Do Deregulated Cas Proteins Induce Genomic Instability in Early-Stage Ovarian Cancer

DTIC Science & Technology

2008-12-01

Klein-Szanto A, Litwin S, Hoelzle MK, Hensley HH, Hamilton TC, Testa JR. RAD001 (Everolimus) delays tumor onset and progression in a transgenic mouse...Mol Biol Cell 2006; 17:1204-17. 10 14. Hensley H, Quinn BA, Wolf RL, Litwin SL, Mabuchi S, Williams SJ, Williams C, Hamilton TC, Connolly DC

The Role of Neuropeptide Y (NPY) In Uncontrolled Alcohol Drinking and Relapse Behavior Resulting From Exposure to Stressful Events

DTIC Science & Technology

2009-11-01

modulating neurobio - logical responses to ethanol and drugs of abuse, including the striatum, nucleus accumbens (NAc), ventral tegmental area (VTA...critically required for the regulation of energy homeostasis in mice. Mol Cell Biol 22, 5027–5035. Rasmussen, D.D., Bryant, C.A., Boldt, B.M., Colasurdo

Role of ets Oncogenes in the Progression of Breast Cancer

DTIC Science & Technology

1998-10-01

8217 References 167 Arias J, Alberts AS, Brindle P, Claret FX, Smeal T, Karin M, May WA, Lessnick SL, Braun BS, Klemsz M, Lewis BC, Feramisco J and Montminy M...0 and Shaw PE. (1994). Mol. Cell. Oncogene, 8, 3459-3464. Biol., 14, 4815-4824. Bories J, Willerford DM, Grevin D, Davidson L, Camus A, Lopez M

Regulation of ATM-Dependent DNA Damage Responses in Breast Cancer by the RhoGEF Net1

DTIC Science & Technology

2014-04-01

1998) Science 279: 509-514. 12. Harper JW, et al., (2007) The DNA Damage Response: Ten years after. Mol. Cell 28; 739-745. 13. Hill R, et al., (2010...RhoGTPases: Biochemistry and Biology. Annu. Rev. Cell Dev. Biol. 21:247-269. 17. Khanna KK, et al., (2001) ATM, a central controller of cellular

Parallel Computing in Protein Structure Topology Determination

DTIC Science & Technology

2008-12-01

model, B) dynamic model. A B 6. REFERENCES Baker, M. L., W. Jiang, et al. (2006). "Ab initio modeling of the herpesvirus VP26 core...skeletons of secondary structures." J Mol Biol 350(3): 571-86. Zhou, Z. H., M. Dougherty, et al. (2000). "Seeing the herpesvirus capsid at 8.5 Å." Science 288(5467): 877-880.

A Chemical Strategy to Trap and Identify Proteins That May Regulate Promoter Hypermethylation in Breast Cancer

DTIC Science & Technology

2007-07-01

This research was supported by W. M. Keck Foundation, the Arnold and Mabel Beckman Foundation, the Camille & Henry Dreyfus Foundation, the...Pegg, Cancer Res. 1990, 50, 6119-6129; b) E. M. Duguid, P. A. Rice , C. He, J. Mol. Biol. 2005, 350, 657-666; c) D. S. Daniels, T. T. Woo, K. X. Luu

Optic Glomeruli: Biological Circuits that Compute Target Identity

DTIC Science & Technology

2013-11-01

vitripennis. Insect Mol. Biol. Suppl. 1:121-36. Strausfeld NJ. 2012. Arthropod Brains. Evolution , Functional Elegance and Historical Significance. Harvard...Neuroscience and Center for Insect Science University of Arizona Tucson, AZ 85721 Contract No. FA8651-10-1-0001 November 2013 FINAL REPORT...PERFORMING ORGANIZATION REPORT NUMBER Department of Neuroscience and Center for Insect Science University of Arizona Tucson, AZ 85721

CD24 as a Potential Therapeutic Target in Prostate Cancer

DTIC Science & Technology

2009-04-01

in CD24/HSA-deficient mice. Blood 89, 1058-1067 (1997). 5. Lohnas, G.L., Roberts , S.F., Pilon, A. & Tramontano, A. Epitope-specific antibody and...4. D. E. Smith et al., Nature 413, 748 (2001). 5. D. N. Fuller et al., J. Mol. Biol. 373, 1113 (2007). 6. D. N. Fuller D. M. Raymer , V. Kottadiel, V

Role of VAPB-MSP, a Novel EphA2 RTK Antagonist in Breast Cancer

DTIC Science & Technology

2012-12-01

13 REFERENCES 1. Arriola E, Marchio C, Tan DS, Drury SC, Lambros MB, et al. (2008) Genomic analysis of the HER2/TOP2A amplicon in breast cancer and...proliferation and branching in mouse mammary epithelium. Mol Biol Cell 12: 1445–1455. 27. Arriola E, Marchio C, Tan DS, Drury SC, Lambros MB, et al

Single-Molecule Analysis of Pre-mRNA Splicing with Colocalization Single-Molecule Spectroscopy (CoSMoS).

PubMed

Braun, Joerg E; Serebrov, Victor

2017-01-01

Recent development of single-molecule techniques to study pre-mRNA splicing has provided insights into the dynamic nature of the spliceosome. Colocalization single-molecule spectroscopy (CoSMoS) allows following spliceosome assembly in real time at single-molecule resolution in the full complexity of cellular extracts. A detailed protocol of CoSMoS has been published previously (Anderson and Hoskins, Methods Mol Biol 1126:217-241, 2014). Here, we provide an update on the technical advances since the first CoSMoS studies including slide surface treatment, data processing, and representation. We describe various labeling strategies to generate RNA reporters with multiple dyes (or other moieties) at specific locations.

Characterization and Use of Temperature-Sensitive Mutations of BRCA1 for the Study of BRCA1 Function

DTIC Science & Technology

2005-01-01

Transcriptional activation by BRCA1. Nature 1996; 382:678-9. tion activation by BRCA1. The mutation would cause a marked 10. Hayes F, Cayanan C, Barilla D...cells was even higher than the Rev Mol Cell Biol 2002; 3:41-9. 20. Hayes F, Cayanan C, Barilla D, Monteiro AN. Functional assay for BRCAI

Oxidative Lung Injury in Virus-Induced Wheezing

DTIC Science & Technology

2012-05-01

Syncytial Virus Infection. Am J Physiol-Lung Cell & Mol Physiol, in press. 1 Annual Progress Report for the period ending 04/30/2012...epithelial cells infected with Respiratory Syncytial Virus: role in viral-induced Interferon Regulatory Factor activation. J Biol Chem. 276:19715-19722...severe RSV bronchiolitis. 2011. Amer J Resp Critic Care Med. 10. Kahn, J . S. 2003. Human metapneumovirus: a newly emerging respiratory pathogen

Computer vision-based automated peak picking applied to protein NMR spectra.

PubMed

Klukowski, Piotr; Walczak, Michal J; Gonczarek, Adam; Boudet, Julien; Wider, Gerhard

2015-09-15

A detailed analysis of multidimensional NMR spectra of macromolecules requires the identification of individual resonances (peaks). This task can be tedious and time-consuming and often requires support by experienced users. Automated peak picking algorithms were introduced more than 25 years ago, but there are still major deficiencies/flaws that often prevent complete and error free peak picking of biological macromolecule spectra. The major challenges of automated peak picking algorithms is both the distinction of artifacts from real peaks particularly from those with irregular shapes and also picking peaks in spectral regions with overlapping resonances which are very hard to resolve by existing computer algorithms. In both of these cases a visual inspection approach could be more effective than a 'blind' algorithm. We present a novel approach using computer vision (CV) methodology which could be better adapted to the problem of peak recognition. After suitable 'training' we successfully applied the CV algorithm to spectra of medium-sized soluble proteins up to molecular weights of 26 kDa and to a 130 kDa complex of a tetrameric membrane protein in detergent micelles. Our CV approach outperforms commonly used programs. With suitable training datasets the application of the presented method can be extended to automated peak picking in multidimensional spectra of nucleic acids or carbohydrates and adapted to solid-state NMR spectra. CV-Peak Picker is available upon request from the authors. gsw@mol.biol.ethz.ch; michal.walczak@mol.biol.ethz.ch; adam.gonczarek@pwr.edu.pl Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Microvesicles as mediators of intercellular communication in cancer.

PubMed

Antonyak, Marc A; Cerione, Richard A

2014-01-01

The discovery that cancer cells generate large membrane-enclosed packets of epigenetic information, known as microvesicles (MVs), that can be transferred to other cells and influence their behavior (Antonyak et al., Small GTPases 3:219-224, 2012; Cocucci et al., Trends Cell Biol 19:43-51, 2009; Rak, Semin Thromb Hemost 36:888-906, 2010; Skog et al., Nat Cell Biol 10:1470-1476, 2008) has added a unique perspective to the classical paracrine signaling paradigm. This is largely because, in addition to growth factors and cytokines, MVs contain a variety of components that are not usually thought to be released into the extracellular environment by viable cells including plasma membrane-associated proteins, cytosolic- and nuclear-localized proteins, as well as nucleic acids, particularly RNA transcripts and micro-RNAs (Skog et al., Nat Cell Biol 10:1470-1476, 2008; Al-Nedawi et al., Nat Cell Biol 10:619-624, 2008; Antonyak et al., Proc Natl Acad Sci U S A 108:4852-4857, 2011; Balaj et al., Nat Commun 2:180, 2011; Choi et al., J Proteome Res 6:4646-4655, 2007; Del Conde et al., Blood 106:1604-1611, 2005; Gallo et al., PLoS One 7:e30679, 2012; Graner et al., FASEB J 23:1541-1557, 2009; Grange et al., Cancer Res 71:5346-5356, 2011; Hosseini-Beheshti et al., Mol Cell Proteomics 11:863-885, 2012; Martins et al., Curr Opin Oncol 25:66-75, 2013; Noerholm et al., BMC Cancer 12:22, 2012; Zhuang et al., EMBO J 31:3513-3523, 2012). When transferred between cancer cells, MVs have been shown to stimulate signaling events that promote cell growth and survival (Al-Nedawi et al., Nat Cell Biol 10:619-624, 2008). Cancer cell-derived MVs can also be taken up by normal cell types that surround the tumor, an outcome that helps shape the tumor microenvironment, trigger tumor vascularization, and even confer upon normal recipient cells the transformed characteristics of a cancer cell (Antonyak et al., Proc Natl Acad Sci U S A 108:4852-4857, 2011; Martins et al., Curr Opin Oncol 25:66-75, 2013; Al-Nedawi et al., Proc Natl Acad Sci U S A 106:3794-3799, 2009; Ge et al., Cancer Microenviron 5:323-332, 2012). Thus, the production of MVs by cancer cells plays crucial roles in driving the expansion of the primary tumor. However, it is now becoming increasingly clear that MVs are also stable in the circulation of cancer patients, where they can mediate long-range effects and contribute to the formation of the pre-metastatic niche, an essential step in metastasis (Skog et al., Nat Cell Biol 10:1470-1476, 2008; Noerholm et al., BMC Cancer 12:22, 2012; Peinado et al., Nat Med 18:883-891, 2012; Piccin et al., Blood Rev 21:157-171, 2007; van der Vos et al., Cell Mol Neurobiol 31:949-959, 2011). These findings, when taken together with the fact that MVs are being aggressively pursued as diagnostic markers, as well as being considered as potential targets for intervention against cancer (Antonyak et al., Small GTPases 3:219-224, 2012; Hosseini-Beheshti et al., Mol Cell Proteomics 11:863-885, 2012; Martins et al., Curr Opin Oncol 25:66-75, 2013; Ge et al., Cancer Microenviron 5:323-332, 2012; Peinado et al., Nat Med 18:883-891, 2012; Piccin et al., Blood Rev 21:157-171, 2007; Al-Nedawi et al., Cell Cycle 8:2014-2018, 2009; Cocucci and Meldolesi, Curr Biol 21:R940-R941, 2011; D'Souza-Schorey and Clancy, Genes Dev 26:1287-1299, 2012; Shao et al., Nat Med 18:1835-1840, 2012), point to critically important roles for MVs in human cancer progression that can potentially be exploited to develop new targeted approaches for treating this disease.

Connexins in Prostate Cancer Initiation and Progression

DTIC Science & Technology

2013-11-01

the Golgi Apparatus for Cargo Transport Prior to Complete Assembly. Mol.Biol.Cell, 17, 4105-4117. 79. Hunziker,W. and Geuze,H. (2011...tumor growth by inducing the assembly of other junctional and signaling complexes? Wild type connexins which form functional gap junctions and mutant...and influences the function of two other important proteins that have been shown to prevent the spread of cancer cells from prostate to distant organs

Genomic Comparison of Escherichia coli O104:H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2

DTIC Science & Technology

2012-11-01

306. 70. Smith DL, Rooks DJ, Fogg PC, Darby AC, Thomson NR, et al. (2012) Comparative genomics of Shiga toxin encoding bacteriophages. BMC Genomics 13...genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev 68: 560–602. 77. Smith DL, Wareing BM, Fogg PCM, Riley LM, Spencer M, et al

Molecular Targeting of Prostate Cancer during Androgen Ablation: Inhibition of CHES1/FOXN3

DTIC Science & Technology

2012-05-01

histone deacetylase restores the DNA damage response in checkpoint- deficient strains of Saccharomyces cerevisiae. Mol Cell Biol 23, 4522-4531. 4. Ji...109,208,031 − 109,208,194 5 164 5.0666 C1orf62 56,874 548,058 TSS_upstream 9 chr16 65,080,679 − 65,080,894 5 216 4.9543 TK2 61,029 20,066 TES_downstream 10

A Polyamine Oxidizing Enzyme as a Drug to Treat Breast Cancer

DTIC Science & Technology

2009-07-01

Paolo ML, Biadene M, Calderone V, Battistutta, R, Scarpa M, Rigo A, Zanot Crystal structure of amine oxidase from bovine serum. J Mol Biol (2005) 346...serum amine oxidase (SAO) as effective treatments for breast cancer using a mouse model. Hopefully, this approach, or a variation thereof, could be...pure enzyme, it is proposed that freshly prepared oxidase is required. In the future, will carry out smaller scale purifications, and only use the

Characterization of an Enantioselective Odorant Receptor in the Yellow Fever Mosquito Aedes aegypti

DTIC Science & Technology

2009-09-15

between insect pheromone receptors expressed in Xenopus oocytes and their cognate pheromone ligands [24,43]. The honey bee Apis mellifera OR11 (AmOR11...136–142. 12. Laska M, Galizia CG (2001) Enantioselectivity of odor perception in honeybees ( Apis mellifera carnica). Behav Neurosci 115: 632–639. 13...Culex quinquefasciatus. Insect Biochem Mol Biol 36: 169–176. 23. Robertson HM, Wanner KW (2006) The chemoreceptor superfamily in the honey bee, Apis

Mechanisms Down-Regulating Sprouty1, a Growth Inhibitor in Prostate Cancer

DTIC Science & Technology

2006-10-01

4139-4147. 6. de Maximy AA, Nakatake Y, Moncada S, Itoh N, Thiery JP, Bellusci S: Cloning and expression pattern of a mouse homologue of Drosophila...22992-22995. 18 10. Gross I, Bassit B, Benezra M, Licht JD: Mammalian sprouty proteins inhibit cell growth and differentiation by preventing ras...Pelletier J, Housman DE : Sequence and structural requirements for high-affinity DNA binding by the WT1 gene product. Mol Cell Biol 1995, 15: 1489-1498

Metabolic Regulation of Caspase 2 in Breast Cancer

DTIC Science & Technology

2011-04-01

S. The apoptosome: physiological, developmental, and pathological modes of regulation. Dev Cell 10, 549-61 ( 2006 ). 3. Baliga, B.C., Read, S.H...Mol Biol Cell 17, 2150-7 ( 2006 ). 9. Bergeron, L. et al. Defects in regulation of apoptosis in caspase-2-deficient mice. Genes Dev 12, 1304-14 (1998...Warburg, O. On the origin of cancer cells. Science 123, 309-14 (1956). 17. Lassus, P., Opitz- Araya , X. & Lazebnik, Y. Requirement for caspase-2 in

T Cell Gene Therapy to Eradicate Disseminated Breast Cancers

DTIC Science & Technology

2012-05-01

examined in a mouse engraftment model. 50x106 mouse T cells transduced with anti-CEA IgTCR and Tandem CARs were injected i.v. into 350 rads γ- irradiated ...proteins in insect cell expression system for testing their effectiveness in inhibiting tick feeding by using them as vaccines to immunize the host...genes essential for sperm development in the male tick Amblyomma hebraeum Koch (Acari: Ixodidae). Insect Biochem Mol Biol. 2008 Jul; 38 (7): 721-729

The Clinical Development of Thalidomide as an Angiogenesis Inhibitor Therapy for Prostate Cancer

DTIC Science & Technology

2006-10-01

LFA-1 and ICAM-1 after in vitro treatment with the anti- TNF - alpha agent thalidomide . Cell Mol Biol (Noisy-le-grand) 2001 Nov;47(7):1105-14. 5...trial has been completed. Data regarding the biologic effects of thalidomide have been generated and analysed. BODY AIM 1. Assessment of...Tumor Necrosis Factor ( TNF )-α prior to and following thalidomide treatment have been assessed in 16 patients. Serum Levels of Interleukin (IL)-6 and

Tick Infestation Risk and Borrelia burgdorferi s.l. Infection-Induced Increase in Host-Finding Efficacy of Female Ixodes ricinus Under Natural Conditions

DTIC Science & Technology

2008-02-14

worldwide, only a few are vaccine -preventable (e.g., tick-borne encephalitis, yellow fever, Japanese encephalitis, and plague). For this reason...western Germany underscore the considerable risk of acquiring Lyme borreliosis in Central Europe. Since no licensed vaccine exists for Lyme borreliosis...Acknowledgements We thank Marco Isack, Sabine Barz, Thorsten Lange, Bernd Bocklet and Dirk Hiller for their assistance with fieldwork. TibMolBiol

Development of the Zebra Danio Model: Carcinogenesis and Gene Transfer Studies

DTIC Science & Technology

1996-09-01

J., and Enomoto, M. (1988). Liver cell carcinomas in the medaka (Oryzias latipes) induced by methylazoxymethanol-acetate. J. Comp. Path. 98, 441-452...accelerate steroid- induced cell division in Xenopus oocytes (Sadler et al., 1986). More recently, ras p21 has been implicated in the transduction of a... induced cell division in Xenopus laevis oocytes. Mol Cell Biol 6:719-722. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989). Molecular Cloning: A

Regulation of Glucose Transport in Quiescent, Lactating, and Neoplastic Mammary Epithelia

DTIC Science & Technology

1999-10-01

accepted subject to minor revision 2. Nemeth, BN, Tsang, ST, Geske , RS, Haney, PM. Golgi targeting of the GLUT1 glucose transporter in lactating mouse...weaning alters glucose transporter targeting in lactating mouse mammary gland. Mol. Biol. Cell 1997; 8, 307a (ASCB poster presentation). 6. Geske , S...Blaise A. Nemeth, Stella W.Y. Tsang, Robert S. Geske , and Peter M. Haney Department of Pediatrics [B.A.N.], University of Wisconsin Children’s Hospital

Clinical validation of 3 commercial real-time reverse transcriptase polymerase chain reaction assays for the detection of Middle East respiratory syndrome coronavirus from upper respiratory tract specimens.

PubMed

Mohamed, Deqa H; AlHetheel, AbdulKarim F; Mohamud, Hanat S; Aldosari, Kamel; Alzamil, Fahad A; Somily, Ali M

2017-04-01

Since discovery of Middle East respiratory syndrome coronavirus (MERS-CoV), a novel betacoronavirus first isolated and characterized in 2012, MERS-CoV real-time reverse transcriptase polymerase chain reaction (rRT-PCR) assays represent one of the most rapidly expanding commercial tests. However, in the absence of extensive evaluations of these assays on positive clinical material of different sources, evaluating their diagnostic effectiveness remains challenging. We describe the diagnostic performance evaluation of 3 common commercial MERS-CoV rRT-PCR assays on a large panel (n = 234) of upper respiratory tract specimens collected during an outbreak episode in Saudi Arabia. Assays were compared to the RealStar® MERS-CoV RT-PCR (Alton Diagnostics, Hamburg, Germany) assay as the gold standard. Results showed i) the TIB MolBiol® LightMix UpE and Orf1a assays (TIB MolBiol, Berlin, Germany) to be the most sensitive, followed by ii) the Anyplex™ Seegene MERS-CoV assay (Seegene, Seoul, Korea), and finally iii) the PrimerDesign™ Genesig® HCoV_2012 assay (PrimerDesign, England, United Kingdom). We also evaluate a modified protocol for the PrimerDesign™ Genesig® HCoV_2012 assay. Copyright © 2017 Elsevier Inc. All rights reserved.

Ca2+ signaling and early embryonic patterning during the blastula and gastrula periods of zebrafish and Xenopus development.

PubMed

Webb, Sarah E; Miller, Andrew L

2006-11-01

It has been proposed that Ca(2+) signaling, in the form of pulses, waves and steady gradients, may play a crucial role in key pattern forming events during early vertebrate development [L.F. Jaffe, Organization of early development by calcium patterns, BioEssays 21 (1999) 657-667; M.J. Berridge, P. Lipp, M.D. Bootman, The versatility and universality of calcium signaling, Nat. Rev. Mol. Cell Biol. 1 (2000) 11-21; S.E. Webb, A.L. Miller, Calcium signalling during embryonic development, Nat. Rev. Mol. Cell Biol. 4 (2003) 539-551]. With reference to the embryos of zebrafish (Danio rerio) and the frog, Xenopus laevis, we review the Ca(2+) signals reported during the Blastula and Gastrula Periods. This developmental window encompasses the major pattern forming events of epiboly, involution, and convergent extension, which result in the establishment of the basic germ layers and body axes [C.B. Kimmel, W.W. Ballard, S.R. Kimmel, B. Ullmann, T.F. Schilling, Stages of embryonic development of the zebrafish, Dev. Dyn. 203 (1995) 253-310]. Data will be presented to support the suggestion that propagating waves (both long and short range) of Ca(2+) release, followed by sequestration, may play a crucial role in: (1) Coordinating cell movements during these pattern forming events and (2) Contributing to the establishment of the basic embryonic axes, as well as (3) Helping to define the morphological boundaries of specific tissue domains and embryonic structures, including future organ anlagen [E. Gilland, A.L. Miller, E. Karplus, R. Baker, S.E. Webb, Imaging of multicellular large-scale rhythmic calcium waves during zebrafish gastrulation, Proc. Natl. Acad. Sci. USA 96 (1999) 157-161; J.B. Wallingford, A.J. Ewald, R.M. Harland, S.E. Fraser, Calcium signaling during convergent extension in Xenopus, Curr. Biol. 11 (2001) 652-661]. The various potential targets of these Ca(2+) transients will also be discussed, as well as how they might integrate with other known pattern forming pathways known to modulate early developmental events (such as the Wnt/Ca(2+)pathway; [T.A. Westfall, B. Hjertos, D.C. Slusarski, Requirement for intracellular calcium modulation in zebrafish dorsal-ventral patterning, Dev. Biol. 259 (2003) 380-391]).

A Generic Protocol for Purifying Disulfide-Bonded Domains and Random Protein Fragments Using Fusion Proteins with SUMO3 and Cleavage by SenP2 Protease.

PubMed

Besir, Hüseyin

2017-01-01

Recombinant expression of heterologous proteins in E. coli is well established for a wide range of proteins, although in many cases, purifying soluble and properly folded proteins remains challenging (Sorensen and Mortensen, J Biotechnol 115:113-128, 2005; Correa and Oppezzo, Methods Mol Biol 1258:27-44, 2015). Proteins that contain disulfide bonds (e.g., cytokines, growth factors) are often particularly difficult to purify in soluble form and still need optimizing of protocols in almost every step of the process (Berkmen, Protein Expr Purif 82:240-251, 2012; de Marco, Microb Cell Fact 11:129, 2012). Expression of disulfide bonded proteins in the periplasm of E. coli is one approach that can help to obtain soluble protein with the correct disulfide bridges forming in the periplasm. This offers the appropriate conditions for disulfide formation although periplasmic expression can also result in low expression levels and incorrect folding of the target protein (Schlapschy and Skerra, Methods Mol Biol 705:211-224, 2011). Generation of specific antibodies often requires a specific antigenic sequence of a protein in order to get an efficient immune response and minimize cross-reactivity of antibodies. Larger proteins like GST (Glutathione-S-transferase) or MBP (maltose binding protein) as solubilizing fusion partners are frequently used to keep antigens soluble and immunize animals. This approach has the disadvantage that the immune response against the fusion partner leads to additional antibodies that need to be separated from the antigen-specific antibodies. For both classes of proteins mentioned above, a protocol has been developed and optimized using the human version of small ubiquitin-like modifier 3 (SUMO3) protein and its corresponding protease SenP2. This chapter describes the experimental steps for expression, purification, refolding, and cleavage that are applicable to both disulfide-bonded proteins with a defined structure and random protein fragments for antibody generation or larger peptides with defined sequence that are difficult express on their own.

The Opposing Roles of Nucleophosmin and the ARF Tumor Suppressor in Breast Cancer

DTIC Science & Technology

2005-04-01

3. Bertwistle, D ., M. Sugimoto, and C . J. Sherr. 2004. Physical and functional interactions of the Arf tumor suppressor protein with nucleophosmin...Kindbeiter, J. C . Sanchez, A. Greco, D . Hochstrasser, and J. J. Diaz. 2002. Functional proteomic analysis of human nucleolus. Mol Biol Cell 13:4100-9...21. Sherr, C . J., and J. D . Weber. 2000. The ARF/p53 pathway. Curr Opin Genet Dev 10:94-9. 22. Spector, D . L., R. L. Ochs, and H. Busch. 1984

The Role of b-Catenin in Mammary Gland Carcinogenesis

DTIC Science & Technology

2002-03-01

Wetering, M., Cavallo, R., Dooijes, D., van Beest , M., van Es, J., Loureiro, J., Ypma, A., hursh, D., Jones, T., Bejsovec, A., Peifer, M., Mortin, M...Transduction Lab - domain of /3-catenin. oratories) and anti-KT3 (Babco) were used as primary Elevated levels of fl-catenin were recently observed in antibodies...1988). Cell, 55, 619 -625. Kolligs FT, Hu G, Dang CV and Fearon ER. (1999). Mol. van de Wetering M, Cavallo R, Dooijes D, van Beest M, van Cell. Biol

Targeting Common but Complex Proteoglycans on Breast Cancer Cells and Stem Cells Using Evolutionary Refined Malaria Proteins

DTIC Science & Technology

2016-08-01

clearance and infect placental cells, thereby causing pregnancy - associated malaria outbreaks in epidemic regions of the world. Prior to this...recognition and activity. Nat. Chem. Biol. 2, 467–473. Holtan, S.G., Creedon, D.J., Haluska, P., and Markovic, S.N. (2009). Cancer and pregnancy : parallels...falciparum involved in pregnancy -associated malaria. Mol. Microbiol. 49, 179–191. Salanti, A., Dahlbäck, M., Turner, L., Nielsen, M.A., Barfod, L

Avoiding microRNA Function Through Alternative Polyandenylation in Prostate Cancer

DTIC Science & Technology

2012-10-01

Similarly to NSD1, Drosophila melanogaster MES-4 catalyses global mono- and dimeth- ylation of H3K36 in vivo, but SET2, the fly orthologue of human...positions of nucleosomes and their modification status within the genomes of humans, C. elegans, D.  melanogaster and mice79–81. In each case...by enhancing recruitment of the MSL complex in Drosophila melanogaster . Mol. Cell. Biol. 28, 3401–3409 (2008). 73. Alekseyenko, A. A. et al. A

Fibronectin Matrix Remodeling in the Regulation of the Inflammatory Response within the Lung: An Early Step in Lung Cancer Progression

DTIC Science & Technology

2011-09-01

such as that which occurs in chronic obstructive pulmonary disease (COPD) and emphysema , is associated with increased risk of lung cancer. These...effect of the fibronectin III-1c peptide on the expression of inflammatory genes by human lung fibroblasts, lung cancer cells, and pulmonary ...CXCR2 in bleomycin-induced pulmonary inflammation and fibrosis. Am J Respir Cell Mol Biol. 2009; 40:410-21. 7. Barnes PJ. New therapies for chronic

Targeting PRMT5 as a Novel Radiosensitization Approach for Primary and Recurrent Prostate Cancer Treatment

DTIC Science & Technology

2015-08-01

6], breast cancer [7], melanoma [8], leukemia and lymphoma [9,10], and glioblastoma [11]. The overexpression of PRMT5 correlatesse 5;NF-Y, Nuclear...multiple human cancers [3 11], though it is unknown how PRMT5 expression is regulated by cancer signaling. In leukemia and lymphoma cells, down...family of tumor suppressors in leukemia and lymphoma cells, Mol. Cell. Biol. 28 (2008) 6262–6277. [10] S. Pal, R.A. Baiocchi, J.C. Byrd, M.R. Grever, S.T

Role of Rad23 and Dsk2 in Nucleotide Excision Repair and Spindle Pole Body Duplication

DTIC Science & Technology

2007-03-01

proteasome. Mol. Cell, 6, 409–419. 14. Saeki, Y., Saitoh, A., Toh-e, A. & Yokosawa , H. (2002). Ubiquitin-like proteins and Rpn10 play cooperative...Sone, T., Toh-e, A. & Yokosawa , H. (2002). Identification of ubiquitin-like protein-binding sub- units of the 26 S proteasome. Biochem. Biophys. Res...Proteasome subunit Rpn1 binds ubiquitin-like protein domains. Nat Cell Biol 2002, 4:725-30. 15. Saeki Y, Sone T, Toh-e A, Yokosawa H: Identification of

Molecular Profiles for Lung Cancer Pathogenesis and Detection in US Veterans

DTIC Science & Technology

2011-10-01

using the BRB-ArrayTools v .4.1.0 developed by Dr. Richard Simon and the BRB-ArrayTools Development Team and then normalized and log-transformed by...C. V Figure 23. Expression of genes located at chromosome 3q26-3q29. RPKM values were obtained for...airway epithelium of cigarette smokers. Am J Respir Cell Mol Biol 2003;29:331-343 14. Spira A, Beane J, Shah V , et al. Effects of cigarette smoke on

P38 Mitogen-Activated Protein Kinase in Metastasis Associated With Transforming Growth Factor Beta

DTIC Science & Technology

2005-06-01

36, 2001. Shin I, Bakin AV, Rodeck U, Brunet A, Arteaga CL. TGFbeta enhances epithelial cell survival via Akt - dependent regulation of FKHRLI. Mol Biol... Akt mediates cell-cycle progression by phosphorylation of p27Kip’ at threonine 157 and modulation of its cellular localization. Nat Med 8:1145-1152...stress fibers. Ectopic- expression and siRNA experiments show that Smad3 and Smad4 mediate up-regulation of tropomyosins and stress fiber formation

Temporal Assessment of Mental Disorders, Smoking, and Hazardous Drinking in United States Troops Deployed in Support of the Operations in Iraq and Afghanistan

DTIC Science & Technology

2012-04-26

drinking may have occurred, since the questionnaire includes only two of ten questions of Alcohol Use Disorders Identification Test (AUDIT).44 The degree...Psychiatric disorders and stages of smoking. Biol Psychiatry. 2004;55(1):69-76. 30. Romberger DJ, Grant K. Alcohol consumption and smoking...from human genetic studies. Mol Psychiatry. 2010;15(6):574-588. 44. Saunders JB, Aasland OG, Babor TF, de la Fuente JR, Grant M. Development of the

Hop stunt viroid: molecular cloning and nucleotide sequence of the complete cDNA copy.

PubMed Central

Ohno, T; Takamatsu, N; Meshi, T; Okada, Y

1983-01-01

The complete cDNA of hop stunt viroid (HSV) has been cloned by the method of Okayama and Berg (Mol.Cell.Biol.2,161-170. (1982] and the complete nucleotide sequence has been established. The covalently closed circular single-stranded HSV RNA consists of 297 nucleotides. The secondary structure predicted for HSV contains 67% of its residues base-paired. The native HSV can possess an extended rod-like structure characteristic of viroids previously established. The central region of the native HSV has a similar structure to the conserved region found in all viroids sequenced so far except for avocado sunblotch viroid. The sequence homologous to the 5'-end of U1a RNA is also found in the sequence of HSV but not in the central conserved region. Images PMID:6312412

Companion Protease Inhibitors for the In Situ Protection of Recombinant Proteins in Plants.

PubMed

Robert, Stéphanie; Jutras, Philippe V; Khalf, Moustafa; D'Aoust, Marc-André; Goulet, Marie-Claire; Sainsbury, Frank; Michaud, Dominique

2016-01-01

We previously described a procedure for the use of plant protease inhibitors as "companion" accessory proteins to prevent unwanted proteolysis of clinically useful recombinant proteins in leaf crude protein extracts (Benchabane et al. Methods Mol Biol 483:265-273, 2009). Here we describe the use of these inhibitors for the protection of recombinant proteins in planta, before their extraction from leaf tissues. A procedure is first described involving inhibitors co-expressed along-and co-migrating-with the protein of interest in host plant cells. An alternative, single transgene scheme is then described involving translational fusions of the recombinant protein and companion inhibitor. These approaches may allow for a significant improvement of protein steady-state levels in leaves, comparable to yield improvements observed with protease-deficient strains of less complex protein expression hosts such as E. coli or yeasts.

Regulation of the Two Delta Crystallin Genes during Lens Development in the Chicken Embryo

DTIC Science & Technology

1991-08-22

Stabilization of tubulin mRNA by inhibition of protein synthesis sea 148 urchin embryos. Mol. Cell. Biol. 8, 3518-3525. Goto, K., Okada, T.S...counts from twenty lens epithelia. Error bars are ± SEM . Symbols: control lens tissue, (square), 0.5 ng/ml actinomycin D, (inverted triangle), 30 ng...Ŝ]-methionine for 5 hr in the absence or presence of actinomycin D (0.5 or 30 M-g/̂ iD • Values are the means ± SEM for ten groups of three lens

New Insights into the Hendra Virus Attachment and Entry Process from Structures of the Virus G Glycoprotein and Its Complex with Ephrin-B2

DTIC Science & Technology

2012-11-05

organization of measles virus fusion complexes. J Virol 83: 10480–10493. 24. Bishop KA, Hickey AC, Khetawat D, Patch JR, Bossart KN, et al. (2008...its receptor, sialyllactose. Structure 13: 803–815. 38. Colf LA, Juo ZS, Garcia KC (2007) Structure of the measles virus hemagglutinin. Nat Struct Mol...Biol 14: 1227–1228. 39. Hashiguchi T, Kajikawa M, Maita N, Takeda M, Kuroki K, et al. (2007) Crystal structure of measles virus hemagglutinin provides

Mechanism of Action of Ribavirin: An Antiviral Drug of Military Importance,

DTIC Science & Technology

1980-06-01

was suspended in 120 mM Tris, 60 mM sodium ace- tate, 3 mM EDTA (pH 7.4) plus 10% glycerol and 0.1% bromophenol blue. Following electrophoresis, gels ... polyacryl - amide gels . J. Mol. Biol. 26:373-387. 2. Browne, M. J. 1979. Mechanism and specificity of action of ri- bavirin. Antimicrob. Agents...of 10 mM EDTA, 1% sodi- um dodecylsulfate (SDS) and 0.4 N sodium acetate (pH 5.2) then ex- tracted twice with a mixture of 50% phenol, 49% chloroform

Avoiding microRNA Function Through Alternative Polyadenylation in Prostate Cancer

DTIC Science & Technology

2012-04-01

H3K36 (REF. 22). Similarly to NSD1, Drosophila melanogaster MES-4 catalyses global mono- and dimeth- ylation of H3K36 in vivo, but SET2, the fly...analysed both the positions of nucleosomes and their modification status within the genomes of humans, C. elegans, D.  melanogaster and mice79–81. In...dosage compensation by enhancing recruitment of the MSL complex in Drosophila melanogaster . Mol. Cell. Biol. 28, 3401–3409 (2008). 73. Alekseyenko, A. A

Simulation of B Cell Affinity Maturation Explains Enhanced Antibody Cross-Reactivity Induced by the Polyvalent Malaria Vaccine AMA1

DTIC Science & Technology

2014-07-01

cell decisions in lymphoid tissue. Mol. Cell . Biol. 28: 4040–4051. 22. Kosmrlj, A., A. K. Jha, E. S. Huseby, M. Kardar, and A. K. Chakraborty. 2008. How...JUL 2014 2. REPORT TYPE 3. DATES COVERED 00-00-2014 to 00-00-2014 4. TITLE AND SUBTITLE Simulation of B Cell Affinity Maturation Explains...8-98) Prescribed by ANSI Std Z39-18 The Journal of Immunology Simulation of B Cell Affinity Maturation Explains Enhanced Antibody Cross-Reactivity

The Role of Ubiquitin E3 Ligase SCF-SKP2 in Prostate Cancer Development

DTIC Science & Technology

2007-02-01

2004; 303:1371-4. 26. Nag A, Bondar T, Shiv S, Raychaudhuri P. The xeroderma pigmentosum group E gene product DDB2 is a specific target of cullin 4A...ubiquitin ligases. Nat Rev Mol Cell Biol 2005; 6:9-20. 2. Nag A, Bondar T, Shiv S, Raychaudhuri P. The xeroderma pigmentosum group E gene product DDB2 is... xeroderma pigmentosum group E patient and the subsequent inability to bind DDB1 (ref. 16). This motif is present in most of the WDR proteins we found (see

Immunobiological Aspects of erbB Receptors in Breast Cancer.

DTIC Science & Technology

1999-08-01

including the time for reviewing instructions,.searching existing data sources, aätherino ’S^f^X^^dt^m^S^ t ^^eÜ^^’^&’a theacollection of information Send...Matozaki, T ., Noguchi, T ., Iwamatsu, A., Yamao, T ., Takahashi, N., Tsuda, M., Takada, T ., and Kasuga, M. (1996) Mol Cell Biol 16,6887-6899. 4...O’Rourke, D. M., Qian, X., Zhang, H.- T ., Davis, J. G., Nute, E., Meinkoth, J., and Greene, M. I. (1997) Proc. Natl. Acad. Sei (USA) 94,3250-3255.1998. 5

Molecular Profiles for Lung Cancer Pathogenesis and Detection in US Veterans

DTIC Science & Technology

2011-10-01

raw image files that were subsequently converted to probe set data. Raw expression data was analyzed using the BRB-ArrayTools v .4.1.0 developed by Dr...epithelium of cigarette smokers. Am J Respir Cell Mol Biol 2003;29:331-343 14. Spira A, Beane J, Shah V , et al. Effects of cigarette smoke on the...human airway epithelial cell transcriptome. Proc Natl Acad Sci U S A 2004;101:10143-10148 15. Spira A, Beane JE, Shah V , et al. Airway epithelial gene

Genomic Instability and Breast Cancer

DTIC Science & Technology

2009-10-01

van Deursen, J., Nussenzweig, A., Paull, T . T ., Alt, F. W., and Chen, J. (2006)Mol. Cell 21, 187–200 7. Huen, M. S., Grant, R ., Manke, I., Minn, K...Science 316, 1198–1202 14. Lechner,M. S., Levitan, I., andDressler, G. R . (2000)Nucleic Acids Res. 28, 2741–2751 15. Cho, Y. W., Hong, T ., Hong, S., Guo...H., Yu, H., Kim, D., Guszczynski, T ., Dressler, G. R ., Copeland, T . D., Kalkum, M., and Ge, K. (2007) J. Biol. Chem. 282, 20395–20406 16. Patel, S. R

Postexposure Protection of Guinea Pigs against a Lethal Ebola Virus Challenge is Conferred by RNA Interference

DTIC Science & Technology

2006-06-15

because its suppression should lead to a nearly total loss of all RNA synthesis , but also because of the absence of similar proteins in mammalian cells...protects mice from fulminant hepatitis. Nat Med 2003; 9:347–51. 12. Ge Q, Filip L, Bai A, Nguyen T, Eisen HN, Chen J. Inhibition of influenza virus...human beta interferon gene in simian cells defective in interferon synthesis . Mol Cell Biol 1986; 6:2279–83. 21. Spann KM, Tran KC, Collins PL

A mathematical analysis of multiple-target SELEX.

PubMed

Seo, Yeon-Jung; Chen, Shiliang; Nilsen-Hamilton, Marit; Levine, Howard A

2010-10-01

SELEX (Systematic Evolution of Ligands by Exponential Enrichment) is a procedure by which a mixture of nucleic acids can be fractionated with the goal of identifying those with specific biochemical activities. One combines the mixture with a specific target molecule and then separates the target-NA complex from the resulting reactions. The target-NA complex is separated from the unbound NA by mechanical means (such as by filtration), the NA is eluted from the complex, amplified by PCR (polymerase chain reaction), and the process repeated. After several rounds, one should be left with the nucleic acids that best bind to the target. The problem was first formulated mathematically in Irvine et al. (J. Mol. Biol. 222:739-761, 1991). In Levine and Nilsen-Hamilton (Comput. Biol. Chem. 31:11-25, 2007), a mathematical analysis of the process was given. In Vant-Hull et al. (J. Mol. Biol. 278:579-597, 1998), multiple target SELEX was considered. It was assumed that each target has a single nucleic acid binding site that permits occupation by no more than one nucleic acid. Here, we revisit Vant-Hull et al. (J. Mol. Biol. 278:579-597, 1998) using the same assumptions. The iteration scheme is shown to be convergent and a simplified algorithm is given. Our interest here is in the behavior of the multiple target SELEX process as a discrete "time" dynamical system. Our goal is to characterize the limiting states and their dependence on the initial distribution of nucleic acid and target fraction components. (In multiple target SELEX, we vary the target component fractions, but not their concentrations, as fixed and the initial pool of nucleic acids as a variable starting condition). Given N nucleic acids and a target consisting of M subtarget component species, there is an M × N matrix of affinities, the (i,j) entry corresponding to the affinity of the jth nucleic acid for the ith subtarget. We give a structure condition on this matrix that is equivalent to the following statement: For any initial pool of nucleic acids such that all N species are represented, the dynamical system defined by the multiple target SELEX process will converge to a unique subset of nucleic acids, each of whose concentrations depend only upon the total nucleic acid concentration, the initial fractional target distribution (both of which are assumed to be the same from round to round), and the overall limiting association constant. (The overall association constant is the equilibrium constant for the system of MN reactions when viewed as a composite single reaction). This condition is equivalent to the statement that every member of a certain family of chemical potentials at infinite target dilution can have at most one critical point. (The condition replaces the statement for single target SELEX that the dynamical system generated via the process always converges to a pool that contains only the nucleic acid that binds best to the target). This suggests that the effectiveness of multiple target SELEX as a separation procedure may not be as useful as single target SELEX unless the thermodynamic properties of these chemical potentials are well understood.

THE MECHANISM OF ACTION OF COLCHICINE

PubMed Central

Wilson, Leslie; Meza, Isaura

1973-01-01

The thermal depolymerization procedure of Stephens (1970. J. Mol. Biol. 47:353) has been employed for solubilization of Strongylocentrotus purpuratus sperm tail outer doublet microtubules with the use of a buffer during solubilization which is of optimal pH and ionic strength for the preservation of colchicine binding activity of chick embryo brain tubulin. Colchicine binding values were corrected for first-order decay during heat solubilization at 50°C (t½ = 5.4 min) and incubation with colchicine at 37°C in the presence of vinblastine sulfate (t½ = 485 min). The colchicine binding properties of heat-solubilized outer doublet tubulin were qualitatively identical with those of other soluble forms of tubulin. The solubilized tubulin (mol wt, 115,000) bound 0.9 ± 0.2 mol of colchicine per mol of tubulin, with a binding constant of 6.3 x 105 liters/mol at 37°C. The colchicine binding reaction was both time and temperature dependent, and the binding of colchicine was prevented in a competitive manner by podophyllotoxin (Ki = 1.3 x 10-6 M). The first-order decay of colchicine binding activity was substantially decreased by the addition of the vinca alkaloids, vinblastine sulfate or vincristine sulfate, thus demonstrating the presence of a vinca alkaloid binding site(s) on the outer doublet tubulin. Tubulin contained within the assembled microtubules did not decay. Intact outer doublet microtubules bound less than 0.001 mol of colchicine per mol of tubulin contained in the microtubules, under conditions where soluble tubulin would have bound 1 mol of colchicine per mol of tubulin (saturating concentration of colchicine, no decay of colchicine binding activity). The presence of colchicine had no effect on the rate of solubilization of outer doublet microtubules during incubation at 37°C. Therefore, the colchicine binding site on tubulin is blocked (not available to bind colchicine) when the tubulin is in the assembled outer doublet microtubules. PMID:4747924

Structural Characterization and Determinants of Specificity of Single-Chain Antibody Inhibitors of Membrane-Type Serine Protease 1

DTIC Science & Technology

2008-03-01

Colman, P. M. (1993). Shape complementarity at protein / protein interfaces . J Mol Biol 234, 946-50. 26. Huang, M., Syed, R., Stura, E. A., Stone, M. J...Å2 of surface area (Table 1). In the apo MT-SP1 structure20, Asp96 forms the bottom of the S4 pocket, allowing a positively charged substrate P4...of surface area that E2 buries on MT-SP1 is larger than the typical antibody/ protein antigen interaction, which averages about 875 Å2 26; 27. This

Complex of a Protective Antibody with its Ebola Virus GP Peptide Epitope: Unusual Features of a Vlambdalx Light Chain

DTIC Science & Technology

2008-01-01

Bioinformatics, 19, ii246–ii255. 52. Lawrence, M. C. & Colman, P. M. (1993). Shape complementarity at protein / protein interfaces . J. Mol. Biol. 234, 946...envelope spike, which is the sole protein expressed on the surface of the Ebola virus and is involved in receptor binding, tropism, and viral entry.6–9 It...variable light chain/heavy chain (VL/VH) interface of 13F6-1-2, ∼1025 Å2 surface area is buried on VL Fig. 1. Nucleotide and translated amino acid

Complex of a Protective Antibody with its Ebola Virus GP Peptide Epitope: Unusual Features of a V lambda x Light Chain

DTIC Science & Technology

2007-10-01

twists. Bioinformatics, 19, ii246–ii255. 52. Lawrence, M. C. & Colman, P. M. (1993). Shape complementarity at protein / protein interfaces . J. Mol. Biol...envelope spike, which is the sole protein expressed on the surface of the Ebola virus and is involved in receptor binding, tropism, and viral entry.6–9 It...26 At the variable light chain/heavy chain (VL/VH) interface of 13F6-1-2, ∼1025 Å2 surface area is buried on VL Fig. 1. Nucleotide and translated amino

Structure-Guided Insights into the Function of Merlin in Neurofibromatosis 2 (NF2)

DTIC Science & Technology

2011-08-01

laboratory of Dr. Lars Pederson (NIEHS-NIH, Research Triangle Park, North Carolina) that harbor entropy mutations on the surface of MBP, and which... mutations . Am J Hum Genet 66: 873–891. 37. Lawrence MC, Colman PM (1993) Shape complementar - ity at protein/protein interfaces. J Mol Biol 234:946–950. 38...Appendices…………………………………………………………………………… 10 3 INTRODUCTION: Neurofibromatosis type 2 (NF2) is caused by inherited or sporadic mutations

Epigenetic Basis for the Regulation of Estrogen Receptor Alpha Activity in Breast Cancer Cells

DTIC Science & Technology

2009-04-01

B) GPER and TESK2 expression after CARM1 silencing in MCF7 was determined by reverse transcription-qPCR and revealed the requirement for CARM1 in...the E2-induced repression of GPER and TESK2. siLUC was used as a control. *, P 0.05; **, P 0.01; ***, P 0.001. (C) Enrichment of Ec3 cluster...sites (blue blocks) near GPER and TESK2 E2-downregulated target genes (red blocks). 3416 LUPIEN ET AL. MOL. CELL. BIOL. at A C Q S E R V IC E /S E R IA

Activation of mTor Signaling by Gene Transduction to Induce Axon Regeneration in the Central Nervous System Following Neural Injury

DTIC Science & Technology

2015-03-01

terminus amino acids of amyloid precursor protein (cAPP). cAPP was found in our recent publication in Gene Therapy (2013) to be the most effective...Therapy. 2012;20:275-86 PubMed PMID: 22008911. 7. Zoncu R, Efeyan A, Sabatini DM. mTOR: from growth signal integration to cancer, diabetes and ageing...NatRevMolCell Biol. 2011;12:21-35. 8. Morita T, Sobue K. Specification of neuronal polarity regulated by local translation of CRMP2 and Tau via the mTOR

Controlling cytoplasmic c-Fos controls tumor growth in the peripheral and central nervous system.

PubMed

Gil, Germán A; Silvestre, David C; Tomasini, Nicolás; Bussolino, Daniela F; Caputto, Beatriz L

2012-06-01

Some 20 years ago c-Fos was identified as a member of the AP-1 family of inducible transcription factors (Angel and Karin in Biochim Biophys Acta 1072:129-157, 1991). More recently, an additional activity was described for this protein: it associates to the endoplasmic reticulum and activates the biosynthesis of phospholipids (Bussolino et al. in FASEB J 15:556-558, 2001), (Gil et al. in Mol Biol Cell 15:1881-1894, 2004), the quantitatively most important components of cellular membranes. This latter activity of c-Fos determines the rate of membrane genesis and consequently of growth in differentiating PC12 cells (Gil et al. in Mol Biol Cell 15:1881-1894, 2004). In addition, it has been shown that c-Fos is over-expressed both in PNS and CNS tumors (Silvestre et al. in PLoS One 5(3):e9544, 2010). Herein, it is shown that c-Fos-activated phospholipid synthesis is required to support membrane genesis during the exacerbated growth characteristic of brain tumor cells. Specifically blocking c-Fos-activated phospholipid synthesis significantly reduces proliferation of tumor cells in culture. Blocking c-Fos expression also prevents tumor progression in mice intra-cranially xeno-grafted human brain tumor cells. In NPcis mice, an animal model of the human disease Neurofibromatosis Type I (Cichowski and Jacks in Cell 104:593-604, 2001), animals spontaneously develop tumors of the PNS and the CNS, provided they express c-Fos (Silvestre et al. in PLoS One 5(3):e9544, 2010). Treatment of PNS tumors with an antisense oligonucleotide that specifically blocks c-Fos expression also blocks tumor growth in vivo. These results disclose cytoplasmic c-Fos as a new target for effectively controlling brain tumor growth.

The VBP and a1/EBP leucine zipper factors bind overlapping subsets of avian retroviral long terminal repeat CCAAT/enhancer elements.

PubMed

Smith, C D; Baglia, L A; Curristin, S M; Ruddell, A

1994-10-01

Two long terminal repeat (LTR) enhancer-binding proteins which may regulate high rates of avian leukosis virus (ALV) LTR-enhanced c-myc transcription during bursal lymphomagenesis have been identified (A. Ruddell, M. Linial, and M. Groudine, Mol. Cell. Biol. 9:5660-5668, 1989). The genes encoding the a1/EBP and a3/EBP binding factors were cloned by expression screening of a lambda gt11 cDNA library from chicken bursal lymphoma cells. The a1/EBP cDNA encodes a novel leucine zipper transcription factor (W. Bowers and A. Ruddell, J. Virol. 66:6578-6586, 1992). The partial a3/EBP cDNA clone encodes amino acids 84 to 313 of vitellogenin gene-binding protein (VBP), a leucine zipper factor that binds the avian vitellogenin II gene promoter (S. Iyer, D. Davis, and J. Burch, Mol. Cell. Biol. 11:4863-4875, 1991). Multiple VBP mRNAs are expressed in B cells in a pattern identical to that previously observed for VBP in other cell types. The LTR-binding activities of VBP, a1/EBP, and B-cell nuclear extract protein were compared and mapped by gel shift, DNase I footprinting, and methylation interference assays. The purified VBP and a1/EBP bacterial fusion proteins bind overlapping but distinct subsets of CCAAT/enhancer elements in the closely related ALV and Rous sarcoma virus (RSV) LTR enhancers. Protein binding to these CCAAT/enhancer elements accounts for most of the labile LTR enhancer-binding activity observed in B-cell nuclear extracts. VBP and a1/EBP could mediate the high rates of ALV and RSV LTR-enhanced transcription in bursal lymphoma cells and many other cell types.

A Method for Decomposition of the Basic Reaction of Biological Macromolecules into Exponential Components

NASA Astrophysics Data System (ADS)

Barabash, Yu. M.; Lyamets, A. K.

2016-12-01

The structural and dynamical properties of biological macromolecules under non-equilibrium conditions determine the kinetics of their basic reaction to external stimuli. This kinetics is multiexponential in nature. This is due to the operation of various subsystems in the structure of macromolecules, as well as the effect of the basic reaction on the structure of macromolecules. The situation can be interpreted as a manifestation of the stationary states of macromolecules, which are represented by monoexponential components of the basic reaction (Monod-Wyman-Changeux model) Monod et al. (J Mol Cell Biol 12:88-118, 1965). The representation of multiexponential kinetics of the basic reaction in the form of a sum of exponential functions (A(t)={sum}_{i=1}^n{a}_i{e}^{-{k}_it}) is a multidimensional optimization problem. To solve this problem, a gradient method of optimization with software determination of the amount of exponents and reasonable calculation time is developed. This method is used to analyze the kinetics of photoinduced electron transport in the reaction centers (RC) of purple bacteria and the fluorescence induction in the granum thylakoid membranes which share a common function of converting light energy.

Thermodynamics of the binding of L-arabinose and of D-galactose to the L-arabinose-binding protein of Escherichia coli.

PubMed

Fukada, H; Sturtevant, J M; Quiocho, F A

1983-11-10

The thermodynamics of the binding of L-arabinose and of D-galactose to the L-arabinose-binding protein of Escherichia coli have been studied by isothermal and scanning calorimetry. The binding reaction with arabinose is characterized by an enthalpy change of -15.3 +/- 0.5 kcal mol-1 at 25 degrees C, and a large decrease in apparent heat capacity, amounting to -0.44 +/- 0.05 kcal K-1 mol-1, which is constant over the temperature range 8 to 30 degrees C. Very similar results were obtained with D-galactose. These calorimetric results have been combined with binding constants determined by equilibrium dialysis (Clark, A. F., Gerken, T. A., and Hogg, R. W. (1982) Biochemistry 21, 2227-2233) to obtain free energy and entropy changes over the range 5 to 30 degrees C, and by extrapolation to 60 degrees C. The protein undergoes reversible unfolding on being heated with an increase in enthalpy at 53.5 degrees C of 151.8 +/- 1.1 kcal mol-1 (169.2 +/- 1.2 kcal mol-1 at 59.0 degrees C) and in apparent heat capacity of 3.16 +/- 0.07 kcal K-1 mol-1. In the presence of arabinose, the unfolding enthalpy is increased to 200.7 +/- 1.8 kcal mol-1 at 59.0 degrees C, the increase being due to the enthalpy of dissociation of the ligand which amounts to 31 kcal mol-1 at the unfolding temperature. The unfolding temperature is increased by the presence of excess arabinose or galactose, an effect which is due solely to displacement by the added ligand of the unfolding-dissociation equilibrium. The thermodynamic data are discussed in connection with the detailed structural information available for this system from x-ray crystallography (Newcomer, M. E., Gilliland, G. L. and Quiocho, F. A. (1981) J. Biol. Chem. 256, 13213-13217, and references cited therein).

PAMLX: a graphical user interface for PAML.

PubMed

Xu, Bo; Yang, Ziheng

2013-12-01

This note announces pamlX, a graphical user interface/front end for the paml (for Phylogenetic Analysis by Maximum Likelihood) program package (Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556; Yang Z. 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591). pamlX is written in C++ using the Qt library and communicates with paml programs through files. It can be used to create, edit, and print control files for paml programs and to launch paml runs. The interface is available for free download at http://abacus.gene.ucl.ac.uk/software/paml.html.

Molecular interactions between single-stranded DNA-binding proteins associated with an essential MCAT element in the mouse smooth muscle alpha-actin promoter.

PubMed

Kelm, R J; Cogan, J G; Elder, P K; Strauch, A R; Getz, M J

1999-05-14

Transcriptional activity of the mouse vascular smooth muscle alpha-actin gene in fibroblasts is regulated, in part, by a 30-base pair asymmetric polypurine-polypyrimidine tract containing an essential MCAT enhancer motif. The double-stranded form of this sequence serves as a binding site for a transcription enhancer factor 1-related protein while the separated single strands interact with two distinct DNA binding activities termed VACssBF1 and 2 (Cogan, J. G., Sun, S., Stoflet, E. S., Schmidt, L. J., Getz, M. J., and Strauch, A. R. (1995) J. Biol. Chem. 270, 11310-11321; Sun, S., Stoflet, E. S., Cogan, J. G., Strauch, A. R., and Getz, M. J. (1995) Mol. Cell. Biol. 15, 2429-2936). VACssBF2 has been recently cloned and shown to consist of two closely related proteins, Puralpha and Purbeta (Kelm, R. J., Elder, P. K., Strauch, A. R., and Getz, M. J. (1997) J. Biol. Chem. 272, 26727-26733). In this study, we demonstrate that Puralpha and Purbeta interact with each other via highly specific protein-protein interactions and bind to the purine-rich strand of the MCAT enhancer in the form of both homo- and heteromeric complexes. Moreover, both Pur proteins interact with MSY1, a VACssBF1-like protein cloned by virtue of its affinity for the pyrimidine-rich strand of the enhancer. Interactions between Puralpha, Purbeta, and MSY1 do not require the participation of DNA. Combinatorial interactions between these three single-stranded DNA-binding proteins may be important in regulating activity of the smooth muscle alpha-actin MCAT enhancer in fibroblasts.

Mechanism of inhibition of HIV-1 integrase by G-tetrad-forming oligonucleotides in Vitro.

PubMed

Jing, N; Marchand, C; Liu, J; Mitra, R; Hogan, M E; Pommier, Y

2000-07-14

The G-tetrad-forming oligonucleotides and have been identified as potent inhibitors of human immunodeficiency virus type 1 integrase (HIV-1 IN) activity (Rando, R. F., Ojwang, J., Elbaggari, A., Reyes, G. R., Tinder, R., McGrath, M. S., and Hogan, M. E. (1995) J. Biol. Chem. 270, 1754-1760; Mazumder, A., Neamati, N., Ojwang, J. O., Sunder, S., Rando, R. F., and Pommier, Y. (1996) Biochemistry 35, 13762-13771; Jing, N., and Hogan, M. E. (1998) J. Biol. Chem. 273, 34992-34999). To understand the inhibition of HIV-1 IN activity by the G-quartet inhibitors, we have designed the oligonucleotides and, composed of three and four G-quartets with stem lengths of 19 and 24 A, respectively. The fact that increasing the G-quartet stem length from 15 to 24 A kept inhibition of HIV-1 IN activity unchanged suggests that the binding interaction occurs between a GTGT loop domain of the G-quartet inhibitors and a catalytic site of HIV-1 IN, referred to as a face-to-face interaction. Docking the NMR structure of (Jing and Hogan (1998)) into the x-ray structure of the core domain of HIV-1 IN, HIV-1 IN-(51-209) (Maignan, S., Guilloteau, J.-P. , Qing, Z.-L., Clement-Mella, C., and Mikol, V. (1998) J. Mol. Biol. 282, 359-368), was performed using the GRAMM program. The statistical distributions of hydrogen bonding between HIV-1 IN and were obtained from the analyses of 1000 random docking structures. The docking results show a high probability of interaction between the GTGT loop residues of the G-quartet inhibitors and the catalytic site of HIV-1 IN, in agreement with the experimental observation.

Production Methods for a Mesenchymal Stem Cell Therapeutic as a Medical Defense Countermeasure

DTIC Science & Technology

2012-02-01

differentiation of murine embryonic stem cells into vascular progenitors. BMC Cell Biol. 2008;9:2. 56. Johnson EA, Dao TL, Kan RK. Status epilepticus ...their undifferentiated and multipotent status . BMC Cell Biol. 2011;12:12. 52. Sun Y, Chen L, Hou XG, Hou WK, Dong JJ, Sun L, et al. Differentiation of

Bioinformatic analysis of the nucleolus.

PubMed

Leung, Anthony K L; Andersen, Jens S; Mann, Matthias; Lamond, Angus I

2003-12-15

The nucleolus is a plurifunctional, nuclear organelle, which is responsible for ribosome biogenesis and many other functions in eukaryotes, including RNA processing, viral replication and tumour suppression. Our knowledge of the human nucleolar proteome has been expanded dramatically by the two recent MS studies on isolated nucleoli from HeLa cells [Andersen, Lyon, Fox, Leung, Lam, Steen, Mann and Lamond (2002) Curr. Biol. 12, 1-11; Scherl, Coute, Deon, Calle, Kindbeiter, Sanchez, Greco, Hochstrasser and Diaz (2002) Mol. Biol. Cell 13, 4100-4109]. Nearly 400 proteins were identified within the nucleolar proteome so far in humans. Approx. 12% of the identified proteins were previously shown to be nucleolar in human cells and, as expected, nearly all of the known housekeeping proteins required for ribosome biogenesis were identified in these analyses. Surprisingly, approx. 30% represented either novel or uncharacterized proteins. This review focuses on how to apply the derived knowledge of this newly recognized nucleolar proteome, such as their amino acid/peptide composition and their homologies across species, to explore the function and dynamics of the nucleolus, and suggests ways to identify, in silico, possible functions of the novel/uncharacterized proteins and potential interaction networks within the human nucleolus, or between the nucleolus and other nuclear organelles, by drawing resources from the public domain.

Subnuclear systems for synthesis of simian virus 40 DNA in vitro.

PubMed Central

Edenberg, H J; Waqar, M A; Huberman, J A

1976-01-01

We have developed two subnuclear systems for synthesis of DNA of simian virus 40 in vitro. We prepare chromatin from infected cells by the method of Hancock [(1974) J. Mol. Biol. 86, 649-663]; these "chromatin bodies" can be disrupted and large debris can be pelleted, leaving a supernatant ("soluble system"). Both chromatin bodies and the soluble system incorporate deoxyribonucleoside triphosphates into nucleoprotein complexes that contain simian virus 40 DNA. The DNA labeled in short pulses sediments in neutral sucrose gradients slightly faster than mature simian virus 40 DNA, as expected for replicating intermediate. When rebanded in alkaline sucrose gradients, about half of the radioactivity is found in short strands (200-300 nucleotides) and half in longer strands (up to full viral size). When these systems are supplemented with a cytoplasmic preparation from HeLa cells, synthesis is stimulated about 5-fold, and the short strands are converted into strands of up to full viral length as well as into covalently closed circles. These subnuclear DNA-replicating systems should be useful for biochemical fractionation and characterization of some of the proteins required for DNA replication. PMID:188037

Beyond gastric adenocarcinoma: Multimodality assessment of common and uncommon gastric neoplasms

PubMed Central

Richman, Danielle M.; Tirumani, Sree Harsha; Hornick, Jason L.; Fuchs, Charles S.; Howard, Stephanie; Krajewski, Katherine; Ramaiya, Nikhil; Rosenthal, Michael

2016-01-01

Despite advances in molecular biology, imaging, and treatment, gastric neoplasms remain a significant cause of morbidity and mortality; gastric adenocarcinoma is the fifth most common malignancy and third most common cause of death worldwide (Brenner et al., Methods Mol Biol 472:467–477, 2009; Howson et al. Epidemiol Rev 8:1–27, 1986; Roder, Gastric Cancer 5(Suppl 1):5–11, 2002; Ferlay et al., GLOBOCAN 2012 v1.0, Cancer Incidence and Mortality Worldwide: IARC CancerBase No. 11 [Internet]. International Agency for Research on Cancer, 2013). Because of both the frequency at which malignant gastric tumors occur as well as the worldwide impact, gastric neoplasms remain important lesions to identify and characterize on all imaging modalities. Despite the varied histologies and behaviors of these neoplasms, many have similar imaging features. Nonetheless, the treatment, management, and prognosis of gastric neoplasms vary by pathology, so it is essential for the radiologist to make every effort to differentiate between these lesions and raise the less common entities as differential diagnostic considerations when appropriate. PMID:27645897

Enzyme activation through the utilization of intrinsic dianion binding energy.

PubMed

Amyes, T L; Malabanan, M M; Zhai, X; Reyes, A C; Richard, J P

2017-03-01

We consider 'the proposition that the intrinsic binding energy that results from the noncovalent interaction of a specific substrate with the active site of the enzyme is considerably larger than is generally believed. An important part of this binding energy may be utilized to provide the driving force for catalysis, so that the observed binding energy represents only what is left over after this utilization' [Jencks,W.P. (1975) Adv. Enzymol. Relat. Areas. Mol. Biol. , , 219-410]. The large ~12 kcal/mol intrinsic substrate phosphodianion binding energy for reactions catalyzed by triosephosphate isomerase (TIM), orotidine 5'-monophosphate decarboxylase and glycerol-3-phosphate dehydrogenase is divided into 4-6 kcal/mol binding energy that is expressed on the formation of the Michaelis complex in anchoring substrates to the respective enzyme, and 6-8 kcal/mol binding energy that is specifically expressed at the transition state in activating the respective enzymes for catalysis. A structure-based mechanism is described where the dianion binding energy drives a conformational change that activates these enzymes for catalysis. Phosphite dianion plays the active role of holding TIM in a high-energy closed active form, but acts as passive spectator in showing no effect on transition-state structure. The result of studies on mutant enzymes is presented, which support the proposal that the dianion-driven enzyme conformational change plays a role in enhancing the basicity of side chain of E167, the catalytic base, by clamping the base between a pair of hydrophobic side chains. The insight these results provide into the architecture of enzyme active sites and the development of strategies for the de novo design of protein catalysts is discussed. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Functional Analysis of the Beclin-1 Tumor Suppressor Interaction with hVps34 (Type-III P13’-kinase) in Breast Cancer Cells

DTIC Science & Technology

2008-06-01

Methods for monitoring autophagy. Int.J Biochem.Cell Biol., 36: 2491-2502, 2004. 13. Scarlatti , F., Bauvy, C., Ventruti, A., Sala, G., Cluzeaud, F...J.Biol.Chem., 279: 18384-18391, 2004. 14. Scarlatti , F., Maffei, R., Beau, I., Codogno, P., and Ghidoni, R. Role of non-canonical Beclin 1- independent

Solid-State NMR Studies of Amyloid Materials: A Protocol to Define an Atomic Model of Aβ(1-42) in Amyloid Fibrils.

PubMed

Xiao, Yiling; McElheny, Dan; Hoshi, Minako; Ishii, Yoshitaka

2018-01-01

Intense efforts have been made to understand the molecular structures of misfolded amyloid β (Aβ) in order to gain insight into the pathological mechanism of Alzheimer's disease. Solid-state NMR spectroscopy (SSNMR) is considered a primary tool for elucidating the structures of insoluble and noncrystalline amyloid fibrils and other amyloid assemblies. In this chapter, we describe a detailed protocol to obtain the first atomic model of the 42-residue human Aβ peptide Aβ(1-42) in structurally homogeneous amyloid fibrils from our recent SSNMR study (Nat Struct Mol Biol 22:499-505, 2015). Despite great biological and clinical interest in Aβ(1-42) fibrils, their structural details have been long-elusive until this study. The protocol is divided into four sections. First, the solid-phase peptide synthesis (SPPS) and purification of monomeric Aβ(1-42) is described. We illustrate a controlled incubation method to prompt misfolding of Aβ(1-42) into homogeneous amyloid fibrils in an aqueous solution with fragmented Aβ(1-42) fibrils as seeds. Next, we detail analysis of Aβ(1-42) fibrils by SSNMR to obtain structural restraints. Finally, we describe methods to construct atomic models of Aβ(1-42) fibrils based on SSNMR results through two-stage molecular dynamics calculations.

Beyond detection: biological physics informing progression and treatment of cancer Beyond detection: biological physics informing progression and treatment of cancer

NASA Astrophysics Data System (ADS)

Newman, T. J.; Thompson, A. M.

2012-12-01

The full text of the Preface is given in the PDF file. References [1] Kaur P et al 2012 Phys. Biol. 9 065001 [2] Lobikin M et al 2012 Phys. Biol. 9 065002 [3] Tanner K 2012 Phys. Biol. 9 065003 [4] Liu S V et al 2012 Phys. Biol. 9 065004 [5] Liao D et al 2012 Phys. Biol. 9 065005 [6] Liao D et al 2012 Phys. Biol. 9 065006 [7] Orlando P A et al 2012 Phys. Biol. 9 065007

EDITORIAL: Annual prizes for best papers

NASA Astrophysics Data System (ADS)

2006-09-01

2005 Roberts Prize The publishers of Physics in Medicine and Biology (PMB) in association with the Institute of Physics and Engineering in Medicine (IPEM) jointly award an annual prize for an article published in PMB during the previous year. The following 14 articles, listed below in chronological order, were rated the best of 2005 based on the (two or three) referees' assessments: P Kundrát et al 2005 Probabilistic two-stage model of cell inactivation by ionizing particles Phys. Med. Biol. 50 1433-47 D Arora et al 2005 Direct thermal dose control of constrained focused ultrasound treatments: phantom and in vivo evaluation Phys. Med. Biol. 50 1919-35 J S Dysart et al 2005 Characterization of Photofrin photobleaching for singlet oxygen dose estimation during photodynamic therapy of MLL cells in vitro Phys. Med. Biol. 50 2597-616 M Defrise et al 2005 Fourier rebinning of time-of-flight PET data Phys. Med. Biol. 50 2749-63 Z Su et al 2005 Systematic investigation of the signal properties of polycrystalline HgI2 detectors under mammographic, radiographic, fluoroscopic and radiotherapy irradiation conditions Phys. Med. Biol. 50 2907-28 E Bräuer-Krisch et al 2005 New irradiation geometry for microbeam radiation therapy Phys. Med. Biol. 50 3103-11 H C Pyo et al 2005 Identification of current density distribution in electrically conducting subject with anisotropic conductivity distribution Phys. Med. Biol. 50 3183-96 R P Findlay et al 2005 Effects of posture on FDTD calculations of specific absorption rate in a voxel model of the human body Phys. Med. Biol. 50 3825-35 G Alexandrakis et al 2005 Tomographic bioluminescence imaging by use of a combined optical-PET (OPET) system: a computer simulation feasibility study Phys. Med. Biol. 50 4225-41 J Keshvari et al 2005 Comparison of radio frequency energy absorption in ear and eye region of children and adults at 900, 1800 and 2450 MHz Phys. Med. Biol. 50 4355-69 J Laufer et al 2005 In vitro measurements of absolute blood oxygen saturation using pulsed near-infrared photoacoustic spectroscopy: accuracy and resolution Phys. Med. Biol. 50 4409-28 Z Cao et al 2005 Optimal number of pinholes in multi-pinhole SPECT for mouse brain imaging---a simulation study Phys. Med. Biol. 50 4609-24 R Dharmakumar et al 2005 A novel microbubble construct for intracardiac or intravascular MR manometry: a theoretical study Phys. Med. Biol. 50 4745-62 R Chopra et al 2005 Method for MRI-guided conformal thermal therapy of prostate with planar transurethral ultrasound heating applicators Phys. Med. Biol. 50 4957-75 The IPEM Publications Committee then assessed and rated these papers in order to choose a winner. We have much pleasure in advising readers that the 2005 Roberts Prize is awarded to: J S Dysart and M S Patterson 2005 Characterization of Photofrin photobleaching for singlet oxygen dose estimation during photodynamic therapy of MLL cells in vitro Phys. Med. Biol. 50 2597-616 2006 Prize for the Highest Cited Paper The annual prize for the most highly cited paper is awarded by the journal publishers to the article published in PMB that has received the most citations1 in the previous 5 years (in this case for the period 2001 to 2005 inclusive). We have much pleasure in advising readers that the 2006 prize is awarded to: P J Keall, V R Kini, S S Vedam and R Mohan 2001 Motion adaptive x-ray therapy: a feasibility study Phys. Med. Biol. 46 1-10 Simon Harris, Publisher Steve Webb, Editor-in-Chief 1 Figures taken from Thomson/ISI

Watching proteins function with time-resolved x-ray crystallography

NASA Astrophysics Data System (ADS)

Šrajer, Vukica; Schmidt, Marius

2017-09-01

Macromolecular crystallography was immensely successful in the last two decades. To a large degree this success resulted from use of powerful third generation synchrotron x-ray sources. An expansive database of more than 100 000 protein structures, of which many were determined at resolution better than 2 Å, is available today. With this achievement, the spotlight in structural biology is shifting from determination of static structures to elucidating dynamic aspects of protein function. A powerful tool for addressing these aspects is time-resolved crystallography, where a genuine biological function is triggered in the crystal with a goal of capturing molecules in action and determining protein kinetics and structures of intermediates (Schmidt et al 2005a Methods Mol. Biol. 305 115-54, Schmidt 2008 Ultrashort Laser Pulses in Biology and Medicine (Berlin: Springer) pp 201-41, Neutze and Moffat 2012 Curr. Opin. Struct. Biol. 22 651-9, Šrajer 2014 The Future of Dynamic Structural Science (Berlin: Springer) pp 237-51). In this approach, short and intense x-ray pulses are used to probe intermediates in real time and at room temperature, in an ongoing reaction that is initiated synchronously and rapidly in the crystal. Time-resolved macromolecular crystallography with 100 ps time resolution at synchrotron x-ray sources is in its mature phase today, particularly for studies of reversible, light-initiated reactions. The advent of the new free electron lasers for hard x-rays (XFELs; 5-20 keV), which provide exceptionally intense, femtosecond x-ray pulses, marks a new frontier for time-resolved crystallography. The exploration of ultra-fast events becomes possible in high-resolution structural detail, on sub-picosecond time scales (Tenboer et al 2014 Science 346 1242-6, Barends et al 2015 Science 350 445-50, Pande et al 2016 Science 352 725-9). We review here state-of-the-art time-resolved crystallographic experiments both at synchrotrons and XFELs. We also outline challenges and further developments necessary to broaden the application of these methods to many important proteins and enzymes of biomedical relevance.

Watching proteins function with time-resolved x-ray crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Šrajer, Vukica; Schmidt, Marius

Macromolecular crystallography was immensely successful in the last two decades. To a large degree this success resulted from use of powerful third generation synchrotron x-ray sources. An expansive database of more than 100 000 protein structures, of which many were determined at resolution better than 2 Å, is available today. With this achievement, the spotlight in structural biology is shifting from determination of static structures to elucidating dynamic aspects of protein function. A powerful tool for addressing these aspects is time-resolved crystallography, where a genuine biological function is triggered in the crystal with a goal of capturing molecules in actionmore » and determining protein kinetics and structures of intermediates (Schmidt et al 2005a Methods Mol. Biol. 305 115–54, Schmidt 2008 Ultrashort Laser Pulses in Biology and Medicine (Berlin: Springer) pp 201–41, Neutze and Moffat 2012 Curr. Opin. Struct. Biol. 22 651–9, Šrajer 2014 The Future of Dynamic Structural Science (Berlin: Springer) pp 237–51). In this approach, short and intense x-ray pulses are used to probe intermediates in real time and at room temperature, in an ongoing reaction that is initiated synchronously and rapidly in the crystal. Time-resolved macromolecular crystallography with 100 ps time resolution at synchrotron x-ray sources is in its mature phase today, particularly for studies of reversible, light-initiated reactions. The advent of the new free electron lasers for hard x-rays (XFELs; 5–20 keV), which provide exceptionally intense, femtosecond x-ray pulses, marks a new frontier for time-resolved crystallography. The exploration of ultra-fast events becomes possible in high-resolution structural detail, on sub-picosecond time scales (Tenboer et al 2014 Science 346 1242–6, Barends et al 2015 Science 350 445–50, Pande et al 2016 Science 352 725–9). We review here state-of-the-art time-resolved crystallographic experiments both at synchrotrons and XFELs. We also outline challenges and further developments necessary to broaden the application of these methods to many important proteins and enzymes of biomedical relevance.« less

Base composition and expression level of human genes.

PubMed

Arhondakis, Stilianos; Auletta, Fabio; Torelli, Giuseppe; D'Onofrio, Giuseppe

2004-01-21

It is well known that the gene distribution is non-uniform in the human genome, reaching the highest concentration in the GC-rich isochores. Also the amino acid frequencies, and the hydrophobicity, of the corresponding encoded proteins are affected by the high GC level of the genes localized in the GC-rich isochores. It was hypothesized that the gene expression level as well is higher in GC-rich compared to GC-poor isochores [Mol. Biol. Evol. 10 (1993) 186]. Several features of human genes and proteins, namely expression level, coding and non-coding lengths, and hydrophobicity were investigated in the present paper. The results support the hypothesis reported above, since all the parameters so far studied converge to the same conclusion, that the average expression level of the GC-rich genes is significantly higher than that of the GC-poor genes.

Aurora kinase B regulates axonal outgrowth and regeneration in the spinal motor neurons of developing zebrafish.

PubMed

Gwee, Serene S L; Radford, Rowan A W; Chow, Sharron; Syal, Monisha D; Morsch, Marco; Formella, Isabel; Lee, Albert; Don, Emily K; Badrock, Andrew P; Cole, Nicholas J; West, Adrian K; Cheung, Steve N S; Chung, Roger S

2018-02-21

Aurora kinase B (AurkB) is a serine/threonine protein kinase with a well-characterised role in orchestrating cell division and cytokinesis, and is prominently expressed in healthy proliferating and cancerous cells. However, the role of AurkB in differentiated and non-dividing cells has not been extensively explored. Previously, we have described a significant upregulation of AurkB expression in cultured cortical neurons following an experimental axonal transection. This is somewhat surprising, as AurkB expression is generally associated only with dividing cells Frangini et al. (Mol Cell 51:647-661, 2013); Hegarat et al. (J Cell Biol 195:1103-1113, 2011); Lu et al. (J Biol Chem 283:31785-31790, 2008); Trakala et al. (Cell Cycle 12:1030-1041, 2014). Herein, we present the first description of a role for AurkB in terminally differentiated neurons. AurkB was prominently expressed within post-mitotic neurons of the zebrafish brain and spinal cord. The expression of AurkB varied during the development of the zebrafish spinal motor neurons. Utilising pharmacological and genetic manipulation to impair AurkB activity resulted in truncation and aberrant motor axon morphology, while overexpression of AurkB resulted in extended axonal outgrowth. Further pharmacological inhibition of AurkB activity in regenerating axons delayed their recovery following UV laser-mediated injury. Collectively, these results suggest a hitherto unreported role of AurkB in regulating neuronal development and axonal outgrowth.

The Drosophila genes CG14593 and CG30106 code for G-protein-coupled receptors specifically activated by the neuropeptides CCHamide-1 and CCHamide-2.

PubMed

Hansen, Karina K; Hauser, Frank; Williamson, Michael; Weber, Stine B; Grimmelikhuijzen, Cornelis J P

2011-01-07

Recently, a novel neuropeptide, CCHamide, was discovered in the silkworm Bombyx mori (L. Roller et al., Insect Biochem. Mol. Biol. 38 (2008) 1147-1157). We have now found that all insects with a sequenced genome have two genes, each coding for a different CCHamide, CCHamide-1 and -2. We have also cloned and deorphanized two Drosophila G-protein-coupled receptors (GPCRs) coded for by genes CG14593 and CG30106 that are selectively activated by Drosophila CCH-amide-1 (EC(50), 2×10(-9) M) and CCH-amide-2 (EC(50), 5×10(-9) M), respectively. Gene CG30106 (symbol synonym CG14484) has in a previous publication (E.C. Johnson et al., J. Biol. Chem. 278 (2003) 52172-52178) been wrongly assigned to code for an allatostatin-B receptor. This conclusion is based on our findings that the allatostatins-B do not activate the CG30106 receptor and on the recent findings from other research groups that the allatostatins-B activate an unrelated GPCR coded for by gene CG16752. Comparative genomics suggests that a duplication of the CCHamide neuropeptide signalling system occurred after the split of crustaceans and insects, about 410 million years ago, because only one CCHamide neuropeptide gene is found in the water flea Daphnia pulex (Crustacea) and the tick Ixodes scapularis (Chelicerata). Copyright © 2010 Elsevier Inc. All rights reserved.

Using sea urchin gametes and zygotes to investigate centrosome duplication.

PubMed

Sluder, Greenfield

2016-01-01

Centriole structure and function in the sea urchin zygote parallel those in mammalian somatic cells. Here, I briefly introduce the properties and attributes of the sea urchin system that make it an attractive platform for the study of centrosome and centriole duplication. These attributes apply to all echinoderms readily available from commercial suppliers: sea urchins, sand dollars, and starfish. I list some of the practical aspects of the system that make it a cost- and time-effective system for experimental work and then list properties that are a "tool kit" that can be used to conduct studies that would not be practical, or in some cases not possible, with mammalian somatic cells. Since centrioles organize and localize the pericentriolar material that nucleates the astral arrays of microtubules (Bobinnec et al. in J Cell Biol 143(6):1575-1589, 1998), the pattern of aster duplication over several cell cycles can be used as a reliable measure for centriole duplication (Sluder and Rieder in J Cell Biol 100(3):887-896, 1985). Descriptions of the methods my laboratory has used to handle and image echinoderm zygotes are reviewed in Sluder et al. (Methods Cell Biol 61:439-472, 1999). Also included is a bibliography of papers that describe additional methods.

The BiolAD-DB system : an informatics system for clinical and genetic data.

PubMed

Nielsen, David A; Leidner, Marty; Haynes, Chad; Krauthammer, Michael; Kreek, Mary Jeanne

2007-01-01

The Biology of Addictive Diseases-Database (BiolAD-DB) system is a research bioinformatics system for archiving, analyzing, and processing of complex clinical and genetic data. The database schema employs design principles for handling complex clinical information, such as response items in genetic questionnaires. Data access and validation is provided by the BiolAD-DB client application, which features a data validation engine tightly coupled to a graphical user interface. Data integrity is provided by the password-protected BiolAD-DB SQL compliant server and database. BiolAD-DB tools further provide functionalities for generating customized reports and views. The BiolAD-DB system schema, client, and installation instructions are freely available at http://www.rockefeller.edu/biolad-db/.

TECHNICAL REPORT

DOE Office of Scientific and Technical Information (OSTI.GOV)

DR. ROBERT SINGER

2007-10-11

Because this DOE grant was abruptly terminated without warning, this group was not able to accomplish the insertion of the biosensor genes into the mouse lines. They have been able to generate some of the mouse lines but have not been able to complete the ones that would give them the model systems that would allow them to investigate metastasis real-time in living tumors at the cellular level. Nonetheless, until the loss of funding, they have made progress in applications of the equipment to biological problems involving RNA and protein movement in living cells. The following products were delivered: (1)more » Imaging of gene expression in living cells and tissues, Singer RH, Lawrence DS, Ovryn B, Condeelis J, J Biomed Optics 10:0514061-0514069, 2005. This paper describes the method for activating single genes within cells and tissues. (2) Single Cell Gene Expression Profiling: Multiplexed Expression Fluorescence in situ Hybridization (FISH): Application to the Analysis of Cultured Cells. Levsky JM, Braut SA, Singer RH, Cell Biology: A Laboratory Handbook Volume 4, eds Celis JE, et al, 121-130. Academic Press, 2005. This paper describes the methodology for single cell expression profiling in tissues. (3) Spatial regulation of beta-actin translation by Src-dependent phosphorylation of ZBP1, Huttelmaier S, Zenklusen D, Lederer M, Dictenberg J, Lorenz M, Meng X, Bassell GJ, Condeelis J, Singer RH, Nature 438:512-515, 2005. This paper describes the mechanism by which the translational repressor of actin mRNA ZBP1 can effect regulation of cell motility and metastasis. (4) Visualization of mRNA translation in living cells, Rodriguez AJ, Shenoy SM, Singer RH, Condeelis J, J Cell Biol 175:67-76, 2006. This work describes a method to visualize mRNA translation in single cells. (5) Imaging mRNA movement from transcription sites to translation sites, Rodriguez AJ, Condeelis J, Singer RH, Dictenberg JB, Semin Cell Dev Biol 18:202-208, 2007. This review describes current technology for visualizing mRNA from birth to death. (6) In vivo dynamics of RNA polymerase II transcription, Darzacq X, Shav-Tal Y, de Turris V, Brody Y, Shenoy SM, Phair RD, Singer RH, Nat Struct Mol Biol 14:796-806, 2007. This paper describes methods for visualizing gene transcription in real time and provides a systems modeling approach to understanding polymerase dynamics. (See News & Views 14:788) (7) Nuclear microenvironment in cancer diagnosis and treatment, Pezo RC, Singer RH, J Cell Biochem in press (2007). This work describes the environmental factors acting on the genes directly. (8) The spatial order of transcription in mammalian cells, Levsky JM, Shenoy SM, Chubb JR, Hall CB, Capodieci P, Singer RH, J Cell Biochem in press (2007). This work describes how active genes are spatially distributed throughout the nucleus. (9) ZBP1 Enhances Cell Polarity and Reduces Metastasis, Lapidus K, Wyckoff J, Mouneimne G, Lorenz M, Soon L, Condeelis J and Singer RH, JCS in press (2007). This work describes the role of the RNA binding protein in cell polarity and metastasis.« less

Two-state protein model with water interactions: Influence of temperature on the intrinsic viscosity of myoglobin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bakk, Audun

2001-06-01

We describe a single-domain protein as a two-state system with water interactions. Around the unfolded apolar parts of the protein we incorporate the hydration effect by introducing hydrogen bonds between the water molecules in order to mimic the {open_quotes}icelike{close_quotes} shell structure. Intrinsic viscosity, proportional to the effective hydrodynamic volume, for sperm whale metmyoglobin is assigned from experimental data in the folded and in the denaturated state. By weighing statistically the two states against the degree of folding, we express the total intrinsic viscosity. The temperature dependence of the intrinsic viscosity, for different chemical potentials, is in good correspondence with experimentalmore » data [P. L. Privalov , J. Mol. Biol. >190, 487 (1986)]. Cold and warm unfolding, common to small globular proteins, is also a result of the model.« less

A full-coordinate model of the polymerase domain of HIV-1 reverse transcriptase and its interaction with a nucleic acid substrate

NASA Technical Reports Server (NTRS)

Setlik, R. F.; Meyer, D. J.; Shibata, M.; Roskwitalski, R.; Ornstein, R. L.; Rein, R.

1994-01-01

We present a full-coordinate model of residues 1-319 of the polymerase domain of HIV-I reverse transcriptase. This model was constructed from the x-ray crystallographic structure of Jacobo-Molina et al. (Jacobo-Molina et al., P.N.A.S. USA 90, 6320-6324 (1993)) which is currently available to the degree of C-coordinates. The backbone and side-chain atoms were constructed using the MAXSPROUT suite of programs (L. Holm and C. Sander, J. Mol. Biol. 218, 183-194 (1991)) and refined through molecular modeling. A seven base pair A-form dsDNA was positioned in the nucleic acid binding cleft to represent the template-primer complex. The orientation of the template-primer complex in the nucleic acid binding cleft was guided by the positions of phosphorus atoms in the crystal structure.

Crystallographic evidence for noncoplanar catalytic aspartic acids in plasmepsin II resides in the Protein Data Bank.

PubMed

Robbins, Arthur H; Dunn, Ben M; Agbandje-McKenna, Mavis; McKenna, Robert

2009-03-01

The carboxylate atoms of the two catalytic aspartic acid residues in aspartic proteases are nearly coplanar and in the uncomplexed form share an in-plane nucleophilic water molecule that is central to the mechanism of these enzymes. This note reports that while reviewing the electron-density maps derived from the deposited data for uncomplexed plasmepsin II from Plasmodium falciparum [Asojo et al. (2003), J. Mol. Biol. 327, 173-181; PDB code 1lf4], it was discovered that the aspartic acid residues in this structure should in fact be distinctly noncoplanar. The crystallographic model from the deposited coordinates has been re-refined against the 1.9 A resolution published diffraction data to an R(cryst) of 21.2% and an R(free) of 22.2%. The catalytic water molecule is present, but the plane of the carboxylate group of Asp214 is rotated by 66 degrees from its original position.

Structural models of antibody variable fragments: A method for investigating binding mechanisms

NASA Astrophysics Data System (ADS)

Petit, Samuel; Brard, Frédéric; Coquerel, Gérard; Perez, Guy; Tron, François

1998-03-01

The value of comparative molecular modeling for elucidating structure-function relationships was demonstrated by analyzing six anti-nucleosome autoantibody variable fragments. Structural models were built using the automated procedure developed in the COMPOSER software, subsequently minimized with the AMBER force field, and validated according to several standard geometric and chemical criteria. Canonical class assignment from Chothia and Lesk's [Chottin and Lesk, J. Mol. Biol., 196 (1987) 901; Chothia et al., Nature, 342 (1989) 877] work was used as a supplementary validation tool for five of the six hypervariable loops. The analysis, based on the hypothesis that antigen binding could occur through electrostatic interactions, reveals a diversity of possible binding mechanisms of anti-nucleosome or anti-histone antibodies to their cognate antigen. These results lead us to postulate that anti-nucleosome autoantibodies could have different origins. Since both anti-DNA and anti-nculeosome autoantibodies are produced during the course of systemic lupus erythematosus, a non-organ specific autoimmune disease, a comparative structural and electrostatic analysis of the two populations of autoantibodies may constitute a way to elucidate their origin and the role of the antigen in tolerance breakdown. The present study illustrates some interests, advantages and limits of a methodology based on the use of comparative modeling and analysis of molecular surface properties.

Segmental isotopic labeling of HIV-1 capsid protein assemblies for solid state NMR.

PubMed

Gupta, Sebanti; Tycko, Robert

2018-02-01

Recent studies of noncrystalline HIV-1 capsid protein (CA) assemblies by our laboratory and by Polenova and coworkers (Protein Sci 19:716-730, 2010; J Mol Biol 426:1109-1127, 2014; J Biol Chem 291:13098-13112, 2016; J Am Chem Soc 138:8538-8546, 2016; J Am Chem Soc 138:12029-12032, 2016; J Am Chem Soc 134:6455-6466, 2012; J Am Chem Soc 132:1976-1987, 2010; J Am Chem Soc 135:17793-17803, 2013; Proc Natl Acad Sci USA 112:14617-14622, 2015; J Am Chem Soc 138:14066-14075, 2016) have established the capability of solid state nuclear magnetic resonance (NMR) measurements to provide site-specific structural and dynamical information that is not available from other types of measurements. Nonetheless, the relatively high molecular weight of HIV-1 CA leads to congestion of solid state NMR spectra of fully isotopically labeled assemblies that has been an impediment to further progress. Here we describe an efficient protocol for production of segmentally labeled HIV-1 CA samples in which either the N-terminal domain (NTD) or the C-terminal domain (CTD) is uniformly 15 N, 13 C-labeled. Segmental labeling is achieved by trans-splicing, using the DnaE split intein. Comparisons of two-dimensional solid state NMR spectra of fully labeled and segmentally labeled tubular CA assemblies show substantial improvements in spectral resolution. The molecular structure of HIV-1 assemblies is not significantly perturbed by the single Ser-to-Cys substitution that we introduce between NTD and CTD segments, as required for trans-splicing.

Mapping Polymerization and Allostery of Hemoglobin S Using Point Mutations

PubMed Central

Weinkam, Patrick; Sali, Andrej

2014-01-01

Hemoglobin is a complex system that undergoes conformational changes in response to oxygen, allosteric effectors, mutations, and environmental changes. Here, we study allostery and polymerization of hemoglobin and its variants by application of two previously described methods: (i) AllosMod for simulating allostery dynamics given two allosterically related input structures and (ii) a machine-learning method for dynamics- and structure-based prediction of the mutation impact on allostery (Weinkam et al. J. Mol. Biol. 2013), now applicable to systems with multiple coupled binding sites such as hemoglobin. First, we predict the relative stabilities of substates and microstates of hemoglobin, which are determined primarily by entropy within our model. Next, we predict the impact of 866 annotated mutations on hemoglobin’s oxygen binding equilibrium. We then discuss a subset of 30 mutations that occur in the presence of the sickle cell mutation and whose effects on polymerization have been measured. Seven of these HbS mutations occur in three predicted druggable binding pockets that might be exploited to directly inhibit polymerization; one of these binding pockets is not apparent in the crystal structure but only in structures generated by AllosMod. For the 30 mutations, we predict that mutation-induced conformational changes within a single tetramer tend not to significantly impact polymerization; instead, these mutations more likely impact polymerization by directly perturbing a polymerization interface. Finally, our analysis of allostery allows us to hypothesize why hemoglobin evolved to have multiple subunits and a persistent low frequency sickle cell mutation. PMID:23957820

Experimental design and multiple response optimization. Using the desirability function in analytical methods development.

PubMed

Candioti, Luciana Vera; De Zan, María M; Cámara, María S; Goicoechea, Héctor C

2014-06-01

A review about the application of response surface methodology (RSM) when several responses have to be simultaneously optimized in the field of analytical methods development is presented. Several critical issues like response transformation, multiple response optimization and modeling with least squares and artificial neural networks are discussed. Most recent analytical applications are presented in the context of analytLaboratorio de Control de Calidad de Medicamentos (LCCM), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, C.C. 242, S3000ZAA Santa Fe, ArgentinaLaboratorio de Control de Calidad de Medicamentos (LCCM), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, C.C. 242, S3000ZAA Santa Fe, Argentinaical methods development, especially in multiple response optimization procedures using the desirability function. Copyright © 2014 Elsevier B.V. All rights reserved.

Locomotor Stability in a Model Swimmer: Coupling Fluid Dynamics, Neurophysiology and Muscle Mechanics

DTIC Science & Technology

2017-07-05

springs which resist deformation. (C) Inset that shows the position of the muscle segments. Cohen, Holmes, Rand, J. Math Biol. 1982 A representative...numbers are the segment number, labeled from head to tail. Cohen, Holmes, Rand, J. Math Biol. 1982 The signals are periodic. Cohen, Holmes, Rand, J... Math Biol. 1982 From head to tail there is a phase lag on each side. Cohen, Holmes, Rand, J. Math Biol. 1982 On a given segment, the signals are in

Rad50S alleles of the Mre11 complex: questions answered and questions raised.

PubMed

Usui, Takehiko; Petrini, John H J; Morales, Monica

2006-08-15

We find that Rad50S mutations in yeast and mammals exhibit constitutive PIKK (PI3-kinase like kinase)-dependent signaling [T. Usui, H. Ogawa, J.H. Petrini, A DNA damage response pathway controlled by Tel1 and the Mre11 complex. Mol. Cell 7 (2001) 1255-1266.; M. Morales, J.W. Theunissen, C.F. Kim, R. Kitagawa, M.B. Kastan, J.H. Petrini, The Rad50S allele promotes ATM-dependent DNA damage responses and suppresses ATM deficiency: implications for the Mre11 complex as a DNA damage sensor. Genes Dev. 19 (2005) 3043-4354.]. The signaling depends on Mre11 complex functions, consistent with its role as a DNA damage sensor. Rad50S is distinct from hypomorphic mutations of Mre11 and Nbs1 in mammals [M. Morales, J.W. Theunissen, C.F. Kim, R. Kitagawa, M.B. Kastan, J.H. Petrini, The Rad50S allele promotes ATM-dependent DNA damage responses and suppresses ATM deficiency: implications for the Mre11 complex as a DNA damage sensor. Genes Dev. 19 (2005) 3043-3054.; J.P. Carney, R.S. Maser, H. Olivares, E.M. Davis, Le M. Beau, J.R. Yates, III, L. Hays, W.F. Morgan, J.H. Petrini, The hMre11/hRad50 protein complex and Nijmegen breakage syndrome: linkage of double-strand break repair to the cellular DNA damage response. Cell 93 (1998) 477-486.; G.S. Stewart, R.S. Maser, T. Stankovic, D.A. Bressan, M.I. Kaplan, N.G. Jaspers, A. Raams, P.J. Byrd, J.H. Petrini, A.M. Taylor, The DNA double-strand break repair gene hMRE11 is mutated in individuals with an ataxia-telangiectasia-like disorder. Cell 99 (1999) 577-587.; B.R. Williams, O.K. Mirzoeva, W.F. Morgan, J. Lin, W. Dunnick, J.H. Petrini, A murine model of nijmegen breakage syndrome. Curr. Biol. 12 (2002) 648-653.; J.W. Theunissen, M.I. Kaplan, P.A. Hunt, B.R. Williams, D.O. Ferguson, F.W. Alt, J.H. Petrini, Checkpoint failure and chromosomal instability without lymphomagenesis in Mre11(ATLD1/ATLD1) mice. Mol. Cell 12 (2003) 1511-1523.] and the Mre11 complex deficiency in yeast [T. Usui, H. Ogawa, J.H. Petrini, A DNA damage response pathway controlled by Tel1 and the Mre11 complex. Mol. Cell 7 (2001) 1255-1266.; D'D. Amours, S.P. Jackson, The yeast Xrs2 complex functions in S phase checkpoint regulation. Genes Dev. 15 (2001) 2238-49. ; M. Grenon, C. Gilbert, N.F. Lowndes, Checkpoint activation in response to double-strand breaks requires the Mre11/Rad50/Xrs2 complex. Nat. Cell Biol. 3 (2001) 844-847. ] where the signaling is compromised. Herein, we describe evidence for chronic signaling by Rad50S and discuss possible mechanisms.

EDITORIAL: Roberts Prize for the best paper published in 2010 Roberts Prize for the best paper published in 2010

NASA Astrophysics Data System (ADS)

Webb, Steve; Harris, Simon

2011-08-01

The publishers of Physics in Medicine and Biology (PMB), IOP Publishing, in association with the journal owners, the Institute of Physics and Engineering in Medicine (IPEM), jointly award an annual prize for the best paper published in PMB during the previous year. The procedure for deciding the winner has been made as thorough as possible, to try to ensure that an outstanding paper wins the prize. We started off with a shortlist of the 10 research papers published in 2010 which were rated the best based on the referees' quality assessments. Following the submission of a short 'case for winning' document by each of the shortlisted authors, an IPEM college of jurors of the status of FIPEM assessed and rated these 10 papers in order to choose a winner, which was then endorsed by the Editorial Board. We have much pleasure in advising readers that the Roberts Prize for the best paper published in 2010 is awarded to M M Paulides et al from Erasmus MC, Rotterdam, The Netherlands, for their paper on hyperthermia treatment: The clinical feasibility of deep hyperthermia treatment in the head and neck: new challenges for positioning and temperature measurement M M Paulides, J F Bakker, M Linthorst, J van der Zee, Z Rijnen, E Neufeld, P M T Pattynama, P P Jansen, P C Levendag and G C van Rhoon 2010 Phys. Med. Biol. 55 2465 Our congratulations go to these authors. Of course all of the shortlisted papers were of great merit, and the full top-10 is listed below (in alphabetical order). Steve Webb Editor-in-Chief Simon Harris Publisher References Alonzo-Proulx O, Packard N, Boone J M, Al-Mayah A, Brock K K, Shen S Z and Yaffe M J 2010 Validation of a method for measuring the volumetric breast density from digital mammograms Phys. Med. Biol. 55 3027 Bian J, Siewerdsen J H, Han X, Sidky E Y, Prince J L, Pelizzari C A and Pan X 2010 Evaluation of sparse-view reconstruction from flat-panel-detector cone-beam CT Phys. Med. Biol. 55 6575 Brun M-A, Formanek F, Yasuda A, Sekine M, Ando N and Eishii Y 2010 Terahertz imaging applied to cancer diagnosis Phys. Med. Biol. 55 4615 Eklund K and Ahnesjö A 2010 Modeling silicon diode dose response factors for small photon fields Phys. Med. Biol. 55 7411 Kolb A, Lorenz E, Judenhofer M S, Renker D, Lankes K and Pichler B J 2010 Evaluation of Geiger-mode APDs for PET block detector designs Phys. Med. Biol. 55 1815 Lobo J and Popescu I A 2010 Two new DOSXYZnrc sources for 4D Monte Carlo simulations of continuously variable beam configurations, with applications to RapidArc, VMAT, TomoTherapy and CyberKnife Phys. Med. Biol. 55 4431 Paulides M M, Bakker J F, Linthorst M, van der Zee J, Rijnen Z, Neufeld E, Pattynama P M T, Jansen P P, Levendag P C and van Rhoon G C 2010 The clinical feasibility of deep hyperthermia treatment in the head and neck: new challenges for positioning and temperature measurement Phys. Med. Biol. 55 2465 Rockne R, Rockhill J K, Mrugala M, Spence A M, Kalet I, Hendrickson K, Lai A, Cloughesy T, Alvord E C Jr and Swanson K R 2010 Predicting the efficacy of radiotherapy in individual glioblastoma patients in vivo: a mathematical modeling approach Phys. Med. Biol. 55 3271 Wertz H et al 2010 Fast kilovoltage/megavoltage (kVMV) breathhold cone-beam CT for image-guided radiotherapy of lung cancer Phys. Med. Biol. 55 4203 Zhang B, MacFadden D, Damyanovich A Z, Rieker M, Stainsby J, Bernstein M, Jaffray D A, Mikulis D and Ménard C 2010 Development of a geometrically accurate imaging protocol at 3 Tesla MRI for stereotactic radiosurgery treatment planning Phys. Med. Biol. 55 6601

EDITORIAL: Roberts Prize for the best paper published in 2009 Roberts Prize for the best paper published in 2009

NASA Astrophysics Data System (ADS)

Webb, Steve; Harris, Simon

2010-07-01

The publishers of Physics in Medicine and Biology (PMB), IOP Publishing, in association with the journal owners, the Institute of Physics and Engineering in Medicine (IPEM), jointly award an annual prize for the best paper published in PMB during the previous year. The procedure for deciding the winner has been made as thorough as possible, to try to ensure that an outstanding paper wins the prize. We started off with a shortlist of the 10 research papers published in 2009 which were rated the best based on the referees' quality assessments. Following the submission of a short 'case for winning' document by each of the shortlisted authors, an IPEM college of jurors of the status of FIPEM assessed and rated these 10 papers in order to choose a winner, which was then endorsed by the Editorial Board. We have a clear, and very worthy, winner this year. We have much pleasure in advising readers that the 2009 Roberts Prize is awarded to E Z Zhang et al from University College London for their paper on photoacoustic tomography. In vivo high resolution 3D photoacoustic imaging of superficial vascular anatomy E Z Zhang, J G Laufer, R B Pedley and P C Beard 2009 Phys. Med. Biol. 54 1035-46 Our congratulations go to these authors. Of course all of the shortlisted papers were of great merit, and the full top-10 is listed below (in alphabetical order). Steve Webb Editor-in-Chief Simon Harris Publisher References Cheng Y-C N , Neelavalli J and Haacke E M 2009 Limitations of calculating field distributions and magnetic susceptibilities in MRI using a Fourier based method Phys. Med. Biol. 54 1169-89 Cho S, Ahn S, Li Q and Leahy R M 2009 Exact and approximate Fourier rebinning of PET data from time-of-flight to non time-of-flight 2009 Phys. Med. Biol. 54 467-84 Davidson S R H, Weersink R A, Haider M A, Gertner M R, Bogaards A, Giewercer D, Scherz A, Sherar M D, Elhilali M, Chin J L, Trachtenberg J and Wilson B C 2009 Treatment planning and dose analysis for interstitial photodynamic therapy of prostate cancer Phys. Med. Biol. 54 2293-313 Hand J W, Shaw A, Sadhoo N, Rajagopal S, Dickinson R J and Gavrilov L R 2009 A random phased array device for delivery of high intensity focused ultrasound Phys. Med. Biol. 54 5675-93 Johnson P, Lee C, Johnson K, Siragusa D and Bolch W E 2009 The influence of patient size on dose conversion coefficients: a hybrid phantom study for adult cardiac catheterization Phys. Med. Biol. 54 3613-29 Paganetti H 2009 Dose to water versus dose to medium in proton beam therapy Phys. Med. Biol. 54 4399-421 Pramanik M, Song K H, Swierczewska M, Green D, Sitharaman B and Wang L V 2009 In vivo carbon nanotube-enhanced non-invasive photoacoustic mapping of the sentinel lymph node Phys. Med. Biol. 54 3291-301 Schöndube H, Stierstorfer K and Noo F 2009 Accurate helical cone-beam CT reconstruction with redundant data 2009 Phys. Med. Biol. 54 4625-44 Tang G, Earl M A and Yu C X 2009 Variable dose rate single-arc IMAT delivered with a constant dose rate and variable angular spacing Phys. Med. Biol. 54 6439-56 Zhang E Z, Laufer J G, Pedley R B and Beard P C 2009 In vivo high resolution 3D photoacoustic imaging of superficial vascular anatomy Phys. Med. Biol. 54 1035-46 For more information on this article see medicalphysicsweb.org

Binding sites for abundant nuclear factors modulate RNA polymerase I-dependent enhancer function in Saccharomyces cerevisiae.

PubMed

Kang, J J; Yokoi, T J; Holland, M J

1995-12-01

The 190-base pair (bp) rDNA enhancer within the intergenic spacer sequences of Saccharomyces cerevisiae rRNA cistrons activates synthesis of the 35S-rRNA precursor about 20-fold in vivo (Mestel,, R., Yip, M., Holland, J. P., Wang, E., Kang, J., and Holland, M. J. (1989) Mol. Cell. Biol. 9, 1243-1254). We now report identification and analysis of transcriptional activities mediated by three cis-acting sites within a 90-bp portion of the rDNA enhancer designated the modulator region. In vivo, these sequences mediated termination of transcription by RNA polymerase I and potentiated the activity of the rDNA enhancer element. Two trans-acting factors, REB1 and REB2, bind independently to sites within the modulator region (Morrow, B. E., Johnson, S. P., and Warner, J. R. (1989) J. Biol. Chem. 264, 9061-9068). We show that REB2 is identical to the ABF1 protien. Site-directed mutagenesis of REB1 and ABF1 binding sites demonstrated uncoupling of RNA polymerase I-dependent termination from transcriptional activation in vivo. We conclude that REB1 and ABF1 are required for RNA polymerase I-dependent termination and enhancer function, respectively, Since REB1 and ABF1 proteins also regulate expression of class II genes and other nuclear functions, our results suggest further similarities between RNA polymerase I and II regulatory mechanisms. Two rDNA enhancers flanking a rDNA minigene stimulated RNA polymerase I transcription in a "multiplicative" fashion. Deletion mapping analysis showed that similar cis-acting sequences were required for enhancer function when positioned upstream or downstream from a rDNA minigene.

A linear lattice model for polyglutamine in CAG-expansion diseases.

PubMed

Bennett, Melanie J; Huey-Tubman, Kathryn E; Herr, Andrew B; West, Anthony P; Ross, Scott A; Bjorkman, Pamela J

2002-09-03

Huntington's disease and several other neurological diseases are caused by expanded polyglutamine [poly(Gln)] tracts in different proteins. Mechanisms for expanded (>36 Gln residues) poly(Gln) toxicity include the formation of aggregates that recruit and sequester essential cellular proteins [Preisinger, E., Jordan, B. M., Kazantsev, A. & Housman, D. (1999) Phil. Trans. R. Soc. London B 354, 1029-1034; Chen, S., Berthelier, V., Yang, W. & Wetzel, R. (2001) J. Mol. Biol. 311, 173-182] and functional alterations, such as improper interactions with other proteins [Cummings, C. J. & Zoghbi, H. Y. (2000) Hum. Mol. Genet. 9, 909-916]. Expansion above the "pathologic threshold" ( approximately 36 Gln) has been proposed to induce a conformational transition in poly(Gln) tracts, which has been suggested as a target for therapeutic intervention. Here we show that structural analyses of soluble huntingtin exon 1 fusion proteins with 16 to 46 glutamine residues reveal extended structures with random coil characteristics and no evidence for a global conformational change above 36 glutamines. An antibody (MW1) Fab fragment, which recognizes full-length huntingtin in mouse brain sections, binds specifically to exon 1 constructs containing normal and expanded poly(Gln) tracts, with affinity and stoichiometry that increase with poly(Gln) length. These data support a "linear lattice" model for poly(Gln), in which expanded poly(Gln) tracts have an increased number of ligand-binding sites as compared with normal poly(Gln). The linear lattice model provides a rationale for pathogenicity of expanded poly(Gln) tracts and a structural framework for drug design.

Balanced branching in transcription termination.

PubMed

Harrington, K J; Laughlin, R B; Liang, S

2001-04-24

The theory of stochastic transcription termination based on free-energy competition [von Hippel, P. H. & Yager, T. D. (1992) Science 255, 809-812 and von Hippel, P. H. & Yager, T. D. (1991) Proc. Natl. Acad. Sci. USA 88, 2307-2311] requires two or more reaction rates to be delicately balanced over a wide range of physical conditions. A large body of work on glasses and large molecules suggests that this balancing should be impossible in such a large system in the absence of a new organizing principle of matter. We review the experimental literature of termination and find no evidence for such a principle, but do find many troubling inconsistencies, most notably, anomalous memory effects. These effects suggest that termination has a deterministic component and may conceivably not be stochastic at all. We find that a key experiment by Wilson and von Hippel [Wilson, K. S. & von Hippel, P. H. (1994) J. Mol. Biol. 244, 36-51] thought to demonstrate stochastic termination was an incorrectly analyzed regulatory effect of Mg(2+) binding.

Crystallization of human estrogenic 17β-hydroxysteroid dehydrogenase under microgravity

NASA Astrophysics Data System (ADS)

Zhu, Dao-Wei; Zhou, Ming; Mao, Ying; Labrie, Fernand; Lin, Sheng-Xiang

1995-11-01

Human 17β-hydroxysteroid dehydrogenase has been crystallized on the ground in the complex form with NADP + and a complete data set of the crystal was primarily collected at 2.9 Å [D.-W. Zhu, X. Lee, R. Breton, D. Ghosh, W. Pangborn, W.L. Duax and S.-X. Lin, J. Mol. Biol. 234 (1993) 242]. To eliminate multiseeding, formation of multicrystals and to obtain higher quality crystals, we carried out the crystallization aboard the Russian MIR space station and crystals were recovered in January, 1994. Crystals of the enzyme were formed in 9 of the total 12 sitting drops in the space mission, in the presence of NADP + or estradiol. This is a first attempt of crystallization of a membrane-associated protein under microgravity in the presence of a detergent. The space experiments showed better results in nucleation number, crystal size and morphology than the ground ones, obtaining crystals diffracting to resolutions between 2.5-2.7 Å. The too early ground mixing has limited a more important improvement of the crystallization.

Sedimentation of knotted polymers

NASA Astrophysics Data System (ADS)

Piili, J.; Marenduzzo, D.; Kaski, K.; Linna, R. P.

2013-01-01

We investigate the sedimentation of knotted polymers by means of stochastic rotation dynamics, a molecular dynamics algorithm that takes hydrodynamics fully into account. We show that the sedimentation coefficient s, related to the terminal velocity of the knotted polymers, increases linearly with the average crossing number nc of the corresponding ideal knot. This provides direct computational confirmation of this relation, postulated on the basis of sedimentation experiments by Rybenkov [J. Mol. Biol.10.1006/jmbi.1996.0876 267, 299 (1997)]. Such a relation was previously shown to hold with simulations for knot electrophoresis. We also show that there is an accurate linear dependence of s on the inverse of the radius of gyration Rg-1, more specifically with the inverse of the Rg component that is perpendicular to the direction along which the polymer sediments. When the polymer sediments in a slab, the walls affect the results appreciably. However, Rg-1 remains to a good precision linearly dependent on nc. Therefore, Rg-1 is a good measure of a knot's complexity.

Lactose carrier protein of Escherichia coli. Transport and binding of 2'-(N-dansyl)aminoethyl beta-D-thiogalactopyranoside and p-nitrophenyl alpha-d-galactopyranoside.

PubMed

Overath, P; Teather, R M; Simoni, R D; Aichele, G; Wilhelm, U

1979-01-09

The elevated level of lactose carrier protein present in cytoplasmic membranes derived from Escherichia coli strain T31RT, which carries the Y gene of the lac operon on a plasmid vector (Teather, R. M., et al. (1978) Mol. Gen. Genet. 159, 239--248), has allowed the detection of a complex between the carrier and the fluorescent substrate 2'-(N-dansyl)-aminoethyl beta-D-thiogalactopyranoside (Dns2-S-Gal). Binding is accompanied by a 50-nm blue shift in the emission maximum of the dansyl residue. The complex (dissociation constant, KD = 30 micron) rapidly dissociates upon addition of competing substrates such as beta-D-galactopyranosyl 1-thio-beta-D-galactopyranoside or upon reaction with the thiol reagent p-chloromercuribenzenesulfonate. Binding of both Dns2-S-Gal and p-nitrophenyl alpha-D-galactopyranoside (alpha-NPG) occurs spontaneously in the absence of an electrochemical potential gradient across the membrane. Comparison of equilibrium binding experiments using Dns2-S-Gal or alpha-NPG and differential labeling of the carrier with radioactive amino acids shows that the carrier binds 1 mol of substrate per mol of polypeptide (molecular weight 30 000). In addition to specific binding to the lactose carrier, Dns2-S-gal binds unspecifically to lipid vesicles or membranes, as described by a partition coefficient, K = 60, resulting in a 25-nm blue shift in the emission maximum of the dansyl group. Both Dns2-S-Gal and alpha-NPG are not only bound by the lactose carrier but also transported across the membrane by this transport protein in cells and membrane vesicles. The fluorescence changes observed with dansylated galactosides in membrane vesicles in the presence of an electrochemical gradient (Schuldiner et al. (1975) J. Biol. Chem. 250, 1361--1370)) are interpreted as an increase in unspecific binding after translocation.

Long-Term Intermittent Exposure to High Altitude Elevates Asymmetric Dimethylarginine in First Exposed Young Adults.

PubMed

Lüneburg, Nicole; Siques, Patricia; Brito, Julio; De La Cruz, Juan José; León-Velarde, Fabiola; Hannemann, Juliane; Ibanez, Cristian; Böger, Rainer H

2017-09-01

Lüneburg, Nicole, Patricia Siques, Julio Brito, Juan José De La Cruz, Fabiola León-Velarde, Juliane Hannemann, Cristian Ibanez, and Rainer Böger. Long-term intermittent exposure to high altitude elevates asymmetric dimethylarginine in first exposed young adults. High Alt Med Biol. 18:226-233, 2017.-Hypoxia-induced dysregulation of pulmonary and cerebral circulation may be related to an impaired nitric oxide (NO) pathway. We investigated the effect of chronic intermittent hypobaric hypoxia (CIH) on metabolites of the NO pathway. We measured asymmetric and symmetric dimethylarginine (ADMA and SDMA) and monomethyl-L-arginine (L-NMMA) and assessed their associations with acclimatization in male draftees (n = 72) undergoing CIH shifts at altitude (3550 m) during 3 months. Sixteen Andean natives living at altitude (3675 m) (chronic hypobaric hypoxia [CH]) were included for comparison. In CIH, ADMA and L-NMMA plasma concentrations increased from 1.14 ± 0.04 to 1.95 ± 0.09 μmol/L (mean ± SE) and from 0.22 ± 0.07 to 0.39 ± 0.03 μmol/L, respectively, (p < 0.001 for both) after 3 months, whereas SDMA did not change. The concentrations of ADMA and L-NMMA were higher in CH (3.48 ± 0.07, 0.53 ± 0.08 μmol/L; p < 0.001) as compared with CIH. In both CIH and CH, ADMA correlated with hematocrit (r 2  = 0.07, p < 0.05; r 2  = 0.26; p < 0.01). In CIH, an association of ADMA levels with poor acclimatization status was observed. We conclude that the endogenous NO synthase inhibitors, ADMA and L-NMMA, are elevated in hypoxia. This may contribute to impaired NO production at altitude and may also be predictive of altitude-associated health impairment.

Long-Term Intermittent Exposure to High Altitude Elevates Asymmetric Dimethylarginine in First Exposed Young Adults

PubMed Central

Siques, Patricia; Brito, Julio; De La Cruz, Juan José; León-Velarde, Fabiola; Hannemann, Juliane; Ibanez, Cristian; Böger, Rainer H.

2017-01-01

Abstract Lüneburg, Nicole, Patricia Siques, Julio Brito, Juan José De La Cruz, Fabiola León-Velarde, Juliane Hannemann, Cristian Ibanez, and Rainer Böger. Long-term intermittent exposure to high altitude elevates asymmetric dimethylarginine in first exposed young adults. High Alt Med Biol. 18:226–233, 2017.—Hypoxia-induced dysregulation of pulmonary and cerebral circulation may be related to an impaired nitric oxide (NO) pathway. We investigated the effect of chronic intermittent hypobaric hypoxia (CIH) on metabolites of the NO pathway. We measured asymmetric and symmetric dimethylarginine (ADMA and SDMA) and monomethyl-L-arginine (L-NMMA) and assessed their associations with acclimatization in male draftees (n = 72) undergoing CIH shifts at altitude (3550 m) during 3 months. Sixteen Andean natives living at altitude (3675 m) (chronic hypobaric hypoxia [CH]) were included for comparison. In CIH, ADMA and L-NMMA plasma concentrations increased from 1.14 ± 0.04 to 1.95 ± 0.09 μmol/L (mean ± SE) and from 0.22 ± 0.07 to 0.39 ± 0.03 μmol/L, respectively, (p < 0.001 for both) after 3 months, whereas SDMA did not change. The concentrations of ADMA and L-NMMA were higher in CH (3.48 ± 0.07, 0.53 ± 0.08 μmol/L; p < 0.001) as compared with CIH. In both CIH and CH, ADMA correlated with hematocrit (r2 = 0.07, p < 0.05; r2 = 0.26; p < 0.01). In CIH, an association of ADMA levels with poor acclimatization status was observed. We conclude that the endogenous NO synthase inhibitors, ADMA and L-NMMA, are elevated in hypoxia. This may contribute to impaired NO production at altitude and may also be predictive of altitude-associated health impairment. PMID:28453332

A simple HPLC method for the comprehensive analysis of cis/trans (Z/E) geometrical isomers of carotenoids for nutritional studies

USDA-ARS?s Scientific Manuscript database

Geometrical isomers of carotenoids behave differently in aspects like stability towards oxidants, bioavailability, vitamin A activity and specificity for enzymes. The availability of HPLC methods for their detailed profiling is therefore advisable to expand our knowledge on their metabolism and biol...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paziresh, M.; Kingston, A. M., E-mail: andrew.kingston@anu.edu.au; Latham, S. J.

Dual-energy computed tomography and the Alvarez and Macovski [Phys. Med. Biol. 21, 733 (1976)] transmitted intensity (AMTI) model were used in this study to estimate the maps of density (ρ) and atomic number (Z) of mineralogical samples. In this method, the attenuation coefficients are represented [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976)] in the form of the two most important interactions of X-rays with atoms that is, photoelectric absorption (PE) and Compton scattering (CS). This enables material discrimination as PE and CS are, respectively, dependent on the atomic number (Z) and density (ρ) of materials [Alvarez and Macovski,more » Phys. Med. Biol. 21, 733 (1976)]. Dual-energy imaging is able to identify sample materials even if the materials have similar attenuation coefficients at single-energy spectrum. We use the full model rather than applying one of several applied simplified forms [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976); Siddiqui et al., SPE Annual Technical Conference and Exhibition (Society of Petroleum Engineers, 2004); Derzhi, U.S. patent application 13/527,660 (2012); Heismann et al., J. Appl. Phys. 94, 2073–2079 (2003); Park and Kim, J. Korean Phys. Soc. 59, 2709 (2011); Abudurexiti et al., Radiol. Phys. Technol. 3, 127–135 (2010); and Kaewkhao et al., J. Quant. Spectrosc. Radiat. Transfer 109, 1260–1265 (2008)]. This paper describes the tomographic reconstruction of ρ and Z maps of mineralogical samples using the AMTI model. The full model requires precise knowledge of the X-ray energy spectra and calibration of PE and CS constants and exponents of atomic number and energy that were estimated based on fits to simulations and calibration measurements. The estimated ρ and Z images of the samples used in this paper yield average relative errors of 2.62% and 1.19% and maximum relative errors of 2.64% and 7.85%, respectively. Furthermore, we demonstrate that the method accounts for the beam hardening effect in density (ρ) and atomic number (Z) reconstructions to a significant extent.« less

Resistance of spacecraft isolates to outer space for planetary protection purposes -first results of the experiment PROTECT of the EXPOSE-E mission.

NASA Astrophysics Data System (ADS)

Horneck, Gerda; Moeller, Ralf

Spore-forming microbes are of particular concern in the context of planetary protection, be-cause their endospores are highly resistant to a variety of environmental extremes, including certain sterilization procedures and the harsh environment of outer space or planetary sur-faces (Nicholson et al., 2000; Horneck et al. 2009). Furthermore, isolates from space craft and space craft assembly facilities have been identified that form spores of an elevated resistance to various physical and chemical conditions, such as ionizing and UV radiation, desiccation and oxidative stress (La Duc et al., 2007). This observation led to the supposition that the spe-cial conditions of ultraclean spacecraft assembly facilities and the applied spacecraft cleaning and decontamination measures cause a selection of the most resistant organisms as survivors. To test this hypothesis, spores of B. pumilus SAFR-032 isolated from these environments as well as spores of the laboratory strain B. subtilis 168 were subjected to selected parameters of space in the experiment PROTECT during the EXPOSE-E mission (February 7, 2008 -September 12, 2009), attached to the EuTEF platform outside of the Columbus module of the International Space Station. The spores were mounted as dry layers onto spacecraft-qualified material (aluminum coupons) and exposed to the following parameters of space, applied sep-arately or in selected combinations: (i) space vacuum, (ii) solar extraterrestrial UV radiation including vacuum-UV, (iii) simulated Mars atmosphere and UV radiation climate, and (iv) galactic cosmic radiation. After recovery, visual inspection showed color changes of the sun-exposed spore samples from white to brownish demonstrating photochemical damage caused by solar extraterrestrial UV radiation. On-going analyses include studies of viability and capabil-ity of repair of damage, mutagenic spectrum, e.g. trp-revertants, rifampicin-resistant mutants, DNA lesion, global gene expression, and genomic and proteomic characterizations using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). First viability studies gave the following survival rates: 20 -30 References: Horneck,G., D.M. Klaus, R.L. Mancinelli (2010) Space microbiology, Microb. Mol. Biol. Rev. (in press) La Duc MT, Dekas A, Osman S, Moissl C, Newcombe D, Venkateswaran K. (2007) Isolation and character-ization of bacteria capable of tolerating the extreme conditions of clean room environments. Appl Environ Microbiol. 73, 2600-11. Nicholson WL, Munakata N, Horneck G, Melosh HJ, and Setlow P (2000) Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments, Microb. Mol. Biol. Rev. 64, 548-572.

Comparative evaluation of neonatal bilirubin using Radiometer whole blood co-oximetry and plasma bilirubin methods from Roche Diagnostics and Ortho Clinical Diagnostics.

PubMed

Lano, Ian Marie; Lyon, Andrew W; Wang, Li; Ruskin, Rob; Lyon, Martha E

2018-03-01

Clinically significant variation has been reported within and between plasma and whole blood total bilirubin methods used to identify neonates for whom clinical intervention for hyperbilirubinemia may be required. To evaluate total bilirubin measurements between the Radiometer whole blood co-oximeter and plasma bilirubin methods from Roche Diagnostics and Ortho Clinical Diagnostics using neonatal specimens. Total bilirubin levels were analyzed by whole blood co-oximetry (Radiometer® ABL90). Specimens were centrifuged and plasma analyzed for total bilirubin with a diazo method (Roche Cobas® C-601) and a reflectance spectrophotometric BuBc dry film method (Ortho Clinical Diagnostics VITROS® 350). Results were evaluated by regression, Bland-Altman comparisons and t-tests. The patient correlation study yielded the following regression equations in μmol/L: a) Radiometer=1.03 Roche - 3.5μmol/L b) Radiometer=0.98 Ortho - 5.7μmol/L c) Roche=0.97 Ortho - 2.4μmol/L. The mean bias over the range of total bilirubin levels examined was -1.0μmol/L for the Radiometer versus the Roche (p≤0.305); -4.4μmol/L for the Radiometer versus Ortho (p≤0.005) and -4.4μmol/L for the Roche versus Ortho (p≤0.002). Whole blood total bilirubin measurement using the Radiometer ABL90 blood gas analyzer provides accurate and precise results compared to the Roche plasma diazo method. Compared to the reflectance spectrophotometric method, results are precise and had a small but statistically significant bias of -4.4μmol/L. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Vitamin C Status of Submariners

DTIC Science & Technology

1980-06-19

one week of collection using a modification of the 2,4- dinitrophenylhydrazine method of Roe and Kuether (14). Before each sampling period, the...KUETHER. The determination of ascorbic acid in whole blood through the 2,4- dinitrophenylhydrazine derivative of dehydroascorbic acid. J. Biol

EDITORIAL: Annual prizes for best papers

NASA Astrophysics Data System (ADS)

2007-07-01

2006 Roberts Prize The publishers of Physics in Medicine and Biology (PMB) in association with the Institute of Physics and Engineering in Medicine (IPEM) jointly award an annual prize for an article published in PMB during the previous year. The following ten articles, listed below in chronological order, were rated the best of 2006 based on the (two or three) referees' assessments: D W Mundy et al 2006 Radiation binary targeted therapy for HER-2 positive breast cancers: assumptions, theoretical assessment and future directions Phys. Med. Biol. 51 1377-91 Y Yang et al 2006 Investigation of optical coherence tomography as an imaging modality in tissue engineering Phys. Med. Biol. 51 1649-59 M Krämer and M Scholz 2006 Rapid calculation of biological effects in ion radiotherapy Phys. Med. Biol. 51 1959-70 P Crespo et al 2006 On the detector arrangement for in-beam PET for hadron therapy monitoring Phys. Med. Biol. 51 2143-63 R J Senden et al 2006 Polymer gel dosimeters with reduced toxicity: a preliminary investigation of the NMR and optical dose-response using different monomers Phys. Med. Biol. 51 3301-14 J Wang et al 2006 FDTD calculation of whole-body average SAR in adult and child models for frequencies from 30 MHz to 3 GHz Phys. Med. Biol. 51 4119-27 C A T Van den Berg et al 2006 The use of MR B+1 imaging for validation of FDTD electromagnetic simulations of human anatomies Phys. Med. Biol. 51 4735-46 S Qin and K W Ferrara 2006 Acoustic response of compliable microvessels containing ultrasound contrast agents Phys. Med. Biol. 51 5065-88 R Kramer et al 2006 Skeletal dosimetry in the MAX06 and the FAX06 phantoms for external exposure to photons based on vertebral 3D-microCT images Phys. Med. Biol. 51 6265-89 R Leiderman et al 2006 Coupling between elastic strain and interstitial fluid flow: ramifications for poroelastic imaging Phys. Med. Biol. 51 6291-313 An IPEM college of jurors then assessed and rated these papers in order to choose a winner. We have much pleasure in advising readers that the 2006 Roberts Prize is awarded to: M Krämer and M Scholz 2006 Rapid calculation of biological effects in ion radiotherapy Phys. Med. Biol. 51 1959-70 2007 Prize for the Highest Cited Paper The annual prize for the most highly cited paper is awarded by the journal publishers (IOP Publishing) to the article published in PMB that has received the most citations1 in the previous 5 years (in this case for the period 2002 to 2006 inclusive). We have much pleasure in advising readers that the 2007 prize is awarded to: S S Vedam, P J Keall, V R Kini, H Mostafavi, H P Shukla and R Mohan 2003 Acquiring a four-dimensional computed tomography dataset using an external respiratory signal Phys. Med. Biol. 48 45-62 Simon Harris, Publisher Steve Webb, Editor-in-Chief 1 Figures taken from Thomson/ISI

Age-related accumulation of pentosidine in aggrecan and collagen from normal and degenerate human intervertebral discs

PubMed Central

Sivan, Sarit Sara; Tsitron, Eve; Wachtel, Ellen; Roughley, Peter; Sakkee, Nico; van der Ham, Frits; Degroot, Jeroen; Maroudas, Alice

2006-01-01

During aging and degeneration, many changes occur in the structure and composition of human cartilaginous tissues, which include the accumulation of the AGE (advanced glycation end-product), pentosidine, in long-lived proteins. In the present study, we investigated the accumulation of pentosidine in constituents of the human IVD (intervertebral disc), i.e. collagen, aggrecan-derived PG (proteoglycan) (A1) and its fractions (A1D1–A1D6) in health and pathology. We found that, after maturity, pentosidine accumulates with age. Over the age range studied, a linear 6-fold increase was observed in pentosidine accumulation for A1 and collagen with respective rates of 0.12 and 0.66 nmol·(g of protein)−1·year−1. Using previously reported protein turnover rate constants (kT) obtained from measurements of the D-isomer of aspartic residue in collagen and aggrecan of human IVD, we could calculate the pentosidine formation rate constants (kF) for these constituents [Sivan, Tsitron, Wachtel, Roughley, Sakkee, van der Ham, DeGroot, Roberts and Maroudas (2006) J. Biol. Chem. 281, 13009–13014; Tsitron (2006) MSc Thesis, Technion-Israel Institute of Technology, Haifa, Israel]. In spite of the comparable formation rate constants obtained for A1D1 and collagen [1.81±0.25 compared with 3.71±0.26 μmol of pentosidine·(mol of lysine)−1·year−1 respectively], the higher pentosidine accumulation in collagen is consistent with its slower turnover (0.005 year−1 compared with 0.134 year−1 for A1D1). Pentosidine accumulation increased with decreasing buoyant density and decreasing turnover of the proteins from the most glycosaminoglycan-rich PG components (A1D1) to the least (A1D6), with respective kF values of 1.81±0.25 and 3.18±0.37 μmol of pentosidine·(mol of lysine)−1·year−1. We concluded that protein turnover is an important determinant of pentosidine accumulation in aggrecan and collagen of human IVD, as was found for articular cartilage. Correlation of pentosidine accumulation with protein half-life in both normal and degenerate discs further supports this finding. PMID:16787390

Studies of a Ras Antagonist in Breast Cancer

DTIC Science & Technology

2005-05-01

growth by Farensylthiosalicylic acid. J Biol Chem 1995; 270: 22268- 22270 . [19] Egozi Y, Weisz B, Gana-Weisz M, Ben-Baruch G, and Kloog Y, Growth...growth by Farensylthiosalisylic acid. J Biol Chem 270(35) (1995) 22268- 22270 . [71] Y. Egozi, B. Weisz, M. Gana-Weisz, G. Ben-Baruch, and Y. Kloog, Growth...G, Marciano D, Egozi Y, Kloog Y 1995 Selective inhibition of Ras- dependent cell growth by farnesylthiosalisylic acid. J Biol Chem 270:22263- 22270 40

Functional Organic Monolayers

DTIC Science & Technology

2005-10-31

Weierstall, K. Downing** and R. M. Glaeser*. J. Struct. Biol. 144, p209. 2003. 292 "A new thin-film phase of pentacene ". J. Wu and J. Spence. J...electron diffraction methods, we have discovered a new phase of pentacene , a material important for attempts to develop organic semiconductors

The protein-protein interactions between SMPI and thermolysin studied by molecular dynamics and MM/PBSA calculations.

PubMed

Adekoya, Olayiwola A; Willassen, Nils-Peder; Sylte, Ingebrigt

2005-04-01

Thermolysin is a zinc-metalloendopeptidase secreted by the gram-positive thermophilic bacterium Bacillus thermoproteolyticus. Thermolysin belongs to the gluzinicin family of enzymes, which is selectively inhibited by Steptomyces metalloproteinase inhibitor (SMPI). Very little is known about the interaction between SMPI and thermolysin. Knowledge about the protein-protein interactions is very important for designing new thermolysin inhibitors with possible industrial or pharmaceutical applications. In the present study, two binding modes between SMPI and thermolysin were studied by 2300 picoseconds (ps) of comparative molecular dynamics (MD) simulations and calculation of the free energy of binding using the molecular mechanics-Poisson-Boltmann surface area (MM/PBSA) method. One of the positions, the 'horizontal arrow head docking' (HAHD) was similar to the previously proposed binding mode by Tate et al. (Tate, S., Ohno, A., Seeram, S. S., Hiraga, K., Oda, K., and Kainosho, M. J. Mol. Biol. 282, 435-446 (1998)). The other position, the 'vertical arrow head docking' (VAHD) was obtained by a manual docking guided by the shape and charge distribution of SMPI and the binding pocket of thermolysin. The calculations showed that SMPI had stronger interactions with thermolysin in the VAHD than in the HAHD complex, and the VAHD complex was considered more realistic than the HAHD complex. SMPI interacted with thermolysin not only at the active site but had auxiliary binding sites contributing to proper interactions. The VAHD complex can be used for designing small molecule inhibitors mimicking the SMPI-thermolysin binding interfaces.

Conditional poliovirus mutants made by random deletion mutagenesis of infectious cDNA.

PubMed Central

Kirkegaard, K; Nelsen, B

1990-01-01

Small deletions were introduced into DNA plasmids bearing cDNA copies of Mahoney type 1 poliovirus RNA. The procedure used was similar to that of P. Hearing and T. Shenk (J. Mol. Biol. 167:809-822, 1983), with modifications designed to introduce only one lesion randomly into each DNA molecule. Methods to map small deletions in either large DNA or RNA molecules were employed. Two poliovirus mutants, VP1-101 and VP1-102, were selected from mutagenized populations on the basis of their host range phenotype, showing a large reduction in the relative numbers of plaques on CV1 and HeLa cells compared with wild-type virus. The deletions borne by the mutant genomes were mapped to the region encoding the amino terminus of VP1. That these lesions were responsible for the mutant phenotypes was substantiated by reintroduction of the sequenced lesions into a wild-type poliovirus cDNA by deoxyoligonucleotide-directed mutagenesis. The deletion of nucleotides encoding amino acids 8 and 9 of VP1 was responsible for the VP1-101 phenotype; the VP1-102 defect was caused by the deletion of the sequences encoding the first four amino acids of VP1. The peptide sequence at the VP1-VP3 proteolytic cleavage site was altered from glutamine-glycine to glutamine-methionine in VP1-102; this apparently did not alter the proteolytic cleavage pattern. The biochemical defects resulting from these mutations are discussed in the accompanying report. Images PMID:2152811

Human oocyte cryopreservation as an adjunct to IVF-embryo transfer cycles.

PubMed

Boldt, Jeffrey; Cline, Donald; McLaughlin, David

2003-06-01

The purpose of this work was to develop methods for successful cryopreservation of human oocytes. Two cryopreservation procedures were used. Method 1 involved use of 1.5 mol/l propanediol (PrOH)-0.1 mol/l sucrose with medium containing sodium (Na) as cryoprotectant medium, seeding at -7 degrees C, and stepwise dilution of cryoprotectant post-thaw. Method 2 used Na-depleted media with 1.5 mol/l PrOH-0.2 mol/l sucrose for freezing, seeding at -6 degrees C, and use of high sucrose (0.5 and 0.2 mol/l) for cryoprotectant removal. The first method was used in seven patients, and gave poor (12.3%) survival results and no pregnancies. The second method was used in 15 patients (16 cycles), and yielded good survival and fertilization rates (74.4 and 59% respectively), with four pregnancies and five healthy infants born to 11 women receiving an embryo transfer. Using Na-depleted media along with other alterations in freezing and thawing procedures, human oocyte cryopreservation can provide excellent survival and pregnancy rates.

G3X-K theory: A composite theoretical method for thermochemical kinetics

NASA Astrophysics Data System (ADS)

da Silva, Gabriel

2013-02-01

A composite theoretical method for accurate thermochemical kinetics, G3X-K, is described. This method is accurate to around 0.5 kcal mol-1 for barrier heights and 0.8 kcal mol-1 for enthalpies of formation. G3X-K is a modification of G3SX theory using the M06-2X density functional for structures and zero-point energies and parameterized for a test set of 223 heats of formation and 23 barrier heights. A reduced perturbation-order variant, G3X(MP3)-K, is also developed, providing around 0.7 kcal mol-1 accuracy for barrier heights and 0.9 kcal mol-1 accuracy for enthalpies, at reduced computational cost. Some opportunities to further improve Gn composite methods are identified and briefly discussed.

Simultaneous square-wave voltammetric determination of aspartame and cyclamate using a boron-doped diamond electrode.

PubMed

Medeiros, Roberta Antigo; de Carvalho, Adriana Evaristo; Rocha-Filho, Romeu C; Fatibello-Filho, Orlando

2008-07-30

A simple and highly selective electrochemical method was developed for the simultaneous determination of aspartame and cyclamate in dietary products at a boron-doped diamond (BDD) electrode. In square-wave voltammetric (SWV) measurements, the BDD electrode was able to separate the oxidation peak potentials of aspartame and cyclamate present in binary mixtures by about 400 mV. The detection limit for aspartame in the presence of 3.0x10(-4) mol L(-1) cyclamate was 4.7x10(-7) mol L(-1), and the detection limit for cyclamate in the presence of 1.0x10(-4) mol L(-1) aspartame was 4.2x10(-6) mol L(-1). When simultaneously changing the concentration of both aspartame and cyclamate in a 0.5 mol L(-1) sulfuric acid solution, the corresponding detection limits were 3.5x10(-7) and 4.5x10(-6) mol L(-1), respectively. The relative standard deviation (R.S.D.) obtained was 1.3% for the 1.0x10(-4) mol L(-1) aspartame solution (n=5) and 1.1% for the 3.0x10(-3) mol L(-1) cyclamate solution. The proposed method was successfully applied in the determination of aspartame in several dietary products with results similar to those obtained using an HPLC method at 95% confidence level.

Human 17β-hydroxysteroid dehydrogenase-ligand complexes: crystals of different space groups with various cations and combined seeding and co-crystallization

NASA Astrophysics Data System (ADS)

Zhu, D.-W.; Han, Q.; Qiu, W.; Campbell, R. L.; Xie, B.-X.; Azzi, A.; Lin, S.-X.

1999-01-01

Human estrogenic 17β-hydroxysteroid dehydrogenase (17β-HSD1) is responsible for the synthesis of active estrogens that stimulate the proliferation of breast cancer cells. The enzyme has been crystallized using a Mg 2+/PEG (3500)/β-octyl glucoside system [Zhu et al., J. Mol. Biol. 234 (1993) 242]. The space group of these crystals is C2. Here we report that cations can affect 17β-HSD1 crystallization significantly. In the presence of Mn 2+ instead of Mg 2+, crystals have been obtained in the same space group with similar unit cell dimensions. In the presence of Li + and Na + instead of Mg 2+, the space group has been changed to P2 12 12 1. A whole data set for a crystal of 17ß-HSD1 complex with progesterone grown in the presence of Li + has been collected to 1.95 Å resolution with a synchrotron source. The cell dimensions are a=41.91 Å, b=108.21 Å, c=117.00 Å. The structure has been preliminarily determined by molecular replacement, yielding important information on crystal packing in the presence of different cations. In order to further understand the structure-function relationship of 17β-HSD1, enzyme complexes with several ligands have been crystallized. As the steroids have very low aqueous solubility, we used a combined method of seeding and co-crystallization to obtain crystals of 17β-HSD1 complexed with various ligands. This method provides ideal conditions for growing complex crystals, with ligands such as 20α-hydroxysteroid progesterone, testosterone and 17β-methyl-estradiol-NADP +. Several complex structures have been determined with reliable electronic density of the bound ligands.

Plakins in development and disease.

PubMed

Sonnenberg, Arnoud; Liem, Ronald K H

2007-06-10

Plakins are large multi-domain molecules that have various functions to link cytoskeletal elements together and to connect them to junctional complexes. Plakins were first identified in epithelial cells where they were found to connect the intermediate filaments to desmosomes and hemidesmosomes [Ruhrberg, C., and Watt, F.M. (1997). The plakin family: versatile organizers of cytoskeletal architecture. Curr Opin Genet Dev 7, 392-397.]. They were subsequently found to be important for the integrity of muscle cells. Most recently, they have been found in the nervous system, where their functions appear to be more complex, including cross-linking of microtubules (MTs) and actin filaments [Leung, C.L., Zheng, M., Prater, S.M., and Liem, R.K. (2001). The BPAG1 locus: Alternative splicing produces multiple isoforms with distinct cytoskeletal linker domains, including predominant isoforms in neurons and muscles. J Cell Biol 154, 691-697., Leung, C.L., Sun, D., Zheng, M., Knowles, D.R., and Liem, R.K. (1999). Microtubule actin cross-linking factor (MACF): a hybrid of dystonin and dystrophin that can interact with the actin and microtubule cytoskeletons. J Cell Biol 147, 1275-1286.]. These plakins have also indicated their relationship to the spectrin superfamily of proteins and the plakins appear to be evolutionarily related to the spectrins, but have diverged to perform different specialized functions. In invertebrates, a single plakin is present in both Drosophila melanogaster and Caenorhabditis elegans, which resemble the more complex plakins found in mammals [Roper, K., Gregory, S.L., and Brown, N.H. (2002). The 'spectraplakins': cytoskeletal giants with characteristics of both spectrin and plakin families. J Cell Sci 115, 4215-4225.]. In contrast, there are seven plakins found in mammals and most of them have alternatively spliced forms leading to a very complex group of proteins with potential tissue specific functions [Jefferson, J.J., Leung, C.L., and Liem, R.K. (2004). Plakins: goliaths that link cell junctions and the cytoskeleton. Nat Rev Mol Cell Biol 5, 542-553.]. In this review, we will first describe the plakins, desmoplakin, plectin, envoplakin and periplakin and then describe two other mammalian plakins, Bullous pemphigoid antigen 1 (BPAG1) and microtubule actin cross-linking factor 1 (MACF1), that are expressed in multiple isoforms in different tissues. We will also describe the relationship of these two proteins to the invertebrate plakins, shortstop (shot) in Drosophila and VAB-10 in C. elegans. Finally, we will describe an unusual mammalian plakin, called epiplakin.

Improving rice models for more reliable prediction of responses of rice yield to CO2 and temperature elevaton

USDA-ARS?s Scientific Manuscript database

Materials and Methods The simulation exercise and model improvement were implemented in phase-wise. In the first modelling activities, the model sensitivities were evaluated to given CO2 concentrations varying from 360 to 720 'mol mol-1 at an interval of 90 'mol mol-1 and air temperature increments...

The host outer membrane proteins OmpA and OmpC are associated with the Shigella phage Sf6 virion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao Haiyan, E-mail: zhaohy@ku.ed; Sequeira, Reuben D., E-mail: sequen@ku.ed; Galeva, Nadezhda A., E-mail: galeva@ku.ed

2011-01-20

Assembly of dsDNA bacteriophage is a precisely programmed process. Potential roles of host cell components in phage assembly haven't been well understood. It was previously reported that two unidentified proteins were present in bacteriophage Sf6 virion (Casjens et al, 2004, J.Mol.Biol. 339, 379-394, Fig. 2A). Using tandem mass spectrometry, we have identified the two proteins as outer membrane proteins (OMPs) OmpA and OmpC from its host Shigella flexneri. The transmission electron cryo-microscopy structure of Sf6 shows significant density at specific sites at the phage capsid inner surface. This density fit well with the characteristic beta-barrel domains of OMPs, thus maymore » be due to the two host proteins. Locations of this density suggest a role in Sf6 morphogenesis reminiscent of phage-encoded cementing proteins. These data indicate a new, OMP-related phage:host linkage, adding to previous knowledge that some lambdoid bacteriophage genomes contain OmpC-like genes that express phage-encoded porins in the lysogenic state.« less

Properties of some monkey DNA sequences obtained by a procedure that enriches for DNA replication origins.

PubMed

Zannis-Hadjopoulos, M; Kaufmann, G; Wang, S S; Lechner, R L; Karawya, E; Hesse, J; Martin, R G

1985-07-01

Twelve clones of monkey DNA obtained by a procedure that enriches 10(3)- to 10(4)-fold for nascent sequences activated early in S phase (G. Kaufmann, M. Zannis-Hadjopoulos, and R. G. Martin, Mol. Cell. Biol. 5:721-727, 1985) have been examined. Only 2 of the 12 ors sequences (origin-enriched sequences) are unique (ors1 and ors8). Three contain the highly reiterated Alu family (ors3, ors9, and ors11). One contains the highly reiterated alpha-satellite family (ors12), but none contain the Kpn family. Those remaining contain middle repetitive sequences. Two examples of the same middle repetitive sequence were found (ors2 and ors6). Three of the middle repetitive sequences (the ors2-ors6 pair, ors5, and ors10) are moderately dispersed; one (ors4) is highly dispersed. The last, ors7, has been mapped to the bona fide replication origin of the D loop of mitochondrial DNA. Of the nine ors sequences tested, half possess snapback (intrachain reannealing) properties.

Characterization of the type I dehydroquinase from Salmonella typhi.

PubMed Central

Moore, J D; Hawkins, A R; Charles, I G; Deka, R; Coggins, J R; Cooper, A; Kelly, S M; Price, N C

1993-01-01

The type I dehydroquinase from the human pathogen Salmonella typhi was overexpressed in an Escherichia coli host and purified to homogeneity. The S. typhi enzyme was characterized in terms of its kinetic parameters, important active-site residues, thermal stability and c.d. and fluorescence properties. In all important respects, the enzyme from S. typhi behaves in a very similar fashion to the well-characterized enzyme from E. coli, including the remarkable conformational stabilization observed on reduction of the substrate/product mixture by NaBH4. This gives confidence that the information from X-ray studies on the S. typhi enzyme [Boys, Fawcett, Sawyer, Moore, Charles, Hawkins, Deka, Kleanthous and Coggins (1992) J. Mol. Biol. 227, 352-355] can be applied to other type I dehydroquinases. Studies of the quenching of fluorescence of the S. typhi enzyme by succinimide show that NaBH4 reduction of the substrate/product imine complex involves a dramatic decrease in the flexibility of the enzyme, with only very minor changes in the overall secondary and tertiary structure. Images Figure 1 PMID:8216229

Conformational Clusters of Phosphorylated Tyrosine.

PubMed

Abdelrasoul, Maha; Ponniah, Komala; Mao, Alice; Warden, Meghan S; Elhefnawy, Wessam; Li, Yaohang; Pascal, Steven M

2017-12-06

Tyrosine phosphorylation plays an important role in many cellular and intercellular processes including signal transduction, subcellular localization, and regulation of enzymatic activity. In 1999, Blom et al., using the limited number of protein data bank (PDB) structures available at that time, reported that the side chain structures of phosphorylated tyrosine (pY) are partitioned into two conserved conformational clusters ( Blom, N.; Gammeltoft, S.; Brunak, S. J. Mol. Biol. 1999 , 294 , 1351 - 1362 ). We have used the spectral clustering algorithm to cluster the increasingly growing number of protein structures with pY sites, and have found that the pY residues cluster into three distinct side chain conformations. Two of these pY conformational clusters associate strongly with a narrow range of tyrosine backbone conformation. The novel cluster also highly correlates with the identity of the n + 1 residue, and is strongly associated with a sequential pYpY conformation which places two adjacent pY side chains in a specific relative orientation. Further analysis shows that the three pY clusters are associated with distinct distributions of cognate protein kinases.

Dictyostelium mutants lacking the cytoskeletal protein coronin are defective in cytokinesis and cell motility

PubMed Central

1993-01-01

Coronin is an actin-binding protein in Dictyostelium discoideum that is enriched at the leading edge of the cells and in projections of the cell surface called crowns. The polypeptide sequence of coronin is distinguished by its similarities to the beta-subunits of trimeric G proteins (E. L. de Hostos, B. Bradtke, F. Lottspeich, R. Guggenheim, and G. Gerisch, 1991. EMBO (Eur. Mol. Biol. Organ.) J. 10:4097-4104). To elucidate the in vivo function of coronin, null mutants have been generated by gene replacement. The mutant cells lacking coronin grow and migrate more slowly than wild-type cells. When these cor- cells grow in liquid medium they become multinucleate, indicating a role of coronin in cytokinesis. To explore this role, coronin has been localized in mitotic wild-type cells by immunofluorescence labeling. During separation of the daughter cells, coronin is strongly accumulated at their distal portions including the leading edges. This contrasts with the localization of myosin II in the cleavage furrow and suggests that coronin functions independently of the conventional myosin in facilitating cytokinesis. PMID:8380174

SAXS fingerprints of aldehyde dehydrogenase oligomers.

PubMed

Tanner, John J

2015-12-01

Enzymes of the aldehyde dehydrogenase (ALDH) superfamily catalyze the nicotinamide adenine dinucleotide-dependent oxidation of aldehydes to carboxylic acids. ALDHs are important in detoxification of aldehydes, amino acid metabolism, embryogenesis and development, neurotransmission, oxidative stress, and cancer. Mutations in genes encoding ALDHs cause metabolic disorders, including alcohol flush reaction (ALDH2), Sjögren-Larsson syndrome (ALDH3A2), hyperprolinemia type II (ALDH4A1), γ-hydroxybutyric aciduria (ALDH5A1), methylmalonic aciduria (ALDH6A1), pyridoxine dependent epilepsy (ALDH7A1), and hyperammonemia (ALDH18A1). We previously reported crystal structures and small-angle X-ray scattering (SAXS) analyses of ALDHs exhibiting dimeric, tetrameric, and hexameric oligomeric states (Luo et al., Biochemistry 54 (2015) 5513-5522; Luo et al., J. Mol. Biol. 425 (2013) 3106-3120). Herein I provide the SAXS curves, radii of gyration, and distance distribution functions for the three types of ALDH oligomer. The SAXS curves and associated analysis provide diagnostic fingerprints that allow rapid identification of the type of ALDH oligomer that is present in solution. The data sets provided here serve as a benchmark for characterizing oligomerization of ALDHs.

Nucleotide sequence of an exceptionally long 5.8S ribosomal RNA from Crithidia fasciculata.

PubMed Central

Schnare, M N; Gray, M W

1982-01-01

In Crithidia fasciculata, a trypanosomatid protozoan, the large ribosomal subunit contains five small RNA species (e, f, g, i, j) in addition to 5S rRNA [Gray, M.W. (1981) Mol. Cell. Biol. 1, 347-357]. The complete primary sequence of species i is shown here to be pAACGUGUmCGCGAUGGAUGACUUGGCUUCCUAUCUCGUUGA ... AGAmACGCAGUAAAGUGCGAUAAGUGGUApsiCAAUUGmCAGAAUCAUUCAAUUACCGAAUCUUUGAACGAAACGG ... CGCAUGGGAGAAGCUCUUUUGAGUCAUCCCCGUGCAUGCCAUAUUCUCCAmGUGUCGAA(C)OH. This sequence establishes that species i is a 5.8S rRNA, despite its exceptional length (171-172 nucleotides). The extra nucleotides in C. fasciculata 5.8S rRNA are located in a region whose primary sequence and length are highly variable among 5.8S rRNAs, but which is capable of forming a stable hairpin loop structure (the "G+C-rich hairpin"). The sequence of C. fasciculata 5.8S rRNA is no more closely related to that of another protozoan, Acanthamoeba castellanii, than it is to representative 5.8S rRNA sequences from the other eukaryotic kingdoms, emphasizing the deep phylogenetic divisions that seem to exist within the Kingdom Protista. Images PMID:7079176

HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales

DOE PAGES

Riccardi, Demian M.; Parks, Jerry M.; Johs, Alexander; ...

2015-03-20

HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods. The library consists of two components: HackaMol, the core that contains classes for storing and manipulating molecular information, and HackaMol::X, the extensions that use the core. We tested the core; it is well-documented and easy to install across computational platforms. Our goal for the extensions is to provide a more flexible space for researchers to develop and share new methods. In this application note, we provide a description of the core classes and two extensions: HackaMol::X::Calculator, anmore » abstract calculator that uses code references to generalize interfaces with external programs, and HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program.« less

HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales.

PubMed

Riccardi, Demian; Parks, Jerry M; Johs, Alexander; Smith, Jeremy C

2015-04-27

HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods. The library consists of two components: HackaMol, the core that contains classes for storing and manipulating molecular information, and HackaMol::X, the extensions that use the core. The core is well-tested, well-documented, and easy to install across computational platforms. The goal of the extensions is to provide a more flexible space for researchers to develop and share new methods. In this application note, we provide a description of the core classes and two extensions: HackaMol::X::Calculator, an abstract calculator that uses code references to generalize interfaces with external programs, and HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program.

HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riccardi, Demian M.; Parks, Jerry M.; Johs, Alexander

HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods. The library consists of two components: HackaMol, the core that contains classes for storing and manipulating molecular information, and HackaMol::X, the extensions that use the core. We tested the core; it is well-documented and easy to install across computational platforms. Our goal for the extensions is to provide a more flexible space for researchers to develop and share new methods. In this application note, we provide a description of the core classes and two extensions: HackaMol::X::Calculator, anmore » abstract calculator that uses code references to generalize interfaces with external programs, and HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program.« less

Tomography of atomic number and density of materials using dual-energy imaging and the Alvarez and Macovski attenuation model

NASA Astrophysics Data System (ADS)

Paziresh, M.; Kingston, A. M.; Latham, S. J.; Fullagar, W. K.; Myers, G. M.

2016-06-01

Dual-energy computed tomography and the Alvarez and Macovski [Phys. Med. Biol. 21, 733 (1976)] transmitted intensity (AMTI) model were used in this study to estimate the maps of density (ρ) and atomic number (Z) of mineralogical samples. In this method, the attenuation coefficients are represented [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976)] in the form of the two most important interactions of X-rays with atoms that is, photoelectric absorption (PE) and Compton scattering (CS). This enables material discrimination as PE and CS are, respectively, dependent on the atomic number (Z) and density (ρ) of materials [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976)]. Dual-energy imaging is able to identify sample materials even if the materials have similar attenuation coefficients at single-energy spectrum. We use the full model rather than applying one of several applied simplified forms [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976); Siddiqui et al., SPE Annual Technical Conference and Exhibition (Society of Petroleum Engineers, 2004); Derzhi, U.S. patent application 13/527,660 (2012); Heismann et al., J. Appl. Phys. 94, 2073-2079 (2003); Park and Kim, J. Korean Phys. Soc. 59, 2709 (2011); Abudurexiti et al., Radiol. Phys. Technol. 3, 127-135 (2010); and Kaewkhao et al., J. Quant. Spectrosc. Radiat. Transfer 109, 1260-1265 (2008)]. This paper describes the tomographic reconstruction of ρ and Z maps of mineralogical samples using the AMTI model. The full model requires precise knowledge of the X-ray energy spectra and calibration of PE and CS constants and exponents of atomic number and energy that were estimated based on fits to simulations and calibration measurements. The estimated ρ and Z images of the samples used in this paper yield average relative errors of 2.62% and 1.19% and maximum relative errors of 2.64% and 7.85%, respectively. Furthermore, we demonstrate that the method accounts for the beam hardening effect in density (ρ) and atomic number (Z) reconstructions to a significant extent.

EDITORIAL: Special section on signal transduction Special section on signal transduction

NASA Astrophysics Data System (ADS)

Shvartsman, Stanislav

2012-08-01

This special section of Physical Biology focuses on multiple aspects of signal transduction, broadly defined as the study of the mechanisms by which cells communicate with their environment. Mechanisms of cell communication involve detection of incoming signals, which can be chemical, mechanical or electromagnetic, relaying these signals to intracellular processes, such as cytoskeletal networks or gene expression systems, and, ultimately, converting these signals to responses such as cell differentiation or death. Given the multiscale nature of signal transduction systems, they must be studied at multiple levels, from the identities and structures of molecules comprising signal detection and interpretation networks, to the systems-level properties of these networks. The 11 papers in this special section illustrate some of the most exciting aspects of signal transduction research. The first two papers, by Marie-Anne Félix [1] and by Efrat Oron and Natalia Ivanova [2], focus on cell-cell interactions in developing tissues, using vulval patterning in worm and cell fate specification in mammalian embryos as prime examples of emergent cell behaviors. Next come two papers from the groups of Julio Saez-Rodriguez [3] and Kevin Janes [4]. These papers discuss how the causal relationships between multiple components of signaling systems can be inferred using multivariable statistical analysis of empirical data. An authoritative review by Zarnitsyna and Zhu [5] presents a detailed discussion of the sequence of signaling events involved in T-cell triggering. Once the structure and components of the signaling systems are determined, they can be modeled using approaches that have been successful in other physical sciences. As two examples of such approaches, reviews by Rubinstein [6] and Kholodenko [7], present reaction-diffusion models of cell polarization and thermodynamics-based models of gene regulation. An important class of models takes the form of enzymatic networks, where a single molecule can participate in multiple types of interactions. Mathematical analysis of these models is discussed in the papers by Del Vecchio [8], Seaton and Krishnan [9], and Hatzimanikatis and colleagues [10]. Finally, all signaling systems are information processing devices. While this point is broadly accepted, there have been only a few attempts to apply information theory to experimental signaling systems. A review by Andre Levchenko and colleagues [11] provides a very clear introduction to information theory and its potential applications to signal transduction in cellular systems. References [1] Félix M-A 2012 Phys. Biol. 9 045001 [2] Oron E and Ivanova N 2012 Phys. Biol. 9 045002 [3] MacNamara A et al 2012 Phys. Biol. 9 045003 [4] Jensen K J and Janes K A 2012 Phys. Biol. 9 045004 [5] Zarnitsyna V and Zhu C 2012 Phys. Biol. 9 045005 [6] Rubinstein B et al 2012 Phys. Biol. 9 045006 [7] Frank T D et al 2012 Phys. Biol. 9 045007 [8] Del Vecchio D et al 2012 Phys. Biol. 9 045008 [9] Seaton D D and Krishnan J 2012 Phys. Biol. 9 045009 [10] Radivojevic A et al 2012 Phys. Biol. 9 045010 [11] Rhee A et al 2012 Phys. Biol. 9 045011

Synthesis of SrAl2O4:Eu2+ phosphors co-doped with Dy3+, Tb3+, Si4+ and optimization of co-doping amount by response surface method

NASA Astrophysics Data System (ADS)

Wang, Huan; Liang, Xiaoping; Liu, Kai; Zhou, Qianqian; Chen, Peng; Wang, Jun; Li, Jianxin

2016-03-01

Dy3+ doped SrAl2O4:Eu2+ phosphors were synthesized by high temperature solid phase method in a weak reducing atmosphere (5% H2 + 95% N2). The relationship between the crushed granularity and the phosphors brightness was studied. The effect of co-doping amount of Dy3+, Tb3+ and Si4+ on the structure and properties of SrAl2O4:Eu2+ via response surface method was investigated. Photoluminescence measurement results showed that the initial afterglow brightness of 0.002 mol% Dy3+ doped SrAl2O4:Eu2+0.002 phosphors decreased after first increased within the sintering temperature range from 1150 to 1400 °C, which created the highest value of 12,101 mcd/m2 at 1300 °C. Numerous coarse particles in the powder ought to be crushed for the practical application, however, the brightness became lower accompanied by the decrease of the granularity. The luminescence property of SrAl2O4:Eu2+ sintered at 1200 °C improved by co-doping Dy3+-Tb3+-Si4+. The results of response surface method showed that the influence extent on the luminescence property was Dy3+ > Tb3+ > Si4+. When the co-doping amount in SrAl2O4:Eu2+0.002 phosphors of Dy3+, Tb3+ and Si4+ was 0.001 mol%, 0.0005 mol% and 0.002 mol%, respectively, the initial afterglow brightness of SrAl2O4 was up to the highest value of 12,231 mcd/m2, which was in good agreement on the predicted maximum value of 12,519 mcd/m2 with the optimum co-doping amount of 0.0015 mol% Dy3+, 0.0005 mol% Tb3+ and 0.0017 mol% Si4+. The brightness of co-doped phosphors not only increased by 56.79% than that of SrAl2O4:Eu2+0.002, Dy3+0.002 sintered at 1200 °C, but also was above that of 1300 °C. The emission spectra results showed that, compared with 0.001 mol% Dy3+ doped phosphor, the emission peak of 0.001 mol% Dy3+-0.001 mol% Tb3+ co-doped phosphor generated red shift and increased by 9.3% in emission intensity; 0.001 mol% Dy3+-0.004 mol% Si4+ and 0.001 mol% Dy3+-0.001 mol% Tb3+-0.004 mol% Si4+ co-doped SrAl2O4:Eu2+0.002 emission peak created blue shift and increased by 37.2% and 47.6% in emission intensity, respectively.

Binding Energy and Catalysis by D-Xylose Isomerase: Kinetic, Product and X-Ray Crystallographic Analysis of Enzyme-Catalyzed Isomerization of (R)-Glyceraldehyde‡, ¶

PubMed Central

Toteva, Maria M.; Silvaggi, Nicholas R.; Allen, Karen N.; Richard, John P.

2011-01-01

D-Xylose isomerase (XI) and triosephosphate isomerase (TIM) catalyze the aldose-ketose isomerization reactions of D-xylose and D-glyceraldehyde 3-phosphate (DGAP), respectively. D-Glyceraldehyde (DGA) is the triose fragment common to the substrates for XI and TIM. The XI-catalyzed isomerization of DGA to give dihydroxyacetone (DHA) in D2O was monitored by 1H NMR spectroscopy and kcat/Km = 0.034 M−1 s−1 was determined for this isomerization at pD 7.0. This is similar to kcat/Km = 0.017 M−1 s−1 for the TIM-catalyzed carbon deprotonation reaction of DGA in D2O at pD 7.0 [Amyes, T. L.; O’Donoghue, A. C. and Richard J. P. (2001) J. Am. Chem. Soc. 123, 11325–11326]. The much larger activation barrier for XI-catalyzed isomerization of D-xylose (kcat/Km = 490 M−1 s−1) than for the TIM-catalyzed isomerization of DGAP (kcat/Km = 9.6 x 106 M−1 s−1) is due to: (i) The larger barrier to conversion of cyclic D-xylose to the reactive linear sugar (5.4 kcal/mol) than for conversion of DGAP hydrate to the free aldehyde (1.7 kcal/mol). (ii) The smaller intrinsic binding energy [Jencks, W. P. (1975) Adv. Enzymol. Relat. Areas Mol. Biol. 43, 219–410] of the terminal ethylene glycol fragment of D-xylose (9.3 kcal/mol) than of the phosphodianion group of DGAP (ca. 12 kcal/mol). The XI-catalyzed isomerization of DGA in D2O at pD 7.0 gives a 90% yield of [1-1H]-DHA and a 10% yield of [1-2H]-DHA, the product of isomerization with deuterium incorporation from solvent D2O. By comparison, the transfer of 3H from labeled hexose substrate to solvent is observed only once in every 109 turnovers for the XI-catalyzed isomerization of [2-3H]-glucose in H2O [Allen, K. N., Lavie, A., Farber, G. K., Glasfeld, A., Petsko, G. A., and Ringe, D. (1994), Biochemistry 33, 1481–1487]. We propose that truncation of the terminal ethylene glycol fragment of D-xylose to give DGA results in a large decrease in the rate of XI-catalyzed isomerization with hydride transfer compared with that for proton transfer. An ultra-high resolution (0.97 Å) X-ray crystal structure was determined for the complex obtained by soaking crystals of XI with 50 mM DGA. The triose binds to XI as the unreactive hydrate, but ligand binding induces metal cofactor movement and conformational changes in active site residues similar to those observed for XI•sugar complexes. PMID:21995300

Biological and Catalytic Conversion of Sugars and Lignin Publications |

Science.gov Websites

mechanism of free and cellulosomal enzyme synergy, ACS Sustainable Chem. Eng. Evaluation of clean Free Energy, J. Amer. Chem. Soc. Process Design and Economics for the Conversion of Lignocellulosic Processive Cellulase with Multiple Absolute Binding Free Energy Methods, J. Biol. Chem. Optimizing Nucleus

Molecular mechanical studies of DNA flexibility: Coupled backbone torsion angles and base-pair openings

PubMed Central

Keepers, Joe W.; Kollman, Peter A.; Weiner, Paul K.; James, Thomas L.

1982-01-01

Molecular mechanics studies have been carried out on “B-DNA-like” structures of [d(C-G-C-G-A-A-T-T-C-G-C-G)]2 and [d(A)]12·[d(T)]12. Each of the backbone torsion angles (ψ, φ, ω, ω′, φ′) has been “forced” to alternative values from the normal B-DNA values (g+, t, g-, g-, t conformations). Compensating torsion angle changes preserve most of the base stacking energy in the double helix. In a second part of the study, one purine N3-pyrimidine N1 distance at a time has been forced to a value of 6 Å in an attempt to simulate the base opening motions required to rationalize proton exchange data for DNA. When the 6-Å constraint is removed, many of the structures revert to the normal Watson-Crick hydrogen-bonded structure, but a number are trapped in structures ≈5 kcal/mol higher in energy than the starting B-DNA structure. The relative energy of these structures, some of which involve a non-Watson-Crick thymine C2(carbonyl)[unk]adenine 6NH2 hydrogen bond, are qualitatively consistent with the ΔH for a “base pair-open state” suggested by Mandal et al. of 4-6 kcal/mol [Mandal, C., Kallenbach, N. R. & Englander, S. W. (1979) J. Mol. Biol. 135, 391-411]. The picture of DNA flexibility emerging from this study depicts the backbone as undergoing rapid motion between local torsional minima on a nanosecond time scale. Backbone motion is mainly localized within a dinucleoside segment and generally not conformationally coupled along the chain or across the base pairs. Base motions are much smaller in magnitude than backbone motions. Base sliding allows imino N—H exchange, but it is localized, and only a small fraction of the N—H groups is exposed at any one time. Stacking and hydrogen bonding cause a rigid core of bases in the center of the molecule accounting for the hydrodynamic properties of DNA. PMID:6957879

Methods for Using Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules

DTIC Science & Technology

2014-08-20

including zero-point energy ( ZPE ) corrections, 43.21 kcal/mol and 50.46 kcal/mol, respectively. The decomposition initiated by trans-HONO elimination can...CCSD(T)/cc-pVTZ level with ZPE corrections) of 47.00 kcal/mol and 48.27 kcal/mol, respectively. Thus, at the CCSD(T)/cc-pVTZ level, the ordering of

The thermochemistry of cubane 50 years after its synthesis: a high-level theoretical study of cubane and its derivatives.

PubMed

Agapito, Filipe; Santos, Rui C; Borges dos Santos, Rui M; Martinho Simões, José A

2015-03-26

The gas-phase enthalpy of formation of cubane (603.4 ± 4 kJ mol(-1)) was calculated using an explicitly correlated composite method (W1-F12). The result obtained for cubane, together with the experimental value for the enthalpy of sublimation, 54.8 ± 2.0 kJ mol(-1), led to 548.6 ± 4.5 kJ mol(-1) for the solid-phase enthalpy of formation. This value is only 6.8 kJ mol(-1) higher than the 50-year-old original calorimetric result. The carbon-hydrogen bond dissociation enthalpy (C-H BDE) of cubane (438.4 ± 4 kJ mol(-1)), together with properties relevant for its experimental determination using gas-phase ion thermochemistry, namely the cubane gas-phase acidity (1704.6 ± 4 kJ mol(-1)), cubyl radical electron affinity (45.8 ± 4 kJ mol(-1)), cubane ionization energy (1435.1 ± 4 kJ mol(-1)), cubyl radical cation proton affinity (918.8 ± 4 kJ mol(-1)), cubane cation appearance energy (1099.6 ± 4 kJ mol(-1)), and cubyl ionization energy (661.2 ± 4 kJ mol(-1)), were also determined. These values were compared with those calculated for unstrained hydrocarbons (viz., methane, ethane, and isobutane). The strain energy of cubane (667.2 kJ mol(-1)) and cubyl radical (689.4 kJ mol(-1)) were independently estimated via quasihomodesmotic reactions. These values were related via a simple model to the C-H BDE in cubane. Taking into account the accuracy of the computational method, the comparison with high-precision experimental results, and the data consistency afforded by the relevant thermodynamic cycles, we claim an uncertainty better than ±4 kJ mol(-1) for the new enthalpy of formation values presented.

Inhibition of a cathepsin L-like cysteine protease by a chimeric propeptide-derived inhibitor.

PubMed

Godat, Emmanuel; Chowdhury, Shafinaz; Lecaille, Fabien; Belghazi, Maya; Purisima, Enrico O; Lalmanach, Gilles

2005-08-09

Like other papain-related cathepsins, congopain from Trypanosoma congolense is synthesized as a zymogen. We have previously identified a proregion-derived peptide (Pcp27), acting as a weak and reversible inhibitor of congopain. Pcp27 contains a 5-mer YHNGA motif, which is essential for selectivity in the inhibition of its mature form [Lalmanach, G., Lecaille, F., Chagas, J. R., Authié, E., Scharfstein, J., Juliano, M. A., and Gauthier, F. (1998) J. Biol. Chem. 273, 25112-25116]. In the work presented here, a homology model of procongopain was generated and subsequently used to model a chimeric 50-mer peptide (called H3-Pcp27) corresponding to the covalent linkage of an unrelated peptide (H3 helix from Antennapedia) to Pcp27. Molecular simulations suggested that H3-Pcp27 (pI = 9.99) maintains an N-terminal helical conformation, and establishes more complementary electrostatic interactions (E(coul) = -25.77 kcal/mol) than 16N-Pcp27, the 34-mer Pcp27 sequence plus the 16 native residues upstream from the proregion (E(coul) = 0.20 kcal/mol), with the acid catalytic domain (pI = 5.2) of the mature enzyme. In silico results correlated with the significant improvement of congopain inhibition by H3-Pcp27 (K(i) = 24 nM), compared to 16N-Pcp27 (K(i) = 1 microM). In addition, virtual alanine scanning of H3 and 16N identified the residues contributing most to binding affinity. Both peptides did not inhibit human cathepsins B and L. In conclusion, these data support the notion that the positively charged H3 helix favors binding, without modifying the selectivity of Pcp27 for congopain.

Simultaneous determination of albumin and low-molecular-mass thiols in plasma by HPLC with UV detection.

PubMed

Borowczyk, Kamila; Wyszczelska-Rokiel, Monika; Kubalczyk, Paweł; Głowacki, Rafał

2015-02-15

In this paper, we describe a simple and robust HPLC based method for determination of total low- and high-molecular-mass thiols, protein S-linked thiols and reduced albumin in plasma. The method is based on derivatization of analytes with 2-chloro-1-methylquinolinium tetrafluoroborate, separation and quantification by reversed-phase liquid chromatography followed by UV detection. Disulfides were converted to their thiol counterparts by reductive cleavage with tris(2-carboxyethyl)phosphine. Linearity in detector response for total thiols was observed over the range of 1-40 μmol L(-1) for Hcy and glutathione (GSH), 5-100 μmol L(-1) for Cys-Gly, 20-300 μmol L(-1) for Cys and 3.1-37.5 μmol L(-1) (0.2-2.4gL(-1)) for human serum albumin (HSA). For the protein S-bound forms these values were as follows: 0.5-30 μmol L(-1) for Hcy and GSH, 2.5-60 μmol L(-1) for Cys-Gly and 5-200 μmol L(-1) for Cys. The LOQs for total HSA, Cys, Hcy, Cys-Gly and GSH were 0.5, 0.2, 0.4, 0.3 and 0.4 μmol L(-1), respectively. The estimated validation parameters for all analytes are more than sufficient to allow the analytical method to be used for monitoring of the total and protein bound thiols as well as redox status of HSA in plasma. Copyright © 2015 Elsevier B.V. All rights reserved.

In situ gas analysis for high pressure applications using property measurements

NASA Astrophysics Data System (ADS)

Moeller, J.; Span, R.; Fieback, T.

2013-10-01

As the production, distribution, and storage of renewable energy based fuels usually are performed under high pressures and as there is a lack of in situ high pressure gas analysis instruments on the market, the aim of this work was to develop a method for in situ high pressure gas analysis of biogas and hydrogen containing gas mixtures. The analysis is based on in situ measurements of optical, thermo physical, and electromagnetic properties in gas mixtures with newly developed high pressure sensors. This article depicts the calculation of compositions from the measured properties, which is carried out iteratively by using highly accurate equations of state for gas mixtures. The validation of the method consisted of the generation and measurement of several mixtures, of which three are presented herein: a first mixture of 64.9 mol. % methane, 17.1 mol. % carbon dioxide, 9 mol. % helium, and 9 mol. % ethane at 323 K and 423 K in a pressure range from 2.5 MPa to 17 MPa; a second mixture of 93.0 mol. % methane, 4.0 mol. % propane, 2.0 mol. % carbon dioxide, and 1.0 mol. % nitrogen at 303 K, 313 K, and 323 K in a pressure range from 1.2 MPa to 3 MPa; and a third mixture of 64.9 mol. % methane, 30.1 mol. % carbon dioxide, and 5.0 mol. % nitrogen at 303 K, 313 K, and 323 K in a pressure range from 2.5 MPa to 4 MPa. The analysis of the tested gas mixtures showed that with measured density, velocity of sound, and relative permittivity the composition can be determined with deviations below 1.9 mol. %, in most cases even below 1 mol. %. Comparing the calculated compositions with the generated gas mixture, the deviations were in the range of the combined uncertainty of measurement and property models.

Interaction Mode between Inclusion Complex of Vitamin K3 with γ- Cyclodextrin and Herring-Sperm DNA.

PubMed

Tang, Yan; Cai, Li; Xue, Kang; Wang, Chunling; Xiong, Xiaoli

2016-05-03

Methods including spectroscopy, electronic chemistry and thermodynamics were used to study the inclusion effect between γ-cyclodextrin (CD) and vitamin K3(K3), as well as the interaction mode between herring-sperm DNA (hsDNA) and γ-CD-K3 inclusion complex. The results from ultraviolet spectroscopic method indicated that VK3 and γ-CD formed 1:1 inclusion complex, with the inclusion constant Kf = 1.02 × 10(4) L/mol, which is based on Benesi-Hildebrand's viewpoint. The outcomes from the probe method and Scatchard methods suggested that the interaction mode between γ-CD-K3 and DNA was a mixture mode, which included intercalation and electrostatic binding effects. The binding constants were K (θ)25°C = 2.16 × 10(4) L/mol, and K(θ)37°C = 1.06 × 10(4) L/mol. The thermodynamic functions of the interaction between γ-CD-K3 and DNA were ΔrHm(θ) = -2.74 × 10(4) J/mol, ΔrSm(θ) = 174.74 J·mol(-1)K(-1), therefore, both ΔrHm(θ) (enthalpy) and ΔrSm(θ) (entropy) worked as driven forces in this action.

A MRCC study of the isomerisation of cyclopropane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lang, Jakub; Švaňa, Matej; Demel, Ondřej

2017-01-19

Mukherjee’s and Brillouin-Wigner multi-reference coupled cluster methods were used to study the isomerization of cyclopropane to propene through a trimethylene/propylidene diradicals. Main aim was to obtain high quality ab-initio data using advanced methods that treat both static and dynamic correlation in the involved species. The MkCCSD(T)/cc-pVQZ activation energy of cyclopropane isomerization via trimethylene is 65.6 kcal/mol, in a good agreement with experimental values in the range 60-65 kcal/mol. The MkCCSD(T)/cc-pV5Z adiabatic singlet-triplet gap in trimethylene is 0.6 kcal/mol, slightly higher than previous CASPT2 result -0.7 kcal/mol by Skancke et al.

Critical Test of Some Computational Chemistry Methods for Prediction of Gas-Phase Acidities and Basicities.

PubMed

Toomsalu, Eve; Koppel, Ilmar A; Burk, Peeter

2013-09-10

Gas-phase acidities and basicities were calculated for 64 neutral bases (covering the scale from 139.9 kcal/mol to 251.9 kcal/mol) and 53 neutral acids (covering the scale from 299.5 kcal/mol to 411.7 kcal/mol). The following methods were used: AM1, PM3, PM6, PDDG, G2, G2MP2, G3, G3MP2, G4, G4MP2, CBS-QB3, B1B95, B2PLYP, B2PLYPD, B3LYP, B3PW91, B97D, B98, BLYP, BMK, BP86, CAM-B3LYP, HSEh1PBE, M06, M062X, M06HF, M06L, mPW2PLYP, mPW2PLYPD, O3LYP, OLYP, PBE1PBE, PBEPBE, tHCTHhyb, TPSSh, VSXC, X3LYP. The addition of the Grimmes empirical dispersion correction (D) to B2PLYP and mPW2PLYP was evaluated, and it was found that adding this correction gave more-accurate results when considering acidities. Calculations with B3LYP, B97D, BLYP, B2PLYPD, and PBE1PBE methods were carried out with five basis sets (6-311G**, 6-311+G**, TZVP, cc-pVTZ, and aug-cc-pVTZ) to evaluate the effect of basis sets on the accuracy of calculations. It was found that the best basis sets when considering accuracy of results and needed time were 6-311+G** and TZVP. Among semiempirical methods AM1 had the best ability to reproduce experimental acidities and basicities (the mean absolute error (mae) was 7.3 kcal/mol). Among DFT methods the best method considering accuracy, robustness, and computation time was PBE1PBE/6-311+G** (mae = 2.7 kcal/mol). Four Gaussian-type methods (G2, G2MP2, G4, and G4MP2) gave similar results to each other (mae = 2.3 kcal/mol). Gaussian-type methods are quite accurate, but their downside is the relatively long computational time.

Unfolding and inactivation during thermal denaturation of an enzyme that exhibits phytase and acid phosphatase activities.

PubMed

Wang, Xiao-Yun; Meng, Fan-Guo; Zhou, Hai-Meng

2004-03-01

The thermostability of an enzyme that exhibits phytase and acid phosphatase activities was studied. Kinetics of inactivation and unfolding during thermal denaturation of the enzyme were compared. The loss of phytase activity on thermal denaturation is most suggestive of a reversible process. As for acid phosphatase activities, an interesting phenomenon was observed; there are two phases in thermal inactivation: when the temperature was between 45 and 50 degrees C, the thermal inactivation could be characterized as an irreversible inactivation which had some residual activity and when the temperature was above 55 degrees C, the thermal inactivation could be characterized as an irreversible process which had no residual activity. The microscopic rate constants for the free enzyme and substrate-enzyme complex were determined by Tsou's method [Adv. Enzymol. Relat. Areas Mol. Biol. 61 (1988) 381]. Fluorescence analyses indicate that when the enzyme was treated at temperatures below 60 degrees C for 60 min, the conformation of the enzyme had no detectable change; when the temperatures were above 60 degrees C, some fluorescence red-shift could be observed with a decrease in emission intensity. The inactivation rates (k(+0)) of free enzymes were faster than those of conformational changes during thermal denaturation at the same temperature. The rapid inactivation and slow conformational changes of phytase during thermal denaturation suggest that inactivation occurs before significant conformational changes of the enzyme, and the active site of this enzyme is situated in a relatively fragile region which makes the active site more flexible than the molecule as a whole.

Differences in α and β polypeptide chains of tubulin resolved by electron microscopy with image reconstruction

PubMed Central

Crepeau, Richard H.; McEwen, Bruce; Edelstein, Stuart J.

1978-01-01

Electron microscopic techniques have been used to reveal two classes of subunits of tubulin in ordered arrays. Presumably the two classes correspond to the α and β polypeptide chains of tubulin that have been distinguished by chemical criteria. The two types of subunits alternate along individual protofilaments in microtubules, microtubule-precursor sheets, and extended zinc-tubulin sheets. The resolution of the two types of polypeptide chains is achieved by improved negative staining methods which produce micrographs with layer lines at 28 Å-1 and 84 Å-1 in optical or computed transforms, in addition to the layer lines at 21 Å-1 and 42 Å-1 described previously [Crepeau, R. H., McEwen, B., Dykes, G. & Edelstein, S. J. (1977) J Mol. Biol. 116, 301-315]. In microtubules or microtubule-precursor sheets, adjacent protofilaments are staggered by about 10 Å, but parallel, in the sense that the α-β vector points in the same direction for all of the protofilaments of the microtubule. However, for the sheets assembled in the presence of zinc, adjacent protofilaments are staggered by about 21 Å and oriented in an antiparallel arrangement with alternate protofilaments related by a 2-fold screw axis. The antiparallel alignment of the protofilaments in the zinc-tubulin sheets accounts for their planarity (no tubular structures are found in the presence of moderate concentrations of zinc), since the intrinsic curvature found with parallel alignment of protofilaments in the absence of zinc would be cancelled by the antiparallel arrangement. Images PMID:283410

Genetics of the connective tissue proteins: Assignment of the gene for human type I procollagen to chromosome 17 by analysis of cell hybrids and microcell hybrids*

PubMed Central

Raj, Cholappadi V. Sundar; Church, Robert L.; Klobutcher, Lawrence A.; Ruddle, Frank H.

1977-01-01

Somatic cell hybrids between mouse and human cell lines have been used to identify the specific chromosome that governs the synthesis of type I procollagen. Fourteen hybrid clones and subclones were derived independently from crosses between mouse parents [LM (thymidine kinase-negative) or A9 (hypoxanthine phosphoribosyltransferase-negative)] and human cells (human diploid lung fibroblasts WI-38 or diploid skin fibroblasts GM5, GM17, and GM9). The cultures were labeled with [3H]proline in modified Eagle's medium without serum. Radioactive procollagens were purified from the medium by the method of Church et al. [(1974) J. Mol. Biol. 86, 785-799]. DEAE-cellulose chromatography was used to separate collagen and type I and type III procollagen. Human type I procollagen was assayed by double immunodiffusion analysis with type I procollagen antibodies prepared by immunizing rabbits with purified human type I procollagen. These analyses combined with karyology and isozyme analyses of each hybrid line have produced evidence for the assignment of the gene for human type I procollagen to chromosome 17. A human microcell-mouse hybrid cell line containing only human chromosome 17 was positive for human type I procollagen, lending further support to the assignment of the human type I procollagen gene to chromosome 17. Finally, by using a hybrid line containing only the long arm of human chromosome 17 translocated onto a mouse chromosome, the type I procollagen gene can be assigned more specifically to the long arm of chromosome 17. Images PMID:412188

Spectrofluorimetric determination of cefixime using terbium-danofloxacin probe

PubMed Central

Manzoori, Jamshid L.; Amjadi, Mohammad; Soltani, Naser; Jouyban, Abolghasem

2014-01-01

Objective(s): Cefixime (Cfx), is a semi-synthetic third-generation oral cephalosporin antibiotic that is prescribed for the treatment of susceptible infections. There are some procedures for the determination of Cfx in pharmaceutical formulations and biological samples. Herein a spectrofluorimetric method was proposed for Cfx determination based on the fluorescence quenching of terbium-danofloxacin (Tb3+-Dano) in the presence of Cfx. Materials and Methods: Cfx was detected based on fluorescence quenching of terbium-danofloxacin (Tb3+-Dano) in the presence of Cfx with maximum excitation and emission wavelengths at 347 nm and 545 nm, respectively. The quenched fluorescence intensity of Tb3+- Dano system is proportional to the concentration of Cfx. The optimum conditions for the determination of Cfx were studied. Results: The maximum response was achieved under optimum conditions of [Tris buffer]= 0.008 mol/l (pH 6.5), [Tb3+]=1×10-4 mol/l and [Dano]=1×10-4 mol/l. The developed method was evaluated in terms of accuracy, precision and limit of detection. The linear concentration ranges for quantification of Cfx were 8.8×10-8-8.8×10-7 mol/l and 1.1×10-7-8.8×10-7 mol/l in standard and human serum samples with the detection limits (S/N=3) of 2.8×10-8 mol/l and 3.9×10-8 mol/l, respectively. The Cfx was determined in pharmaceutical tablets and spiked serum samples and the results were satisfactory. Conclusion: This method is simple, practical and relatively interference-free for determination of Cfx in pharmaceutical tablets and serum samples. PMID:24904718

Moderate severity heart failure does not involve a downregulation of myocardial fatty acid oxidation

DTIC Science & Technology

2004-10-01

malonyl-CoA-sensitive form of carnitine palmitoyltransferase is not local - ized exclusively in the outer membrane of rat liver mitochondria . J Biol...for the isolation of fresh mitochondria , both subsarcolemmal and interfibrillar. Analytic methods. Detailed analytic methods have been previously cited...populations of mitochondria , the subsarcolemmal and inter- fibrillar, were isolated from hearts of normal and HF dogs using the procedure of Palmer et al

PMMA microreactor for chemiluminescence detection of Cu (II) based on 1,10-Phenanthroline-hydrogen peroxide reaction.

PubMed

Chen, Xueye; Shen, Jienan; Li, Tiechuan

2016-01-01

A microreactor for the chemiluminescence detection of copper (II) in water samples, based on the measurement of light emitted from the copper (II) catalysed oxidation of 1,10-phenanthroline by hydrogen peroxide in basic aqueous solution, is presented. Polymethyl methacrylate (PMMA) was chose as material for fabricating the microreactor with mill and hot bonding method. Optimized reagents conditions were found to be 6.3 × 10(-5)mol/L 1,10-phenanthroline, 1.5 × 10(-3)mol/L hydrogen peroxide, 7.0 × 10(-2)mol/L sodium hydroxide and 2.4 × 10(-5)mol/L Hexadecyl trimethyl ammonium Bromide (CTMAB). In the continuous flow injection mode the system can perform fully automated detection with a reagent consumption of only 3.5 μL each time. The linear range of the Cu (II) ions concentration was 1.5 × 10(-8) mol/L to 1.0 × 10(-4) mol/L, and the detection limit was 9.4 × 10(-9)mol/L with the S/N ratio of 4. The relative standard deviation was 3.0 % for 2.0 × 10(-6) mol/L Cu (II) ions (n = 10). The most obvious features of the detection method are simplicity, rapidity and easy fabrication of the microreactor.

Research on modified the estimates of NOx emissions combined the OMI and ground-based DOAS technique

NASA Astrophysics Data System (ADS)

Zhang, Qiong; Li*, Ang; Xie, Pinhua; Hu, Zhaokun; Wu, Fengcheng; Xu, Jin

2017-04-01

A new method to calibrate nitrogen dioxide (NO2) lifetimes and emissions from point sources using satellite measurements base on the mobile passive differential optical absorption spectroscopy (DOAS) and multi axis differential optical absorption spectroscopy (MAX-DOAS) is described. It is based on using the Exponentially-Modified Gaussian (EMG) fitting method to correct the line densities along the wind direction by fitting the mobile passive DOAS NO2 vertical column density (VCD). An effective lifetime and emission rate are then determined from the parameters of the fit. The obtained results were then compared with the results acquired by fitting OMI (Ozone Monitoring Instrument) NO2 using the above fitting method, the NOx emission rate was about 195.8mol/s, 160.6mol/s, respectively. The reason why the latter less than the former may be because the low spatial resolution of the satellite.

Applications of Random Differential Equations to Engineering Science. Wave Propagation in Turbulent Media and Random Linear Hyperbolic Systems.

DTIC Science & Technology

1981-11-10

1976), 745-754. 4. (with W. C. Tam) Periodic and traveling wave solutions to Volterra - Lotka equation with diffusion. Bull. Math. Biol. 38 (1976), 643...with applications [17,19,20). (5) A general method for reconstructing the mutual coherent function of a static or moving source from the random

Pyrolysis kinetics and thermal behavior of waste sawdust biomass using thermogravimetric analysis.

PubMed

Mishra, Ranjeet Kumar; Mohanty, Kaustubha

2018-03-01

The present study reports pyrolysis behavior of three waste biomass using thermogravimetric analysis to determine kinetic parameters at five different heating rates. Physiochemical characterization confirmed that these biomass have the potential for fuel and energy production. Pyrolysis experiments were carried out at five different heating rates (5-25 °C min -1 ). Five model-free methods such as Kissinger-Akahira-Sunose (KAS), Ozawa-Flynn-Wall (OFW), Friedman, Coats-Redfern, and distributed activation energy (DAEM) were used to calculate the kinetic parameters. The activation energy was found to be 171.66 kJ mol -1 , 148.44 kJ mol -1 , and 171.24 kJ mol -1 from KAS model; 179.29 kJ mol -1 , 156.58 kJ mol -1 , and 179.47 kJ mol -1 from OFW model; 168.58 kJ mol -1 , 181.53 kJ mol -1 , and 184.61 kJ mol -1 from Friedman model; and 206.62 kJ mol -1 , 171.63 kJ mol -1 , and 160.45 kJ mol -1 from DAEM model for PW, SW, AN biomass respectively. The calculated kinetic parameters are in good agreement with other reported biomass. Copyright © 2017 Elsevier Ltd. All rights reserved.

Advances in the Visualization and Analysis of Boundary Layer Flow in Swimming Fish

DTIC Science & Technology

2005-02-01

caudal-fin amputation on the kinematics and metabolic rate of underyearling sockeye salmon ( Oncorhynchus nerka ) at steady swimming speeds. J. Exp. Biol...caudal-fin amputation on the kinematics and metabolic rate of underyearling sockeye salmon ( Oncorhynchus nerka ) at steady swimming speeds. J. Exp. Biol

Light-regulated phosphorylation of maize phosphoenolpyruvate carboxykinase plays a vital role in its activity.

PubMed

Chao, Qing; Liu, Xiao-Yu; Mei, Ying-Chang; Gao, Zhi-Fang; Chen, Yi-Bo; Qian, Chun-Rong; Hao, Yu-Bo; Wang, Bai-Chen

2014-05-01

Phosphoenolpyruvate carboxykinase (PEPCK)-the major decarboxylase in PEPCK-type C4 plants-is also present in appreciable amounts in the bundle sheath cells of NADP-malic enzyme-type C4 plants, such as maize (Zea mays), where it plays an apparent crucial role during photosynthesis (Wingler et al., in Plant Physiol 120(2):539-546, 1999; Furumoto et al., in Plant Mol Biol 41(3):301-311, 1999). Herein, we describe the use of mass spectrometry to demonstrate phosphorylation of maize PEPCK residues Ser55, Thr58, Thr59, and Thr120. Western blotting indicated that the extent of Ser55 phosphorylation dramatically increases in the leaves of maize seedlings when the seedlings are transferred from darkness to light, and decreases in the leaves of seedlings transferred from light to darkness. The effect of light on phosphorylation of this residue is opposite that of the effect of light on PEPCK activity, with the decarboxylase activity of PEPCK being less in illuminated leaves than in leaves left in the dark. This inverse relationship between PEPCK activity and the extent of phosphorylation suggests that the suppressive effect of light on PEPCK decarboxylation activity might be mediated by reversible phosphorylation of Ser55.

Temporal and tissue-specific regulation of a Brassica napus stearoyl-acyl carrier protein desaturase gene.

PubMed Central

Slocombe, S P; Piffanelli, P; Fairbairn, D; Bowra, S; Hatzopoulos, P; Tsiantis, M; Murphy, D J

1994-01-01

The nucleotide sequence of a Brassica napus stearoyl-acyl carrier protein desaturase gene (Bn10) is presented. This gene is one member of a family of four closely related genes expressed in oilseed rape. The expression of the promoter of this gene in transgenic tobacco was found to be temporally regulated in the developing seed tissues. However, the promoter was also particularly active in other oleogenic tissues such as the tapetum and pollen grains. This raises the interesting question of whether seed-expressed lipid synthesis genes are regulated by separate tissue-specific determinants or by a single factor common to all oleogenic tissues. Parts of the plants undergoing rapid development such as the components of immature flowers and seedlings also exhibited high levels of promoter activity. These tissues are likely to have an elevated requirement for membrane lipid synthesis. Stearoyl-acyl carrier protein desaturase transcript levels have previously been shown to be temporally regulated in the B. napus embryo (S.P. Slocombe, I. Cummins, R.P. Jarvis, D.J. Murphy [1992] Plant Mol Biol 20: 151-155). Evidence is presented demonstrating the induction of desaturase mRNA by abscisic acid in the embryo. PMID:8016261

The Peptide Near the C Terminus Regulates Receptor CAR Nuclear Translocation Induced by Xenochemicals in Mouse Liver

PubMed Central

Zelko, Igor; Sueyoshi, Tatsuya; Kawamoto, Takeshi; Moore, Rick; Negishi, Masahiko

2001-01-01

In response to phenobarbital (PB) and other PB-type inducers, the nuclear receptor CAR translocates to the mouse liver nucleus (T. Kawamoto et al., Mol. Cell. Biol. 19:6318–6322, 1999). To define the translocation mechanism, fluorescent protein-tagged human CAR (hCAR) was expressed in the mouse livers using the in situ DNA injection and gene delivery systems. As in the wild-type hCAR, the truncated receptor lacking the C-terminal 10 residues (i.e., AF2 domain) translocated to the nucleus, indicating that the PB-inducible translocation is AF2 independent. Deletion of the 30 C-terminal residues abolished the receptor translocation, and subsequent site-directed mutagenesis delineated the PB-inducible translocation activity of the receptor to the peptide L313GLL316AEL319. Ala mutations of Leu313, Leu316, or Leu319 abrogated the translocation of CAR in the livers, while those of Leu312 or Leu315 did not affect the nuclear translocation. The leucine-rich peptide dictates the nuclear translocation of hCAR in response to various PB-type inducers and appears to be conserved in the mouse and rat receptors. PMID:11283262

Accurate Cell Division in Bacteria: How Does a Bacterium Know Where its Middle Is?

NASA Astrophysics Data System (ADS)

Howard, Martin; Rutenberg, Andrew

2004-03-01

I will discuss the physical principles lying behind the acquisition of accurate positional information in bacteria. A good application of these ideas is to the rod-shaped bacterium E. coli which divides precisely at its cellular midplane. This positioning is controlled by the Min system of proteins. These proteins coherently oscillate from end to end of the bacterium. I will present a reaction-diffusion model that describes the diffusion of the Min proteins, and their binding/unbinding from the cell membrane. The system possesses an instability that spontaneously generates the Min oscillations, which control accurate placement of the midcell division site. I will then discuss the role of fluctuations in protein dynamics, and investigate whether fluctuations set optimal protein concentration levels. Finally I will examine cell division in a different bacteria, B. subtilis. where different physical principles are used to regulate accurate cell division. See: Howard, Rutenberg, de Vet: Dynamic compartmentalization of bacteria: accurate division in E. coli. Phys. Rev. Lett. 87 278102 (2001). Howard, Rutenberg: Pattern formation inside bacteria: fluctuations due to the low copy number of proteins. Phys. Rev. Lett. 90 128102 (2003). Howard: A mechanism for polar protein localization in bacteria. J. Mol. Biol. 335 655-663 (2004).

Dysregulated human Tyrosyl-DNA phosphodiesterase I acts as cellular toxin

PubMed Central

Cuya, Selma M.; Comeaux, Evan Q.; Wanzeck, Keith; Yoon, Karina J.; van Waardenburg, Robert C.A.M.

2016-01-01

Tyrosyl-DNA phosphodiesterase I (TDP1) hydrolyzes the drug-stabilized 3’phospho-tyrosyl bond formed between DNA topoisomerase I (TOPO1) and DNA. TDP1-mediated hydrolysis uses a nucleophilic histidine (Hisnuc) and a general acid/base histidine (Hisgab). A Tdp1Hisgab to Arg mutant identified in patients with the autosomal recessive neurodegenerative disease SCAN1 causes stabilization of the TDP1-DNA intermediate. Based on our previously reported Hisgab-substitutions inducing yeast toxicity (Gajewski et al. J. Mol. Biol. 415, 741-758, 2012), we propose that converting TDP1 into a cellular poison by stabilizing the covalent enzyme-DNA intermediate is a novel therapeutic strategy for cancer treatment. Here, we analyzed the toxic effects of two TDP1 catalytic mutants in HEK293 cells. Expression of human Tdp1HisnucAla and Tdp1HisgabAsn mutants results in stabilization of the covalent TDP1-DNA intermediate and induces cytotoxicity. Moreover, these mutants display reduced in vitro catalytic activity compared to wild type. Co-treatment of Tdp1mutant with topotecan shows more than additive cytotoxicity. Overall, these results support the hypothesis that stabilization of the TDP1-DNA covalent intermediate is a potential anti-cancer therapeutic strategy. PMID:27893431

Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe[superscript 2+] metal-ion preference

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jackson, Colin J.; Hadler, Kieran S.; Carr, Paul D.

2011-09-28

The structure of a malonate-bound form of the glycerophosphodiesterase from Enterobacter aerogenes, GpdQ, has been refined at a resolution of 2.2 {angstrom} to a final R factor of 17.1%. The structure was originally solved to 2.9 {angstrom} resolution using SAD phases from Zn{sup 2+} metal ions introduced into the active site of the apoenzyme [Jackson et al. (2007), J. Mol. Biol. 367, 1047-1062]. However, the 2.9 {angstrom} resolution was insufficient to discern significant details of the architecture of the binuclear metal centre that constitutes the active site. Furthermore, kinetic analysis revealed that the enzyme lost a significant amount of activitymore » in the presence of Zn2+, suggesting that it is unlikely to be a catalytically relevant metal ion. In this communication, a higher resolution structure of GpdQ is presented in which malonate is visibly coordinated in the active site and analysis of the native metal-ion preference is presented using atomic absorption spectroscopy and anomalous scattering. Catalytic implications of the structure and its Fe{sup 2+} metal-ion preference are discussed.« less

Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe[supscript 2+] metal-ion preference

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jackson, Colin J.; Hadler, Kieran S.; Carr, Paul D.

2010-09-20

The structure of a malonate-bound form of the glycerophosphodiesterase from Enterobacter aerogenes, GpdQ, has been refined at a resolution of 2.2 {angstrom} to a final R factor of 17.1%. The structure was originally solved to 2.9 {angstrom} resolution using SAD phases from Zn{sup 2+} metal ions introduced into the active site of the apoenzyme [Jackson et al. (2007), J. Mol. Biol. 367, 1047-1062]. However, the 2.9 {angstrom} resolution was insufficient to discern significant details of the architecture of the binuclear metal centre that constitutes the active site. Furthermore, kinetic analysis revealed that the enzyme lost a significant amount of activitymore » in the presence of Zn{sup 2+}, suggesting that it is unlikely to be a catalytically relevant metal ion. In this communication, a higher resolution structure of GpdQ is presented in which malonate is visibly coordinated in the active site and analysis of the native metal-ion preference is presented using atomic absorption spectroscopy and anomalous scattering. Catalytic implications of the structure and its Fe{sup 2+} metal-ion preference are discussed.« less

Modeling polymorphic transformation of rotating bacterial flagella in a viscous fluid

NASA Astrophysics Data System (ADS)

Ko, William; Lim, Sookkyung; Lee, Wanho; Kim, Yongsam; Berg, Howard C.; Peskin, Charles S.

2017-06-01

The helical flagella that are attached to the cell body of bacteria such as Escherichia coli and Salmonella typhimurium allow the cell to swim in a fluid environment. These flagella are capable of polymorphic transformation in that they take on various helical shapes that differ in helical pitch, radius, and chirality. We present a mathematical model of a single flagellum described by Kirchhoff rod theory that is immersed in a fluid governed by Stokes equations. We perform numerical simulations to demonstrate two mechanisms by which polymorphic transformation can occur, as observed in experiments. First, we consider a flagellar filament attached to a rotary motor in which transformations are triggered by a reversal of the direction of motor rotation [L. Turner et al., J. Bacteriol. 182, 2793 (2000), 10.1128/JB.182.10.2793-2801.2000]. We then consider a filament that is fixed on one end and immersed in an external fluid flow [H. Hotani, J. Mol. Biol. 156, 791 (1982), 10.1016/0022-2836(82)90142-5]. The detailed dynamics of the helical flagellum interacting with a viscous fluid is discussed and comparisons with experimental and theoretical results are provided.

Synthetic Fab Fragments that Bind the HIV-1 gp41 Heptad Repeat Regions

PubMed Central

Liu, Yanyun; Regula, Lauren K.; Stewart, Alex; Lai, Jonathan R.

2011-01-01

Recent work has demonstrated that antibody phage display libraries containing restricted diversity in the complementarity determining regions (CDRs) can be used to target a wide variety of antigens with high affinity and specificity. In the most extreme case, antibodies whose combining sites are comprised of only two residues – tyrosine and serine – have been identified against several protein antigens. [F. A. Fellouse, B. Li, D. M. Compaan, A. A. Peden, S. G. Hymowitz, and S. S. Sidhu, J. Mol. Biol., 348 (2005) 1153–1162.] Here, we report the isolation and characterization of antigen-binding fragments (Fabs) from such “minimalist” diversity synthetic antibody libraries that bind the heptad repeat regions of human immunodeficiency virus type 1 (HIV-1) gp41. We show that these Fabs are highly specific for the HIV-1 epitope and comparable in affinity to a single chain variable fragment (scFv) derived from a natural antibody repertoire that targets the same region. Since the heptad repeat regions of HIV-1 gp41 are required for viral entry, these Fabs have potential for use in therapeutic, research, or diagnostic applications. PMID:21925149

Involvement of tyrosine residues, N-terminal amino acids, and beta-alanine in insect cuticular sclerotization.

PubMed

Andersen, Svend Olav

2007-09-01

During sclerotization of insect cuticle the acyldopamines, N-acetyldopamine (NADA) and N-beta-alanyldopamine (NBAD), are oxidatively incorporated into the cuticular matrix, thereby hardening and stabilizing the material by forming crosslinks between the proteins in the cuticular matrix and by forming polymers filling the intermolecular spaces in the cuticle. Sclerotized cuticle from the locust, Schistocerca gregaria, and the beetle, Tenebrio molitor, was hydrolyzed in dilute hydrochloric acid, and from the hydrolysates some components presumably degradation products of cuticular crosslinks were isolated. In two of the components, the sidechain of 3,4-dihydroxyacetophenone was linked to the amino groups of glycine and beta-alanine, respectively, and in the third component to the phenolic group of tyrosine. These three compounds, glycino-dihydroxyacetophenone, beta-alanino-dihydroxyacetophenone, and O-tyrosino-dihydroxyacetophenone, as well as the previously reported compound, lysino-dihydroxyacetophenone [Andersen, S.O., Roepstorff, P., 2007. Aspects of cuticular sclerotization in the locust, Schistocerca gregaria, and the beetle, Tenebrio molitor. Insect Biochem. Mol. Biol. 37, 223-234], are suggested to be degradation products of cuticular crosslinks, in which amino acid residues formed linkages to both the alpha- and beta-positions of the sidechain of acyldopamines.

On-line Adaptive Radiation Treatment of Prostate Cancer

DTIC Science & Technology

2009-01-01

12]. For intensity modulated radiation therapy (IMRT) plans , the beamlet weight can be re-optimized on a daily basis to mini- mize the dose to the OAR...Thongphiew D, Wang Z, Mathayomchan B, Chankong V, Yoo S, et al. On-line re-optimization of prostate IMRT plans for adaptive radiation therapy . Phys Med Biol...time. The treatment planning method for VMAT however is not mature. We are developing a robust VMAT treatment planning method which incorporates

Evaluation of a third party enzymatic ammonia method for use on the Roche Cobas 6000 (c501) automated platform.

PubMed

Seiden-Long, Isolde; Schnabl, Kareena; Skoropadyk, Wendy; Lennon, Nola; McKeage, Arlayne

2014-08-01

Adaptation of the Randox Enzymatic Manual UV Ammonia method to be used on the Roche Cobas 6000 (c501) automated analyzer platform. The Randox ammonia reagent was evaluated for precision, linearity, accuracy and interference from hemolysis, icterus and lipemia on the Roche c501 analyzer. Comparison studies were conducted for the Randox reagent between Roche c501, Siemens Vista, Ortho Vitros 250, and Beckman DxC methods. The Randox reagent demonstrates acceptable within-run (L1=65 μmol/L, CV 3.4% L2=168 μmol/L, CV 1.9%) and between-run precision (L1=29 μmol/L, CV 7.3% L2=102 μmol/L, CV 3.0%), Analytical Measurement Range (7-940 μmol/L), and accuracy. The method interference profile is superior for the Randox method (hemolysis index up to 600, icteric index up to 60, lipemic index up to 100) as compared to the Roche method (hemolysis index up to 200, icteric index up to 10, lipemic index up to 50). Comparison was very good between the Randox reagent and two other wet chemistry platforms. The Randox Enzymatic Manual UV Ammonia reagent is an available alternative to the Roche Cobas c501 reagent. The method is more robust to endogenous interferences and less prone to instrument error flags, thus allowing the majority of clinical specimens to be reported without additional sample handling at our institution. Copyright © 2014 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

A comparison of the coupled cluster and internally contracted averaged coupled-pair functional levels of theory for the calculation of the MCH2(+) binding energies for M = Sc to Cu

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Partridge, Harry; Scuseria, Gustavo E.

1992-01-01

The correlation contribution to the M-C binding energy for the MCH2(+) systems can exceed 100 kcal/mol. At the self-consistent field (SCF) level, these systems can be more than 50 kcal/mol above the fragment energies. In spite of the poor zeroth-order reference, the coupled cluster single and double excitation method with a perturbational estimate of triple excitations, CCSD(T), method is shown to provide an accurate description of these systems. The maximum difference between the CCSD(T) and internally contracted averaged coupled-pair functional binding energies is 1.5 kcal/mol for CrCH2(+), with the remaining systems agreeing to within 1.0 kcal/mol.

Spectroscopic analysis on the resveratrol-DNA binding interactions at physiological pH

NASA Astrophysics Data System (ADS)

Zhang, Shufang; Sun, Xuejun; Jing, Zhihong; Qu, Fengli

2011-11-01

The interaction of resveratrol with calf thymus deoxyribonucleic acid (ctDNA) under physiological conditions (Tris-HCl buffer solutions, pH 7.4) was studied by spectroscopy, fluorescence spectroscopy and viscosity measurement method, respectively. Results indicated that a complex of resveratrol with ctDNA was formed with a binding constant of K17 °C = 5.49 × 10 3 L mol -1 and K37 °C = 1.90 × 10 4 L mol -1. The fluorescence quenching mechanism of acridine orange (AO)-ctDNA by resveratrol was shown to be a static quenching type. The thermodynamic parameters of the complex were calculated by a double reciprocal method: ΔHms=4.64×10 J mol, ΔSms=231.8 J K mol and ΔGms=-2.54×10 J mol (37 °C). Spectroscopic techniques together with viscosity determination provided evidences of intercalation mode of binding for the interaction between resveratrol and ctDNA.

Curing kinetics of 4,4‧-Methylenebis epoxy and m-Xylylenediamine

NASA Astrophysics Data System (ADS)

Li, Z. R.; Li, X. D.; Guo, X. Y.

2017-11-01

In this paper, the curing kinetics of 4,4‧-Methylenebis epoxy resin(TGDDM) and m-Xylylenediamine(m-XDA) was investigated by non-isothermal differential scanning calorimetry(DSC) at various heating rates. Selected non-isothermal methods for analyzing curing kinetics were compared. The activation energy(E) and the correlation coefficient(R) were obtained by different isoconversional methods. The reaction order(n) was obtained by the activation energy in different isoconversional methods for the by Crane equation. The results show that the apparent activation energy are 65.23kJ/mol, 52.20 kJ/mol and 66.10 kJ/mol by using the method of Kissinger, Friedman and F-W-O, the reaction order are 0.911, 0.729 and 0.923 by using the method of Kissinger, Friedman and F-W-O.

Taxonomic revision of true morels (Morchella) in Canada and the United States

USDA-ARS?s Scientific Manuscript database

Recent molecular phylogenetic studies by Taskin et al. (Fungal Genet. Biol. 47:672-682. 2010; Mycologia [in press]) and O'Donnell et al. (Fungal Genet. Biol. 48:252-265. 2011) revealed the existence of at least 50 species of Morchella worldwide and demonstrated a high degree of continental endemism ...

Isolation and structures of glycoprotein-derived free oligosaccharides from the unfertilized eggs of Scyliorhinus caniculus. Characterization of the sequences galactose(alpha 1-4)galactose(beta 1-3)-N-acetylglucosamine and N-acetylneuraminic acid(alpha 2-6)galactose(beta 1-3)-N-acetylglucosamine.

PubMed

Plancke, Y; Delplace, F; Wieruszeski, J M; Maes, E; Strecker, G

1996-01-15

As previously reported [Ishii, K., Iwasaki, M., Inoue, S., Kenny, P. T. M., Komura, H. & Inoue, Y. (1989) J. Biol. Chem. 264, 1623-1630; Inoue, S., Iwasaki, M., Ishii, K., Kitajima, K. & Inoue, Y. (1989) J. Biol. Chem. 264, 18520-185261, the unfertilized eggs of two different species of fresh-water fish, Plecoglossus altivelis and Tribodolon hakonensis, contain relatively large amounts of free sialooligosaccharides. These oligosaccharides were found to derive from glycophosphoproteins, owing to the activity of a peptide - N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase [Iwasaki, M., Seko, A., Kitajima, K., Inoue, Y. & Inoue, S. (1992) J. Biol. Chem. 267, 24287-24296; Seko, A., Kitajima, K., Inoue, Y. & Inoue, S. (1991) J. Biol. Chem. 266, 22110-22114]. Here we describe a new type of free oligosaccharides, isolated from unfertilized eggs of Scyliorhinus caniculus. From the structural analysis, based upon 1H-NMR spectroscopy, the following glycan units are proposed.[Formula: see text

Results of the Second U.S. Manned Suborbital Space Flight, July 21, 1961

DTIC Science & Technology

1961-07-21

Alpha - ketoglutaric ...... Neg. Neg. Neg. Neg . .............................. Isocitric ............... 0 to 10...M.: An Accurate Method for the Determination of Blood Urea Nitrogen by Direct Nesslerization. Jour. Biol. Chem., vol. 143, 1942, pp. 531-544. Calcium ...DIEHL, H., and FI.LINGBOE, J. L.: Indicator for Titration of Calcium in Presence of Magnesium With Disodium. Dihy- drogen Ethylene

Removal of pharmaceutical and personal care products (PPCPs) under nitrifying and denitrifying conditions.

PubMed

Suarez, Sonia; Lema, Juan M; Omil, Francisco

2010-05-01

The contribution of volatilization, sorption and transformation to the removal of 16 Pharmaceutical and Personal Care Products (PPCPs) in two lab-scale conventional activated sludge reactors, working under nitrifying (aerobic) and denitrifying (anoxic) conditions for more than 1.5 years, have been assessed. Pseudo-first order biological degradation rate constants (k(biol)) were calculated for the selected compounds in both reactors. Faster degradation kinetics were measured in the nitrifying reactor compared to the denitrifying system for the majority of PPCPs. Compounds could be classified according to their k(biol) into very highly (k(biol)>5Lg(SS)(-1)d(-1)), highly (175%) and anoxic (>65%) conditions, whereas naproxen (NPX), ethinylestradiol (EE2), roxithromycin (ROX) and erythromycin (ERY) were only significantly transformed in the aerobic reactor (>80%). The anti-depressant citalopram (CTL) was moderately biotransformed under both, aerobic and anoxic conditions (>60% and >40%, respectively). Some compounds, as carbamazepine (CBZ), diazepam (DZP), sulfamethoxazole (SMX) and trimethoprim (TMP), manifested high resistance to biological transformation. Solids Retention Time (SRT(aerobic) >50d and <50d; SRT(anoxic) >20d and <20d) had a slightly positive effect on the removal of FLX, NPX, CTL, EE2 and natural estrogens (increase in removal efficiencies <10%). Removal of diclofenac (DCF) in the aerobic reactor was positively affected by the development of nitrifying biomass and increased from 0% up to 74%. Similarly, efficient anoxic transformation of ibuprofen (75%) was observed after an adaptation period of 340d. Temperature (16-26 degrees C) only had a slight effect on the removal of CTL which increased in 4%.

Explicitly Representing the Solvation Shell in Continuum Solvent Calculations

PubMed Central

Svendsen, Hallvard F.; Merz, Kenneth M.

2009-01-01

A method is presented to explicitly represent the first solvation shell in continuum solvation calculations. Initial solvation shell geometries were generated with classical molecular dynamics simulations. Clusters consisting of solute and 5 solvent molecules were fully relaxed in quantum mechanical calculations. The free energy of solvation of the solute was calculated from the free energy of formation of the cluster and the solvation free energy of the cluster calculated with continuum solvation models. The method has been implemented with two continuum solvation models, a Poisson-Boltzmann model and the IEF-PCM model. Calculations were carried out for a set of 60 ionic species. Implemented with the Poisson-Boltzmann model the method gave an unsigned average error of 2.1 kcal/mol and a RMSD of 2.6 kcal/mol for anions, for cations the unsigned average error was 2.8 kcal/mol and the RMSD 3.9 kcal/mol. Similar results were obtained with the IEF-PCM model. PMID:19425558

Thermal conductivity of ZrO2-4mol%Y2O3 thin coatings by pulsed thermal imaging method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jang, Byung-Koog; Sun, Jiangang; Kim, Seongwon

Thin ZrO2-4mol% Y2O3 coatings were deposited onto ZrO2 substrates by electron beam-physical vapor deposition. The coated samples revealed a feather-like columnar microstructure. The main phase of the ZrO2-4mol% Y2O3 coatings was the tetragonal phase. To evaluate the influence of the coating’s thickness on the thermal conductivity of thin ZrO2-4mol% Y2O3 coatings, the pulsed thermal imaging method was employed to obtain the thermal conductivity of the coating layer in the two-layer (coating and substrate) samples with thickness between 56 and 337 micrometers. The thermal conductivity of the coating layer was successfully evaluated and compared well with those obtained by the lasermore » flash method for similar coatings. The thermal conductivity of coatings shows an increasing tendency with an increase in the coating’s thickness.« less

New potentiometric and spectrophotometric methods for the determination of dextromethorphan in pharmaceutical preparations.

PubMed

Elmosallamy, Mohamed A F; Amin, Alaa S

2014-01-01

New, simple and convenient potentiometric and spectrophotometric methods are described for the determination of dextromethorphan hydrobromide (DXM) in pharmaceutical preparations. The potentiometric technique is based on developing a potentiometric sensor incorporating the dextromethorphan tetrakis(p-chlorophenyl)borate ion-pair complex as an electroactive species in a plasticized PVC matrix membrane with o-nitophenyl octyl ether or dioctyl phthalate. The sensor shows a rapid near Nernstian response of over 1 × 10(-5) - 1 × 10(-2) mol L(-1) dextromethorphan in the pH range of 3.0 - 9.0. The detection limit is 2 × 10(-6) mol L(-1) DXM and the response time is instantaneous (2 s). The proposed spectrophotometric technique involves the reaction of DXM with eriochrom black T (EBT) to form an ion-associate complex. Solvent extraction is used to improve the selectivity of the method. The optimal extraction and reaction conditions have been studied, and the analytical characteristics of the method have been obtained. Linearity is obeyed in the range of 7.37 - 73.7 × 10(-5) mol L(-1) DXM, and the detection limit of the method is 1.29 × 10(-5) mol L(-1). The relative standard deviation (RSD) and relative error for six replicate measurements of 3.685 × 10(-4) mol L(-1) are 0.672 and 0.855%, respectively. The interference effect of some excepients has also been tested. The drug contents in pharmaceutical preparations were successfully determined by the proposed methods by applying the standard-addition technique.

Probing phenylalanine/adenine pi-stacking interactions in protein complexes with explicitly correlated and CCSD(T) computations.

PubMed

Copeland, Kari L; Anderson, Julie A; Farley, Adam R; Cox, James R; Tschumper, Gregory S

2008-11-13

To examine the effects of pi-stacking interactions between aromatic amino acid side chains and adenine bearing ligands in crystalline protein structures, 26 toluene/(N9-methyl)adenine model configurations have been constructed from protein/ligand crystal structures. Full geometry optimizations with the MP2 method cause the 26 crystal structures to collapse to six unique structures. The complete basis set (CBS) limit of the CCSD(T) interaction energies has been determined for all 32 structures by combining explicitly correlated MP2-R12 computations with a correction for higher-order correlation effects from CCSD(T) calculations. The CCSD(T) CBS limit interaction energies of the 26 crystal structures range from -3.19 to -6.77 kcal mol (-1) and average -5.01 kcal mol (-1). The CCSD(T) CBS limit interaction energies of the optimized complexes increase by roughly 1.5 kcal mol (-1) on average to -6.54 kcal mol (-1) (ranging from -5.93 to -7.05 kcal mol (-1)). Corrections for higher-order correlation effects are extremely important for both sets of structures and are responsible for the modest increase in the interaction energy after optimization. The MP2 method overbinds the crystal structures by 2.31 kcal mol (-1) on average compared to 4.50 kcal mol (-1) for the optimized structures.

Do older adults use the Method of Loci? Results from the ACTIVE Study

PubMed Central

Gross, Alden L.; Brandt, Jason; Bandeen-Roche, Karen; Carlson, Michelle C.; Stuart, Elizabeth A.; Marsiske, Michael; Rebok, George W.

2013-01-01

Background The method of loci (MoL) is a complex visuospatial mnemonic strategy. Previous research suggests older adults could potentially benefit from using the MoL, but that it is too attentionally demanding for them to use in practice. We evaluated the hypotheses that training can increase the use of MoL, and that MoL use is associated with better memory. Methods We analyzed skip patterns on response forms for the Auditory Verbal Learning Test (AVLT) in the Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE, n=1,401) trial using 5 years of longitudinal follow-up. Results At baseline, 2% of participants skipped spaces. Fewer than 2% of control participants skipped spaces at any visit across 5 years, but 25% of memory-trained participants, taught the MoL, did so. Participants who skipped spaces used more serial clustering, a hallmark of the MoL (p<0.001). Trained participants who skipped spaces showed greater memory improvement after training than memory-trained participants who did not skip spaces (Cohen's d=0.84, P=0.007), and did not differ in the subsequent rate of long-term memory decline through up to 5 years of follow-up. Conclusion Despite being attentionally demanding, this study suggests that after training, the MoL is used by up to 25% of older adults, and that its use is associated with immediate memory improvement that was sustained through the course of follow-up. Findings are consistent with the notion that older adults balance complexity with novelty in strategy selection, and that changes in strategies used following memory training result in observable qualitative and quantitative differences in memory performance. PMID:24625044

Conditioning of renewable silver amalgam film electrode for the characterization of clothianidin and its determination in selected samples by adsorptive square-wave voltammetry.

PubMed

Brycht, Mariola; Skrzypek, Sławomira; Guzsvány, Valéria; Berenji, Janoš

2013-12-15

A new square-wave adsorptive stripping voltammetric (SWAdSV) method was developed for the determination of the neonicotinoid insecticide clothianidin (Clo), based on its reduction at a renewable silver amalgam film electrode (Hg(Ag)FE). The key point of the procedure is the pretreatment of the Hg(Ag)FE by applying the appropriate conditioning potential (-1.70 V vs. Ag/AgCl reference electrode). Under the optimized voltammetric conditions, such pretreatment resulted in the peak for the Clo reduction in Britton-Robinson buffer pH 9.0 at about -0.60 V, which was used for the analytical purpose. The developed SWAdSV procedure made it possible to determine Clo in the concentration range of 6.0×10(-7)-7.0×10(-6) mol L(-1) (LOD=1.8×10(-7) mol L(-1), LOQ=6.0×10(-7) mol L(-1)) and 7.0×10(-6)-4.0×10(-5) mol L(-1) (LOD=1.3×10(-6) mol L(-1), LOQ=4.2×10(-6) mol L(-1)). The repeatability, precision, and the recovery of the method were determined. The effect of common interfering pesticides was also investigated. Standard addition method was successfully applied and validated for the determination of Clo in spiked Warta River water, corn seeds samples, and in corn seeds samples treated with the commercial formulation PONCHO 600 FS. © 2013 Elsevier B.V. All rights reserved.

Studies to Control Endemic Typhoid Fever in Chile

DTIC Science & Technology

1984-07-14

Malmaceda PGP, Acosta JJV, Arrasco VG. La fiebre tifoidea en el nino senor de dos anos. Biol. Ned. Hosp. Inf. Rex. 38:473, 1981. 11. Kumate J...Penaloza JL, Llausas’A. La fiebre tifoidea en el primer ano de la vida. Biol. Red. Bosp. Inf. 31:925, 1974. 12. Herrera P, Cuellar A. Samanellosis tifica en

A comparison of the Method of Lines to finite difference techniques in solving time-dependent partial differential equations. [with applications to Burger equation and stream function-vorticity problem

NASA Technical Reports Server (NTRS)

Kurtz, L. A.; Smith, R. E.; Parks, C. L.; Boney, L. R.

1978-01-01

Steady state solutions to two time dependent partial differential systems have been obtained by the Method of Lines (MOL) and compared to those obtained by efficient standard finite difference methods: (1) Burger's equation over a finite space domain by a forward time central space explicit method, and (2) the stream function - vorticity form of viscous incompressible fluid flow in a square cavity by an alternating direction implicit (ADI) method. The standard techniques were far more computationally efficient when applicable. In the second example, converged solutions at very high Reynolds numbers were obtained by MOL, whereas solution by ADI was either unattainable or impractical. With regard to 'set up' time, solution by MOL is an attractive alternative to techniques with complicated algorithms, as much of the programming difficulty is eliminated.

A multi-level quantum mechanics and molecular mechanics study of SN2 reaction at nitrogen: NH2Cl + OH(-) in aqueous solution.

PubMed

Lv, Jing; Zhang, Jingxue; Wang, Dunyou

2016-02-17

We employed a multi-level quantum mechanics and molecular mechanics approach to study the reaction NH2Cl + OH(-) in aqueous solution. The multi-level quantum method (including the DFT method with both the B3LYP and M06-2X exchange-correlation functionals and the CCSD(T) method, and both methods with the aug-cc-pVDZ basis set) was used to treat the quantum reaction region in different stages of the calculation in order to obtain an accurate potential of mean force. The obtained free energy activation barriers at the DFT/MM level of theory yielded a big difference of 21.8 kcal mol(-1) with the B3LYP functional and 27.4 kcal mol(-1) with the M06-2X functional respectively. Nonetheless, the barrier heights become very close when shifted from DFT to CCSD(T): 22.4 kcal mol(-1) and 22.9 kcal mol(-1) at CCSD(T)(B3LYP)/MM and CCSD(T)(M06-2X)/MM levels of theory, respectively. The free reaction energy obtained using CCSD(T)(M06-2X)/MM shows an excellent agreement with the one calculated using the available gas-phase data. Aqueous solution plays a significant role in shaping the reaction profile. In total, the water solution contributes 13.3 kcal mol(-1) and 14.6 kcal mol(-1) to the free energy barrier heights at CCSD(T)(B3LYP)/MM and CCSD(T)(M06-2X)/MM respectively. The title reaction at nitrogen is a faster reaction than the corresponding reaction at carbon, CH3Cl + OH(-).

MolTalk – a programming library for protein structures and structure analysis

PubMed Central

Diemand, Alexander V; Scheib, Holger

2004-01-01

Background Two of the mostly unsolved but increasingly urgent problems for modern biologists are a) to quickly and easily analyse protein structures and b) to comprehensively mine the wealth of information, which is distributed along with the 3D co-ordinates by the Protein Data Bank (PDB). Tools which address this issue need to be highly flexible and powerful but at the same time must be freely available and easy to learn. Results We present MolTalk, an elaborate programming language, which consists of the programming library libmoltalk implemented in Objective-C and the Smalltalk-based interpreter MolTalk. MolTalk combines the advantages of an easy to learn and programmable procedural scripting with the flexibility and power of a full programming language. An overview of currently available applications of MolTalk is given and with PDBChainSaw one such application is described in more detail. PDBChainSaw is a MolTalk-based parser and information extraction utility of PDB files. Weekly updates of the PDB are synchronised with PDBChainSaw and are available for free download from the MolTalk project page following the link to PDBChainSaw. For each chain in a protein structure, PDBChainSaw extracts the sequence from its co-ordinates and provides additional information from the PDB-file header section, such as scientific organism, compound name, and EC code. Conclusion MolTalk provides a rich set of methods to analyse and even modify experimentally determined or modelled protein structures. These methods vary in complexity and are thus suitable for beginners and advanced programmers alike. We envision MolTalk to be most valuable in the following applications: 1) To analyse protein structures repetitively in large-scale, i.e. to benchmark protein structure prediction methods or to evaluate structural models. The quality of the resulting 3D-models can be assessed by e.g. calculating a Ramachandran-Sasisekharan plot. 2) To quickly retrieve information for (a limited number of) macro-molecular structures, i.e. H-bonds, salt bridges, contacts between amino acids and ligands or at the interface between two chains. 3) To programme more complex structural bioinformatics software and to implement demanding algorithms through its portability to Objective-C, e.g. iMolTalk. 4) To be used as a front end to databases, e.g. PDBChainSaw. PMID:15096277

MolTalk--a programming library for protein structures and structure analysis.

PubMed

Diemand, Alexander V; Scheib, Holger

2004-04-19

Two of the mostly unsolved but increasingly urgent problems for modern biologists are a) to quickly and easily analyse protein structures and b) to comprehensively mine the wealth of information, which is distributed along with the 3D co-ordinates by the Protein Data Bank (PDB). Tools which address this issue need to be highly flexible and powerful but at the same time must be freely available and easy to learn. We present MolTalk, an elaborate programming language, which consists of the programming library libmoltalk implemented in Objective-C and the Smalltalk-based interpreter MolTalk. MolTalk combines the advantages of an easy to learn and programmable procedural scripting with the flexibility and power of a full programming language. An overview of currently available applications of MolTalk is given and with PDBChainSaw one such application is described in more detail. PDBChainSaw is a MolTalk-based parser and information extraction utility of PDB files. Weekly updates of the PDB are synchronised with PDBChainSaw and are available for free download from the MolTalk project page http://www.moltalk.org following the link to PDBChainSaw. For each chain in a protein structure, PDBChainSaw extracts the sequence from its co-ordinates and provides additional information from the PDB-file header section, such as scientific organism, compound name, and EC code. MolTalk provides a rich set of methods to analyse and even modify experimentally determined or modelled protein structures. These methods vary in complexity and are thus suitable for beginners and advanced programmers alike. We envision MolTalk to be most valuable in the following applications:1) To analyse protein structures repetitively in large-scale, i.e. to benchmark protein structure prediction methods or to evaluate structural models. The quality of the resulting 3D-models can be assessed by e.g. calculating a Ramachandran-Sasisekharan plot.2) To quickly retrieve information for (a limited number of) macro-molecular structures, i.e. H-bonds, salt bridges, contacts between amino acids and ligands or at the interface between two chains.3) To programme more complex structural bioinformatics software and to implement demanding algorithms through its portability to Objective-C, e.g. iMolTalk.4) To be used as a front end to databases, e.g. PDBChainSaw.

AC Conductivity and Dielectric Properties of Borotellurite Glass

NASA Astrophysics Data System (ADS)

Taha, T. A.; Azab, A. A.

2016-10-01

Borotellurite glasses with formula 60B2O3-10ZnO-(30 - x)NaF- xTeO2 ( x = 0 mol.%, 5 mol.%, 10 mol.%, and 15 mol.%) have been synthesized by thermal melting. X-ray diffraction (XRD) analysis confirmed that the glasses were amorphous. The glass density ( ρ) was determined by the Archimedes method at room temperature. The density ( ρ) and molar volume ( V m) were found to increase with increasing TeO2 content. The direct-current (DC) conductivity was measured in the temperature range from 473 K to 623 K, in which the electrical activation energy of ionic conduction increased from 0.27 eV to 0.48 eV with increasing TeO2 content from 0 mol.% to 15 mol.%. The dielectric parameters and alternating-current (AC) conductivity ( σ ac) were investigated in the frequency range from 1 kHz to 1 MHz and temperature range from 300 K to 633 K. The AC conductivity and dielectric constant decreased with increasing TeO2 content from 0 mol.% to 15 mol.%.

A Novel Nanosecond Pulsed Power Unit for the Formation of ·OH in Water

NASA Astrophysics Data System (ADS)

Li, Shengli; Hu, Sheng; Zhang, Han

2012-04-01

A novel nanosecond pulsed power unit was developed for plasma treatment of wastewater, based on the theory of magnetic pulse compression and semiconductor opening switch (SOS). The peak value, rise time and pulse duration of the output voltage were observed to be -51 kV, 60 ns and 120 ns, respectively. The concentrations of ·OH generated by the novel nanosecond pulsed plasma power were determined using the method of high-performance liquid chromatography (HPLC). The results showed that the concentrations of ·OH increased with the increase in peak voltage, and the generation rates of ·OH were 4.1 × 10-10 mol/s, 5.7 × 10-10 mol/s, and 7.7 × 10-10 mol/s at 30 kV, 35 kV, and 40 kV, respectively. The efficiency of OH generation was found to be independent of the input parameters for applied power, with an average value of 3.23×10-12 mol/J obtained.

Interactions of solvent with the heme region of methemoglobin and fluoro-methemoglobin.

PubMed

Koenig, S H; Brown, R D; Lindstrom, T R

1981-06-01

It is now more than 20 years since Davidson and collaborators (1957, Biochim. Biophys, Acta. 26:370-373; J. Mol. Biol. 1:190-191) applied the theoretical ideas of Bloembergen et al. (1948. Phys. Rev. 73:679-712) on outer sphere magnetic relaxation of solvent protons to studies of solutions of methemoglobin. From then on, there has been debate regarding the relative contributions to paramagnetic solvent proton relaxation by inner sphere (ligand-exchange) effects and by outer sphere (diffusional) effects in methemoglobin solutions. Gupta and Mildvan (1975. J. Biol. Chem 250:146-253) extended the early measurements, attributed the relatively small paramagnetic effects to exchange with solvent of the water ligand of the heme-Fe3+ ion, and interpreted their data to indicate cooperativity and an alkaline Bohr effect in the presence of inositol hexaphosphate. They neglected the earlier discussions entirely, and made no reference to outer sphere effects. We have measured the relaxation rate of solvent protons as a function of magnetic field for solutions of methemoglobin, under a variety of conditions of pH and temperature, and have given careful consideration to the relatively large diamagnetic corrections that are necessary by making analogous measurements on oxyhemoglobin, carbonmonoxyhemoglobin, and cyano- and azide-methemoglobin. (The latter two, because of their short electronic relaxation times, behave as though diamagnetic). We show that the paramagnetic contribution to solvent relaxation can be dominated by outer sphere effects, a result implying that many conclusions, including those of Gupta and Mildvan, require reexamination. Finally, we present data for fluoro-methemoglobin, which relaxes solvent protons an order of magnitude better than does methemoglobin. Here one has a startling breakdown of the dogma that has been the basis for interpreting many ligand-replacement studies; in contrast to the prevailing view that replacement of a water ligand of a protein-bound paramagnetic ion by another ligand should decrease relaxation rates, replacement of H2O by F- increases the relaxation rate drastically. The data can all be reconciled, however, with what is anticipated from knowledge of ligand interactions in the heme region.

Crystal structure of the coat protein from the GA bacteriophage: model of the unassembled dimer.

PubMed Central

Ni, C. Z.; White, C. A.; Mitchell, R. S.; Wickersham, J.; Kodandapani, R.; Peabody, D. S.; Ely, K. R.

1996-01-01

There are four groups of RNA bacteriophages with distinct antigenic and physicochemical properties due to differences in surface residues of the viral coat proteins. Coat proteins also play a role as translational repressor during the viral life cycle, binding an RNA hairpin within the genome. In this study, the first crystal structure of the coat protein from a Group II phage GA is reported and compared to the Group I MS2 coat protein. The structure of the GA dimer was determined at 2.8 A resolution (R-factor = 0.20). The overall folding pattern of the coat protein is similar to the Group I MS2 coat protein in the intact virus (Golmohammadi R, Valegård K, Fridborg K, Liljas L. 1993, J Mol Biol 234:620-639) or as an unassembled dimer (Ni Cz, Syed R, Kodandapani R. Wickersham J, Peabody DS, Ely KR, 1995, Structure 3:255-263). The structures differ in the FG loops and in the first turn of the alpha A helix. GA and MS2 coat proteins differ in sequence at 49 of 129 amino acid residues. Sequence differences that contribute to distinct immunological and physical properties of the proteins are found at the surface of the intact virus in the AB and FG loops. There are six differences in potential RNA contact residues within the RNA-binding site located in an antiparallel beta-sheet across the dimer interface. Three differences involve residues in the center of this concave site: Lys/Arg 83, Ser/Asn 87, and Asp/Glu 89. Residue 87 was shown by molecular genetics to define RNA-binding specificity by GA or MS2 coat protein (Lim F. Spingola M, Peabody DS, 1994, J Biol Chem 269:9006-9010). This sequence difference reflects recognition of the nucleotide at position -5 in the unpaired loop of the translational operators bound by these coat proteins. In GA, the nucleotide at this position is a purine whereas in MS2, it is a pyrimidine. PMID:8976557

Crystal structure of the coat protein from the GA bacteriophage: model of the unassembled dimer.

PubMed

Ni, C Z; White, C A; Mitchell, R S; Wickersham, J; Kodandapani, R; Peabody, D S; Ely, K R

1996-12-01

There are four groups of RNA bacteriophages with distinct antigenic and physicochemical properties due to differences in surface residues of the viral coat proteins. Coat proteins also play a role as translational repressor during the viral life cycle, binding an RNA hairpin within the genome. In this study, the first crystal structure of the coat protein from a Group II phage GA is reported and compared to the Group I MS2 coat protein. The structure of the GA dimer was determined at 2.8 A resolution (R-factor = 0.20). The overall folding pattern of the coat protein is similar to the Group I MS2 coat protein in the intact virus (Golmohammadi R, Valegård K, Fridborg K, Liljas L. 1993, J Mol Biol 234:620-639) or as an unassembled dimer (Ni Cz, Syed R, Kodandapani R. Wickersham J, Peabody DS, Ely KR, 1995, Structure 3:255-263). The structures differ in the FG loops and in the first turn of the alpha A helix. GA and MS2 coat proteins differ in sequence at 49 of 129 amino acid residues. Sequence differences that contribute to distinct immunological and physical properties of the proteins are found at the surface of the intact virus in the AB and FG loops. There are six differences in potential RNA contact residues within the RNA-binding site located in an antiparallel beta-sheet across the dimer interface. Three differences involve residues in the center of this concave site: Lys/Arg 83, Ser/Asn 87, and Asp/Glu 89. Residue 87 was shown by molecular genetics to define RNA-binding specificity by GA or MS2 coat protein (Lim F. Spingola M, Peabody DS, 1994, J Biol Chem 269:9006-9010). This sequence difference reflects recognition of the nucleotide at position -5 in the unpaired loop of the translational operators bound by these coat proteins. In GA, the nucleotide at this position is a purine whereas in MS2, it is a pyrimidine.

Structure of the Fusarium oxysporum endoglucanase I with a nonhydrolyzable substrate analogue: substrate distortion gives rise to the preferred axial orientation for the leaving group.

PubMed

Sulzenbacher, G; Driguez, H; Henrissat, B; Schülein, M; Davies, G J

1996-12-03

Endoglucanase I (EG I) is a cellulase, from glycosyl hydrolase family 7, which cleaves the beta-1,4 linkages of cellulose with overall retention of configuration. The structure of the EG I from Fusarium oxysproum, complexed to a nonhydrolyzable thiooligosaccharide substrate analogue, has been determined by X-ray crystallography at a resolution of 2.7 A utilizing the 4-fold noncrystallographic symmetry present in the asymmetric unit. The electron density map clearly reveals the presence of three glucosyl units of the inhibitor, consistent with the known number of sugar-binding subsites, located at the active site of the enzyme in the -2, -1, and +1 subsites, i.e., actually spanning the point of enzymatic cleavage. The pyranose ring at the point of potential enzymatic cleavage is clearly distorted from the standard 4C1 chair as was originally suggested for beta-retaining enzymes by Phillips [Ford, L.O., Johnson, L.N., Machin, P. A., Phillips, D.C., & Tijan, T. (1974) J. Mol. Biol, 88, 349-371]. The distortion observed goes beyond the "sofa" conformation observed in previous studies and results in a conformation whose salient feature is the resulting quasi-axial orientation for the glycosidic bond and leaving group, as predicted by stereoelectronic theory. An almost identical conformation has recently been observed in a complex of chitobiase with its unhydrolyzed substrate [Tews, I., Perrakis, A., Oppenheim, A., Dauter, Z., Wilson, K. S., & Vorgias, C. E. (1996) Nat. Struct. Biol. 3, 638-648]. The striking similarity between these two complexes extends beyond the almost identical pyranose ring distortion. The overlap of the two respective sugars places the enzymatic nucleophile of endoglucanase I in coincidence with the C2 acetamido oxygen of N-acetylglucosamine in the catalytic site of the chitobiase, substantiating the involvement of this group in the catalytic mechanism of chitobiase and related chitinolytic enzymes. The endoglucanase I complex with the thiosaccharide substrate analogue clearly illustrates the potential of nonhydrolyzable sulfur-linked oligosaccharides in the elucidation of substrate binding and catalysis by glycosyl hydrolases.

Electrophoresis-chemiluminescence detection of phenols catalyzed by hemin.

PubMed

Shu, Lu; Zhu, Jinkun; Wang, Qingjiang; He, Pingang; Fang, Yuzhi

2014-09-01

Based on the catalytic activity of hemin, an efficient biocatalyst, an indirect capillary electrophoresis-chemiluminescence (CE-CL) detection method for phenols using a hemin-luminol-hydrogen peroxide system was developed. Through a series of static injection experiments, hemin was found to perform best in a neutral solution rather than an acidic or alkaline medium. Although halide ions such as Br(-) and F(-) could further enhance the CL signal catalyzed by hemin, it is difficult to apply these conditions to this CE-CL detection system because of the self-polymerization of hemin, as it hinders the CE process. The addition of concentrated ammonium hydroxide to an aqueous/dimethyl sulfoxide solution of hemin-luminol afforded a stable CE-CL baseline. The indirect CE-CL detection of five phenols using this method gave the following limits of detections: 4.8 × 10(-8) mol/L (o-sec-butylphenol), 4.9 × 10(-8) mol/L (o-cresol), 5.4 × 10(-8) mol/L (m-cresol), 5.3 × 10(-8) mol/L (2,4-dichlorophenol) and 7.1 × 10(-8) mol/L (phenol). Copyright © 2013 John Wiley & Sons, Ltd.

Sensitive determination of norepinephrine, synephrine, and isoproterenol by capillary electrophoresis with indirect electrochemiluminescence detection.

PubMed

Liu, Yan-Ming; Cao, Jun-Tao; Zheng, Yan-Li; Chen, Yong-Hong

2008-07-01

A new and sensitive method for the determination of norepinephrine (NE), synephrine, and isoproterenol was developed by CE separation and indirect electrochemiluminescence detection (ECL) based on their quenching effects on the tris(2,2'-bipyridyl)-ruthenium(II)/tripropylamine (TPA) system. The conditions for CE separation and ECL detection were investigated in detail. Under the optimum conditions, the three analytes were well separated within 9 min. The LODs (S/N = 3) in standard solution are 2.6 x 10(-8) mol/L for NE, 6.6 x 10(-9) mol/L for synephrine and 8.4 x 10(-8) mol/L for isoproterenol, respectively. The precisions of intraday and interday are less than 4.4 and 6.1%, respectively. The LOQs (S/N = 10) in real human urine samples are 2.6 x 10(-7) mol/L for NE, 8.8 x 10(-8 ) mol/L for synephrine, and 8.8 x 10(-7) mol/L for isoproterenol, respectively. The applicability of the proposed method was illustrated in the determination of 20 human urine samples from diabetic patients and healthy persons. The results obtained indicated that the level of NE in patients (mean value 0.41 micromol/L) was higher than that in healthy persons (mean value 0.24 micromol/L).

Multipoint Binding of the SLP-76 SH2 Domain to ADAP Is Critical for Oligomerization of SLP-76 Signaling Complexes in Stimulated T Cells

PubMed Central

Coussens, Nathan P.; Hayashi, Ryo; Brown, Patrick H.; Balagopalan, Lakshmi; Balbo, Andrea; Akpan, Itoro; Houtman, Jon C. D.; Barr, Valarie A.; Schuck, Peter; Appella, Ettore

2013-01-01

The adapter molecules SLP-76 and LAT play central roles in T cell activation by recruiting enzymes and other adapters into multiprotein complexes that coordinate highly regulated signal transduction pathways. While many of the associated proteins have been characterized, less is known concerning the mechanisms of assembly for these dynamic and potentially heterogeneous signaling complexes. Following T cell receptor (TCR) stimulation, SLP-76 is found in structures called microclusters, which contain many signaling complexes. Previous studies showed that a mutation to the SLP-76 C-terminal SH2 domain nearly abolished SLP-76 microclusters, suggesting that the SH2 domain facilitates incorporation of signaling complexes into microclusters. S. C. Bunnell, A. L. Singer, D. I. Hong, B. H. Jacque, M. S. Jordan, M. C. Seminario, V. A. Barr, G. A. Koretzky, and L. E. Samelson, Mol. Cell. Biol., 26:7155–7166, 2006). Using biophysical methods, we demonstrate that the adapter, ADAP, contains three binding sites for SLP-76, and that multipoint binding to ADAP fragments oligomerizes the SLP-76 SH2 domain in vitro. These results were complemented with confocal imaging and functional studies of cells expressing ADAP with various mutations. Our results demonstrate that all three binding sites are critical for SLP-76 microcluster assembly, but any combination of two sites will partially induce microclusters. These data support a model whereby multipoint binding of SLP-76 to ADAP facilitates the assembly of SLP-76 microclusters. This model has implications for the regulation of SLP-76 and LAT microclusters and, as a result, T cell signaling. PMID:23979596

Multipoint binding of the SLP-76 SH2 domain to ADAP is critical for oligomerization of SLP-76 signaling complexes in stimulated T cells.

PubMed

Coussens, Nathan P; Hayashi, Ryo; Brown, Patrick H; Balagopalan, Lakshmi; Balbo, Andrea; Akpan, Itoro; Houtman, Jon C D; Barr, Valarie A; Schuck, Peter; Appella, Ettore; Samelson, Lawrence E

2013-11-01

The adapter molecules SLP-76 and LAT play central roles in T cell activation by recruiting enzymes and other adapters into multiprotein complexes that coordinate highly regulated signal transduction pathways. While many of the associated proteins have been characterized, less is known concerning the mechanisms of assembly for these dynamic and potentially heterogeneous signaling complexes. Following T cell receptor (TCR) stimulation, SLP-76 is found in structures called microclusters, which contain many signaling complexes. Previous studies showed that a mutation to the SLP-76 C-terminal SH2 domain nearly abolished SLP-76 microclusters, suggesting that the SH2 domain facilitates incorporation of signaling complexes into microclusters. S. C. Bunnell, A. L. Singer, D. I. Hong, B. H. Jacque, M. S. Jordan, M. C. Seminario, V. A. Barr, G. A. Koretzky, and L. E. Samelson, Mol. Cell. Biol., 26:7155-7166, 2006). Using biophysical methods, we demonstrate that the adapter, ADAP, contains three binding sites for SLP-76, and that multipoint binding to ADAP fragments oligomerizes the SLP-76 SH2 domain in vitro. These results were complemented with confocal imaging and functional studies of cells expressing ADAP with various mutations. Our results demonstrate that all three binding sites are critical for SLP-76 microcluster assembly, but any combination of two sites will partially induce microclusters. These data support a model whereby multipoint binding of SLP-76 to ADAP facilitates the assembly of SLP-76 microclusters. This model has implications for the regulation of SLP-76 and LAT microclusters and, as a result, T cell signaling.

Reporting of sex as a variable in cardiovascular studies using cultured cells

PubMed Central

2011-01-01

Background Chromosomal complement, including that provided by the sex chromosomes, influences expression of proteins and molecular signaling in every cell. However, less than 50% of the scientific studies published in 2009 using experimental animals reported sex as a biological variable. Because every cell has a sex, we conducted a literature review to determine the extent to which sex is reported as a variable in cardiovascular studies on cultured cells. Methods Articles from 10 cardiovascular journals with high impact factors (Circulation, J Am Coll Cardiol, Eur Heart J, Circ Res, Arterioscler Thromb Vasc Biol, Cardiovasc Res, J Mol Cell Cardiol, Am J Physiol Heart Circ Physiol, J Heart Lung Transplant and J Cardiovasc Pharmacol) and published in 2010 were searched using terms 'cultured' and 'cells' in any order to determine if the sex of those cells was reported. Studies using established cell lines were excluded. Results Using two separate search strategies, we found that only 25 of 90 articles (28%) and 20 of 101 articles (19.8%) reported the sex of cells. Of those reporting the sex of cells, most (68.9%; n = 31) used only male cells and none used exclusively female cells. In studies reporting the sex of cells of cardiovascular origin, 40% used vascular smooth-muscle cells, and 30% used stem/progenitor cells. In studies using cells of human origin, 35% did not report the sex of those cells. None of the studies using neonatal cardiac myocytes reported the sex of those cells. Conclusions The complement of sex chromosomes in cells studied in culture has the potential to affect expression of proteins and 'mechanistic' signaling pathways. Therefore, consistent with scientific excellence, editorial policies should require reporting sex of cells used in in vitro experiments. PMID:22060014

Fundamental Studies in the Molecular Basis of Laser Induced Retinal Damage.

DTIC Science & Technology

1984-09-01

C. Hannemann , H. and Sochtig, E. (1979) Nature 277, 143-145. 25. Richards, J. M. and Swislocki, N. 1. (1979) J. Biol. Chem. 254, 6857-6860. 26...and Yamada, E. (1981) Biomedical Res. 2, 177-193. 51. Roof, D. J. and Heuser, J. E. (1982) J. Cell Biol. 95, 487-500. 52. Hagins, W. A. and Jennings , W

Evaluation of Genomic Instability as an Early Event in the Progression of Breast Cancer

DTIC Science & Technology

2007-04-01

theory of marginotomy. J. Theor. Biol. 41:181-90. 8. Watson, J. D. 1972. The origin of concatemeric T7 DNA. Nat. New Biol. 239:197-201. 9. Karlseder...concentrations were measured 6 using the Picogreen® dsDNA quantitation assay (Molecular Probes, Eugene, OR) using a λ phage DNA as the standard as

Routine internal- and external-quality control data in clinical laboratories for estimating measurement and diagnostic uncertainty using GUM principles.

PubMed

Magnusson, Bertil; Ossowicki, Haakan; Rienitz, Olaf; Theodorsson, Elvar

2012-05-01

Healthcare laboratories are increasingly joining into larger laboratory organizations encompassing several physical laboratories. This caters for important new opportunities for re-defining the concept of a 'laboratory' to encompass all laboratories and measurement methods measuring the same measurand for a population of patients. In order to make measurement results, comparable bias should be minimized or eliminated and measurement uncertainty properly evaluated for all methods used for a particular patient population. The measurement as well as diagnostic uncertainty can be evaluated from internal and external quality control results using GUM principles. In this paper the uncertainty evaluations are described in detail using only two main components, within-laboratory reproducibility and uncertainty of the bias component according to a Nordtest guideline. The evaluation is exemplified for the determination of creatinine in serum for a conglomerate of laboratories both expressed in absolute units (μmol/L) and relative (%). An expanded measurement uncertainty of 12 μmol/L associated with concentrations of creatinine below 120 μmol/L and of 10% associated with concentrations above 120 μmol/L was estimated. The diagnostic uncertainty encompasses both measurement uncertainty and biological variation, and can be estimated for a single value and for a difference. This diagnostic uncertainty for the difference for two samples from the same patient was determined to be 14 μmol/L associated with concentrations of creatinine below 100 μmol/L and 14 % associated with concentrations above 100 μmol/L.

Application of headspace solid phase microextraction for study of noncovalent interaction of borneol with human serum albumin

PubMed Central

Hu, Liang; Chen, Dong-ying

2009-01-01

Aim: To investigate noncovalent interactions between borneol and human serum albumin (HSA) under near-physiological conditions. Methods: A 65-μm polydimethylsiloxane (PDMS) fiber was selected for sampling. The extraction temperature was kept at 37 °C, and the extraction time was optimized at 10 min. Borneol solutions of different concentrations were equilibrated in 600 μmol/L HSA and 67 mmol/L phosphate buffer solution (pH 7.4, 37 °C) for 24 h prior to solid phase microextraction (SPME) using headspace mode. The binding properties were obtained based on the calculation of extracted borneol amount using gas chromatography (GC) determination. Results: The headspace SPME extraction method avoided disturbance from the HSA binding matrix. The recovery showed good linearity for the borneol concentrations over the range of 0.4–16.3 μmol/L with a regression coefficient (R2) of 0.9998. The limit of detection and lower limit of quantitation were determined to be 0.01 μmol/L and 0.4 μmol/L, respectively. The binding constant and the percentage binding rate were estimated to be 2.4×103(mol/L)-1 and 59.5%, respectively. Conclusion: Headspace SPME coupled to GC is a simple, sensitive and rapid method for the study of borneol binding to HSA. The method may be applied in the determination of other protein binding properties in human plasma. PMID:19890364

Method and basis set dependence of anharmonic ground state nuclear wave functions and zero-point energies: application to SSSH.

PubMed

Kolmann, Stephen J; Jordan, Meredith J T

2010-02-07

One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy surfaces (PESs) constructed using a variety of method and basis set combinations. The ZPE of SSSH, which is approximately 29 kJ mol(-1) at the CCSD(T)/6-31G* level of theory, has a 4 kJ mol(-1) dependence on the treatment of electron correlation. The anharmonic ZPEs are consistently 0.3 kJ mol(-1) lower in energy than the harmonic ZPEs calculated at the Hartree-Fock and MP2 levels of theory, and 0.7 kJ mol(-1) lower in energy at the CCSD(T)/6-31G* level of theory. Ideally, for sub-kJ mol(-1) thermochemical accuracy, ZPEs should be calculated using correlated methods with as big a basis set as practicable. The ground state nuclear wave function of SSSH also has significant method and basis set dependence. The analysis of the nuclear wave function indicates that SSSH is localized to a single symmetry equivalent global minimum, despite having sufficient ZPE to be delocalized over both minima. As part of this work, modifications to the interpolated PES construction scheme of Collins and co-workers are presented.

Method and basis set dependence of anharmonic ground state nuclear wave functions and zero-point energies: Application to SSSH

NASA Astrophysics Data System (ADS)

Kolmann, Stephen J.; Jordan, Meredith J. T.

2010-02-01

One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy surfaces (PESs) constructed using a variety of method and basis set combinations. The ZPE of SSSH, which is approximately 29 kJ mol-1 at the CCSD(T)/6-31G∗ level of theory, has a 4 kJ mol-1 dependence on the treatment of electron correlation. The anharmonic ZPEs are consistently 0.3 kJ mol-1 lower in energy than the harmonic ZPEs calculated at the Hartree-Fock and MP2 levels of theory, and 0.7 kJ mol-1 lower in energy at the CCSD(T)/6-31G∗ level of theory. Ideally, for sub-kJ mol-1 thermochemical accuracy, ZPEs should be calculated using correlated methods with as big a basis set as practicable. The ground state nuclear wave function of SSSH also has significant method and basis set dependence. The analysis of the nuclear wave function indicates that SSSH is localized to a single symmetry equivalent global minimum, despite having sufficient ZPE to be delocalized over both minima. As part of this work, modifications to the interpolated PES construction scheme of Collins and co-workers are presented.

DFT and ab initio study of the unimolecular decomposition of the lowest singlet and triplet states of nitromethane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manaa, M.R.; Fried, L.E.

1998-11-26

The fully optimized potential energy curves for the unimolecular decomposition of the lowest singlet and triplet states of nitromethane through the C-NO{sub 2} bond dissociation pathway are calculated using various DFT and high-level ab initio electronic structure methods. The authors perform gradient corrected density functional theory (DFT) and multiconfiguration self-consistent field (MCSCF) to conclusively demonstrate that the triplet state of nitromethane is bound. The adiabatic curve of this state exhibits a 33 kcal/mol energy barrier as determined at the MCSCF level. DFT methods locate this barrier at a shorter C-N bond distance with 12--16 kcal/mol lower energy than does MCSCF.more » In addition to MCSCF and DFT, quadratic configuration interactions with single and double substitutions (QCISD) calculations are also performed for the singlet curve. The potential energy profiles of this state predicted by FT methods based on Becke`s 1988 exchange functional differ by as much as 17 kcal/mol from the predictions of MCSCF and QCISD in the vicinity of the equilibrium structure. The computational methods predict bond dissociation energies 5--9 kcal/mol lower than the experimental value. DFT techniques based on Becke`s 3-parameter exchange functional show the best overall agreement with the higher level methods.« less

Optimized MOL-PCR for Characterization of Microbial Pathogens.

PubMed

Wuyts, Véronique; Roosens, Nancy H C; Bertrand, Sophie; Marchal, Kathleen; De Keersmaecker, Sigrid C J

2016-01-06

Characterization of microbial pathogens is necessary for surveillance, outbreak detection, and tracing of outbreak sources. This unit describes a multiplex oligonucleotide ligation-PCR (MOL-PCR) optimized for characterization of microbial pathogens. With MOL-PCR, different types of markers, like unique sequences, single-nucleotide polymorphisms (SNPs) and indels, can be simultaneously analyzed in one assay. This assay consists of a multiplex ligation for detection of the markers, a singleplex PCR for signal amplification, and hybridization to MagPlex-TAG beads for readout on a Luminex platform after fluorescent staining. The current protocol describes the MOL-PCR, as well as methods for DNA isolation, probe design, and data interpretation and it is based on an optimized MOL-PCR assay for subtyping of Salmonella Typhimurium. Copyright © 2016 John Wiley & Sons, Inc.

Vasorelaxant and antihypertensive effects of formononetin through endothelium-dependent and -independent mechanisms

PubMed Central

SUN, Tao; LIU, Rui; CAO, Yong-xiao

2011-01-01

Aim: To investigate the mechanisms underlying the vasorelaxant effect of formononetin, an O-methylated isoflavone, in isolated arteries, and its antihypertensive activity in vivo. Methods: Arterial rings of superior mesenteric arteries, renal arteries, cerebral basilar arteries, coronary arteries and abdominal aortas were prepared from SD rats. Isometric tension of the arterial rings was recorded using a myograph system. Arterial pressure was measured using tail-cuff method in spontaneously hypertensive rats. Results: Formononetin (1–300 μmol/L) elicited relaxation in arteries of the five regions that were pre-contracted by KCl (60 mmol/L), U46619 (1 μmol/L) or phenylephrine (10 μmol/L). The formononetin-induced relaxation was reduced by removal of endothelium or by pretreatment with L-NAME (100 μmol/L). Under conditions of endothelium denudation, formononetin (10, 30, and 100 μmol/L) inhibited the contraction induced by KCl and that induced by CaCl2 in Ca2+-free depolarized medium. In the absence of extracellular Ca2+, formononetin (10, 30, and 100 μmol/L) depressed the constriction caused by phenylephrine (10 μmol/L), but did not inhibit the tonic contraction in response to the addition of CaCl2 (2 mmol/L). The contraction caused by caffeine (30 mmol/L) was not inhibited by formononetin (100 μmol/L). Formononetin (10 and 100 μmol/L) reduced the change rate of Ca2+-fluorescence intensity in response to KCl (50 mmol/L). In spontaneously hypertensive rats, formononetin (5, 10, and 20 mg/kg) slowly lowered the systolic, diastolic and mean arterial pressure. Conclusion: Formononetin causes vasodilatation via two pathways: (1) endothelium-independent pathway, probably due to inhibition of voltage-dependent Ca2+ channels and intracellular Ca2+ release; and (2) endothelium-dependent pathway by releasing NO. Both the pathways may contribute to its antihypertensive effect. PMID:21818108

Breast Cancer Resistance to Cyclophosphamide and Other Oxazaphosphorines

DTIC Science & Technology

1998-10-01

Zr-75 and T-47D cells, colon carcinoma C cells, and salivary gland Warthin tumors and mucoepidermoid carcinomas), although otherwise seemingly...cytosolic class-3 aldehyde dehydrogenase by Warthin tumors and mucoepidermoid carcinomas of the parotid gland. Arch. Oral Biol., 41:597-605, 1996...specific cytosolic class-3 aldehyde dehydrogenase by Warthin tumours and mucoepidermoid carcinomas of the parotid gland. Archiv. Oral Biol., 41:597-605

Laser Hazards Bibliography, January 1991

DTIC Science & Technology

1991-01-31

retinitis pigmentosa , Adv Exp Med Biol, 77: 233-247 (1977). 3. Agarwal, L. P., and Malik, S. R. K., Solar retinitis , Br J Ophth, 43: 366-370 (1959). 4. Al... Retinitis pigmentosa : clinical management based on current concepts, Adv Exp Med Biol, 77: 181-195 (1977). 557. Wolbarsht, M. L., Safe Ocular Levels for IR...270 C. Optical Radiation Hazards - General Reviews ............ 271 D. Retinal Burns from Lasers

Reductive trapping of substrate to bovine plasma amine oxidase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hartmann, C.; Klinman, J.P.

1987-01-25

Plasma amine oxidases catalyze the oxidative deamination of amines to aldehydes, followed by a 2e- reduction of O/sub 2/ to H/sub 2/O/sub 2/. Pyrroloquinoline quinone (PQQ), previously believed to be restricted to prokaryotes, has recently been proposed to be the cofactor undergoing reduction in the first half-reaction of bovine plasma amine oxidase (Ameyama, M., Hayashi, U., Matsushita, K., Shinagawa, E., and Adachi, O. (1984) Agric. Biol. Chem. 48, 561-565; Lobenstein-Verbeek, C. L., Jongejan, J. A., Frank, J., and Duine, J. A. (1984) FEBS Lett. 170, 305-309). This result is unexpected, since model studies with PQQ implicate Schiff's base formation betweenmore » a reactive carbonyl and substrates, whereas experiments with bovine plasma amine oxidase have failed to provide evidence for a carbonyl cofactor. We have, therefore, re-examined putative adducts between substrate and enzyme-bound cofactor, employing a combination of (/sup 14/C)benzylamine and (/sup 3/H)NaCNBH/sub 3/. The use of the relatively weak reductant, NaCNBH/sub 3/, affords Schiff's base specificity and permits the study of enzyme below pH 7.0. As we show, enzyme can only be inactivated by NaCNBH/sub 3/ in the presence of substrate, leading to the incorporation of 1 mol of (/sup 14/C)benzylamine/mol of enzyme subunit at complete inactivation. By contrast, we are unable to detect any labeling with (/sup 3/H)NaCNBH/sub 3/, analogous to an earlier study with (/sup 3/H)NaCNBH/sub 4/ (Suva, R. H., and Abeles, R. H. (1978) Biochemistry 17, 3538-3545). We conclude, first, that our inability to obtain adducts containing both carbon 14 and tritium rules out the reductive trapping either of amine substrate with pyridoxal phosphate or of aldehyde product with a lysyl side chain and, second, that the observed pattern of labeling is fully consistent with the presence of PQQ at the active site of bovine plasma amine oxidase.« less

Linkage of Organic Anion Transporter-1 to Metabolic Pathways through Integrated “Omics”-driven Network and Functional Analysis*

PubMed Central

Ahn, Sun-Young; Jamshidi, Neema; Mo, Monica L.; Wu, Wei; Eraly, Satish A.; Dnyanmote, Ankur; Bush, Kevin T.; Gallegos, Tom F.; Sweet, Douglas H.; Palsson, Bernhard Ø.; Nigam, Sanjay K.

2011-01-01

The main kidney transporter of many commonly prescribed drugs (e.g. penicillins, diuretics, antivirals, methotrexate, and non-steroidal anti-inflammatory drugs) is organic anion transporter-1 (OAT1), originally identified as NKT (Lopez-Nieto, C. E., You, G., Bush, K. T., Barros, E. J., Beier, D. R., and Nigam, S. K. (1997) J. Biol. Chem. 272, 6471–6478). Targeted metabolomics in knockouts have shown that OAT1 mediates the secretion or reabsorption of many important metabolites, including intermediates in carbohydrate, fatty acid, and amino acid metabolism. This observation raises the possibility that OAT1 helps regulate broader metabolic activities. We therefore examined the potential roles of OAT1 in metabolic pathways using Recon 1, a functionally tested genome-scale reconstruction of human metabolism. A computational approach was used to analyze in vivo metabolomic as well as transcriptomic data from wild-type and OAT1 knock-out animals, resulting in the implication of several metabolic pathways, including the citric acid cycle, polyamine, and fatty acid metabolism. Validation by in vitro and ex vivo analysis using Xenopus oocyte, cell culture, and kidney tissue assays demonstrated interactions between OAT1 and key intermediates in these metabolic pathways, including previously unknown substrates, such as polyamines (e.g. spermine and spermidine). A genome-scale metabolic network reconstruction generated some experimentally supported predictions for metabolic pathways linked to OAT1-related transport. The data support the possibility that the SLC22 and other families of transporters, known to be expressed in many tissues and primarily known for drug and toxin clearance, are integral to a number of endogenous pathways and may be involved in a larger remote sensing and signaling system (Ahn, S. Y., and Nigam, S. K. (2009) Mol. Pharmacol. 76, 481–490, and Wu, W., Dnyanmote, A. V., and Nigam, S. K. (2011) Mol. Pharmacol. 79, 795–805). Drugs may alter metabolism by competing for OAT1 binding of metabolites. PMID:21757732

Purification, substrate specificity, and classification of tripeptidyl peptidase II.

PubMed

Bålöw, R M; Tomkinson, B; Ragnarsson, U; Zetterqvist, O

1986-02-15

An extralysosomal tripeptide-releasing aminopeptidase was recently discovered in rat liver (Bålöw, R.-M., Ragnarsson, U., and Zetterqvist, O. (1983) J. Biol. Chem. 258, 11622-11628). In the present work this tripeptidyl peptidase is shown to occur in several rat tissues and in human erythrocytes. The erythrocyte enzyme was purified about 80,000-fold from a hemolysate while the rat liver enzyme was purified about 4,000-fold from a homogenate. Upon polyacrylamide gel electrophoresis in sodium dodecyl sulfate under reducing conditions more than 90% of the protein was represented by a polypeptide of Mr 135,000 in both cases. In addition, the two enzymes eluted at similar positions in the various chromatographic steps, showed similar specific activity, and had a pH optimum around 7.5. A tryptic pentadecapeptide from the alpha-chain of human hemoglobin, Val-Gly-Ala-His-Ala-Gly-Glu-Tyr-Gly-Ala-Glu-Ala-Leu-Glu-Arg, i.e. residues 17-31, was found to be sequentially cleaved by the erythrocyte enzyme into five tripeptides, beginning from the NH2 terminus. Chromogenic tripeptidylamides showed various rates of hydrolysis at pH 7.5. With Ala-Ala-Phe-4-methyl-7-coumarylamide, Km was 16 microM and Vmax 13 mumol min-1 . mg-1, comparable to the standard substrate Arg-Arg-Ala-Ser(32P)-Val-Ala values (Km 13 microM and Vmax 24 mumol . min-1 . mg-1). The tripeptidyl peptidase of human erythrocytes was classified as a serine peptidase from its irreversible inhibition by phenylmethanesulfonyl fluoride and diisopropyl fluorophosphate. The rate of inhibition was decreased by the presence of an efficient competitive inhibitor, Val-Leu-Arg-Arg-Ala-Ser-Val-Ala (Ki 1.5 microM). [3H]Diisopropylphosphate was incorporated to the extent of 0.7-0.9 mol/mol of Mr 135,000 subunit, which confirms the high purity of the enzyme.

Chromatin Structure and Breast Cancer Radiosensitivity

DTIC Science & Technology

2006-10-01

for growth arrest induced by human polynucleotide phosphorylase (hPNPaseold-35) in human melanoma cells. J Biol Chem. 278:24542-24551 (2003). 5...regulatory proteins on human telomeres. Methods in Molecular Biology. 241: 329-339. 9. Hunt CR, Dix DJ, Sharma GG, Pandita RK, Gupta A, Funk M, and...break response network in meiosis . DNA Repair 3:1149-1164. 12. Shahrabani-Gargir L, Pandita TK and Werner H (2004) Ataxia-telangiectasia

MR Imaging Based Treatment Planning for Radiotherapy of Prostate Cancer

DTIC Science & Technology

2007-02-01

developed practical methods for heterogeneity correction for MRI - based dose calculations (Chen et al 2007). 6) We will use existing Monte Carlo ... Monte Carlo verification of IMRT dose distributions from a commercial treatment planning optimization system, Phys. Med. Biol., 45:2483-95 (2000) Ma...accuracy and consistency for MR based IMRT treatment planning for prostate cancer. A short paper entitled “ Monte Carlo dose verification of MR image based

Molecular Imaging of Ovarian Carcinoma Angiogenesis

DTIC Science & Technology

2007-03-01

peptides have also been labeled with 18F through electrophilic substitution method (71). The direct fluorination strategy resulted in multiple side...ligand with integrin αvβ3. Substitution of the amino acid in position 4 (D-Phe in lead structure) with tyrosine allows electrophilic radiohalogenation...Hamacher K, Stoecklin G. A comparative study of n.c.a. fluorine -18 labeling of proteins via acylation and photochemical conjugation. Nucl Med Biol. 1996;23

Chemiluminescence detection of peroxynitrite with flow injection

NASA Astrophysics Data System (ADS)

Kang, Dai; Evmiridis, Nick P.; Vlessidis, Athanasios; Zhou, Yikai

2001-09-01

Peroxynitrite is an important derivative made by nitric oxide in vivo. It can make damages in many kinds of tissue and cells. Its research value in heart disease and cancer is a very high. A sensitive, specific method for analysis of peroxynitrite is described. In this method, chemiluminescence reaction between perodynitrite and luminol was used to detect with flow injection system. The assay has a detection limit of 2 by 10-8 mol L-1, and linear range of 5 by 10-8 mol L-1 to 5 by 10-5 mol L-1. The application o f flow injection system offers the possibility to establish biosensor for real-time detection of perodynitrite.

The method of lines in three dimensional fracture mechanics

NASA Technical Reports Server (NTRS)

Gyekenyesi, J.; Berke, L.

1980-01-01

A review of recent developments in the calculation of design parameters for fracture mechanics by the method of lines (MOL) is presented. Three dimensional elastic and elasto-plastic formulations are examined and results from previous and current research activities are reported. The application of MOL to the appropriate partial differential equations of equilibrium leads to coupled sets of simultaneous ordinary differential equations. Solutions of these equations are obtained by the Peano-Baker and by the recurrance relations methods. The advantages and limitations of both solution methods from the computational standpoint are summarized.

Sealing and External Sterilization of a Sample Container

NASA Technical Reports Server (NTRS)

Bar-Cohen, Yoseph; Badescu, Mircea; Bao, Xiaoqi; Sherrit, Stewart; Olorunsola, Ayoola

2008-01-01

A method of (1) sealing a sample of material acquired in a possibly b iologically contaminated ("dirty") environment into a hermetic conta iner, (2) sterilizing the outer surface of the container, then (3) d elivering the sealed container to a clean environment has been propos ed. The method now proposed was originally intended to be used to ret urn samples from Mars to Earth, but could also be used on Earth to t ransport material samples acquired in environments that contain biol ogical hazards and/or, in some cases, chemical hazards.

Development of a standard reference material containing 22 chlorinated hydrocarbon gases at 1 μmol/mol in nitrogen.

PubMed

Li, Ning; Du, Jian; Yang, Jing; Fan, Qiang; Tian, Wen

2017-11-01

A gas standard mixture containing 22 chlorinated hydrocarbons in high purity nitrogen was prepared using a two-step weighing method and a gasifying apparatus developed in-house. The concentration of each component was determined using a gas chromatograph with flame ionization detection (GC/FID). Linear regression analysis of every component was performed using the gas standard mixture with concentrations ranging from 1 to 10 μmol/mol, showing the complete gasification of volatile organic compound (VOCs) species in a selected cylinder. Repeatability was also examined to ensure the reliability of the preparation method. In addition, no significant difference was observed between domestic treated and imported treated cylinders, which were conducive to reduction of the cost of raw materials. Moreover, the results of stability testing at different pressures and long-term stability tests indicated that the gas standard at 1 μmol/mol level with relative expanded uncertainties of 5% was stable above 2 MPa for a minimum of 12 months. Finally, a quantity comparison was conducted between the gas standard and a commercial gas standard from Scott Specialty Gases (now Air Liquide America Specialty Gases). The excellent agreement of every species suggested the favorable accuracy of our gas standard. Therefore, this reference material can be applied to routine observation of VOCs and for other purposes.

NMR determination of the global structure of the 113Cd derivative of desulforedoxin: investigation of the hydrogen bonding pattern at the metal center.

PubMed Central

Goodfellow, B. J.; Rusnak, F.; Moura, I.; Domke, T.; Moura, J. J.

1998-01-01

Desulforedoxin (Dx) is a simple homodimeric protein isolated from Desulfovibrio gigas (Dg) containing a distorted rubredoxin-like center with one iron coordinated by four cysteinyl residues (7.9 kDa with 36 amino acids per monomer). In order to probe the geometry and the H-bonding at the active site of Dx, the protein was reconstituted with 113Cd and the solution structure determined using 2D NMR methods. The structure of this derivative was initially compared with the NMR solution structure of the Zn form (Goodfellow BJ et al., 1996, J Biol Inorg Chem 1:341-353). Backbone amide protons for G4, D5, G13, L11 NH, and the Q14 NH side-chain protons, H-bonded in the X-ray structure, were readily exchanged with solvent. Chemical shift differences observed for amide protons near the metal center confirm the H-bonding pattern seen in the X-ray model (Archer M et al., 1995, J Mol Biol 251:690-702) and also suggest that H-bond lengths may vary between the Fe, Zn, and 113Cd forms. The H-bonding pattern was further probed using a heteronuclear spin echo difference (HSED) experiment; the results confirm the presence of NH-S H-bonds inferred from D2O exchange data and observed in the NMR family of structures. The presence of "H-bond mediated" coupling in Dx indicates that the NH-S H-bonds at the metal center have significant covalent character. The HSED experiment also identified an intermonomer "through space" coupling for one of the L26 methyl groups, indicating its proximity to the 113Cd center in the opposing monomer. This is the first example of an intermonomer "through space" coupling. Initial structure calculations produced subsets of NMR families with the S of C28 pointing away from or toward the L26 methyl: only the subset with the C28 sulfur pointing toward the L26 methyl could result in a "through space" coupling. The HSED result was therefore included in the structure calculations. Comparison of the Fe, Zn, and 113Cd forms of Dx suggests that the geometry of the metal center and the global fold of the protein does not vary to any great extent, although the H-bond network varies slightly when Cd is introduced. The similarity between the H-bonding pattern seen at the metal center in Dx, Rd (including H-bonded and through space-mediated coupling), and many zinc-finger proteins suggests that these H-bonds are structurally vital for stabilization of the metal centers in these proteins. PMID:9568899

NMR determination of the global structure of the 113Cd derivative of desulforedoxin: investigation of the hydrogen bonding pattern at the metal center.

PubMed

Goodfellow, B J; Rusnak, F; Moura, I; Domke, T; Moura, J J

1998-04-01

Desulforedoxin (Dx) is a simple homodimeric protein isolated from Desulfovibrio gigas (Dg) containing a distorted rubredoxin-like center with one iron coordinated by four cysteinyl residues (7.9 kDa with 36 amino acids per monomer). In order to probe the geometry and the H-bonding at the active site of Dx, the protein was reconstituted with 113Cd and the solution structure determined using 2D NMR methods. The structure of this derivative was initially compared with the NMR solution structure of the Zn form (Goodfellow BJ et al., 1996, J Biol Inorg Chem 1:341-353). Backbone amide protons for G4, D5, G13, L11 NH, and the Q14 NH side-chain protons, H-bonded in the X-ray structure, were readily exchanged with solvent. Chemical shift differences observed for amide protons near the metal center confirm the H-bonding pattern seen in the X-ray model (Archer M et al., 1995, J Mol Biol 251:690-702) and also suggest that H-bond lengths may vary between the Fe, Zn, and 113Cd forms. The H-bonding pattern was further probed using a heteronuclear spin echo difference (HSED) experiment; the results confirm the presence of NH-S H-bonds inferred from D2O exchange data and observed in the NMR family of structures. The presence of "H-bond mediated" coupling in Dx indicates that the NH-S H-bonds at the metal center have significant covalent character. The HSED experiment also identified an intermonomer "through space" coupling for one of the L26 methyl groups, indicating its proximity to the 113Cd center in the opposing monomer. This is the first example of an intermonomer "through space" coupling. Initial structure calculations produced subsets of NMR families with the S of C28 pointing away from or toward the L26 methyl: only the subset with the C28 sulfur pointing toward the L26 methyl could result in a "through space" coupling. The HSED result was therefore included in the structure calculations. Comparison of the Fe, Zn, and 113Cd forms of Dx suggests that the geometry of the metal center and the global fold of the protein does not vary to any great extent, although the H-bond network varies slightly when Cd is introduced. The similarity between the H-bonding pattern seen at the metal center in Dx, Rd (including H-bonded and through space-mediated coupling), and many zinc-finger proteins suggests that these H-bonds are structurally vital for stabilization of the metal centers in these proteins.

Activation mechanism of a noncanonical RNA-dependent RNA polymerase.

PubMed

Garriga, Damià; Navarro, Aitor; Querol-Audí, Jordi; Abaitua, Fernando; Rodríguez, José F; Verdaguer, Núria

2007-12-18

Two lineages of viral RNA-dependent RNA polymerases (RDRPs) differing in the organization (canonical vs. noncanonical) of the palm subdomain have been identified. Phylogenetic analyses indicate that both lineages diverged at a very early stage of the evolution of the enzyme [Gorbalenya AE, Pringle FM, Zeddam JL, Luke BT, Cameron CE, Kalmakoff J, Hanzlik TN, Gordon KH, Ward VK (2002) J Mol Biol 324:47-62]. Here, we report the x-ray structure of a noncanonical birnaviral RDRP, named VP1, in its free form, bound to Mg(2+) ions, and bound to a peptide representing the polymerase-binding motif of the regulatory viral protein VP3. The structure of VP1 reveals that the noncanonical connectivity of the palm subdomain maintains the geometry of the catalytic residues found in canonical polymerases but results in a partial blocking of the active site cavity. The VP1-VP3 peptide complex shows a mode of polymerase activation in which VP3 binding promotes a conformational change that removes the steric blockade of the VP1 active site, facilitating the accommodation of the template and incoming nucleotides for catalysis. The striking structural similarities between birnavirus (dsRNA) and the positive-stranded RNA picornavirus and calicivirus RDRPs provide evidence supporting the existence of functional and evolutionary relationships between these two virus groups.

Notes on the birth-death prior with fossil calibrations for Bayesian estimation of species divergence times.

PubMed

Dos Reis, Mario

2016-07-19

Constructing a multi-dimensional prior on the times of divergence (the node ages) of species in a phylogeny is not a trivial task, in particular, if the prior density is the result of combining different sources of information such as a speciation process with fossil calibration densities. Yang & Rannala (2006 Mol. Biol. Evol 23, 212-226. (doi:10.1093/molbev/msj024)) laid out the general approach to combine the birth-death process with arbitrary fossil-based densities to construct a prior on divergence times. They achieved this by calculating the density of node ages without calibrations conditioned on the ages of the calibrated nodes. Here, I show that the conditional density obtained by Yang & Rannala is misspecified. The misspecified density can sometimes be quite strange-looking and can lead to unintentionally informative priors on node ages without fossil calibrations. I derive the correct density and provide a few illustrative examples. Calculation of the density involves a sum over a large set of labelled histories, and so obtaining the density in a computer program seems hard at the moment. A general algorithm that may provide a way forward is given.This article is part of the themed issue 'Dating species divergences using rocks and clocks'. © 2016 The Author(s).

Ars insulator identified in sea urchin possesses an activity to ensure the transgene expression in mouse cells.

PubMed

Tajima, Shoji; Shinohara, Keiko; Fukumoto, Maiko; Zaitsu, Reiko; Miyagawa, Junichi; Hino, Shinjiro; Fan, Jun; Akasaka, Koji; Matsuoka, Masao

2006-04-01

Sea urchin arylsulfatase (Ars) gene locus has features of an insulator, i.e., blocking of enhancer and promoter interaction, and protection of a transgene against positional effects [Akasaka et al. (1999) Cell. Mol. Biol. 45, 555-565]. To examine the effect of Ars insulator on long-term expression of a transgene, the insulator was inserted into LTR of retrovirus vector harboring hrGFP gene as a reporter, and then introduced into mouse myoblast cells. The isolated clones transduced with the reporter gene with or without Ars insulator were cultured for more than 20 wk in the absence of a selection reagent, and the expression of hrGFP was periodically determined. Expression of hrGFP in four clones transduced with the reporter gene without Ars insulator was completely silenced after 20 wk of culture. On the other hand, hrGFP was expressed in all clones with Ars insulator inserted in one of the two different orientations. Histone H3 deacetylation and DNA methylation of the 5'LTR promoter region, signs for heterochromatin and silencing, were suppressed in the clones that were expressing hrGFP. Ars insulator is effective in maintaining a transgene in mouse cells in an orientation-dependent manner, and will be a useful tool to ensure stable expression of a transgene.

A light-driven proton pump from Haloterrigena turkmenica: Functional expression in Escherichia coli membrane and coupling with a H{sup +} co-transporter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kamo, Naoki; Hashiba, Tsuyoshi; Kikukawa, Takashi

2006-03-10

A gene encoding putative retinal protein was cloned from Haloterrigena turkmenica (JCM9743). The deduced amino acid sequence was most closely related to that of deltarhodopsin, which functions as a light-driven H{sup +} pump and was identified in a novel strain Haloterrigena sp. arg-4 (K. Ihara, T. Uemura, I. Katagiri, T. Kitajima-Ihara, Y. Sugiyama, Y. Kimura, Y. Mukohata, Evolution of the archaeal rhodopsins: Evolution rate changes by gene duplication and functional differentiation, J. Mol. Biol. 285 (1999) 163-174. GenBank Accession No. AB009620). Thus, we called the present protein H. turkmenica deltarhodopsin (HtdR) in this report. Differing from the Halobacterium salinarum bacteriorhodopsinmore » (bR), functional expression of HtdR was achieved in Escherichia coli membrane with a high yield of 10-15mg protein/L culture. The photocycle of purified HtdR was similar to that of bR. The photo-induced electrogenic proton pumping activity of HtdR was verified. We co-expressed both HtdR and EmrE, a proton-coupled multi-drug efflux transporter in E. coli, and the cells successfully extruded ethidium, a substrate of EmrE, on illumination.« less

Association of Rpn10 with high molecular weight complex is enhanced during retinoic acid-induced differentiation of neuroblastoma cells.

PubMed

Tayama, Yoko; Kawahara, Hiroyuki; Minami, Ryosuke; Shimada, Masumi; Yokosawa, Hideyoshi

2007-12-01

The ubiquitin-binding Rpn10 protein serves as an ubiquitin receptor that delivers client proteins to the 26S proteasome, the protein degradation complex. It has been suggested that the ubiquitin-dependent protein degradation is critical for neuronal differentiation and for preventing neurodegenerative diseases. Our previous study indicated the importance of Rpn10 in control of cellular differentiation (Shimada et al., Mol Biol Cell 17:5356-5371, 2006), though the functional relevance of Rpn10 in neuronal cell differentiation remains a mystery to be uncovered. In the present study, we have examined the level of Rpn10 in a proteasome-containing high molecular weight (HMW) protein fraction prepared from the mouse neuroblastoma cell line Neuro2a. We here report that the protein level of Rpn10 in HMW fraction from un-differentiated Neuro2a cells was significantly lower than that of other cultured cell lines. We have found that retinoic acid-induced neural differentiation of Neuro2a cells significantly stimulates the incorporation of Rpn10 into HMW fractions, although the amounts of 26S proteasome subunits were not changed. Our findings provide the first evidence that the modulation of Rpn10 is linked to the control of retinoic acid-induced differentiation of neuroblastoma cells.

Phylogenetic mixtures and linear invariants for equal input models.

PubMed

Casanellas, Marta; Steel, Mike

2017-04-01

The reconstruction of phylogenetic trees from molecular sequence data relies on modelling site substitutions by a Markov process, or a mixture of such processes. In general, allowing mixed processes can result in different tree topologies becoming indistinguishable from the data, even for infinitely long sequences. However, when the underlying Markov process supports linear phylogenetic invariants, then provided these are sufficiently informative, the identifiability of the tree topology can be restored. In this paper, we investigate a class of processes that support linear invariants once the stationary distribution is fixed, the 'equal input model'. This model generalizes the 'Felsenstein 1981' model (and thereby the Jukes-Cantor model) from four states to an arbitrary number of states (finite or infinite), and it can also be described by a 'random cluster' process. We describe the structure and dimension of the vector spaces of phylogenetic mixtures and of linear invariants for any fixed phylogenetic tree (and for all trees-the so called 'model invariants'), on any number n of leaves. We also provide a precise description of the space of mixtures and linear invariants for the special case of [Formula: see text] leaves. By combining techniques from discrete random processes and (multi-) linear algebra, our results build on a classic result that was first established by James Lake (Mol Biol Evol 4:167-191, 1987).

Preparation and thermoluminescent dosimetry features of high sensitivity LiF:Mg,Ce phosphor

NASA Astrophysics Data System (ADS)

Shoushtari, M. K.; Zahedifar, M.; Sadeghi, E.

2018-04-01

Thermoluminescence (TL) kinetics and dosimetry features of newly produced LiF doped with Mg and Ce were investigated. Different contents of Mg (0-1 mol%) and Ce (0-2 mol%) were introduced in host material by melting method. The most TL sensitivity of the fabricated phosphor was obtained at 0.7 and 0.05 mol% concentrations of Mg and Ce impurities, respectively. The optimum pre-irradiation annealing regime of the synthesized LiF-based material was found at 350 °C for 10 min. Kinetic parameters of LiF:Mg,Ce dosimeter were obtained using different methods of computerized glow curve deconvolution (CGCD), initial rise (IR) and isothermal decay (ID). A good conformity are observed between the results obtained from different kinetic analysis methods. Other TL features such as fading, dose response and reusability were also examined.

Adsorption as a method of doping 3-mol%-yttria-stabilized zirconia powder with copper oxides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seidensticker, J.R.; Mayo, M.J.; Osseo-Asare, K.

The adsorption behavior of Cu[sup 2+] on 3-mol%-yttria-stabilized tetragonal zirconia polycrystalline (3Y-TZP) powder was studied. There is a window of pH values (10 < pH < 11) where adsorption may be used as a method of doping 3Y-TZP with Cu[sup 2+]. The maximum mole percent of the CuO additions is determined by the specific surface area of the 3Y-TZP powder; a powder with a specific surface area of 16.1 m[sup 2]/g is limited to about 1 mol% CuO. Compacts made from powders doped with CuO using this method exhibited an enhancement in superplasticity comparable to that observed in other studiesmore » using samples doped with CuO by attrition milling.« less

Neurovascular and Autonomic Dysfunction Associated with Gulf War Illness Pain

DTIC Science & Technology

2016-10-01

pyridostigmine and organophosphorus pesticides with human cholinesterases." Chem Biol Interact 190(2-3): 79-83. Wilson, B. W., F. J. Rusli, M. K. Yan Tam...vitro kinetic interactions of DEET, pyridostigmine and organophosphorus pesticides with human cholinesterases." Chem Biol Interact 190(2-3): 79-83...that can accompany pain symptoms in veterans with GWI. 2. Keywords: pain, autonomic, nociceptor, blood flow, pesticides , pyridostigmine bromide

The Big Bang of tissue growth: Apical cell constriction turns into tissue expansion.

PubMed

Janody, Florence

2018-03-05

How tissue growth is regulated during development and cancer is a fundamental question in biology. In this issue, Tsoumpekos et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201705104) and Forest et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201705107) identify Big bang (Bbg) as an important growth regulator of the Drosophila melanogaster wing imaginal disc. © 2018 Janody.

Solvent effects and potential of mean force study of the SN2 reaction of CH3+CN‑ in water

NASA Astrophysics Data System (ADS)

Li, Chen; Liu, Peng; Li, Yongfang; Wang, Dunyou

2018-03-01

We used a combined quantum mechanics and molecular mechanics (QM/MM) method to investigate the solvent effects and potential of mean force of the CH3F+CN‑ reaction in water. Comparing to gas phase, the water solution substantially affects the structures of the stationary points along the reaction path. We quantitatively obtained the solvent effects’ contributions to the reaction: 1.7 kcal/mol to the activation barrier and ‑26.0 kcal/mol to the reaction free energy. The potential mean of force calculated with the density functional theory/MM theory has a barrier height at 19.7 kcal/mol, consistent with the experimental result at 23.0 kcal/mol; the calculated reaction free energy at ‑43.5 kcal/mol is also consistent with the one estimated based on the gas-phase data at ‑39.7 kcal/mol. Project supported by the National Natural Science Foundation of China (Grant No. 11774206) and Taishan Scholarship Fund from Shandong Province, China.

Comparative study on the pyrolysis behaviour and kinetics of two macroalgae biomass (Gracilaria changii and Gelidium pusillum) by thermogravimetric analysis

NASA Astrophysics Data System (ADS)

Roslee, A. N.; Munajat, N. F.

2017-10-01

Macroalgae are often referred as seaweed and could be significant biomass resource for the production of numerous energy carriers including biofuels. In this study, the chemical composition of Gracilaria changii (G. changii) and Gelidium pusillum (G. pusillum) were determined through proximate and ultimate analysis and the thermal degradation behaviour of G. changii and G. pusillum were investigated via thermogravimetric analysis (TGA) in determining the important main composition to be considered as biomass fuels. It has found the pyrolysis of G. changii and G. pusillum consists of three stages and stage II is the main decomposition stage with major mass loss of around 52.16% and 44.42%, respectively. The TGA data were then used for determination of kinetic parameters of the pyrolysis process using three model-free methods: Kissinger, Kissinger-Akahira-Sunose (KAS) and Flynn-Wall-Ozawa (FWO). The apparent activation energy calculated by using Kissinger method for G. changii was lower than G. Pusillum, i.e.173.12 kJ/mol and 193.22 kJ/mol, respectively. The activation energies calculated from KAS and FWO methods were increased with increasing the pyrolysis conversion with average activation energies of 172.32 kJ/mol and 181.19 kJ/mol for G. changii while for G. pusillum (177.42 kJ/mol and 187.4 kJ/mol). G. pusillum has lower and wider distribution of activation energy and revealed that the pyrolysis process for G. changii was easier than G. pusillum. These data provide information for further application for designing and modelling in thermochemical conversion system of macroalgae biomass.

Kinetics of the Strain-Promoted Oxidation-Controlled Cycloalkyne-1,2-quinone Cycloaddition: Experimental and Theoretical Studies.

PubMed

Escorihuela, Jorge; Das, Anita; Looijen, Wilhelmus J E; van Delft, Floris L; Aquino, Adelia J A; Lischka, Hans; Zuilhof, Han

2018-01-05

Stimulated by its success in both bioconjugation and surface modification, we studied the strain-promoted oxidation-controlled cycloalkyne-1,2-quinone cycloaddition (SPOCQ) in three ways. First, the second-order rate constants and activation parameters (ΔH ⧧ ) were determined of various cyclooctynes reacting with 4-tert-butyl-1,2-quinone in a SPOCQ reaction, yielding values for ΔH ⧧ of 4.5, 7.3, and 12.1 kcal/mol, for bicyclo[6.1.0]non-4-yne (BCN), cyclooctyne (OCT), and dibenzoazacyclooctyne (DIBAC), respectively. Second, their reaction paths were investigated in detail by a range of quantum mechanical calculations. Single-configuration theoretical methods, like various DFT and a range of MP2-based methods, typically overestimate this barrier by 3-8 kcal/mol (after inclusion of zero-point energy, thermal, and solvation corrections), whereas MP2 itself underestimates the barrier significantly. Only dispersion-corrected DFT methods like B97D (yielding 4.9, 6.4, and 12.1 kcal/mol for these three reactions) and high-level CCSD(T) and multireference multiconfiguration AQCC ab initio approaches (both yielding 8.2 kcal/mol for BCN) give good approximations of experimental data. Finally, the multireference methods show that the radical character in the TS is rather small, thus rationalizing the use of single-reference methods like B97D and SCS-MP2 as intrinsically valid approaches.

Kinetics of the Strain-Promoted Oxidation-Controlled Cycloalkyne-1,2-quinone Cycloaddition: Experimental and Theoretical Studies

PubMed Central

2017-01-01

Stimulated by its success in both bioconjugation and surface modification, we studied the strain-promoted oxidation-controlled cycloalkyne–1,2-quinone cycloaddition (SPOCQ) in three ways. First, the second-order rate constants and activation parameters (ΔH⧧) were determined of various cyclooctynes reacting with 4-tert-butyl-1,2-quinone in a SPOCQ reaction, yielding values for ΔH⧧ of 4.5, 7.3, and 12.1 kcal/mol, for bicyclo[6.1.0]non-4-yne (BCN), cyclooctyne (OCT), and dibenzoazacyclooctyne (DIBAC), respectively. Second, their reaction paths were investigated in detail by a range of quantum mechanical calculations. Single-configuration theoretical methods, like various DFT and a range of MP2-based methods, typically overestimate this barrier by 3–8 kcal/mol (after inclusion of zero-point energy, thermal, and solvation corrections), whereas MP2 itself underestimates the barrier significantly. Only dispersion-corrected DFT methods like B97D (yielding 4.9, 6.4, and 12.1 kcal/mol for these three reactions) and high-level CCSD(T) and multireference multiconfiguration AQCC ab initio approaches (both yielding 8.2 kcal/mol for BCN) give good approximations of experimental data. Finally, the multireference methods show that the radical character in the TS is rather small, thus rationalizing the use of single-reference methods like B97D and SCS-MP2 as intrinsically valid approaches. PMID:29260879

Analytical performances of a new enzymatic assay for hemoglobin A1c.

PubMed

Jaisson, Stéphane; Desmons, Aurore; Renard, Benoît; Chevelle, Benjamin; Leroy, Nathalie; Gillery, Philippe

2014-07-01

HbA1c is considered the gold standard for the follow-up of diabetic patients and a new diagnostic tool for diabetes mellitus, which implies the availability of reliable assay methods. We have evaluated a new assay developed by Abbott Laboratories, based on the enzymatic quantification of HbA1c by a fructosyl dipeptide oxidase using Architect analyzers. Precision, linearity, correlation with a HPLC method, accuracy and potential impact interferences on HbA1c measurement have been evaluated. Intra-day and between-day CVs were lower than 1.2% and linearity was excellent from 19 mmol/mol (3.9%) to 163 mmol/mol (17.1%). The results were well correlated with those obtained by the HPLC (Variant II device, kit NU - BioRad): HbA1c [Architect, mmol/mol]=0.986×HbA1c [Variant II, mmol/mol]+0.713 (r=0.998, n=109). This method provided consistent results with IFCC titrated quality control samples. Classical interferences in HbA1c assays (i.e. labile HbA1c, carbamylated hemoglobin, triglycerides or bilirubin) did not have an impact on HbA1c quantification by this method. This new enzymatic assay proved to be a robust and reliable method for HbA1c measurement suitable for routine practice in clinical chemistry laboratories. Copyright © 2014 Elsevier B.V. All rights reserved.

NOTE: Fluoroscopic gating without implanted fiducial markers for lung cancer radiotherapy based on support vector machines

NASA Astrophysics Data System (ADS)

Cui, Ying; Dy, Jennifer G.; Alexander, Brian; Jiang, Steve B.

2008-08-01

Various problems with the current state-of-the-art techniques for gated radiotherapy have prevented this new treatment modality from being widely implemented in clinical routine. These problems are caused mainly by applying various external respiratory surrogates. There might be large uncertainties in deriving the tumor position from external respiratory surrogates. While tracking implanted fiducial markers has sufficient accuracy, this procedure may not be widely accepted due to the risk of pneumothorax. Previously, we have developed a technique to generate gating signals from fluoroscopic images without implanted fiducial markers using template matching methods (Berbeco et al 2005 Phys. Med. Biol. 50 4481-90, Cui et al 2007b Phys. Med. Biol. 52 741-55). In this note, our main contribution is to provide a totally different new view of the gating problem by recasting it as a classification problem. Then, we solve this classification problem by a well-studied powerful classification method called a support vector machine (SVM). Note that the goal of an automated gating tool is to decide when to turn the beam ON or OFF. We treat ON and OFF as the two classes in our classification problem. We create our labeled training data during the patient setup session by utilizing the reference gating signal, manually determined by a radiation oncologist. We then pre-process these labeled training images and build our SVM prediction model. During treatment delivery, fluoroscopic images are continuously acquired, pre-processed and sent as an input to the SVM. Finally, our SVM model will output the predicted labels as gating signals. We test the proposed technique on five sequences of fluoroscopic images from five lung cancer patients against the reference gating signal as ground truth. We compare the performance of the SVM to our previous template matching method (Cui et al 2007b Phys. Med. Biol. 52 741-55). We find that the SVM is slightly more accurate on average (1-3%) than the template matching method, when delivering the target dose. And the average duty cycle is 4-6% longer. Given the very limited patient dataset, we cannot conclude that the SVM is more accurate and efficient than the template matching method. However, our preliminary results show that the SVM is a potentially precise and efficient algorithm for generating gating signals for radiotherapy. This work demonstrates that the gating problem can be considered as a classification problem and solved accordingly.

Concentration sensor based on a tilted fiber Bragg grating for anions monitoring

NASA Astrophysics Data System (ADS)

Melo, L. B.; Rodrigues, J. M. M.; Farinha, A. S. F.; Marques, C. A.; Bilro, L.; Alberto, N.; Tomé, J. P. C.; Nogueira, R. N.

2014-08-01

The ubiquity and importance of anions in many crucial roles accounts for the current high interest in the design and preparation of effective sensors for these species. Therefore, a tilted fiber Bragg grating sensor was fabricated to investigate individual detection of different anion concentrations in ethyl acetate, namely acetate, fluoride and chloride. The influence of the refractive index on the transmission spectrum of a tilted fiber Bragg grating was determined by developing a new demodulation method. This is based on the calculation of the standard deviation between the cladding modes of the transmission spectrum and its smoothing function. The standard deviation method was used to monitor concentrations of different anions. The sensor resolution obtained for the anion acetate, fluoride and chloride is 79 × 10-5 mol/dm3, 119 × 10-5 mol/dm3 and 78 × 10-5 mol/dm3, respectively, within the concentration range of (39-396) × 10-5 mol/dm3.

Multipolar Electrostatic Energy Prediction for all 20 Natural Amino Acids Using Kriging Machine Learning.

PubMed

Fletcher, Timothy L; Popelier, Paul L A

2016-06-14

A machine learning method called kriging is applied to the set of all 20 naturally occurring amino acids. Kriging models are built that predict electrostatic multipole moments for all topological atoms in any amino acid based on molecular geometry only. These models then predict molecular electrostatic interaction energies. On the basis of 200 unseen test geometries for each amino acid, no amino acid shows a mean prediction error above 5.3 kJ mol(-1), while the lowest error observed is 2.8 kJ mol(-1). The mean error across the entire set is only 4.2 kJ mol(-1) (or 1 kcal mol(-1)). Charged systems are created by protonating or deprotonating selected amino acids, and these show no significant deviation in prediction error over their neutral counterparts. Similarly, the proposed methodology can also handle amino acids with aromatic side chains, without the need for modification. Thus, we present a generic method capable of accurately capturing multipolar polarizable electrostatics in amino acids.

The Influence of Conditions on Synthesis Hydroxyapatite By Chemical Precipitation Method

NASA Astrophysics Data System (ADS)

Zhu, Jianping; Kong, Deshuang; Zhang, Yin; Yao, Nengjian; Tao, Yaqiu; Qiu, Tai

2011-10-01

Particles of Hydroxyapatite (HAp) were synthesized by means of chemical precipitation method, under atmosphere pressure. The starting solution with the Ca/P ratio of 1.67 was prepared by mixing 0.167 mol·dm-3 Ca(NO3)2·4H2O, 0.100 mol·dm-3 (NH4)2HPO4, 0.500 mol·dm-3 (NH2)2CO and 0.10 mol·dm-3 HNO3 aqueous solutions. The hydroxyapatite were prepared by heating the solution at 80 °C for 24 hour and then at 90°C for 72 hour. Then followed, the dry powers were heat treatment at 660°C temperatures for 8 hour. The obtained powder was analyzed using XRD, XRF, FT-IR, SEM, TG-DTA. The results showed that obtained HAp powers were greatly influenced by synthetic conditions. HAp powders with various morphologies, such as sphere, rod, layered, dumbbell, fibre, scaly, were obtained by controlling the synthetic conditions.

Microstructure and Properties of KSr2Nb5O15 Ceramics with Excess K+

NASA Astrophysics Data System (ADS)

Wang, Min; Gao, Feng; Xu, Jie; Zhang, Chaochao; Qin, Mengjie; Wang, Li; Guo, Yiting

2017-03-01

KSr2Nb5O15- xK (KSN- xK, x = 0 mol.%, 4 mol.%, 8 mol.%, 12 mol.%, 16 mol.%, and 20 mol.%) lead-free ferroelectric ceramics have been prepared by a buried sintering method using needle-like KSN particles synthesized by molten salt synthesis, and their microstructure, dielectric properties, and infrared transmittance investigated. The results suggest that the KSN- xK ceramics had simplex tungsten bronze structure for x ≤ 12 mol.%, but K2Nb8O21 secondary phase appeared at higher x. Excess K+ compensated the shortage of A-site ions in KSN crystallites, alleviated lattice distortion, and drove the KSN component closer to stoichiometric ratio, all of which increased the Curie temperature. The dielectric relaxor behavior of the ceramics was enhanced as the excess K+ content was increased. The dielectric constant, dielectric tunability, and infrared transmittance initially increased then decreased with increasing x. The specimen with 12 mol.% excess K+ showed optimum electrical properties, including maximum infrared transmittance of ˜60%. This work confirms that A-site vacancies in KSN can be compensated by excess K+, and that this effect can be used to adjust the local composition, alleviate structural distortion of the oxygen octahedron, enhance the Curie temperature, etc.

Pyrolysis characteristics and kinetics of oil-based drilling cuttings in shale gas developing

NASA Astrophysics Data System (ADS)

Huang, Chuan; Li, Tong; Xu, Tengtun; Zeng, Yunmin; Song, Xue

2018-03-01

In this paper, the thermal behavior of waste oil-based drilling cuttings (from shale gas fields in Chongqing) was examined at different heating rates ranging from 5 to 15 °C min-1 in inert atmosphere using a sync analyzer of thermogravimetry (TG) and differential scanning calorimetry (DSC). Four methods were used to analyze the distributions and variations of kinetics parameter (active energy (E) and frequency gene (A)): Coats-Redfern and other three iso-conversion rate methods (Flynn-Wall-Ozawa, Vyazovkin and Friedman). The experimental results indicated that the process consists of three steps, i.e., water evaporation, volatilization of light oil component and heavy oil cracking. TG curves moved toward higher temperature zone caused by thermal hysteresis with the increase of temperature rising rate. For volatilization of lightweight components, the E calculated by three iso-conversion rate methods changed a little with conversion, and had almost the same results as the CR method (14.39˜20.08 kJ.mol-1). For reactions of heavy oil cracking with mixed mechanism, corresponding E rose gradually with the increase of reaction time. The CR method shows nonlinear trends and the reaction models and kinetic parameters cannot be extracted from CR curves. The results by three iso-conversion methods showed that apparent activation energy was given as 155.74˜561.10 kJ.mol-1, 141.06˜524.96 kJ.mol-1 and 74.37˜605.10 kJ.mol-1, respectively.

The role of leaf height in plant competition for sunlight: analysis of a canopy partitioning model.

PubMed

Nevai, Andrew L; Vance, Richard R

2008-01-01

A global method of nullcline endpoint analysis is employed to determine the outcome of competition for sunlight between two hypothetical plant species with clonal growth form that differ solely in the height at which they place their leaves above the ground. This difference in vertical leaf placement, or canopy partitioning, produces species differences in sunlight energy capture and stem metabolic maintenance costs. The competitive interaction between these two species is analyzed by considering a special case of a canopy partitioning model (RR Vance and AL Nevai, J. Theor. Biol. 2007, 245:210-219; AL Nevai and RR Vance, J. Math. Biol. 2007, 55:105-145). Nullcline endpoint analysis is used to partition parameter space into regions within which either competitive exclusion or competitive coexistence occurs. The principal conclusion is that two clonal plant species which compete for sunlight and place their leaves at different heights above the ground but differ in no other way can, under suitable parameter values, experience stable coexistence even though they occupy an environment which varies neither over horizontal space nor through time.

An Extended Ab Initio and Theoretical Thermodynamics Studies of the Bergman Reaction and the Energy Splitting of the Singlet Ortho-, Meta-, and Para-Benzynes

NASA Technical Reports Server (NTRS)

Lindh, Roland; Lee, Timothy J.; Bernhardsson, Anders; Persson, B. Joakim; Karlstroem, Gunnar; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The autoaromatization of (Z)-hex-3-ene-1,5-diyne to the singlet biradical para-benzyne has been reinvestigated by state of the art ab initio methods. Previous CCSD(T)/6-31G(d,p) and CASPT2[0]/ANO[C(5s4p2d1f)/H(3s2p)] calculations estimated the the reaction heat at 298 K to be 8-10 and 4.9 plus or minus 3.2 kcal/mol, respectively. Recent NO- and oxygen-dependent trapping experiments and collision-induced dissociation threshold energy experiments estimate the heat of reaction to be 8.5 plus or minus 1.0 at 470 K (recomputed to 9.5 plus or minus 1.0 at 298 K) and 8.4 plus or minus 3.0 kcal/mol at 298 K, respectively. New theoretical estimates at 298 K predict the values at the basis set limit for the CCSD(T) and CASPT2(g1) methods to be 12.7 plus or minus 2.0 and 5.4 plus or minus 2.0 kcal/mol, respectively. The experimentally predicted electronic contribution to the heat of activation is 28.6 kcal/mol. This can be compared with 25.5 and 29.8 kcal/mol from the CASPT2[g1] and the CCSD(T) methods, respectively. The new study has in particular improved on the one-particle basis set for the CCSD(T) method as compared to earlier studies. For the CASPT2 investigation the better suited CASPT2[g1] approximation is utilized. The original CASPT2 method, CASPT2[0], systematically favors open shell systems relative to closed shell systems. This was previously corrected empirically. The study shows that the energy difference between CCSD(T) and CASPT2[g1] at the basis set limit is estimated to be 7 plus or minus 2 kcal/mol. The study also demonstrates that the estimated heat of reaction is very sensitive to the quality of the basis set.

The Mechanism of Blood Function and Production After Injury.

DTIC Science & Technology

1980-02-01

radioactive 59Fe labeled red cell dilution method described by Garcia7 . Red cell 2,3 diphosphoglycerate levels were measured using a commercial kit...and protein depleted rats was also associated with elevated 2,3 diphosphoglycerate levels (p<.05)(Table IV) suggesting partial compensation for anemic...Brewer, G.J.: The relationship between red cell 2,3 diphosphoglycerate and levels of hemoglobin in the human. Proc.Soc. Exp.Biol.Med. 150(1): 215-9

Stability of Cucumber Necrosis Virus at the Quasi-6-Fold Axis Affects Zoospore Transmission.

PubMed

Sherman, Michael B; Kakani, Kishore; Rochon, D'Ann; Jiang, Wen; Voss, Neil R; Smith, Thomas J

2017-10-01

Cucumber necrosis virus (CNV) is a member of the genus Tombusvirus and has a monopartite positive-sense RNA genome. CNV is transmitted in nature via zoospores of the fungus Olpidium bornovanus As with other members of the Tombusvirus genus, the CNV capsid swells when exposed to alkaline pH and EDTA. We previously demonstrated that a P73G mutation blocks the virus from zoospore transmission while not significantly affecting replication in plants (K. Kakani, R. Reade, and D. Rochon, J Mol Biol 338:507-517, 2004, https://doi.org/10.1016/j.jmb.2004.03.008). P73 lies immediately adjacent to a putative zinc binding site (M. Li et al., J Virol 87:12166-12175, 2013, https://doi.org/10.1128/JVI.01965-13) that is formed by three icosahedrally related His residues in the N termini of the C subunit at the quasi-6-fold axes. To better understand how this buried residue might affect vector transmission, we determined the cryo-electron microscopy structure of wild-type CNV in the native and swollen state and of the transmission-defective mutant, P73G, under native conditions. With the wild-type CNV, the swollen structure demonstrated the expected expansion of the capsid. However, the zinc binding region at the quasi-6-fold at the β-annulus axes remained intact. By comparison, the zinc binding region of the P73G mutant, even under native conditions, was markedly disordered, suggesting that the β-annulus had been disrupted and that this could destabilize the capsid. This was confirmed with pH and urea denaturation experiments in conjunction with electron microscopy analysis. We suggest that the P73G mutation affects the zinc binding and/or the β-annulus, making it more fragile under neutral/basic pH conditions. This, in turn, may affect zoospore transmission. IMPORTANCE Cucumber necrosis virus (CNV), a member of the genus Tombusvirus , is transmitted in nature via zoospores of the fungus Olpidium bornovanus While a number of plant viruses are transmitted via insect vectors, little is known at the molecular level as to how the viruses are recognized and transmitted. As with many spherical plant viruses, the CNV capsid swells when exposed to alkaline pH and EDTA. We previously demonstrated that a P73G mutation that lies inside the capsid immediately adjacent to a putative zinc binding site (Li et al., J Virol 87:12166-12175, 2013, https://doi.org/10.1128/JVI.01965-13) blocks the virus from zoospore transmission while not significantly affecting replication in plants (K. Kakani, R. Reade, and D. Rochon, J Mol Biol 338:507-517, 2004, https://doi.org/10.1016/j.jmb.2004.03.008). Here, we show that the P73G mutant is less stable than the wild type, and this appears to be correlated with destabilization of the β-annulus at the icosahedral 3-fold axes. Therefore, the β-annulus appears not to be essential for particle assembly but is necessary for interactions with the transmission vector. Copyright © 2017 American Society for Microbiology.

Stability of Cucumber Necrosis Virus at the Quasi-6-Fold Axis Affects Zoospore Transmission

PubMed Central

Sherman, Michael B.; Kakani, Kishore; Rochon, D'Ann; Jiang, Wen; Voss, Neil R.

2017-01-01

ABSTRACT Cucumber necrosis virus (CNV) is a member of the genus Tombusvirus and has a monopartite positive-sense RNA genome. CNV is transmitted in nature via zoospores of the fungus Olpidium bornovanus. As with other members of the Tombusvirus genus, the CNV capsid swells when exposed to alkaline pH and EDTA. We previously demonstrated that a P73G mutation blocks the virus from zoospore transmission while not significantly affecting replication in plants (K. Kakani, R. Reade, and D. Rochon, J Mol Biol 338:507–517, 2004, https://doi.org/10.1016/j.jmb.2004.03.008). P73 lies immediately adjacent to a putative zinc binding site (M. Li et al., J Virol 87:12166–12175, 2013, https://doi.org/10.1128/JVI.01965-13) that is formed by three icosahedrally related His residues in the N termini of the C subunit at the quasi-6-fold axes. To better understand how this buried residue might affect vector transmission, we determined the cryo-electron microscopy structure of wild-type CNV in the native and swollen state and of the transmission-defective mutant, P73G, under native conditions. With the wild-type CNV, the swollen structure demonstrated the expected expansion of the capsid. However, the zinc binding region at the quasi-6-fold at the β-annulus axes remained intact. By comparison, the zinc binding region of the P73G mutant, even under native conditions, was markedly disordered, suggesting that the β-annulus had been disrupted and that this could destabilize the capsid. This was confirmed with pH and urea denaturation experiments in conjunction with electron microscopy analysis. We suggest that the P73G mutation affects the zinc binding and/or the β-annulus, making it more fragile under neutral/basic pH conditions. This, in turn, may affect zoospore transmission. IMPORTANCE Cucumber necrosis virus (CNV), a member of the genus Tombusvirus, is transmitted in nature via zoospores of the fungus Olpidium bornovanus. While a number of plant viruses are transmitted via insect vectors, little is known at the molecular level as to how the viruses are recognized and transmitted. As with many spherical plant viruses, the CNV capsid swells when exposed to alkaline pH and EDTA. We previously demonstrated that a P73G mutation that lies inside the capsid immediately adjacent to a putative zinc binding site (Li et al., J Virol 87:12166–12175, 2013, https://doi.org/10.1128/JVI.01965-13) blocks the virus from zoospore transmission while not significantly affecting replication in plants (K. Kakani, R. Reade, and D. Rochon, J Mol Biol 338:507–517, 2004, https://doi.org/10.1016/j.jmb.2004.03.008). Here, we show that the P73G mutant is less stable than the wild type, and this appears to be correlated with destabilization of the β-annulus at the icosahedral 3-fold axes. Therefore, the β-annulus appears not to be essential for particle assembly but is necessary for interactions with the transmission vector. PMID:28724762

Exploring the World of Phospholipids and Their Interactions with Proteins: The Work of William Dowhan

PubMed Central

2012-01-01

The Gene Encoding the Phosphatidylinositol Transfer Protein Is Essential for Cell Growth (Aitken, J. F., van Heusden, G. P., Temkin, M., and Dowhan, W. (1990) J. Biol. Chem. 265, 4711–4717) A Phospholipid Acts as a Chaperone in Assembly of a Membrane Transport Protein (Bogdanov, M., Sun, J., Kaback, H. R., and Dowhan, W. (1996) J. Biol. Chem. 271, 11615–11618) PMID:22427432

Bibliography of Ticks and Tickborne Diseases from Homer (About 800 B.C.) to 31 December 1981. Volume 7.

DTIC Science & Technology

1982-05-01

Oklahoma. Brt. J.". Nu-tr..-f Arch. Pediat., Barcelona Brit. J. Nutr. BRITISH JOURNAL OF NUTRITION . ARCHIVOS DE PEDIATRIA. BARCELONA. London. Arh. Biol...INTERNATIONAL. The CEUTICAL CHEMISTRY. Nw York, Journal of Stock Breeding, Animal London Health, Nutrition and Husbandry. Surrey. J. Neurocyt. Med...INSTITUT. Tiflis. J. Therm. Biol. Nutr. Rep. Internat. JOURNAL OF THERMAL BIOLOGY. NUTRITION REPORTS INTERNATIONAL. Sutton Bonington, England. Los

A 3-Component System of Competition and Diffusion.

DTIC Science & Technology

1983-08-01

assume * that the distribution of the populations are determined by competition of’ Lotka - Volterra - * Gause type and simple diffusion. Suppose ui(t,x...diffusive Lotka - Volterra system with three species can have a stable non-constant equilibrium solutions. J. Math. Biol., (in press). [7] Kishimoto, K., Mimura...M. and Yoshida, K., Stable spatlo-temporal oscillations of diffusive Lotka - Volterra systems with three or more species, to appear in J. Math. Biol

Centrosome Amplification: A Potential Marker of Breast Cancer Agressiveness

DTIC Science & Technology

2006-07-01

centrosome amplification. Introduction of DNA damage in the MCF-7 cell line by treatment with hydroxyurea (HU) or daunorubicin (DR) resulted in the...cycles of DNA synthesis and mitotic division in hydroxyurea - arrested Chinese hamster ovary cells. J Cell Biol, 130: 105-115, 1995. 23. D’Assoro, A. B...from cycles of DNA synthesis and mitotic division in hydroxyurea -arrested Chinese hamster ovary cells. J Cell Biol, 1995. 130(1): p. 105-15. 22

Gas-phase acidities of nitrated azoles as determined by the extended kinetic method and computations.

PubMed

Nichols, Charles M; Old, William M; Lineberger, W Carl; Bierbaum, Veronica M

2015-01-15

Making use of the extended kinetic method and the alternative method for data analysis, we have experimentally determined ΔH°acid (kcal/mol) for six mononitrated azole species (2-nitropyrrole = 337.0, 3-nitropyrrole = 335.8, 3-nitropyrazole = 330.5, 4-nitropyrazole = 329.5, 2-nitroimidazole = 327.4, and 4-nitroimidazole = 325.0). We report an absolute uncertainty of ±2.2 kcal/mol that arises from the uncertainties of the reference acids; the relative values are known within 0.4 kcal/mol. Combining these experimental ΔH°acid values with ΔS°acid values calculated at the B3LYP/aug-cc-pVTZ level of theory, we report ΔG°acid (kcal/mol) for the nitroazoles (2-nitropyrrole = 329.4, 3-nitropyrrole = 328.4, 3-nitropyrazole = 323.1, 4-nitropyrazole = 322.0, 2-nitroimidazole = 319.7, and 4-nitroimidazole = 317.6); the absolute uncertainties are ±2.4 kcal/mol. In addition to the experimental studies, we have computationally investigated the gas-phase acidities and electron affinities of the azoles in this work, as well as higher-order aza- and dinitro-substituted azoles. We discuss trends in the stabilities of the deprotonated azoles based on aza substitution and nitro group placement. 4-Nitroimidazole has already found use as the anionic component in ionic liquids, and we propose that the additional nitrated azolate ions are potential candidates for the anionic component of ionic liquids.

Is HO3 minimum cis or trans? An analytic full-dimensional ab initio isomerization path.

PubMed

Varandas, A J C

2011-05-28

The minimum energy path for isomerization of HO(3) has been explored in detail using accurate high-level ab initio methods and techniques for extrapolation to the complete basis set limit. In agreement with other reports, the best estimates from both valence-only and all-electron single-reference methods here utilized predict the minimum of the cis-HO(3) isomer to be deeper than the trans-HO(3) one. They also show that the energy varies by less than 1 kcal mol(-1) or so over the full isomerization path. A similar result is found from valence-only multireference configuration interaction calculations with the size-extensive Davidson correction and a correlation consistent triple-zeta basis, which predict the energy difference between the two isomers to be of only Δ = -0.1 kcal mol(-1). However, single-point multireference calculations carried out at the optimum triple-zeta geometry with basis sets of the correlation consistent family but cardinal numbers up to X = 6 lead upon a dual-level extrapolation to the complete basis set limit of Δ = (0.12 ± 0.05) kcal mol(-1). In turn, extrapolations with the all-electron single-reference coupled-cluster method including the perturbative triples correction yield values of Δ = -0.19 and -0.03 kcal mol(-1) when done from triple-quadruple and quadruple-quintuple zeta pairs with two basis sets of increasing quality, namely cc-cpVXZ and aug-cc-pVXZ. Yet, if added a value of 0.25 kcal mol(-1) that accounts for the effect of triple and perturbative quadruple excitations with the VTZ basis set, one obtains a coupled cluster estimate of Δ = (0.14 ± 0.08) kcal mol(-1). It is then shown for the first time from systematic ab initio calculations that the trans-HO(3) isomer is more stable than the cis one, in agreement with the available experimental evidence. Inclusion of the best reported zero-point energy difference (0.382 kcal mol(-1)) from multireference configuration interaction calculations enhances further the relative stability to ΔE(ZPE) = (0.51 ± 0.08) kcal mol(-1). A scheme is also suggested to model the full-dimensional isomerization potential-energy surface using a quadratic expansion that is parametrically represented by a Fourier analysis in the torsion angle. The method illustrated at the raw and complete basis-set limit coupled-cluster levels can provide a valuable tool for a future analysis of the available (incomplete thus far) experimental rovibrational data. This journal is © the Owner Societies 2011

Evaluation of the Giggenbach bottle method using artificial fumarolic gases

NASA Astrophysics Data System (ADS)

Lee, S.; Jeong, H. Y.

2013-12-01

Volcanic eruption is one of the most dangerous natural disasters. Mt. Baekdu, located on the border between North Korea and China, has been recently showing multiple signs of its eruption. The magmatic activity of a volcano strongly affects the composition of volcanic gases, which can provide a useful tool for predicting the eruption. Among various volcanic gas monitoring methods, the Giggenbach bottle method involves the on-site sampling of volcanic gases and the subsequent laboratory analysis, thus making it possible to detect a range of volcanic gases at low levels. In this study, we aim to evaluate the effectiveness of the Giggenbach bottle method and develop the associated analytical tools using artificial fumarolic gases with known compositions. The artificial fumarolic gases are generated by mixing CO2, CO, H2S, SO2, Ar, and H2 gas streams with a N2 stream sparged through an acidic medium containing HCl and HF. The target compositions of the fumarolic gases are selected to cover those reported for various volcanoes under different tectonic environments as follows: CO2 (2-12 mol %), CO (0.3-1 mol %), H2S (0.7-2 mol %), SO2 (0.6-4 mol %), Ar (0.3-0.7 mol %), H2 (0.3-0.7 mol %), HCl (0.2-1 mol %), and HF (< 0.015 mol %). The artificial fumarolic gases are collected into an evacuated bottle partially filled with 4 M NaOH solution containing 0.5 mM Cd(CH3COO)2. While non-condensable components such as CO, Ar, H2, and N2 accumulate in the headspace of the bottle, acidic components including CO2, SO2, HCl, and HF dissolve into the alkaline solution. In case of H2S, it reacts with dissolved Cd2+ to precipitate as CdS(s). The gas accumulated in the headspace can be analyzed for CO, Ar, H2, and N2 on a gas chromatography. The alkaline solution is first separated from yellowish CdS precipitates by filtration, and then pretreated with hydrogen peroxide to oxidize dissolved SO2 (H2SO3) to SO42-. The resultant solution can be analyzed for SO2 as SO42-, HCl as Cl-, and HF as F- on an ion chromatography and CO2 on an ionic carbon analyzer. Also, the amount of H2S can be determined by measuring the remaining dissolved Cd2+ on an inductively coupled plasma-mass spectrometry.

Sample preparation and UHPLC-FD analysis of pteridines in human urine.

PubMed

Tomšíková, H; Solich, P; Nováková, L

2014-07-01

Elevated levels of pteridines can indicate the activation of cellular immune system by certain diseases. No work dealing with the simultaneous determination of urinary neopterin, biopterin and their reduced forms has been published. Therefore, a new SPE-UHPLC-FD method for the analysis of these compounds has been developed. The main emphasis was put on the stability of dihydroforms during the sample processing and storage. As a stabilizing agent, dithiothreitol, at various concentrations, and various pH values (3.8-9.8) of working solutions were tested. Chromatographic separation was performed under HILIC isocratic conditions on BEH Amide column. The method was linear for the calibration standard solutions in the range of 10-10,000 ng/ml (dihydroforms) and 0.5-1000 ng/ml (oxidized forms), and for real samples in the range of 25-1000 ng/ml (dihydroforms) and 1-100 ng/ml (oxidized forms). The development of a new SPE sample preparation method was carried out on different types of sorbents (based on a mixed-mode cation exchange, porous graphitic carbon and a polymer comprising hydrophilic and hydrophobic components). Final validation was performed on a MCAX SPE column. Method accuracy ranged from 76.9 to 121.9%. The intra- and inter-day precision did not exceed 10.7%. The method provided high sensitivity for the use in routine clinical measurements of urine (LLOQ 1 ng/ml for oxidized forms and 25 ng/ml for dihydroforms). Average concentrations of biopterin, neopterin, and dihydrobiopterin found in urine of healthy persons were related to the mol of creatinine (66.8, 142.3, and 257.3 μmol/mol of creatinine, respectively) which corresponded to the literature data. The concentration of dihydroneopterin obtained using our method was 98.8 μmol/mol of creatinine. Copyright © 2014 Elsevier B.V. All rights reserved.

The energy separation between the classical and nonclassical isomers of protonated acetylene - An extensive study in one- and n-particle space saturation

NASA Technical Reports Server (NTRS)

Lindh, Roland; Rice, Julia E.; Lee, Timothy J.

1991-01-01

The energy separation between the classical and nonclassical forms of protonated acetylene has been reinvestigated in light of the recent experimentally deduced lower bound to this value of 6.0 kcal/mol. The objective of the present study is to use state-of-the-art ab initio quantum mechanical methods to establish this energy difference to within chemical accuracy (i.e., about 1 kcal/mol). The one-particle basis sets include up to g-type functions and the electron correlation methods include single and double excitation coupled-cluster (CCSD), the CCSD(T) extension, multireference configuration interaction, and the averaged coupled-pair functional methods. A correction for zero-point vibrational energies has also been included, yielding a best estimate for the energy difference between the classical and nonclassical forms of 3.7 + or - 1.3 kcal/mol.

Chemiluminescence determination of ferulic acid by flow-injection analysis using cerium(IV) sensitized by rhodamine 6G.

PubMed

Wang, Ju Peng; Li, Nian Bing; Luo, Hong Qun

2008-11-01

A simple, sensitive and rapid flow-injection chemiluminescence method has been developed for the determination of ferulic acid based on the chemiluminescence reaction of ferulic acid with rhodamine 6G and ceric sulfate in sulphuric acid medium. Strong chemiluminescence signal was observed when ferulic acid was injected into the acidic ceric sulfate solution in a flow-cell. The present method allowed the determination of ferulic acid in the concentration range of 8.0 x 10(-6) to 1.0 x 10(-4) mol l(-1) and the detection limit for ferulic acid was 8.7 x 10(-9) mol l(-1). The relative standard deviation was 2.4% for 10 replicate analyses of 1.0 x 10(-5) mol l(-1) ferulic acid. The proposed method was applied to the determination of ferulic acid in Taita Beauty Essence samples with satisfactory results.

Chemiluminescence determination of ferulic acid by flow-injection analysis using cerium(IV) sensitized by rhodamine 6G

NASA Astrophysics Data System (ADS)

Wang, Ju Peng; Li, Nian Bing; Luo, Hong Qun

2008-11-01

A simple, sensitive and rapid flow-injection chemiluminescence method has been developed for the determination of ferulic acid based on the chemiluminescence reaction of ferulic acid with rhodamine 6G and ceric sulfate in sulphuric acid medium. Strong chemiluminescence signal was observed when ferulic acid was injected into the acidic ceric sulfate solution in a flow-cell. The present method allowed the determination of ferulic acid in the concentration range of 8.0 × 10 -6 to 1.0 × 10 -4 mol l -1 and the detection limit for ferulic acid was 8.7 × 10 -9 mol l -1. The relative standard deviation was 2.4% for 10 replicate analyses of 1.0 × 10 -5 mol l -1 ferulic acid. The proposed method was applied to the determination of ferulic acid in Taita Beauty Essence samples with satisfactory results.

Vitamin A determination in milk samples based on the luminol-periodate chemiluminescence system.

PubMed

Rishi, Lubna; Yaqoob, Mohammad; Waseem, Amir; Nabi, Abdul

2014-01-01

A simple and rapid flow injection (FI) method for the determination of retinyl acetate is reported based on its enhancing effect on the luminol-periodate chemiluminescence (CL) system in an alkaline medium. The detection limit (3s×blank) was 8.0×10⁻⁸ mol L⁻¹, with an injection throughput of 90 h⁻¹. The method allows linear increase of CL intensity over the retinyl acetate concentration range of 1.0-100×10⁻⁷ mol L⁻¹ (R²=0.9996) with relative standard deviations of 2.4% (n=10) for 5.0×10⁻⁷ mol L⁻¹. The key chemical and physical variables (reagent concentrations, flow rates, sample volume, and photomultiplier tube (PMT) voltage) were optimized and potential interferences were investigated. The method was successfully applied to human milk, fresh cow's milk and infant milk-based formulas and the results were in good agreement with the previously reported HPLC method. A brief discussion on the possible CL reaction mechanism is also presented.

Kinetic analysis of manure pyrolysis and combustion processes.

PubMed

Fernandez-Lopez, M; Pedrosa-Castro, G J; Valverde, J L; Sanchez-Silva, L

2016-12-01

Due to the depletion of fossil fuel reserves and the environmental issues derived from their use, biomass seems to be an excellent source of renewable energy. In this work, the kinetics of the pyrolysis and combustion of three different biomass waste samples (two dairy manure samples before (Pre) and after (Dig R) anaerobic digestion and one swine manure sample (SW)) was studied by means of thermogravimetric analysis. In this work, three iso-conversional methods (Friedman, Flynn-Wall-Ozawa (FWO) and Kissinger-Akahira-Sunose (KAS)) were compared with the Coats-Redfern method. The E a values of devolatilization stages were in the range of 152-170kJ/mol, 148-178kJ/mol and 156-209kJ/mol for samples Pre, Dig R and SW, respectively. Concerning combustion process, char oxidation stages showed lower E a values than that obtained for the combustion devolatilization stage, being in the range of 140-175kJ/mol, 178-199kJ/mol and 122-144kJ/mol for samples Pre, Dig R and SW, respectively. These results were practically the same for samples Pre and Dig R, which means that the kinetics of the thermochemical processes were not affected by anaerobic digestion. Finally, the distributed activation energy model (DAEM) and the pseudo-multi component stage model (PMSM) were applied to predict the weight loss curves of pyrolysis and combustion. DAEM was the best model that fitted the experimental data. Copyright © 2016 Elsevier Ltd. All rights reserved.

Thermodynamic characterization of three polymorphic forms of piracetam.

PubMed

Picciochi, Ricardo; Diogo, Hermínio P; da Piedade, Manuel E Minas

2011-02-01

Combustion calorimetry, solution calorimetry, and differential scanning calorimetry (DSC) were used to determine the standard (p° = 0.1 MPa) molar enthalpies of formation of Forms I, II, and III piracetam at 298.15 K, namely, Δ(f) H(m)° (C(6)H(10)O(2)N(2), cr I) = -520.6 ± 1.6 kJ·mol(-1), Δ(f) H(m)° (C(6)H(10)O(2)N(2), cr II) = -523.8 ± 1.6 kJ·mol(-1), and Δ(f) H(m)° (C(6)H(10)O(2)N(2), cr III) = -524.1 ± 1.6 kJ·mol(-1). The enthalpy of formation of gaseous piracetam at 298.15 K was also derived as Δ(f) H(m)° (C(6)H(10)O(2)N(2), g) = -401.3 ± 2.1 kJ·mol(-1), by combining the standard molar enthalpy of formation of Form II piracetam with the corresponding enthalpy of sublimation, Δ(sub) H(m)° (C(6) H(10) O(2) N(2), cr II) = 122.5 ± 1.4 kJ·mol(-1), obtained by drop-sublimation Calvet microcalorimetry and the Knudsen effusion method. The Δ(f) H(m)° (C(6)H(10)O(2)N(2), g) value was used to assess the corresponding predictions by the B3LYP/cc-pVTZ (-335.3 kJ·mol(-1)), G3MP2 (-388.7 kJ·mol(-1)), and CBS-QB3 (-402.8 kJ·mol(-1)) methods, based on the calculation of the atomization enthalpy of piracetam. Finally, the results of the solution and DSC experiments indicate that the stability hierarchy of Forms I, II, and III piracetam at 298.15 K, for which there was conflicting evidence in the literature, is III > II > I. Copyright © 2010 Wiley-Liss, Inc.

Energy transfer and 2.0 μm emission in Tm{sup 3+}/Ho{sup 3+} co-doped α-NaYF{sub 4} single crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, Zhigang; Yang, Shuo; Xia, Haiping, E-mail: hpxcm@nbu.edu.cn

2016-04-15

Highlights: • Cubic NaYF{sub 4} single crystals co-doped with ∼1.90 mol% Tm{sup 3+} and various Ho{sup 3+} concentrations were grown by Bridgman method. • The maximum fluorescence lifetime was 23.23 ms for Tm{sup 3+} (1.90 mol%)/Ho{sup 3+} (3.89 mol%) co-doped α-NaYF{sub 4}. • The obtained energy transfer rate (W{sub ET}) and energy transfer efficiency (η) of Tm{sup 3+}:{sup 3}F{sub 4} are 1077 s{sup −1} and 95.0%, respectively. • The maximum emission cross section reached 1.06 × 10{sup −20} cm{sup 2}. - Abstract: Cubic NaYF{sub 4} single crystals co-doped with ∼1.90 mol% Tm{sup 3+} and various Ho{sup 3+} concentrations were grownmore » by Bridgman method. The energy transfer from Tm{sup 3+} to Ho{sup 3+} and the optimum fluorescence emission around 2.04 μm of Ho{sup 3+} ion were investigated based on the measured absorption spectra, emission spectra, emission cross section and decay curves under excitation of 800 nm LD. The emission intensity at 2.04 μm increased with the increase of Ho{sup 3+} concentration from 0.96 mol% to 3.89 mol% when the concentration of Tm{sup 3+} was held constantly at ∼1.90 mol%. Moreover, the maximum emission cross section reached 1.06 × 10{sup −20} cm{sup 2} and the maximum fluorescence lifetime was 23.23 ms for Tm{sup 3+}(1.90 mol%)/Ho{sup 3+}(3.89 mol%) co-doped one. According to the measured lifetime of Tm{sup 3+} single-doped and Tm{sup 3+}/Ho{sup 3+} co-doped samples, the maximum energy transfer efficiency of Tm{sup 3+}:{sup 3}F{sub 4} level was 95.0%. Analysis on the fluorescence dynamics indicated that electric dipole–dipole is dominant for the energy transfer from Tm{sup 3+} to Ho{sup 3+}.« less

Comparative evaluation of antiplatelet effect of lycopene with aspirin and the effect of their combination on platelet aggregation: An in vitro study

PubMed Central

Sawardekar, Swapna B.; Patel, Tejal C.; Uchil, Dinesh

2016-01-01

Introduction: The objective was to compare antiplatelet effect of lycopene with aspirin and to study effect of combination of the two on platelet aggregation in vitro, using platelets from healthy volunteers. Materials and Methods: Platelets were harvested; platelet count of platelet-rich plasma adjusted to 2.5 Χ 105/μL. Aspirin (140 μmol/L) and lycopene (4, 6, 8, 10, and 12 μmol/L) were studied in vitro against adenosine-5’- diphosphate (ADP) (2.5 μM/L) and collagen Results: All the concentrations of lycopene (4–12 μmol/L) exhibited reduction in maximum platelet aggregation induced by aggregating agents ADP and collagen (P < 0.01 vs. vehicle) and were comparable with aspirin. Lycopene at concentration 10 μmol/L showed maximum platelet inhibition (47.05% ± 19.56%) against ADP, whereas lycopene at concentration 8 μmol/L showed maximum platelet inhibition (54.26% ± 30.71%) against collagen. Four μmol/L of lycopene combined with 140 μmol/L and 70 μmol/L aspirin showed greater inhibition of platelets as compared to aspirin 140 μmol/L alone, against both ADP and collagen. Conclusion: The study favorably compares lycopene and aspirin with respect to their antiplatelet activities against ADP and collagen. Lycopene can be considered as a potential target for modifying the thrombotic and pro-inflammatory events associated with platelet activation. PMID:26997718

n-Nucleotide circular codes in graph theory.

PubMed

Fimmel, Elena; Michel, Christian J; Strüngmann, Lutz

2016-03-13

The circular code theory proposes that genes are constituted of two trinucleotide codes: the classical genetic code with 61 trinucleotides for coding the 20 amino acids (except the three stop codons {TAA,TAG,TGA}) and a circular code based on 20 trinucleotides for retrieving, maintaining and synchronizing the reading frame. It relies on two main results: the identification of a maximal C(3) self-complementary trinucleotide circular code X in genes of bacteria, eukaryotes, plasmids and viruses (Michel 2015 J. Theor. Biol. 380, 156-177. (doi:10.1016/j.jtbi.2015.04.009); Arquès & Michel 1996 J. Theor. Biol. 182, 45-58. (doi:10.1006/jtbi.1996.0142)) and the finding of X circular code motifs in tRNAs and rRNAs, in particular in the ribosome decoding centre (Michel 2012 Comput. Biol. Chem. 37, 24-37. (doi:10.1016/j.compbiolchem.2011.10.002); El Soufi & Michel 2014 Comput. Biol. Chem. 52, 9-17. (doi:10.1016/j.compbiolchem.2014.08.001)). The univerally conserved nucleotides A1492 and A1493 and the conserved nucleotide G530 are included in X circular code motifs. Recently, dinucleotide circular codes were also investigated (Michel & Pirillo 2013 ISRN Biomath. 2013, 538631. (doi:10.1155/2013/538631); Fimmel et al. 2015 J. Theor. Biol. 386, 159-165. (doi:10.1016/j.jtbi.2015.08.034)). As the genetic motifs of different lengths are ubiquitous in genes and genomes, we introduce a new approach based on graph theory to study in full generality n-nucleotide circular codes X, i.e. of length 2 (dinucleotide), 3 (trinucleotide), 4 (tetranucleotide), etc. Indeed, we prove that an n-nucleotide code X is circular if and only if the corresponding graph [Formula: see text] is acyclic. Moreover, the maximal length of a path in [Formula: see text] corresponds to the window of nucleotides in a sequence for detecting the correct reading frame. Finally, the graph theory of tournaments is applied to the study of dinucleotide circular codes. It has full equivalence between the combinatorics theory (Michel & Pirillo 2013 ISRN Biomath. 2013, 538631. (doi:10.1155/2013/538631)) and the group theory (Fimmel et al. 2015 J. Theor. Biol. 386, 159-165. (doi:10.1016/j.jtbi.2015.08.034)) of dinucleotide circular codes while its mathematical approach is simpler. © 2016 The Author(s).

[Determination of H2S in Rat Intestinal Perfusion Solution Based on Fluorescence Analysis].

PubMed

Hou, Jun-feng; Li, Xin-xia; Shen, Xue-ru; Huojia, Miliban; Guan, Ming

2015-08-01

Under alkaline conditions, Fluorescein mercury has strong fluorescence, however, when it met S(2-), its fluorescence would quench, in view of the above, a fluorescence method for determination of H2S in biological samples was established. In the 0.1 mol · L(-1) NaOH dilution, when the concentration of fluorescein Mercury and Na2S was 5.0 × 10(-5) and 1.0 × 10(-5) mol · L(-1) respectively, the fluorescence intensity of system was determined at 522 nm. The results showed that, at the range of 4.0 × 10(-7)~2.0 × 10(-6) mol · L(-1), the concentration decreasing of H2S and fluorescence intensity had good linear relationship, r=0.9980, the RSD of precision test was 4.59% (n=7), the detection limit was 3.5 × 10(-8) mol · L(-1), the content of H2S in the sample were 1.01 × 10(-6) and 1.15 × 10(-6) mol · L(-1), and the recovery rate was 95.8%~101.0%, the method has the advantages of simple operation, high sensitivity, good selectivity, can accurately determine of H2S in intestinal perfused solution, and provides the basis for the determination of endogenous H2S.

Validation of a reversed-phase high-performance liquid chromatographic method for the determination of free amino acids in rice using l-theanine as the internal standard.

PubMed

Liyanaarachchi, G V V; Mahanama, K R R; Somasiri, H P P S; Punyasiri, P A N

2018-02-01

The study presents the validation results of the method carried out for analysis of free amino acids (FAAs) in rice using l-theanine as the internal standard (IS) with o-phthalaldehyde (OPA) reagent using high-performance liquid chromatography-fluorescence detection. The detection and quantification limits of the method were in the range 2-16μmol/kg and 3-19μmol/kg respectively. The method had a wide working range from 25 to 600μmol/kg for each individual amino acid, and good linearity with regression coefficients greater than 0.999. Precision measured in terms of repeatability and reproducibility, expressed as percentage relative standard deviation (% RSD) was below 9% for all the amino acids analyzed. The recoveries obtained after fortification at three concentration levels were in the range 75-105%. In comparison to l-norvaline, findings revealed that l-theanine is suitable as an IS and the validated method can be used for FAA determination in rice. Copyright © 2017 Elsevier Ltd. All rights reserved.

Biological Conversion of Glycerol to Ethanol by Enterobacter aerogenes

NASA Astrophysics Data System (ADS)

Nwachukwu, Raymond E. S.

In a search to turn the economically and environmentally non-valuable "waste" streams of biodiesel production into a profitable byproduct, a mutant strain of Enterobacter aerogenes ATCC 13048 was developed by six-tube subculturing technique. This technique is based on the principle of adaptive evolution, and involved subculturing the bacterium in a tryptic soy broth without dextrose (TSB) containing specific glycerol and ethanol concentration for six consecutive times. Then, the six consecutive subculturing was repeated in a fresh TSB of higher glycerol and ethanol concentrations. A new mutant strain, E. aerogenes S012, which could withstand a combination of 200 g/l glycerol and 30 g/l ethanol concentrations, was developed. The wild and mutant strains were used for the fermentation of pure (P-) and recovered (R-) glycerol. Taguchi and full factorial methods of design of experiments were used to screen and optimize the important process factors that influence the microbial production of ethanol. A statistically sound regression model was used to establish the mathematical relationship between the process variables and ethanol production. Temperature of 38°C, agitation speed of 200 rpm, pH of 6.3-6.6, and microaerobic condition were the optimum process conditions. Different pretreatment methods to recover glycerol from the crude glycerol and the subsequent fermentation method showed that direct acidification using 85% H3PO4 was the best. The R-glycerol contained 51% pure glycerol and 21% methanol. The wild strain, E. aerogenes ATCC 13048, produced only 12 g/l and 12.8 g/l ethanol from 20 g/l P- and R-glycerol respectively, and could not utilize higher glycerol concentrations. The mutant, E. aerogenes S012, produced ethanol amount and yield of 43 g/l and 1.12 mol/mol-glycerol from P-glycerol, respectively within 96 h. It also produced ethanol amount and yield of 26.8 g/l and 1.07 mol/mol-glycerol, respectively, from R-glycerol within the same duration. In a fermentation to estimate hydrogen production using a respirometer, the hydrogen yield and volumetric rate of 1.06 mol/mol-glycerol and 217 ml/l/h, respectively were obtained from 6% P-glycerol in 72 h by E. aerogenes S012. The result was higher from R-glycerol, which produced hydrogen yield and productivity of 1.83 mol/mol-glycerol and 326 ml/l/h, respectively.

Laser Hazards Bibliography

DTIC Science & Technology

1989-10-31

Report LA-3204, Los Alamos Scientific Laboratory, University of California, Los Alamos, NM (6 October 1964). 95. Craik , K. J. W., On the effects of...surgery (letter), Am J Opt, 97(5): 658-9,8 (May 1984). 437. Scott, Jennifer , "The computation of temperature rises in the human eye induced by infrared...radiation," Phys Med Biol, 33(2): 243-257 (1988). 438. Scott, Jennifer , "A finite modelof heat transport in the human eye," Phsy Med Biol, 33(2): 227-241

Targeting Midbodies in Ovarian Cancer Stem Cells as a Therapeutic Strategy

DTIC Science & Technology

2013-10-01

functional spindle assembly. Nat. Cell Biol. 13, 1406–1414. Ori-McKenney, K.M., Jan, L.Y., and Jan, Y.-N. (2012). Golgi outposts shape dendrite morphology...1899. Yadav, S., and Linstedt, A.D. (2011). Golgi positioning. Cold Spring Harb. Perspect . Biol. 3, 3. Zhang, H., Squirrell, J.M., and White, J.G. (2008...implications for recy- cling endosome function . This new liaison has additional impli- cations for a variety of biological processes including cilia

Role of p53 in cdk Inhibitor VMY-1-103-induced Apoptosis in Prostate Cancer

DTIC Science & Technology

2013-11-01

DAOY medulloblastoma cells, which have a p53 mutation (6). In order to examine if this holds true in prostate cancer cell lines, I stably transfected...disrupts chromosome organization and delays metaphase progression in medulloblastoma cells. Cancer Biol Ther. 2011 Nov 1;12(9):818-26  Other...1-103 is a novel CDK inhibitor that disrupts chromosome organization and delays metaphase progression in medulloblastoma cells. Cancer Biol Ther

The canonical equation of adaptive dynamics for life histories: from fitness-returns to selection gradients and Pontryagin's maximum principle.

PubMed

Metz, Johan A Jacob; Staňková, Kateřina; Johansson, Jacob

2016-03-01

This paper should be read as addendum to Dieckmann et al. (J Theor Biol 241:370-389, 2006) and Parvinen et al. (J Math Biol 67: 509-533, 2013). Our goal is, using little more than high-school calculus, to (1) exhibit the form of the canonical equation of adaptive dynamics for classical life history problems, where the examples in Dieckmann et al. (J Theor Biol 241:370-389, 2006) and Parvinen et al. (J Math Biol 67: 509-533, 2013) are chosen such that they avoid a number of the problems that one gets in this most relevant of applications, (2) derive the fitness gradient occurring in the CE from simple fitness return arguments, (3) show explicitly that setting said fitness gradient equal to zero results in the classical marginal value principle from evolutionary ecology, (4) show that the latter in turn is equivalent to Pontryagin's maximum principle, a well known equivalence that however in the literature is given either ex cathedra or is proven with more advanced tools, (5) connect the classical optimisation arguments of life history theory a little better to real biology (Mendelian populations with separate sexes subject to an environmental feedback loop), (6) make a minor improvement to the form of the CE for the examples in Dieckmann et al. and Parvinen et al.

Determination of Trace Amounts of Lead Using the Flotation-spectrophotometric method

PubMed Central

Shiri, Sabah; Delpisheh, Ali; Haeri, Ali; Poornajaf, Abdolhossein; Golzadeh, Babak; Shiri, Sina

2011-01-01

The present study describes a simple and highly selective method for separation, preconcentration and spectrophotometric determination of extremely low concentrations of lead. It is based on flotation of a complex of Pb2+ ions and Alizarin yellow between aqueous and n-hexane interface at pH = 6. The proposed procedure is also applied for determination of lead in both tap water and prepared sea water samples. Beer’s Law was obeyed over the concentration range of 3.86 × 10–8 To 8.20 × 10–7 molL−1 (8–170 ngmL−1) with an apparent molar absorptivity of 1.33 × 106 molL−1 cm−1 for a 100 mL aliquot of the water sample. The detection limit (n = 10) was 8.7 × 10–9 molL−1 (1.0 ngmL−1) and the Relative standard deviation (R.S.D), (n = 10) for 7.2 × 10–7 molL−1 (150 ngmL−1) of Pb (II) was 4.36%. A notable advantage of the method is that the determination of Pb (II) is free from the interference of almost all cations and ions found in the environment and waste water samples. The determination of Pb (II) in tap and synthetic seawater samples was also carried out by the present method. The results were satisfactorily comparable so that the applicability of the proposed method was confirmed to the real samples.

Utility of gold nanoparticles in luminescence determination of trovafloxacin: comparison of chemiluminescence and fluorescence detection.

PubMed

Alarfaj, Nawal A; El-Tohamy, Maha F

2015-12-01

Two novel sensitive sequential injection chemiluminescence analysis and fluorescence methods for trovafloxacin mesylate detection have been developed. The methods were based on the enhancement effect of gold nanoparticles on luminol-ferricyanide-trovafloxacin and europium(III)-trovafloxacin complex systems. The optimum conditions for both detection methods were investigated. The chemiluminescence signal was emitted due to the enhanced effect of gold nanoparticles on the reaction of luminol-ferricyanide-trovafloxacin in an alkaline medium. The response was linear over a concentration range of 1.0 × 10(-9) to 1.0 × 10(-2) mol/L (%RSD = 1.3), (n = 9, r = 0.9991) with a detection limit of 1.7 × 10(-10) mol/L (S/N = 3). The weak fluorescence intensity signal of the oxidation complex of europium(III)-trovafloxacin was strongly enhanced by gold nanoparticles and detected at λex = 330 and λem = 540 nm. Fluorescence detection enabled the determination of trovafloxacin mesylate over a linear range of 1.0 × 10(-8) to 1.0 × 10(-3) mol/L (%RSD = 1.2), (n = 6, r = 0.9993) with a detection limit of 3.3 × 10(-9) mol/L. The proposed methods were successfully applied to the determination of the studied drug in its bulk form and in pharmaceutical preparations. The results were treated statistically and compared with those obtained from other reported methods. Copyright © 2015 John Wiley & Sons, Ltd.

Monitoring of urinary calcium and phosphorus excretion in preterm infants: comparison of 2 methods.

PubMed

Staub, Eveline; Wiedmer, Nicolas; Staub, Lukas P; Nelle, Mathias; von Vigier, Rodo O

2014-04-01

Premature babies require supplementation with calcium (Ca) and phosphorus (P) to prevent metabolic bone disease of prematurity. To guide mineral supplementation, 2 methods of monitoring urinary excretion of Ca and P are used: urinary Ca or P concentration and Ca/creatinine (Crea) or P/Crea ratios. We compare these 2 methods in regards to their agreement on the need for mineral supplementation. Retrospective chart review of 230 premature babies with birth weight <1500 g, undergoing screening of urinary spot samples from day 21 of life and fortnightly thereafter. Hypothetical cutoff values for urine Ca or P concentration (1 mmol/L) and urine Ca/Crea ratio (0.5 mol/mol) or P/Crea ratio (4 mol/mol) were applied to the sample results. The agreement on whether to supplement the respective minerals based on the results with the 2 methods was compared. Multivariate general linear models sought to identify patient characteristics to predict discordant results. A total of 24.8% of cases did not agree on the indication for Ca supplementation, and 8.8% for P. Total daily Ca intake was the only patient characteristic associated with discordant results. With the intention to supplement the respective mineral, comparison of urinary mineral concentration with mineral/Crea ratio is moderate for Ca and good for P. The results do not allow identifying superiority of either method on the decision as to which babies require Ca and/or P supplements.

Determination of Trace Amounts of Lead Using the Flotation-spectrophotometric method

PubMed Central

Shiri, Sabah; Delpisheh, Ali; Haeri, Ali; Poornajaf, Abdolhossein; Golzadeh, Babak; Shiri, Sina

2010-01-01

The present study describes a simple and highly selective method for separation, preconcentration and spectrophotometric determination of extremely low concentrations of lead. It is based on flotation of a complex of Pb2+ ions and Alizarin yellow between aqueous and n-hexane interface at pH = 6. The proposed procedure is also applied for determination of lead in both tap water and prepared sea water samples. Beer’s Law was obeyed over the concentration range of 3.86 × 10−8 To 8.20 × 10−7 molL−1 (8–170 ngmL−1) with an apparent molar absorptivity of 1.33 × 106 molL−1 cm−1 for a 100 mL aliquot of the water sample. The detection limit (n = 10) was 8.7 × 10−9 molL−1 (1.0 ngmL−1) and the Relative standard deviation (R.S.D), (n = 10) for 7.2 × 10−7 molL−1 (150 ngmL−1) of Pb (II) was 4.36%. A notable advantage of the method is that the determination of Pb (II) is free from the interference of almost all cations and ions found in the environment and waste water samples. The determination of Pb (II) in tap and synthetic seawater samples was also carried out by the present method. The results were satisfactorily comparable so that the applicability of the proposed method was confirmed to the real samples. PMID:21234287

Comparative Mg(2+)-dependent sequential covalent binding stoichiometries of 3'-O-(4-benzoyl)benzoyl adenosine 5'-diphosphate of MF1, TF1, and the alpha 3 beta 3 core complex of TF1. The binding change motif is independent of the F1 gamma delta epsilon subunits.

PubMed

Aloise, P; Kagawa, Y; Coleman, P S

1991-06-05

Three F1 preparations, the beef heart (MF1) and thermophilic bacterium (TF1) holoenzymes, and the alpha 3 beta 3 "core" complex of TF1 reconstituted from individually expressed alpha and beta subunits, were compared as to their kinetic and binding stoichiometric responses to covalent photoaffinity labeling with BzATP and BzADP (+/- Mg2+). Each enzyme displayed an enhanced pseudo-first order rate of photoinhibition and one-third of the sites covalent binding to a catalytic site for full inhibition, plus, but not minus Mg2+. Titration of near stoichiometric [MgBzADP]/[F1] ratios during photolysis disclosed two sequential covalent binding patterns for each enzyme; a high affinity binding corresponding to unistoichiometric covalent association concomitant with enzyme inhibition, followed by a low affinity multisite-saturating covalent association. Thus, in the absence of the structural asymmetry inducing gamma delta epsilon subunits of the holoenzyme, the sequential binding of nucleotide at putative catalytic sites on the alpha 3 beta 3 complex of any F1 appears sufficient to effect binding affinity changes. With MF1, final covalent saturation of BzADP-accessible sites was achieved with 2 mol of BzADP/mol of enzyme, but with TF1 or its alpha 3 beta 3 complex, saturation required 3 mol of BzADP/mol of enzyme. Such differential final labeling stoichiometries could arise because of the endogenous presence of 1 nucleotide already bound to one of the 3 potential catalytic sites on normally prepared MF1, whereas TF1, possessing no endogenous nucleotide, has 3 vacant BzADP-accessible sites. Kinetics measurements revealed that regardless of the incremental extent of inhibition of the TF1 holoenzyme by BzADP during photolysis, the two higher apparent Km values (approximately 1.5 x 10(-4) and approximately 10(-3) M, respectively) of the progressively inactivated incubation are unchanged relative to fully unmodified enzyme. As reported for BzATP (or BzADP) and MF1 (Ackerman, S.H., Grubmeyer, C., and Coleman, P.S. (1987) J. Biol. Chem. 262, 13765-13772), this supports the fact that the photocovalent inhibition of F1 is a one-hit one-kill phenomenon. Isoelectric focusing gels revealed that [3H]BzADP covalently modifies both TF1 and MF1 exclusively on the beta subunit, whether or not Mg2+ is present. A single 19-residue [3H]BzADP-labeled peptide was resolved from a tryptic digest of MF1, and this peptide corresponded with the one believed to contain at least a portion of the beta subunit catalytic site domain (i.e. beta Ala-338----beta Arg-356).

Gas-phase acidities of cysteine-polyalanine peptides I: A(3,4)CSH and HSCA(3,4).

PubMed

Ren, Jianhua; Tan, John P; Harper, Robert T

2009-10-15

The gas-phase acidities of four cysteine-polyalanine peptides, A(3,4)CSH and HSCA(3,4), were determined using the extended Cooks kinetic method with full entropy analysis. A triple-quadrupole mass spectrometer with an electrospray interface was employed for the experimental study. The ion activation was achieved via collision-induced dissociation (CID) experiments. The deprotonation enthalpies (Delta(acid)H) of the peptides were determined to be 332.2 +/- 2.0 kcal/mol (A(3)CSH), 325.9 +/- 2.0 kcal/mol (A(4)CSH), 319.3 +/- 3.0 kcal/mol (HSCA(3)), and 319.2 +/- 4.0 kcal/mol (HSCA(4)). The deprotonation entropies (Delta(acid)S) of the peptides were estimated based on the entropy term (Delta(DeltaS)) and the deprotonation entropies of the reference acids. By using the deprotonation enthalpies and entropies, the gas-phase acidities (Delta(acid)G) of the peptides were derived: 325.0 +/- 2.0 kcal/mol (A(3)CSH), 320.2 +/- 2.0 kcal/mol (A(4)CSH), 316.3 +/- 3.0 kcal/mol (HSCA(3)), and 315.4 +/- 4.0 kcal/mol (HSCA(4)). Conformations and energetic information of the peptides were calculated through simulated annealing (Tripos), geometry optimization (AM1), and single-point energy calculations (B3LYP/6-31+G(d)), respectively. The calculated theoretical deprotonation enthalpies (Delta(acid)H) of 334.2 kcal/mol (A(3)CSH), 327.7 kcal/mol (A(4)CSH), 320.6 kcal/mol (HSCA(3)), and 318.6 kcal/mol (HSCA(4)) are in good agreement with the experimentally determined values. Both the experimental and computational studies suggest that the two N-terminal cysteine peptides, HSCA(3,4), are significantly more acidic than the corresponding C-terminal ones, A(3,4)CSH. The high acidities of the former are likely due to the helical conformational effects for which the thiolate anion may be strongly stabilized by the interaction with the helix macrodipole.

Voltammetric method for the determination of sildenafil citrate (Viagra) in pure form and in pharmaceutical formulations.

PubMed

Tyszczuk, Katarzyna; Korolczuk, Mieczyslaw

2010-06-01

A highly sensitive and simple voltammetric method for the determination of sildenafil citrate (SC) was developed. The method is based on the accumulation by adsorption of SC on a lead film modified glassy carbon electrode (LF/GCE) and then the reduction of SC throughout the stripping step. During the determinations of SC at the lead film electrode three adsorptive stripping voltammetric peaks at -1.2, -1.33 and -1.45V were observed. The respective response selected for identification and quantification has been evaluated with respect to the composition and pH of the supporting electrolyte, the potential and the time of the lead film formation, the potential and the time of the SC accumulation and other variables. Experimental results indicate an excellent linear correlation between the peak current and concentration in the range of 2x10(-9)-1.5x10(-7)mol/L (for peaks 1 and 2) and 1x10(-8)-1.5x10(-7)mol/L (for the peak 3). The detection limits (LOD) for SC following 30s of accumulation time were equal to 9x10(-10)mol/L (for peaks 1 and 2) and 4.5x10(-9)mol/L (for the peak 3). The method was successfully applied to the determination of SC in the tablets (Viagra 25 and Viagra 50) and average the contents were in close agreement with those quoted by the manufacturer and with those obtained by the reported spectrophotometric method and voltammetric method using a hanging mercury drop electrode. Copyright 2009 Elsevier B.V. All rights reserved.

Expression, purification, crystallization and preliminary X-ray analysis of the Met244Ala variant of catalase–peroxidase (KatG) from the haloarchaeon Haloarcula marismortui

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ten-i, Tomomi; Kumasaka, Takashi; Higuchi, Wataru

2007-11-01

The Met244Ala variant of the H. marismortui KatG enzyme was expressed in haloarchaeal host cells and purified to homogeneity. The variant was crystallized using the hanging-drop vapour-diffusion method with ammonium sulfate and NaCl as precipitants. The reddish-brown rod-shaped crystals obtained belong to the monoclinic space group C2, with unit-cell parameters a = 315.24, b = 81.04, c = 74.77 Å, β = 99.81°. The covalent modification of the side chains of Trp95, Tyr218 and Met244 within the active site of Haloarcula marismortui catalase–peroxidase (KatG) appears to be common to all KatGs and has been demonstrated to be particularly significant formore » its bifunctionality [Smulevich et al. (2006 ▶), J. Inorg. Biochem.100, 568–585; Jakopitsch, Kolarich et al. (2003 ▶), FEBS Lett.552, 135–140; Jakopitsch, Auer et al. (2003 ▶), J. Biol. Chem.278, 20185–20191; Jakopitsch et al. (2004 ▶), J. Biol. Chem.279, 46082–46095; Regelsberger et al. (2001 ▶), Biochem. Soc. Trans.29, 99–105; Ghiladi, Knudsen et al. (2005 ▶), J. Biol. Chem.280, 22651–22663; Ghiladi, Medzihradzky et al. (2005 ▶), Biochemistry, 44, 15093–15105]. The Met244Ala variant of the H. marismortui KatG enzyme was expressed in haloarchaeal host cells and purified to homogeneity. The variant showed a complete loss of catalase activity, whereas the peroxidase activity of this mutant was highly enhanced owing to an increase in its affinity for the peroxidatic substrate. The variant was crystallized using the hanging-drop vapour-diffusion method with ammonium sulfate and NaCl as precipitants. The reddish-brown rod-shaped crystals obtained belong to the monoclinic space group C2, with unit-cell parameters a = 315.24, b = 81.04, c = 74.77 Å, β = 99.81°. A crystal frozen using lithium sulfate as the cryoprotectant diffracted to beyond 2.0 Å resolution. Preliminary X-ray analysis suggests the presence of a dimer in the asymmetric unit.« less

Molecular Analysis of Motility in Metastatic Mammary Adenocarcinoma Cells

DTIC Science & Technology

1996-09-01

elements of epidermoid carcinoma (A43 1) cells. J. Cell. Biol. 103: 87-94 Winkler, M. (1988). Translational regulation in sea urchin eggs: a complex...and Methods. Error bars show SEM . Figure 2. Rhodamine-actin polymerizes preferentially at the tips of lamellipods in EGF- stimulated cells. MTLn3...lamellipods. B) rhodamine-actin intensity at the cell center. Data for each time point is the average and SEM of 15 different cells. Images A and B

Focused ultrasound transducer spatial peak intensity estimation: a comparison of methods

NASA Astrophysics Data System (ADS)

Civale, John; Rivens, Ian; Shaw, Adam; ter Haar, Gail

2018-03-01

Characterisation of the spatial peak intensity at the focus of high intensity focused ultrasound transducers is difficult because of the risk of damage to hydrophone sensors at the high focal pressures generated. Hill et al (1994 Ultrasound Med. Biol. 20 259-69) provided a simple equation for estimating spatial-peak intensity for solid spherical bowl transducers using measured acoustic power and focal beamwidth. This paper demonstrates theoretically and experimentally that this expression is only strictly valid for spherical bowl transducers without a central (imaging) aperture. A hole in the centre of the transducer results in over-estimation of the peak intensity. Improved strategies for determining focal peak intensity from a measurement of total acoustic power are proposed. Four methods are compared: (i) a solid spherical bowl approximation (after Hill et al 1994 Ultrasound Med. Biol. 20 259-69), (ii) a numerical method derived from theory, (iii) a method using measured sidelobe to focal peak pressure ratio, and (iv) a method for measuring the focal power fraction (FPF) experimentally. Spatial-peak intensities were estimated for 8 transducers at three drive powers levels: low (approximately 1 W), moderate (~10 W) and high (20-70 W). The calculated intensities were compared with those derived from focal peak pressure measurements made using a calibrated hydrophone. The FPF measurement method was found to provide focal peak intensity estimates that agreed most closely (within 15%) with the hydrophone measurements, followed by the pressure ratio method (within 20%). The numerical method was found to consistently over-estimate focal peak intensity (+40% on average), however, for transducers with a central hole it was more accurate than using the solid bowl assumption (+70% over-estimation). In conclusion, the ability to make use of an automated beam plotting system, and a hydrophone with good spatial resolution, greatly facilitates characterisation of the FPF, and consequently gives improved confidence in estimating spatial peak intensity from measurement of acoustic power.

An optical chemical sensor for thorium (IV) determination based on thorin.

PubMed

Rastegarzadeh, S; Pourreza, N; Saeedi, I

2010-01-15

A selective method for the determination of thorium (IV) using an optical sensor is described. The sensing membrane is prepared by immobilization of thorin-methyltrioctylammonium ion pair on triacetylcellulose polymer. The sensor produced a linear response for thorium (IV) concentration in the range of 6.46 x 10(-6) to 9.91 x 10(-5)mol L(-1) with detection limit of 1.85 x 10(-6)mol L(-1). The regeneration of optode was accomplished completely at a short time (less than 20s) with 0.1 mol L(-1) of oxalate ion solution. The relative standard deviation for ten replicate measurements of 2.15 x 10(-5) and 8.62 x 10(-5)mol L(-1) of thorium was 2.71 and 1.65%, respectively. The optode membrane exhibits good selectivity for thorium (IV) over several other ionic species and are comparable to those obtained in case of spectrophotometric determination of thorium using thorin in solution. A good agreement with the ICP-MS and spiked method was achieved when the proposed optode was applied to the determination of thorium (IV) in dust and water samples.

Micelle-enhanced and terbium-sensitized spectrofluorimetric determination of gatifloxacin and its interaction mechanism

NASA Astrophysics Data System (ADS)

Guo, Changchuan; Wang, Lei; Hou, Zhun; Jiang, Wei; Sang, Lihong

2009-05-01

A terbium-sensitized spectrofluorimetric method using an anionic surfactant, sodium dodecyl benzene sulfonate (SDBS), was developed for the determination of gatifloxacin (GFLX). A coordination complex system of GFLX-Tb 3+-SDBS was studied. It was found that SDBS significantly enhanced the fluorescence intensity of the complex (about 11-fold). Optimal experimental conditions were determined as follows: excitation and emission wavelengths of 331 and 547 nm, pH 7.0, 2.0 × 10 -4 mol l -1 terbium (III), and 2.0 × 10 -4 mol l -1 SDBS. The enhanced fluorescence intensity of the system (Δ If) showed a good linear relationship with the concentration of GFLX over the range of 5.0 × 10 -10 to 5.0 × 10 -8 mol l -1 with a correlation coefficient of 0.9996. The detection limit (3 σ) was determined as 6.0 × 10 -11 mol l -1. This method has been successfully applied to the determination of GFLX in pharmaceuticals and human urine/serum samples. Compared with most of other methods reported, the rapid and simple procedure proposed in the text offers higher sensitivity, wider linear range, and better stability. The interaction mechanism of the system is also studied by the research of ultraviolet absorption spectra, surface tension, solution polarity and fluorescence polarization.

Hydration Resistance of Y2O3 Doped CaO and Its Application to Melting Titanium Alloys

NASA Astrophysics Data System (ADS)

Fanlong, Meng; Zhiwei, Cheng; Guangyao, Chen; Xionggang, Lu; Chonghe, Li

Various amount Y2O3(1-8 mol%) doped CaO powder was synthesized by the solid state reaction method, the pellete and crucible were fabricated by the cold isostatic pressing and were sintered at 1750°C for 4h. The microstructural characterization was revealed by X-ray diffraction(XRD) and scanning electron microscopy(SEM).The XRD results showed that when Y2O3 doped 2 mol%, metastable CaY2O4 phase existed in CaO grain boundary, when Y2O3 doped 3 mol%-8 mol%, in addition to the above structure, Y2O3 phase also be found in CaO grain boundary. Hydration experiment results showed when Y2O3 doped 0 mol%-4 mol%, CaO had excellent hydration resistance performance, Y2O3 doped 2 mol% had the best hydration resistance, its weight addition stored after 7 weeks (49 days) was only about 0.2 wt%. Melting experiment results showed that it was no reaction between crucible and alloy layer. Oxygen, calcium, titanium, nickle and yttrium element not diffusion between the CaO crucible and TiNi alloy, it was no oxygen content increase after melting.

Nine Different Chemical Species and Action Mechanisms of Pancreatic Lipase Ligands Screened Out from Forsythia suspensa Leaves All at One Time.

PubMed

Chen, Tinggui; Li, Yayun; Zhang, Liwei

2017-05-12

It is difficult to screen out as many active components as possible from natural plants all at one time. In this study, subfractions of Forsythia suspensa leaves were firstly prepared; then, their inhibitive abilities on pancreatic lipase were tested; finally, the highest inhibiting subfraction was screened by self-made immobilized pancreatic lipase. Results showed that nine ligands, including eight inhibitors and one promotor, were screened out all at one time. They were three flavonoids (rutin, IC 50 : 149 ± 6.0 μmol/L; hesperidin, 52.4 μmol/L; kaempferol-3- O -rutinoside, isolated from F. suspensa leaves for the first time, IC 50 notably reached 2.9 ± 0.5 μmol/L), two polyphenols (chlorogenic acid, 3150 ± 120 μmol/L; caffeic acid, 1394 ± 52 μmol/L), two lignans (phillyrin, promoter; arctigenin, 2129 ± 10.5 μmol/L), and two phenethyl alcohol (forsythiaside A, 2155 ± 8.5 μmol/L; its isomer). Their action mechanisms included competitive inhibition, competitive promotion, noncompetitive inhibition, and uncompetitive inhibition. In sum, using the appropriate methods, more active ingredients can be simply and quickly screened out all at one time from a complex natural product system. In addition, F. suspensa leaves contain numerous inhibitors of pancreatic lipase.

Calpain-Dependent Proteolysis of the Androgen Receptor

DTIC Science & Technology

2009-11-01

Cancer 1999;84:6–9. 17. Lakshmikuttyamma A, Selvakumar P, Kanthan R , Kanthan SC, Sharma RK. Overexpression of m-calpain in human colorectal...determinants of calpain cleavage. J Biol Chem 2004;279:20775–85. 10. Rios-Doria J, Day KC, Kuefer R , et al. The role of calpain in the proteolytic...prostate carcinoma cell line, 22Rv1. In vitro Cell Dev Biol 1999;35:403–9. 15. Gupta AK, Cerniglia GJ, Mick R , McKenna WG, Muschel RJ. HIV protease

Regulation of ATM-Dependent DNA Damage Responses in Breast Cancer by the RhoGEF Net1

DTIC Science & Technology

2013-04-01

Science 279: 509-514. 5. Jaffe AB. et al., (2010) RhoGTPases: Biochemistry and Biology. Annu. Rev. Cell Dev. Biol. 21:247-269. 6. Rossman KL, et al...exchange factor Net1 is regulated by nuclear sequestration. J. Biol. Chem. 277:17, 14581-14588. 17. Harper JW, et al., (2007) The DNA Damage Response: Ten...Research (AACR) Annual Meeting and 2013 Annual Cancer Research Biochemistry Retreat Regulation of ATM-dependent DNA damage signaling in human breast

Highly Efficient Catalytic Hydrogen Evolution from Ammonia Borane Using the Synergistic Effect of Crystallinity and Size of Noble-Metal-Free Nanoparticles Supported by Porous Metal-Organic Frameworks.

PubMed

Liu, Penglong; Gu, Xiaojun; Kang, Kai; Zhang, Hao; Cheng, Jia; Su, Haiquan

2017-03-29

A series of nonprecious metal nanoparticles (NPs) supported by metal-organic framework MIL-101 were synthesized using four methods and their catalytic performance on hydrogen evolution from ammonia borane (NH 3 BH 3 ) was studied. The results showed that the crystalline Co NPs with size of 4.5-8.5 and 14.5-24.5 nm had low activities featuring the total turnover frequency (TOF) values of 9.9 and 4.5 mol H2 mol cat -1 min -1 , respectively. In contrast, the amorphous Co NPs with size of 1.6-2.6 and 13.5-24.5 nm exhibited high activities featuring the total TOF values of 51.4 and 22.3 mol H2 mol cat -1 min -1 , respectively. The remarkably different activities could be ascribed to the different crystallinity and size of Co NPs in the catalysts. Moreover, the ultrasound-assisted in situ method was also successfully applied to bimetallic systems, and MIL-101-supported amorphous CuCo, FeCo and NiCo NPs had the catalytic activities with total TOF values of 51.7, 50.8, and 44.3 mol H2 mol cat -1 min -1 , respectively, which were the highest in the values of the reported non-noble metal Co-based catalysts. The present approach, namely, using the synergistic effect of crystallinity and size of metal NPs, may offer a new prospect for high-performance and low-cost nanocatalysts.

Possible role of organic peroxides in the detection of irradiated food

NASA Astrophysics Data System (ADS)

Shengchu, Qi; Jilan, Wu; Yan, Zhu

1993-07-01

In order to determine the level of organic peroxides induced by autooxidation, random sampling of pork has been performed with ˜ 300 analytical data. The organic peroxide content in unirradiated pork has been estimated as (5.4±3.0)X10 -5mol.kg -1. The dependence of yield of peroxide in pork, minced meat and braised chicken on absorbed dose has been investigated. For killing trichinae 0.5˜1 kGy is used, the quantity of peroxide in pork will be 2X10 -4mol.kg -1 (or 4X10 -4 mol.kg -1 for 1 kGy), which is 3.7˜7.4 times greater than the background. If 3 kGy is used to eliminate Samonella, the quantity of peroxides in pork will be 1.3X10 -3mol.kg -1., which approaches 24 times greater than the average value of background. When minced meat was irradiated in the presence of air, a chain reaction takes place with G (organic peroxides) value 30.2. Radiation processing dose of braised chicken for shelf-life extension is ˜ 9kGy, organic peroxide content in braised chicken fat is 32.5X10 -4mol.kg -1, which is about 14.7 times greater than average value (2.2X10 -4mol.kg -1) in unirradiated one. Applying peroxide method to qualitatively detect the irradiated food containing fat is satisfactory. Recombining with measuring ESR signal of irradiated bone will cause the method of detection more accurate and perfect.

Properties of the LiCl-KCl-Li2O system as operating medium for pyro-chemical reprocessing of spent nuclear fuel

NASA Astrophysics Data System (ADS)

Mullabaev, Albert; Tkacheva, Olga; Shishkin, Vladimir; Kovrov, Vadim; Zaikov, Yuriy; Sukhanov, Leonid; Mochalov, Yuriy

2018-03-01

Crystallization temperatures (liquidus and solidus) in the LiCl-Li2O and (LiCl-KCl)-Li2O systems with the KCl content of 10 and 20 mol.% were obtained with independent methods of thermal analysis using cooling curves, isothermal saturation, and differential scanning calorimetry. The linear sweep voltammetry was applied to control the time of the equilibrium establishment in the molten system after the Li2O addition, which depended on the composition of the base melt and the concentration of Li2O. The fragments of the binary LiCl-Li2O and quazi-binary [LiCl-KCl(10 mol.%)]-Li2O and [LiCl-KCl(20 mol.%)]-Li2O phase diagrams in the Li2O concentration range from 0 to 12 mol.% were obtained. The KCl presence in the LiCl-KCl-Li2O molten mixture in the amount of 10 and 20 mol.% reduces the liquidus temperature by 30 and 80°, respectively, but the region of the homogeneous molten state of the system is considerably narrowed, which complicates its practical application. The Li2O solubility in the molten LiCl, LiCl-KCl(10 mol.%) and LiCl-KCl(20 mol.%) decreases with increasing the KCl content and is equal to 11.5, 7.7 and 3.9 mol.% at 650°С, respectively. The LiCl-KCl melt with 10 mol.% KCl can be recommended for practical use as a medium for the SNF pyro-chemical reprocessing at temperature below 700 °C.

Successful application of the DBLOC method to the hydroxylation of camphor by cytochrome p450

PubMed Central

Jerome, Steven V.; Hughes, Thomas F.

2015-01-01

Abstract The activation barrier for the hydroxylation of camphor by cytochrome P450 was computed using a mixed quantum mechanics/molecular mechanics (QM/MM) model of the full protein‐ligand system and a fully QM calculation using a cluster model of the active site at the B3LYP/LACVP*/LACV3P** level of theory, which consisted of B3LYP/LACV3P** single point energies computed at B3LYP/LACVP* optimized geometries. From the QM/MM calculation, a barrier height of 17.5 kcal/mol was obtained, while the experimental value was known to be less than or equal to 10 kcal/mol. This process was repeated using the D3 correction for hybrid DFT in order to investigate whether the inadequate treatment of dispersion interaction was responsible for the overestimation of the barrier. While the D3 correction does reduce the computed barrier to 13.3 kcal/mol, it was still in disagreement with experiment. After application of a series of transition metal optimized localized orbital corrections (DBLOC) and without any refitting of parameters, the barrier was further reduced to 10.0 kcal/mol, which was consistent with the experimental results. The DBLOC method to C—H bond activation in methane monooxygenase (MMO) was also applied, as a second, independent test. The barrier in MMO was known, by experiment, to be 15.4 kcal/mol.1 After application of the DBLOC corrections to the MMO barrier compute by B3LYP, in a previous study, and accounting for dispersion with Grimme's D3 method, the unsigned deviation from experiment was improved from 3.2 to 2.3 kcal/mol. These results suggested that the combination of dispersion plus localized orbital corrections could yield significant quantitative improvements in modeling the catalytic chemistry of transition‐metal containing enzymes, within the limitations of the statistical errors of the model, which appear to be on the order of approximately 2 kcal/mole. PMID:26441133

Homozygous Expression of Mutant ELOVL4 Leads to Seizures and Death in a Novel Animal Model of Very Long-Chain Fatty Acid Deficiency.

PubMed

Hopiavuori, Blake R; Deák, Ferenc; Wilkerson, Joseph L; Brush, Richard S; Rocha-Hopiavuori, Nicole A; Hopiavuori, Austin R; Ozan, Kathryn G; Sullivan, Michael T; Wren, Jonathan D; Georgescu, Constantin; Szweda, Luke; Awasthi, Vibhudutta; Towner, Rheal; Sherry, David M; Anderson, Robert E; Agbaga, Martin-Paul

2018-02-01

Lipids are essential components of the nervous system. However, the functions of very long-chain fatty acids (VLC-FA; ≥ 28 carbons) in the brain are unknown. The enzyme ELOngation of Very Long-chain fatty acids-4 (ELOVL4) catalyzes the rate-limiting step in the biosynthesis of VLC-FA (Agbaga et al., Proc Natl Acad Sci USA 105(35): 12843-12848, 2008; Logan et al., J Lipid Res 55(4): 698-708, 2014), which we identified in the brain as saturated fatty acids (VLC-SFA). Homozygous mutations in ELOVL4 cause severe neuropathology in humans (Ozaki et al., JAMA Neurol 72(7): 797-805, 2015; Mir et al., BMC Med Genet 15: 25, 2014; Cadieux-Dion et al., JAMA Neurol 71(4): 470-475, 2014; Bourassa et al., JAMA Neurol 72(8): 942-943, 2015; Aldahmesh et al., Am J Hum Genet 89(6): 745-750, 2011) and are post-natal lethal in mice (Cameron et al., Int J Biol Sci 3(2): 111-119, 2007; Li et al., Int J Biol Sci 3(2): 120-128, 2007; McMahon et al., Molecular Vision 13: 258-272, 2007; Vasireddy et al., Hum Mol Genet 16(5): 471-482, 2007) from dehydration due to loss of VLC-SFA that comprise the skin permeability barrier. Double transgenic mice with homozygous knock-in of the Stargardt-like macular dystrophy (STDG3; 797-801_AACTT) mutation of Elovl4 with skin-specific rescue of wild-type Elovl4 expression (S + Elovl4 mut/mut mice) develop seizures by P19 and die by P21. Electrophysiological analyses of hippocampal slices showed aberrant epileptogenic activity in S + Elovl4 mut/mut mice. FM1-43 dye release studies showed that synapses made by cultured hippocampal neurons from S + Elovl4 mut/mut mice exhibited accelerated synaptic release kinetics. Supplementation of VLC-SFA to cultured hippocampal neurons from mutant mice rescued defective synaptic release to wild-type rates. Together, these studies establish a critical, novel role for ELOVL4 and its VLC-SFA products in regulating synaptic release kinetics and epileptogenesis. Future studies aimed at understanding the molecular mechanisms by which VLC-SFA regulate synaptic function may provide new targets for improved seizure therapies.

Dopant occupancy and UV-VIS-NIR spectroscopy of Mg (0, 4, 5 and 6 mol.%):Dy:LiNbO3 crystal

NASA Astrophysics Data System (ADS)

Dai, Li; Liu, Chunrui; Han, Xianbo; Wang, Luping; Tan, Chao; Yan, Zhehua; Xu, Yuheng

2017-09-01

A series of Dy:LiNbO3 crystals with x mol.% Mg2+ ions (x =0, 4, 5 and 6 mol.%) were grown by the Czochralski method. The effective segregation coefficient of Mg2+ and Dy3+ ions was studied by the inductively coupled plasma-atomic emission spectrometry (ICP-AES). UV-VIS-NIR absorption spectra and Judd-Ofelt theory were used to investigate their spectroscopic properties. J-O intensity parameters (Ω2 = 7.53 × 10-20cm2, Ω4 = 6.98 × 10-20cm2, and Ω6 = 3.09 × 10-20cm2) and larger spectroscopic quality factor (X = 2.26) for Mg:(6 mol.%)Dy:LiNbO3 crystals were obtained.

Decrease of serum carnitine levels in patients with or without gastrointestinal cancer cachexia

PubMed Central

Malaguarnera, Mariano; Risino, Corrado; Gargante, Maria Pia; Oreste, Giovanni; Barone, Gloria; Tomasello, Anna Veronica; Costanzo, Mario; Cannizzaro, Matteo Angelo

2006-01-01

AIM: To evaluate the levels of serum carnitine in patients with cancer in digestive organs and to compare them with other cancers in order to provide new insights into the mechanisms of cachexia. METHODS: Fifty-five cachectic patients with or without gastrointestinal cancer were enrolled in the present study. They underwent routine laboratory investigations, including examination of the levels of various forms of carnitine present in serum (i.e., long-chain acylcarnitine, short-chain acylcarnitine, free carnitine, and total carnitine). These values were compared with those found in 60 cancer patients in good nutritional status as well as with those of 30 healthy control subjects. RESULTS: When the cachectic patients with gastro-intestinal cancer were compared with the cachectic patients without gastrointestinal cancer, the difference was -6.8 μmol/L in free carnitine (P < 0.005), 0.04 μmol/L in long chain acylcarnitine (P < 0.05), 8.7 μmol/L in total carnitine (P < 0.001). In the cachectic patients with or without gastrointestinal cancer, the difference was 12.2 μmol/L in free carnitine (P < 0.001), 4.60 μmol/L in short chain acylcarnitine (P < 0.001), and 0.60 μmol /L in long-chain acylcarnitine (P < 0.005) and 17.4 μmol/L in total carnitine (P < 0.001). In the cachectic patients with gastrointestinal cancer and the healthy control subjects, the difference was 15.5 μmol/L in free carnitine (P < 0.001), 5.2 μmol /L in short-chain acylcarnitine (P < 0.001), 1.0 μmol/L in long chain acylcarnitine (P < 0.001), and 21.8 μmol/L in total carnitine (P < 0.001). CONCLUSION: Low serum levels of carnitine in terminal neoplastic patients are decreased greatly due to the decreased dietary intake and impaired endogenous synthesis of this substance. These low serum carnitine levels also contribute to the progression of cachexia in cancer patients. PMID:16874868

EDITORIAL Complexity of advanced radiation therapy necessitates multidisciplinary inquiry into dose reconstruction and risk assessment Complexity of advanced radiation therapy necessitates multidisciplinary inquiry into dose reconstruction and risk assessment

NASA Astrophysics Data System (ADS)

Newhauser, Wayne

2010-07-01

The availability of low-cost, high-performance computing is rapidly transforming the landscape of cancer research. Computational techniques are playing an increasingly important role and have become the third major method of scientific inquiry, supplementing traditional methods of observation and theory. This evolution began in the 1940s when high-performance computing techniques were developed for military applications, including radiation transport calculations. These same basic methods are still widely utilized in a broad spectrum of computational problems in medicine, including radiation cancer therapy (Rogers 2006, Spezi 2010) and radiologic diagnostic imaging (Doi 2006, Kalender 2006). Supercomputing is also now being used to study the genetics and genomics of cancer (Geurts van Kessel 2010), with application to gene sequencing (Mardis 2008), genome-wide association studies (Pearson and Manolio 2008), biomolecular dynamics (Sanbonmatsu and Tung 2007) and systems biology (Wolkenhauer et al 2010). The extensive and growing body of literature is evidence of a remarkable expansion of activity and enormous boost to cancer research from the application of high-performance computing. Early successes were facilitated by inexpensive computing resources and advances in modeling algorithms. Many contemporary models require extensive approximations and phenomenological approaches. In fact, many critical problems remain computationally intractable; the underlying physical and biological processes are simply too complex to model with contemporary theory and computing capacity. In the future, a vast stream of new insights will flow from studies that use increasingly exact models and first-principles approaches. Hence, in the war on cancer the present status of computational research could be summarized as the beginning of the beginning. For these reasons, there is a vital need for scientists and clinicians to periodically discuss progress and future plans regarding computational cancer research, particularly research involving supercomputing. In April 2010, a symposium entitled '4th Joint Symposium on Computational Medical Physics: The Nexus of Research on Cancer, Radiation, and Supercomputing: Dawn of a Golden Age?' was convened at Rice University in Houston, Texas. One objective of this symposium was to provide researchers and clinicians with an overview of recent progress in advanced radiation therapy. Another was to review basic concepts and methods from a wide variety of disciplines related to cancer radiation therapy, including supercomputing, physics, informatics, imaging, and epidemiology. The symposium featured current issues and controversies and, in particular, a review of recent advances in research on proton and photon therapies. Sessions included Current Issues in Proton Therapy for Pediatric Cancers; Current Issues in Advanced Radiotherapy for Prostate Cancer; Charged Particles in Space and Military Applications; Recent Advances in Radiation Epidemiology; Advanced Computing Techniques: Perspectives from Cancer Researchers and Computer Scientists; Radiobiologic, Dosimetric, and Outcomes Modeling; Imaging and Informatics, and a Young Investigators' Symposium. The complete program is available at www.regonline.com/joint_symposium. The symposium was attended by more than 100 delegates who delivered 47 oral presentations. The delegates included leading scientists and clinicians from the fields of epidemiology, particle physics, medical physics, mathematics, oncology, and cancer prevention. This issue of Physics in Medicine and Biology contains 13 original research articles based on selected presentations from the symposium. Each article underwent the journal's usual rigorous peer review process; we are grateful to the many individuals who contributed to this issue, including the publishing editor, board members, referees, and of course the authors, all of whom generously shared their time and expertise. The majority of articles from the symposium are interrelated and focus on dose and risk assessments related to radiation exposures from advanced radiation therapies. These research topics have become increasingly complex and require the combined expertise of researchers with highly specialized and diverse investigational skills. Innovative multidisciplinary teams will be needed to achieve breakthroughs and, ultimately, to translate the research into clinical practice (Disis and Slattery 2010). The symposium's scientific goals included fostering and promoting such multidisciplinary teams, which will work to solve these complex problems and thereby improve cancer outcomes. To help clarify how the 13 articles each contribute to the goal of improving cancer outcomes, a brief digression is necessary. The proportion of patients surviving their cancers for five years or more is large and increasing (Jemal et al 2009). Unfortunately, in survivors who received radiation therapy, the prevalence of radiogenic late effects is likewise large and increasing (cf Altekruse et al 2010, Meadows et al 2009, Hudson et al 2009, Friedman et al 2010), with the potential to become a public health issue of considerable scale (Travis 2006). A multitude of late effects are associated with radiation exposure, including the development of second cancers, cardiac toxicity, cognitive deficits, and musculoskeletal growth abnormalities in children. In modern radiation therapy, much effort is devoted to developing personalized treatments that control the tumor while minimizing acute toxicities to surrounding healthy tissues; comparatively less attention has been paid to minimizing late effects (Durante and Loeffler 2010). In recent years, however, there has been an encouraging increase in research activities seeking to quantify radiation exposures (Stovall et al 2006) and the associated risks of late effects from modern external-beam therapies (Xu et al 2008). In this issue, Zhang et al (2010) report on Monte Carlo and analytical models to predict the stray radiation exposure in a patient receiving proton radiotherapy. In this study, the authors focused on stray neutron radiation that emanated from the treatment unit. Despite the complexity of high-energy neutron dosimetry, the authors succeeded in developing a relatively simple analytical model to predict these exposures. This finding is important because, with further development, it could provide a method to predict stray radiation exposures as an enhanced form of routine treatment planning. Fontenot et al (2010) report on methods to evaluate uncertainties in comparative risk assessments; knowledge of uncertainties is vital to determine the limits of applicability in these assessments, which may in turn affect clinical and policy decisions. Howell et al (2010a) report on the accuracy of a widely used radiation treatment planning system. In particular, they investigated the system's dosimetric accuracy outside the treatment beam, e.g. due to scatter and leakage radiation from external-beam photon therapy. This study provides important illustrative evidence of the need to carefully validate dose algorithms in out-of-field regions. In a related study, Howell et al (2010b) developed a methodology to estimate doses to partially in-field and out-of-field organs. Scarboro et al (2010) report on the impact of organ size and position on out-of-field dose estimates. Taddei et al (2010a) report on the targeting accuracy of a novel device that can be used to treat age-related macular degeneration, the leading cause of blindness in the developed world. Taddei et al (2010b) report on the risks of radiogenic second cancers following proton and photon radiation therapies for liver cancer. Taddei et al (2010c) also compare the risks of radiogenic second cancers from secondary neutrons for a boy and a girl after receiving craniospinal irradiation with passively scattered proton beams. Scanned-beam proton therapy is presently considered the technologically most complex beam delivery approach and is used in only a few centers worldwide. Coutrakon et al (2010) reported on an investigation of dosimetric errors associated with the delivery of scanned proton beams. Titt et al (2010) report on a novel method to adjust the size of scanned proton beams. This study is important because our inability to produce very small beam spot sizes has been an obstacle to realizing the full clinical potential of this technique. Yepes et al (2010) report on the speedup and accuracy of a fast proton dose algorithm that uses an array of graphics processing units; this technique represents a nascent low-cost alternative to the traditional approach of high-performance computing using central processing units. Radiation exposures from kilovoltage computed tomography (CT) procedures have increased dramatically, with the fraction of collective effective dose from CT exposures rising from 3% in the early 1980s to 49% in 2006 (NCRP 2009). Proton CT is an emerging technology that may enable reductions in both proton range uncertainties and the imaging dose to the patient relative to comparable kilovoltage CT techniques. Erdelyi (2010) reports on uncertainties in electron densities estimated using proton CT. Finally, Cheung et al (2010) report on the suitability of advanced composite fiducial markers for localization of the prostate in proton therapy. Their analysis is particularly important because approximately 60% of the proton treatment capacity in the United States is used for patients with prostate cancer. The symposium was the fourth of a series entitled 'Symposia on Computational Cancer Research'. The symposia have alternately been hosted by The University of Texas M D Anderson Cancer Center, Rice University, and Northern Illinois University. The fifth joint symposium will be held in Houston, on 5-7 April 2011, and will focus on survivorship issues after childhood cancers (www.regonline.com/5thjointsymposium). On behalf of the symposium organizing committee, I hope to see you there. Wayne Newhauser, The University of Texas M D Anderson Cancer Center, USA Chairman of 4th Joint Symposium Organizing Committee and Guest Editor References Altekruse S F et al (ed) SEER Cancer Statistics Review, 1975--2007 (Bethesda, MD: National Cancer Institute) (http://seer.cancer.gov/csr/1975_2007/) based on November 2009 SEER data submission, posted to the SEER website, 2010 Cheung J, Kudchadker R J, Zhu X R, Lee A K and Newhauser W D 2010 Dose perturbations and image artifacts caused by carbon-coated ceramic and stainless steel fiducials used in proton therapy for prostate cancer Phys. Med. Biol. 55 7135-47 Coutrakon G, Wang N, Miller D W and Yang Y 2010 Dose error analysis for a scanned proton beam delivery system Phys. Med. Biol. 55 7081-96 Disis M L and Slattery J T 2010 The road we must take: multidisciplinary team science Sci. Transl. Med. 2 22cm9 Doi K 2006 Diagnostic imaging over the last 50 years: research and development in medical imaging science and technology Phys. Med. Biol. 51 R5-27 Durante M and Loeffler J S 2010 Charged particles in radiation oncology Nat. Rev. Clin. Oncol. 7 37-43 Erdelyi B 2010 Electron density uncertainties in proton computed tomography Phys. Med. Biol. 55 7121-34 Fontenot J D, Bloch C, Followill D, Titt U, Zhang M and Newhauser W D 2010 Estimate of the uncertainties in the relative risk of secondary malignant neoplasms following proton therapy and intensity-modulated photon therapy Phys. Med. Biol. 55 6987-98 Friedman D L, Whitton J, Leisenring W, Mertens A C, Hammond S, Stovall M, Donaldson S S, Meadows A T, Robison L L and Neglia J P 2010 Subsequent neoplasms in 5-year survivors of childhood cancer: the Childhood Cancer Survivor Study J. Natl Cancer Inst. 102 1083-95 Geurts van Kessel A 2010 The 'omics' of cancer Cancer Genet. Cytogenet. 203 37-42 Howell R M, Scarboro S B, Kry S F and Yaldo D Z 2010a Accuracy of out-of-field dose calculations by a commercial treatment planning system Phys. Med. Biol. 55 6999-7008 Howell R M, Scarboro S B, Taddei P J, Krishnan S, Kry S F and Newhauser W D 2010b Methodology for determining doses to in-field, out-of-field and partially in-field organs for late effects studies in proton radiotherapy Phys. Med. Biol. 55 7009-23 Hudson M M, Mulrooney D A, Bowers D C, Sklar C A, Green D M, Donaldson S S, Oeffinger K C, Neglia J P, Meadows A T and Robison L L 2009 High-risk populations identified in Childhood Cancer Survivor Study investigations: implications for risk-based surveillance J. Clin. Oncol. 27 2405-14 Jemal A, Siegel R, Ward E, Hao Y, Xu J and Thun M J 2009 Cancer statistics, 2009 CA Cancer J. Clin. 59 225-49 Kalender W A 2006 X-ray computed tomography Phys. Med. Biol. 51 R29-43 Mardis E R 2008 Next-generation DNA sequencing methods Annu. Rev. Genomics Hum. Genet. 9 387-402 Meadows A T, Friedman D L, Neglia J P, Mertens A C, Donaldson S S, Stovall M, Hammond S, Yasui Y and Inskip P D 2009 Second neoplasms in survivors of childhood cancer: findings from the Childhood Cancer Survivor Study cohort J. Clin. Oncol. 27 2356-62 NCRP (National Council on Radiation Protection and Measurements) 2009 Ionizing radiation exposure of the population of the United States {\\it NCRP Report No. 160} (Bethesda, MD: NCRP) Pearson T A and Manolio T A 2008 How to interpret a genome-wide association study JAMA 299 1335-44 Rogers D W 2006 Fifty years of Monte Carlo simulations for medical physics Phys. Med. Biol. 51 R287-301 Sanbonmatsu K Y and Tung C S 2007 High performance computing in biology: multimillion atom simulations of nanoscale systems J. Struct. Biol. 157 470-80 Scarboro S B, Stovall M, White A, Smith S A, Yaldo D, Kry S F and Howell R M 2010 Effect of organ size and position on out-of-field dose distributions during radiation therapy Phys. Med. Biol. 55 7025-36 Spezi E (ed) 2010 Special section: Selected papers from the Second European Workshop on Monte Carlo Treatment Planning (MCTP2009) Phys. Med. Biol. 55 (16) 4431-614 Stovall M, Weathers R, Kasper C, Smith S A, Travis L, Ron E and Kleinerman R 2006 Dose reconstruction for therapeutic and diagnostic radiation exposures: use in epidemiological studies Radiat. Res. 166 141-57 Taddei P J, Chell E, Hansen S, Gertner M and Newhauser W D 2010a Assessment of targeting accuracy of a low-energy stereotactic radiosurgery treatment for age-related macular degeneration Phys. Med. Biol. 55 7037-54 Taddei P J, Howell R M, Krishnan S, Scarboro S B, Mirkovic D and Newhauser W D 2010b Risk of second malignant neoplasm following proton versus intensity-modulated photon radiotherapies for hepatocellular carcinoma Phys. Med. Biol. 55 7055-65 Taddei P J, Mahajan A, Mirkovic D, Zhang R, Giebeler A, Kornguth D, Harvey M, Woo S and Newhauser W D 2010c Predicted risks of second malignant neoplasm incidence and mortality due to secondary neutrons in a girl and boy receiving proton craniospinal irradiation Phys. Med. Biol. 55 7067-80 Titt U, Mirkovic D, Sawakuchi G O, Perles L A, Newhauser W D, Taddei P J and Mohan R 2010 Adjustment of the lateral and longitudinal size of scanned proton beam spots using a pre-absorber to optimize penumbrae and delivery efficiency Phys. Med. Biol. 55 7097-106 Travis L B 2006 The epidemiology of second primary cancers Cancer Epidemiol. Biomarkers Prev. 15 2020-6 Wolkenhauer O et al 2010 Systems biologists seek fuller integration of systems biology approaches in new cancer research programs Cancer Res. 70 12-3 Xu X G, Bednarz B and Paganetti H 2008 A review of dosimetry studies on external-beam radiation treatment with respect to second cancer induction Phys. Med. Biol. 53 R193-241 Yepes P, Mirkovic D and Taddei P J 2010 A GPU implementation of a track-repeating algorithm for proton radiotherapy dose calculations Phys. Med. Biol. 55 7107-20 Zhang R, P\\'{e}rez-And\\'{u}jar A, Fontenot J D, Taddei P J and Newhauser W D 2010 An analytic model of neutron ambient dose equivalent and equivalent dose for proton radiotherapy Phys. Med. Biol. 55 6975-85

Interior region-of-interest reconstruction using a small, nearly piecewise constant subregion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taguchi, Katsuyuki; Xu Jingyan; Srivastava, Somesh

2011-03-15

Purpose: To develop a method to reconstruct an interior region-of-interest (ROI) image with sufficient accuracy that uses differentiated backprojection (DBP) projection onto convex sets (POCS) [H. Kudo et al., ''Tiny a priori knowledge solves the interior problem in computed tomography'', Phys. Med. Biol. 53, 2207-2231 (2008)] and a tiny knowledge that there exists a nearly piecewise constant subregion. Methods: The proposed method first employs filtered backprojection to reconstruct an image on which a tiny region P with a small variation in the pixel values is identified inside the ROI. Total variation minimization [H. Yu and G. Wang, ''Compressed sensing basedmore » interior tomography'', Phys. Med. Biol. 54, 2791-2805 (2009); W. Han et al., ''A general total variation minimization theorem for compressed sensing based interior tomography'', Int. J. Biomed. Imaging 2009, Article 125871 (2009)] is then employed to obtain pixel values in the subregion P, which serve as a priori knowledge in the next step. Finally, DBP-POCS is performed to reconstruct f(x,y) inside the ROI. Clinical data and the reconstructed image obtained by an x-ray computed tomography system (SOMATOM Definition; Siemens Healthcare) were used to validate the proposed method. The detector covers an object with a diameter of {approx}500 mm. The projection data were truncated either moderately to limit the detector coverage to diameter 350 mm of the object or severely to cover diameter 199 mm. Images were reconstructed using the proposed method. Results: The proposed method provided ROI images with correct pixel values in all areas except near the edge of the ROI. The coefficient of variation, i.e., the root mean square error divided by the mean pixel values, was less than 2.0% or 4.5% with the moderate or severe truncation cases, respectively, except near the boundary of the ROI. Conclusions: The proposed method allows for reconstructing interior ROI images with sufficient accuracy with a tiny knowledge that there exists a nearly piecewise constant subregion.« less

Metabolic stability of new anticonvulsants in body fluids and organ homogenates.

PubMed

Marszałek, Dorota; Goldnik, Anna; Pluciński, Franciszek; Mazurek, Aleksander P; Jakubiak, Anna; Lis, Ewa; Tazbir, Piotr; Koziorowska, Agnieszka

2012-01-01

The stability as a function of time of compounds with established anticonvulsant activity: picolinic acid benzylamide (Pic-BZA), picolinic acid 2-fluorobenzylamide (Pic-2-F-BZA), picolinic acid 3-fluorobenzylamide (Pic-3-F-BZA), picolinic acid 4-fluorobenzylamide (Pic-4-F-BZA) and picolinic acid 2-methylbenzylamide (Pic-2-Me-BZA) in body fluids and homogenates of body organs were determined after incubation. It was found that they decompose relatively rapidly in liver and kidney and are stable against enzymes present in body fluids and some organs. These results are consistent with the bond strength expressed as total energy of amide bonds (calculated by quantum chemical methods) in the studied anticonvulsants. The calculated values of the amide bond energy are: 199.4 kcal/mol, 200.2 kcal/mol, 207.5 kcal/mol, 208.4 kcal/mol and 198.2 kcal/mol, respectively. The strength of the amide bonds in the studied anticonvulsants correctly reflects their stability in liver or kidney.

Estimation of Cell Proliferation Dynamics Using CFSE Data

PubMed Central

Banks, H.T.; Sutton, Karyn L.; Thompson, W. Clayton; Bocharov, Gennady; Roose, Dirk; Schenkel, Tim; Meyerhans, Andreas

2010-01-01

Advances in fluorescent labeling of cells as measured by flow cytometry have allowed for quantitative studies of proliferating populations of cells. The investigations (Luzyanina et al. in J. Math. Biol. 54:57–89, 2007; J. Math. Biol., 2009; Theor. Biol. Med. Model. 4:1–26, 2007) contain a mathematical model with fluorescence intensity as a structure variable to describe the evolution in time of proliferating cells labeled by carboxyfluorescein succinimidyl ester (CFSE). Here, this model and several extensions/modifications are discussed. Suggestions for improvements are presented and analyzed with respect to statistical significance for better agreement between model solutions and experimental data. These investigations suggest that the new decay/label loss and time dependent effective proliferation and death rates do indeed provide improved fits of the model to data. Statistical models for the observed variability/noise in the data are discussed with implications for uncertainty quantification. The resulting new cell dynamics model should prove useful in proliferation assay tracking and modeling, with numerous applications in the biomedical sciences. PMID:20195910

Determination of ampicillin sodium using the cupric oxide nanoparticles-luminol-H2 O2 chemiluminescence reaction.

PubMed

Iranifam, Mortaza; Kharameh, Merhnaz Khabbaz

2014-09-01

A simple and sensitive chemiluminescence (CL) method has been developed for the determination of ampicillin sodium at submicromolar levels. The method is based on the inhibitory effect of ampicillin sodium on the cupric oxide nanoparticles (CuO NPs)-luminol-H2 O2 CL reaction. Experimental parameters affecting CL inhibition including concentrations of CuO NPs, luminol, H2 O2 and NaOH were optimized. Under optimum conditions, the calibration plot was linear in the analyte concentration range 4.0 × 10(-7) -4.0 × 10(-6) mol/L. The limit of detection was 2.6 × 10(-7) mol/L and the relative standard deviation (RSD) for six replicate determinations of 1 × 10(-6) mol/L ampicillin sodium was 4.71%. Also, X-ray diffraction (XRD) and transmission electron microscopy (TEM) analysis were employed to characterize the CuO NPs. The utility of the proposed method was demonstrated by determining ampicillin sodium in pharmaceutical preparation. Copyright © 2013 John Wiley & Sons, Ltd.

Flow injection chemiluminescence determination of naphazoline hydrochloride in pharmaceuticals.

PubMed

Iranifam, Mortaza; Sorouraddin, Mohammad H

2014-02-01

A simple and sensitive flow injection chemiluminescence (FI-CL) method was developed for the determination of naphazoline hydrochloride (NPZ). The method is based on the enhancing effect of NPZ on the weak CL signal from the reaction of KIO4 with H2 O2 . Experimental parameters that affected the CL signal, including the pH of the KIO4 solution, concentrations of KIO4 , H2 O2 and disodium-EDTA and flow rate were optimized. Under the optimum conditions, the increment of CL intensity was linearly proportional to the concentration of NPZ in the range 5.0 × 10(-6) to 70 × 10(-6) mol/L. The detection limit was 1.0 × 10(-6) mol/L and the relative standard deviation for 50 × 10(-6) mol/L NPZ solution was 2.8% (n = 11). In addition, a high throughput of 120 samples/h was achieved. The utility of this method was demonstrated by determining NPZ in pharmaceuticals. Copyright © 2013 John Wiley & Sons, Ltd.

Flow-injection chemiluminescence determination of diazepam by oxidation with N-bromosuccinimide.

PubMed

Han, Suqin; Jia, Shize; Guo, Liang

2013-01-01

A rapid and sensitive flow-injection chemiluminescence (FI-CL) method is described for the determination of diazepam based on its reaction with N-bromosuccinimide (NBS) in alkaline medium in the presence of dichlorofluorescein (DCF) as an effective energy-transfer agent. Under optimum conditions, the proposed method allowed the measurement of diazepam over the range of 2.0 × 10(-6) to 2.0 × 10(-4) mol/L with a detection limit of 5.0 × 10(-7) mol/L. The relative standard deviation for 11 parallel measurements of 2.0 × 10(-5) mol/L diazepam was 2.1%. The method was applied satisfactorily for the determination of diazepam in pharmaceutical preparations, and the results agree well with those obtained by spectrophotometry. The use of the proposed system for the determination of diazepam in urine and plasma samples was also tested. The possible mechanism of the chemiluminescence reaction is discussed briefly. Copyright © 2012 John Wiley & Sons, Ltd.

Determination of traces of 237Np in environmental samples by ICP-MS after separation using TOA extraction chromatography.

PubMed

Ji, Y Q; Li, J Y; Luo, S G; Wu, T; Liu, J L

2001-09-01

A simple, rapid, cost-efficient, and robust method for separation of 237Np with an extraction chromatographic column (TOA: tri-n-octylamine on Teflon powder) is outlined in detail and further improved for direct ICP-MS analysis. The column efficiently retained 237Np in 2 mol L(-1) HNO3 medium and all of the 237Np was easily eluted with 0.02 mol L(-1) oxalic acid in 0.16 mol L(-1) HNO3 at 95 degrees C. The separated solutions were free from most matrix elements and were aspirated into the ICP-MS directly. The decontamination factor for 238U is more than 10(4). The instrumental detection limit for 237Np was 0.46 pg mL(-1), which corresponds to 1.2 x 10(-5) Bq mL(-1). The method is more rapid than traditional radiometric techniques. It is also considered to be more suitable for environmental monitoring than existing methods based on TOA.

The method of loci as a mnemonic device to facilitate learning in endocrinology leads to improvement in student performance as measured by assessments

PubMed Central

Rizvi, Farwa; Syed, Anjum; Shahid, Aqueel; Manzoor, Hana

2014-01-01

Cognitive psychology has demonstrated that the way knowledge is structured in memory determines the ability to retain, recall, and use it to solve problems. The method of loci (MOL) is a mnemonic device that relies on spatial relationships between “loci” (e.g., locations on a familiar route or rooms in a familiar building) to arrange and recollect memorial content. In the present study, we hypothesized that the use of MOL leads to better understanding of the topic among students, which can be observed through better student performance on assessments. Students were divided into two groups: group 1 was taught insulin and diabetes mellitus through didactic lectures and a self-directed learning session, whereas group 2 was taught insulin and diabetes mellitus through didactic lectures and MOL. Memory palaces for insulin and diabetes mellitus were generated by students under supervision of the teacher and taught by students as well. A questionnaire survey and open-ended questions were given to the participants. Group 2, which underwent didactic lectures followed by a MOL interactive session, showed significantly improved performance on the assessments compared with group 1, which had been taught through didactic lectures and a self-directed learning session. Descriptive analysis showed that all students found MOL to be a helpful technique. PMID:25039085

Huperzine A derivative M3 protects PC12 cells against sodium nitroprusside-induced apoptosis

PubMed Central

Ning, Na; Hu, Jin-feng; Yuan, Yu-he; Zhang, Xin-yuan; Dai, Jun-gui; Chen, Nai-hong

2012-01-01

Aim: To investigate the effects of M3, a derivative of huperzine A, on the apoptosis induced by sodium nitroprusside (SNP) in PC12 cells. Methods: Cell viability was detected using MTT method. Apoptosis was examined with annexin V/prodium iodide (PI) stain. The levels of reactive oxygen species (ROS) were measured using fluorophotometric quantitation. The amount of malonaldehyde (MDA) was determined with MDA detection kits. The expression of caspase-3 and Hsp70 were analyzed using Western blotting. Results: Exposure of PC12 cells to SNP (200 μmol/L) for 24 h decreased the cell viability to 69.0% of that in the control group. Pretreatment with M3 (10 μmol/L) or huperzine A (10 μmol/L) significantly protected the cells against SNP-induced injury and apoptosis; the ratio of apoptotic bodies in PC12 cells was decreased from 27.3% to 15.0%. Pretreatment with M3 (10 μmol/L) significantly decreased ROS and MDA levels, and increased the expression of Hsp70 in the cells. Quercetin (10 μmol/L) blocked the protective effect of M3, while did not influence on that of huperzine A. Conclusion: M3 protects PC12 cells against SNP-induced apoptosis, possible due to ROS scavenging and Hsp70 induction. PMID:22120967

Interactions of vitamin K3 with herring-sperm DNA using spectroscopy and electrochemistry.

PubMed

Huang, Jianhang; Wang, Xingming; Fei, Dan; Ding, Lisheng

2010-10-01

By means of ultraviolet-visible (UV-Vis) and fluorescence spectra, the binding ratio between vitamin K(3) and herring-sperm DNA in a physiological pH environment (pH = 7.40) was determined as n(K3):n(DNA) = 2:1, and the binding constants of vitamin K(3) binding to DNA at different temperatures were determined as K(θ)(298K) = 1.28 × 10(5) L·mol(-1) and K(θ)(310K) = 7.19 × 10(4) L·mol(-1), which were confirmed using the double reciprocal method are Δ(r)H(m)(θ) = -3.57 × 10(4) J·mol(-1), Δ(r)G(m)(θ) = -2.92 × 10(4) J·mol(-1), and Δ(r)S(m)(θ) = 217.67 J·mol(-1)K(-1). The driving power of this process was enthalpy. An intercalation binding of the vitamin K(3) with DNA was supported by a competitive experiment using acridine orange (AO) as a spectral probe. By combination analysis of the Scatchard method and cyclic voltammetry, we suggested that the interaction mode between vitamin K(3) and herring-sperm DNA would be a mixed mode. The quinonoid, duality fused-ring of vitamin K(3) can intercalate into the base pairs of DNA, and there is an electrostatic binding along with intercalation binding.

New highly sensitive and selective fluorescent terbium complex for the detection of aluminium ions

NASA Astrophysics Data System (ADS)

Anwar, Zeinab M.; Ibrahim, Ibrahim A.; Kamel, Rasha M.; Abdel-Salam, Enas T.; El-Asfoury, Mahmoud H.

2018-02-01

A highly sensitive and selective spectrofluorimetric method has been developed for the rapid determination of aluminium ions. The method is based on the fluorescence enhancement of Tb complex with 3,4-dimetyl-thieno[2,3 b] thiophene-2,5-dicarboxylic acid (LN) after addition trace amount of aluminium ions. The fluorescence of the probe is monitored at the characteristic an emission wavelength of Tb3+ at 545 nm with excitation at 300 nm. Optimum detection was obtained in DMSO-H2O (2:8, v/v) and at pH 6.0 using MOPSO buffer. Under the optimum conditions linear calibration curves were obtained from 0.5 μ mol L-1 to 20 μ mol L-1 with detection limit of 0.1 μ mol L-1. Effect of interference of other ions was studied.

A new multiplex method for the diagnosis of peroxisomal disorders allowing simultaneous determination of plasma very-long-chain fatty acids, phytanic, pristanic, docosahexaenoic and bile acids by high-performance liquid chromatography-atmospheric pressure chemical ionization-tandem mass spectrometry.

PubMed

Semeraro, Michela; Rizzo, Cristiano; Boenzi, Sara; Cappa, Marco; Bertini, Enrico; Antonetti, Giacomo; Dionisi-Vici, Carlo

2016-07-01

Peroxisomal disorders (PDs) present with wide phenotypic variability. An appropriate diagnosis requires a complete analysis of peroxisomal metabolites. We developed a multiplex LC-MS/MS method, using atmospheric pressure chemical ionization allowing the simultaneous determination in plasma of very-long-chain fatty acids, phytanic, pristanic, docosahexaenoic acids and di- and tri-hydroxycolestanoic bile acids. Two hundred microliters of plasma extracted with acetonitrile and 200μl extracted with hexane after an acid hydrolysis were combined, evaporated, dissolved in 10μl of methanol and analyzed. The acquisition was in negative-ion mode using multiple reaction monitoring. The method was validated analytically and clinically. Linearity was 0.1-200μmol/l for docosanoic, cis-13-docosenoic, tetracosanoic, cis-15-tetracosenoic and phytanic acids; 0.01-10μmol/l for hexacosanoic acid; 0.02-20μmol/l for di-hydroxycolestanoic, tri-hydroxycolestanoic and pristanic acids; 0.3-300μmol/l for docosahexaenoic acid. Intra-day and inter-day CVs were below 3.88 and 3.98 respectively for all compounds. Samples from patients with known peroxisomal disorders were compared with controls and the method allowed to confirm the diagnosis in all subjects with a 100% sensitivity. The advantage of this multiplex method is to allow in a single chromatographic run the simultaneous determination of a large number of peroxisome biomarkers with a simple preparative phase without derivatization. Copyright © 2016 Elsevier B.V. All rights reserved.

EDITORIAL: Roberts Prize for the best paper published in 2012 Roberts Prize for the best paper published in 2012

NASA Astrophysics Data System (ADS)

Cherry, Simon; Ruffle, Jon

2013-08-01

The publishers of Physics in Medicine and Biology (PMB), IOP Publishing, in association with the journal owners, the Institute of Physics and Engineering in Medicine (IPEM), jointly award the Roberts prize for the best paper published in PMB during the previous year. The procedure for deciding the winner is a two-stage process. First, a shortlist of contenders is drawn up based on those papers that had the best referees' quality assessments, with a further quality check and endorsement by the Editorial Board. The papers on the shortlist are then reviewed by a specially convened IPEM committee consisting of members with fellow status. This committee reads the shortlisted papers and selects the winner. We have much pleasure in advising readers that the Roberts Prize for the best paper published in 2012 is awarded to Michel Defrise, Ahmadreza Rezaei and Johan Nuyts from the Vrije Universiteit Brussels and the Katholieke Universiteit Leuven, Belgium for their breakthrough paper that describes how the information needed for attenuation correction in PET imaging can be extracted, to within a constant, from time-of-flight emission data: Time-of-flight PET data determine the attenuation sinogram up to a constant 2012 Phys. Med. Biol. 57 885 Michel Defrise1, Ahmadreza Rezaei2 and Johan Nuyts2 1Department of Nuclear Medicine, Vrije Universiteit Brussel, B-1090 Brussels, Belgium 2Department of Nuclear Medicine, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium This paper represents an important and timely contribution to the literature as time-of-flight PET scanners are now offered by several manufacturers. In hybrid PET/CT scanners, the PET attenuation correction, necessary for quantitative reconstruction of the tracer distribution, can be derived directly from the CT data. Sometimes, however, the PET and CT scans may be poorly aligned due to patient motion and other approaches are needed. In addition, hybrid PET/MRI scanners also, have been developed recently, and in these scanners attenuation correction of the PET data is a particularly difficult challenge as there is no direct relationship between MR signal intensity and tissue attenuation for 511 keV photons. This paper offers a possible path forwards for attenuation correction in these circumstances by exploiting consistency conditions in tandem with time-of-flight information and proves under these circumstances that the data for PET attenuation correction can be determined to within a constant. Our congratulations go to these authors. Of course all of the shortlisted papers were of an extremely high standard, and merit recognition by the community. They are listed below in alphabetical order. We also would like to thank the PMB Editorial Board and the IPEM Committee members for their hard work in assessing the papers. Simon R Cherry Editor-in-Chief Jon Ruffle Publisher References Buhr H, Büermann L, Gerlach M, Krumrey M and Rabus H 2012 Measurement of the mass energy-absorption coefficient of air for x-rays in the range from 3 keV to 60 keV Phys. Med. Biol. 57 8231 Chen W, Unkelbach J, Trofimov A, Madden T, Kooy H, Bortfeld T and Craft D 2012 Including robustness in multi-criteria optimization for intensity modulated proton therapy Phys. Med. Biol. 57 591 Clasie B M, Sharp G C, Seco J, Flanz J B and Kooy H M 2012 Numerical solutions of the gamma index in two and three dimensions Phys. Med. Biol. 57 6981 Connell T, Alexander A, Evans M and Seuntjens J 2012 An experimental feasibility study on the use of scattering foil free beams for modulated electron radiotherapy Phys. Med. Biol. 57 3259 Defrise M, Rezaei A and Nuyts J 2012 Time-of-flight PET data determine the attenuation sinogram up to a constant Phys. Med. Biol. 57 885 Dowdell S J, Clasie B, Depauw N, Metcalfe P, Rosenfeld A B, Kooy H M, Flanz J B and Paganetti H 2012 Monte Carlo study of the potential reduction in out-of-field dose using a patient-specific aperture in pencil beam scanning proton therapy Phys. Med. Biol. 57 2829 Scott A J D, Kumar S, Nahum A E and Fenwick J D 2012 Characterizing the influence of detector density on dosimeter response in non-equilibrium small photon fields Phys. Med. Biol. 57 4461 Stam M K, Crijns S P M, Zonnenberg B A, Barendrecht M M, van Vulpen M, Lagendijk J J W and Raaymakers B W 2012 Navigators for motion detection during real-time MRI-guided radiotherapy Phys. Med. Biol. 57 6797 Xia T, Alessio A M, De Man B, Manjeshwar R, Asma E and Kinahan P E 2012 Ultra-low dose CT attenuation correction for PET/CT Phys. Med. Biol. 57 309 Yamaguchi M et al 2012 Beam range estimation by measuring bremsstrahlung Phys. Med. Biol. 57 2843 For more information on this article, see medicalphysicsweb.org

Preclinical and Clinical Development of Low Dose Methamphetamine for the Treatment of Traumatic Brain Injury

DTIC Science & Technology

2014-04-01

methods of treating or reducing the occurrence of neuronal cell damage in a subject having a transient cerebral hypoxia and/or ischemic condition (e.g...2006. Signal trans- duction of MEK/ERK and PI3K/Akt activation by hypoxia /reoxygenation in renal epithelial cells . Eur. J. Cell Biol. 85, 1189e1199...cognitive impairment. The dentate gyrus region of the hippocampus contains a population of self-perpetuating neural stem cells . These cells

Yin and Yang of Heparanase in Breast Cancer Initiation

DTIC Science & Technology

2014-09-01

significance of heparanase in cancer metastasis and angiogenesis. Int J Biochem Cell Biol 38: 2018 -2039, 2006 2. Gotte M, Yip GW: Heparanase...Methods Plasmids. The C-terminus of the HPR1 gene (encoding amino acid 413-543) was cloned into a RCAS vector digested with a PacI and Cla I. An...contained a cleaved Pac I site. This fragment was directly ligated into Not I/PacI- digested RCAS-C. The following plasmid designated as RCAS-8C was used

Phytoplankton Productivity in an Arctic Fjord (West Greenland): Estimating Electron Requirements for Carbon Fixation and Oxygen Production

PubMed Central

Hancke, Kasper; Dalsgaard, Tage; Sejr, Mikael Kristian; Markager, Stiig; Glud, Ronnie Nøhr

2015-01-01

Accurate quantification of pelagic primary production is essential for quantifying the marine carbon turnover and the energy supply to the food web. Knowing the electron requirement (Κ) for carbon (C) fixation (Κ C) and oxygen (O2) production (Κ O2), variable fluorescence has the potential to quantify primary production in microalgae, and hereby increasing spatial and temporal resolution of measurements compared to traditional methods. Here we quantify Κ C and Κ O2 through measures of Pulse Amplitude Modulated (PAM) fluorometry, C fixation and O2 production in an Arctic fjord (Godthåbsfjorden, W Greenland). Through short- (2h) and long-term (24h) experiments, rates of electron transfer (ETRPSII), C fixation and/or O2 production were quantified and compared. Absolute rates of ETR were derived by accounting for Photosystem II light absorption and spectral light composition. Two-hour incubations revealed a linear relationship between ETRPSII and gross 14C fixation (R2 = 0.81) during light-limited photosynthesis, giving a Κ C of 7.6 ± 0.6 (mean ± S.E.) mol é (mol C)−1. Diel net rates also demonstrated a linear relationship between ETRPSII and C fixation giving a Κ C of 11.2 ± 1.3 mol é (mol C)−1 (R2 = 0.86). For net O2 production the electron requirement was lower than for net C fixation giving 6.5 ± 0.9 mol é (mol O2)−1 (R2 = 0.94). This, however, still is an electron requirement 1.6 times higher than the theoretical minimum for O2 production [i.e. 4 mol é (mol O2)−1]. The discrepancy is explained by respiratory activity and non-photochemical electron requirements and the variability is discussed. In conclusion, the bio-optical method and derived electron requirement support conversion of ETR to units of C or O2, paving the road for improved spatial and temporal resolution of primary production estimates. PMID:26218096

Quantum mechanics study of repulsive π-π interaction and flexibility of phenyl moiety in the iron azodioxide complex

NASA Astrophysics Data System (ADS)

Liu, Yuemin; Liu, Yucheng; Murru, Siva; Tzeng, Nianfeng; Srivastava, Radhey S.

2015-10-01

In this study, repulsive π-π interactions within iron azodioxide complex Fe[Ph(O)NN(O)Ph]3 were quantum mechanically characterized using DFT, MP2 and CCSD(T) methods. Flexibility of six phenyl moieties in this complex structure was also investigated by structural optimization approach using the DFT methods. Our MP2 and CCSD(T) calculations of the closest pair provided interaction energy of 6.62 and 8.29 kcal/mol respectively, which indicate a strongest repulsion among these intra-molecular π-π interactions. Interaction energy of the particular π-π pair calculated from 24 hybrid DFT methods ranges from 4.56 kcal/mol from BHandH method to 15.15 kcal/mol from O3LYP method. Cares should be exercised when interpreting interaction energy and geometry optimization from DFT simulation of systems containing π-π interaction. Comparison between the DFT results and the benchmark CCSD(T) results shows that the DFT calculations of π-π interaction are reasonable but still need to be interpreted with caution. Furthermore, MP2 interaction energy of -44.69 kcal/mol between two substituted π systems/phenyl rings Ph(O)N-moieties suggested that above energetically unfavorable π-π interaction can be compensated by the covalent bond N-N in a single ligand Ph(O)NN(O)Ph, which allows for a reasonable stability across the complex molecules. Optimizations of the entire complex molecule using B3LYP and M06HF methods produced a large variation of π-π distances and orientations, which implied that the complex molecule may perform catalysis at room temperature.

A new spectrophotometric method for determination of EDTA in water using its complex with Mn(III)

NASA Astrophysics Data System (ADS)

Andrade, Carlos Eduardo O.; Oliveira, André F.; Neves, Antônio A.; Queiroz, Maria Eliana L. R.

2016-11-01

EDTA is an important ligand used in many industrial products as well as in agriculture, where it is employed to assist in phytoextraction procedures and the absorption of nutrients by plants. Due to its intensive use and recalcitrance, it is now considered an emerging pollutant in water, so there is great interest in techniques suitable for its monitoring. This work proposes a method based on formation of the Mn(III)-EDTA complex after oxidation of the Mn(II)-EDTA complex by PbO2 immobilized on cyanoacrylate spheres. A design of experiments (DOE) based on the Doehlert matrix was used to determine the optimum conditions of the method, and the influence of the variables was evaluated using a multiple linear regression (MLR) model. The optimized method presented a linear response in the range from 0.77 to 100.0 μmol L- 1, with analytical sensitivity of 7.7 × 103 L mol- 1, a coefficient of determination of 0.999, and a limit of detection of 0.23 μmol L- 1. The method was applied using samples fortified at different concentration levels, and the recoveries achieved were between 97.0 and 104.9%.

A meiotic DNA polymerase from a mushroom, Agaricus bisporus.

PubMed Central

Takami, K; Matsuda, S; Sono, A; Sakaguchi, K

1994-01-01

A meiotic DNA polymerase [DNA nucleotidyltransferase (DNA-directed), EC 2.7.7.7], which likely has a role in meiotic DNA repair, was isolated from a mushroom, Agaricus bisporus. The purified fraction displays three bands in SDS/PAGE, at molecular masses of 72 kDa, 65 kDa and 36 kDa. Optimal activity is at pH 7.0-8.0 in the presence of 5 mM Mg2+ and 50 mM KCl and at 28-30 degrees C, which is the temperature for meiosis. This enzyme is resistant to N-ethylmaleimide and sensitive to 2',3'-dideoxythymidine 5'-triphosphate, suggesting that it is a beta-like DNA polymerase. These characteristics are similar to those of Coprinus DNA polymerase beta [Sakaguchi and Lu (1982) Mol. Cell. Biol. 2, 752-757]. In Western-blot analysis, the antiserum against the Coprinus polymerase reacts only with the 65 kDa band, which coincides with the molecular mass of the Coprinus polymerase. Western-blot analysis also showed that the antiserum could react with crude extracts not only from the Agaricales family, to which Agaricus and Coprinus belong, but also from different mushroom families and Saccharomyces. The Agaricus polymerase activity can be found only in the meiotic-cell-rich fraction, but the enzyme is also present in the somatic cells in an inactive state. Images Figure 2 Figure 5 Figure 6 PMID:8172591

The BOS1 gene encodes an essential 27-kD putative membrane protein that is required for vesicular transport from the ER to the Golgi complex in yeast

PubMed Central

1991-01-01

We recently described the identification of BOS1 (Newman, A., J. Shim, and S. Ferro-Novick. 1990. Mol. Cell. Biol. 10:3405-3414.). BOS1 is a gene that in multiple copy suppresses the growth and secretion defect of bet1 and sec22, two mutants that disrupt transport from the ER to the Golgi complex in yeast. The ability of BOS1 to specifically suppress mutants blocked at a particular stage of the secretory pathway suggested that this gene encodes a protein that functions in this process. The experiments presented in this study support this hypothesis. Specifically, the BOS1 gene was found to be essential for cellular growth. Furthermore, cells depleted of the Bos1 protein fail to transport pro-alpha-factor and carboxypeptidase Y (CPY) to the Golgi apparatus. This defect in export leads to the accumulation of an extensive network of ER and small vesicles. DNA sequence analysis predicts that Bos1 is a 27-kD protein containing a putative membrane- spanning domain. This prediction is supported by differential centrifugation experiments. Thus, Bos1 appears to be a membrane protein that functions in conjunction with Bet1 and Sec22 to facilitate the transport of proteins at a step subsequent to translocation into the ER but before entry into the Golgi apparatus. PMID:2007627

The double nucleation model for sickle cell haemoglobin polymerization: full integration and comparison with experimental data.

PubMed

Medkour, Terkia; Ferrone, Frank; Galactéros, Frédéric; Hannaert, Patrick

2008-06-01

Sickle cell haemoglobin (HbS) polymerization reduces erythrocyte deformability, causing deleterous vaso-occlusions. The double-nucleation model states that polymers grow from HbS aggregates, the nuclei, (i) in solution (homogeneous nucleation), (ii) onto existing polymers (heterogeneous nucleation). When linearized at initial HbS concentration, this model predicts early polymerization and its characteristic delay-time (Ferrone et al. J Mol Biol 183(4):591-610, 611-631, 1985). Addressing its relevance for describing complete polymerization, we constructed the full, non-linearized model (Simulink), The MathWorks). Here, we compare the simulated outputs to experimental progress curves (n = 6-8 different [HbS], 3-6 mM range, from Ferrone's group). Within 10% from start, average root mean square (rms) deviation between simulated and experimental curves is 0.04 +/- 0.01 (25 degrees C, n = 8; mean +/- standard error). Conversely, for complete progress curves, averaged rms is 0.48 +/- 0.04. This figure is improved to 0.13 +/- 0.01 by adjusting heterogeneous pathway parameters (p < 0.01): the nucleus stability (sigma(2) micro( cc ): + 40%), and the fraction of polymer surface available for nucleation (phi), from 5e(-7), (3 mM) to 13 (6 mM). Similar results are obtained at 37 degrees C. We conclude that the physico-chemical description of heterogeneous nucleation warrants refinements in order to capture the whole HbS polymerization process.

Evaluating the quality of NMR structures by local density of protons.

PubMed

Ban, Yih-En Andrew; Rudolph, Johannes; Zhou, Pei; Edelsbrunner, Herbert

2006-03-01

Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. 2005 Wiley-Liss, Inc.

Tandem repeats of the 5' non-transcribed spacer of Tetrahymena rDNA function as high copy number autonomous replicons in the macronucleus but do not prevent rRNA gene dosage regulation.

PubMed Central

Pan, W J; Blackburn, E H

1995-01-01

The rRNA genes in the somatic macronucleus of Tetrahymena thermophila are normally on 21 kb linear palindromic molecules (rDNA). We examined the effect on rRNA gene dosage of transforming T.thermophila macronuclei with plasmid constructs containing a pair of tandemly repeated rDNA replication origin regions unlinked to the rRNA gene. A significant proportion of the plasmid sequences were maintained as high copy circular molecules, eventually consisting solely of tandem arrays of origin regions. As reported previously for cells transformed by a construct in which the same tandem rDNA origins were linked to the rRNA gene [Yu, G.-L. and Blackburn, E. H. (1990) Mol. Cell. Biol., 10, 2070-2080], origin sequences recombined to form linear molecules bearing several tandem repeats of the origin region, as well as rRNA genes. The total number of rDNA origin sequences eventually exceeded rRNA gene copies by approximately 20- to 40-fold and the number of circular replicons carrying only rDNA origin sequences exceeded rRNA gene copies by 2- to 3-fold. However, the rRNA gene dosage was unchanged. Hence, simply monitoring the total number of rDNA origin regions is not sufficient to regulate rRNA gene copy number. Images PMID:7784211

Linker DNA accessibility in chromatin fibers of different conformations: a reevaluation.

PubMed Central

Zlatanova, J; Leuba, S H; Yang, G; Bustamante, C; van Holde, K

1994-01-01

New studies on chromatin fiber morphology, using the technique of scanning force microscopy (SFM), have caused us to reexamine recent analysis of nuclease digestion of chromatin. Chicken erythrocyte chromatin fibers, glutaraldehyde-fixed at 0, 10, and 80 mM NaCl, were imaged with the help of SFM. The chromatin fibers possessed a loose three-dimensional 30-nm structure even in the absence of added salt. This structure slightly condensed upon addition of 10 mM NaCl, and highly compacted, irregularly segmented fibers were observed at 80 mM NaCl. This sheds new light upon our previously reported analysis of the kinetics of digestion by soluble and membrane-immobilized micrococcal nuclease [Leuba, S. H., Zlatanova, J. & van Holde, K. (1994) J. Mol. Biol. 235, 871-880]. While the low-ionic-strength fibers were readily digested, the highly compacted structure formed at 80 mM NaCl was refractory to nuclease attack, implying that the linkers were fully accessible in the low-ionic-strength conformation but not in the condensed fibers. We now find that cleavage of the linker DNA by a small molecule, methidiumpropyl-EDTA-Fe(II), proceeds for all types of conformations at similar rates. Thus, steric hindrance is responsible for the lack of accessibility to micrococcal nuclease in the condensed fiber. Taken in total the data suggest that reexamination of existing models of chromatin conformation is warranted. Images PMID:8202481

Characterization of B61, the ligand for the Eck receptor protein-tyrosine kinase.

PubMed

Shao, H; Pandey, A; O'Shea, K S; Seldin, M; Dixit, V M

1995-03-10

B61 was originally described as a novel secreted tumor necrosis factor-alpha-inducible gene product in endothelial cells (Holzman, L. B., Marks, R. M., and Dixit, V. M. (1990) Mol. Cell. Biol. 10, 5830-5838). It was recently discovered that soluble recombinant B61 could serve as a ligand for the Eck receptor protein-tyrosine kinase, a member of the Eph/Eck subfamily of receptor protein-tyrosine kinases (Bartley, T.D., Hunt, R. W., Welcher, A. A., Boyle, W. J., Parker, V. P., Lindberg, R. A., Lu, H. S., Colombero, A. M., Elliott, R. L., Guthrie, R. A., Holst, P. L., Skrine, J. D., Toso, R. J., Zhang, M., Fernandez, E., Trail, G., Yarnum, B., Yarden, Y., Hunter, T., and Fox, G. M. (1994) Nature 368, 558-560). We now show that B61 can also exist as a cell surface glycosylphosphatidyl-inositol-linked protein that is capable of activating the Eck receptor protein-tyrosine kinase, the first such report of a receptor protein-tyrosine kinase ligand that is glycosylphosphatidylinositol-linked. In addition, the expression patterns of B61 and Eck during mouse ontogeny were determined by in situ hybridization. Both were found to be highly expressed in the developing lung and gut, while Eck was preferentially expressed in the thymus. Finally, the gene for B61 was localized to a specific position on mouse chromosome 3 by interspecific back-cross analysis.

Cyclin D1 down-regulation is essential for DBC2's tumor suppressor function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoshihara, Takashi; Collado, Denise; Hamaguchi, Masaaki

2007-07-13

The expression of tumor suppressor gene DBC2 causes certain breast cancer cells to stop growing [M. Hamaguchi, J.L. Meth, C. Von Klitzing, W. Wei, D. Esposito, L. Rodgers, T. Walsh, P. Welcsh, M.C. King, M.H. Wigler, DBC2, a candidate for a tumor suppressor gene involved in breast cancer, Proc. Natl. Acad. Sci. USA 99 (2002) 13647-13652]. Recently, DBC2 was found to participate in diverse cellular functions such as protein transport, cytoskeleton regulation, apoptosis, and cell cycle control [V. Siripurapu, J.L. Meth, N. Kobayashi, M. Hamaguchi, DBC2 significantly influences cell cycle, apoptosis, cytoskeleton, and membrane trafficking pathways. J. Mol. Biol. 346more » (2005) 83-89]. Its tumor suppression mechanism, however, remains unclear. In this paper, we demonstrate that DBC2 suppresses breast cancer proliferation through down-regulation of Cyclin D1 (CCND1). Additionally, the constitutional overexpression of CCND1 prevented the negative impact of DBC2 expression on their growth. Under a CCND1 promoter, the expression of CCNE1 exhibited the same protective effect. Our results indicate that the down-regulation of CCND1 is an essential step for DBC2's growth suppression of cancer cells. We believe that this discovery contributes to a better understanding of DBC2's tumor suppressor function.« less

Proflavine binding to poly(rC-rA) inverts the CD spectrum but not the helix handedness.

PubMed

Westhof, E; Sundaralingam, M

1984-08-01

The interaction of proflavine hemisulfate with the sodium salt of poly(rC-rA) in solution (unbuffered) yields an inverted (mirror-like) circular dichroism (CD) spectrum to that of the free poly(rC-rA). Simultaneously, an induced negative Cotton effect appears in the proflavine band region with a maximum at 467 nm and a slight shoulder at 420 nm. This observation may be explained as resulting from the formation of a poly(rC-rA).proflavine complex with the polynucleotide existing as a right-handed parallel chain duplex with the proflavine intercalated between the CpA sequence and not the ApC sequence. The intercalation geometry here is expected to be analogous to that found in the crystal structure of the dinucleotide CpA.proflavine complex (Westhof et al. J. Mol. Biol., 1981) which forms a miniature right-handed helix. Although normally an inverted spectra could be attributed to a reversal in the helix handedness, the similarity in the 31P nuclear magnetic resonance spectra between the free and proflavine bound poly(rC-rA) indicates that their handedness is the same. The inverted CD spectrum may be a result of the different stacking orientation between the intercalated proflavine and the A-A base-pair on one hand and the triply hydrogen bonded protonated C-C base-pair on the other.

Nuclear factors that bind to the enhancer region of nondefective Friend murine leukemia virus.

PubMed Central

Manley, N R; O'Connell, M A; Sharp, P A; Hopkins, N

1989-01-01

Nondefective Friend murine leukemia virus (MuLV) causes erythroleukemia when injected into newborn NFS mice, while Moloney MuLV causes T-cell lymphoma. Exchange of the Friend virus enhancer region, a sequence of about 180 nucleotides including the direct repeat and a short 3'-adjacent segment, for the corresponding region in Moloney MuLV confers the ability to cause erythroid disease on Moloney MuLV. We have used the electrophoretic mobility shift assay and methylation interference analysis to identify cellular factors which bind to the Friend virus enhancer region and compared these with factors, previously identified, that bind to the Moloney virus direct repeat (N. A. Speck and D. Baltimore, Mol. Cell. Biol. 7:1101-1110, 1987). We identified five binding sites for sequence-specific DNA-binding proteins in the Friend virus enhancer region. While some binding sites are present in both the Moloney and Friend virus enhancers, both viruses contain unique sites not present in the other. Although none of the factors identified in this report which bind to these unique sites are present exclusively in T cells or erythroid cells, they bind to three regions of the enhancer shown by genetic analysis to encode disease specificity and thus are candidates to mediate the tissue-specific expression and distinct disease specificities encoded by these virus enhancer elements. Images PMID:2778872

Gentamicin Binds to the Megalin Receptor as a Competitive Inhibitor Using the Common Ligand Binding Motif of Complement Type Repeats

PubMed Central

Dagil, Robert; O'Shea, Charlotte; Nykjær, Anders; Bonvin, Alexandre M. J. J.; Kragelund, Birthe B.

2013-01-01

Gentamicin is an aminoglycoside widely used in treatments of, in particular, enterococcal, mycobacterial, and severe Gram-negative bacterial infections. Large doses of gentamicin cause nephrotoxicity and ototoxicity, entering the cell via the receptor megalin. Until now, no structural information has been available to describe the interaction with gentamicin in atomic detail, and neither have any three-dimensional structures of domains from the human megalin receptor been solved. To address this gap in our knowledge, we have solved the NMR structure of the 10th complement type repeat of human megalin and investigated its interaction with gentamicin. Using NMR titration data in HADDOCK, we have generated a three-dimensional model describing the complex between megalin and gentamicin. Gentamicin binds to megalin with low affinity and exploits the common ligand binding motif previously described (Jensen, G. A., Andersen, O. M., Bonvin, A. M., Bjerrum-Bohr, I., Etzerodt, M., Thogersen, H. C., O'Shea, C., Poulsen, F. M., and Kragelund, B. B. (2006) J. Mol. Biol. 362, 700–716) utilizing the indole side chain of Trp-1126 and the negatively charged residues Asp-1129, Asp-1131, and Asp-1133. Binding to megalin is highly similar to gentamicin binding to calreticulin. We discuss the impact of this novel insight for the future structure-based design of gentamicin antagonists. PMID:23275343

Gibbs motif sampling: detection of bacterial outer membrane protein repeats.

PubMed Central

Neuwald, A. F.; Liu, J. S.; Lawrence, C. E.

1995-01-01

The detection and alignment of locally conserved regions (motifs) in multiple sequences can provide insight into protein structure, function, and evolution. A new Gibbs sampling algorithm is described that detects motif-encoding regions in sequences and optimally partitions them into distinct motif models; this is illustrated using a set of immunoglobulin fold proteins. When applied to sequences sharing a single motif, the sampler can be used to classify motif regions into related submodels, as is illustrated using helix-turn-helix DNA-binding proteins. Other statistically based procedures are described for searching a database for sequences matching motifs found by the sampler. When applied to a set of 32 very distantly related bacterial integral outer membrane proteins, the sampler revealed that they share a subtle, repetitive motif. Although BLAST (Altschul SF et al., 1990, J Mol Biol 215:403-410) fails to detect significant pairwise similarity between any of the sequences, the repeats present in these outer membrane proteins, taken as a whole, are highly significant (based on a generally applicable statistical test for motifs described here). Analysis of bacterial porins with known trimeric beta-barrel structure and related proteins reveals a similar repetitive motif corresponding to alternating membrane-spanning beta-strands. These beta-strands occur on the membrane interface (as opposed to the trimeric interface) of the beta-barrel. The broad conservation and structural location of these repeats suggests that they play important functional roles. PMID:8520488

Preferential cleavage sites for Sau3A restriction endonuclease in human ribosomal DNA.

PubMed

Kupriyanova, N S; Kirilenko, P M; Netchvolodov, K K; Ryskov, A P

2000-07-21

Previous studies of cloned ribosomal DNA (rDNA) variants isolated from the cosmid library of human chromosome 13 have revealed some disproportion in representativity of different rDNA regions (N. S. Kupriyanova, K. K. Netchvolodov, P. M. Kirilenko, B. I. Kapanadze, N. K. Yankovsky, and A. P. Ryskov, Mol. Biol. 30, 51-60, 1996). Here we show nonrandom cleavage of human rDNA with Sau3A or its isoshizomer MboI under mild hydrolysis conditions. The hypersensitive cleavage sites were found to be located in the ribosomal intergenic spacer (rIGS), especially in the regions of about 5-5.5 and 11 kb upstream of the rRNA transcription start point. This finding is based on sequencing mapping of the rDNA insert ends in randomly selected cosmid clones of human chromosome 13 and on the data of digestion kinetics of cloned and noncloned human genomic rDNA with Sau3A and MboI. The results show that a methylation status and superhelicity state of the rIGS have no effect on cleavage site sensitivity. It is interesting that all primary cleavage sites are adjacent to or entering into Alu or Psi cdc 27 retroposons of the rIGS suggesting a possible role of neighboring sequences in nuclease accessibility. The results explain nonequal representation of rDNA sequences in the human genomic DNA library used for this study. Copyright 2000 Academic Press.

Diabetes Complications at Presentation and One Year by Glycated Haemoglobin at Diagnosis in a Multiethnic and Diverse Socioeconomic Population: Results from the South London Diabetes Study.

PubMed

Azam, Mohsin; Marwood, Lindsey; Ismail, Khalida; Evans, Tyrrell; Sivaprasad, Sobha; Winkley, Kirsty; Amiel, Stephanie Anne

2015-01-01

Background. WHO's recommendation of HbA1c ≥ 48 mmol/mol (6.5%) as diagnostic for type 2 diabetes mellitus (T2DM) was adopted by three UK London boroughs in May 2012. The South London Diabetes (SOUL-D) study has recruited people with newly diagnosed T2DM since 2008. We compared participants diagnosed before May 2012 with HbA1c < 48 mmol/mol to those with diagnostic HbA1c ≥ 48 mmol/mol. Methods. A prospective cohort study of newly diagnosed T2DM participants from 96 primary care practices, comparing demographic and biomedical variables between those with diagnostic HbA1c < 48 mmol/mol or HbA1c ≥ 48 mmol/mol at recruitment and after one year. Results. Of 1488 participants, 22.8% had diagnostic HbA1c < 48 mmol/mol. They were older and more likely to be white (p < 0.05). At recruitment and one year, there were no between-group differences in the prevalence of diabetic complications, except that those diagnosed with HbA1c < 48 mmol/mol had more sensory neuropathy at recruitment (p = 0.039) and, at one year, had new myocardial infarction (p = 0.012) but less microalbuminuria (p = 0.012). Conclusions. Use of HbA1c ≥ 48 mmol/mol as the sole T2DM diagnostic criterion may miss almost a quarter of those previously diagnosed in South London yet HbA1c < 48 mmol/mol may not exclude clinically important diabetes.

Diabetes Complications at Presentation and One Year by Glycated Haemoglobin at Diagnosis in a Multiethnic and Diverse Socioeconomic Population: Results from the South London Diabetes Study

PubMed Central

Azam, Mohsin; Marwood, Lindsey; Ismail, Khalida; Evans, Tyrrell; Sivaprasad, Sobha; Winkley, Kirsty; Amiel, Stephanie Anne

2015-01-01

Background. WHO's recommendation of HbA1c ≥ 48 mmol/mol (6.5%) as diagnostic for type 2 diabetes mellitus (T2DM) was adopted by three UK London boroughs in May 2012. The South London Diabetes (SOUL-D) study has recruited people with newly diagnosed T2DM since 2008. We compared participants diagnosed before May 2012 with HbA1c < 48 mmol/mol to those with diagnostic HbA1c ≥ 48 mmol/mol. Methods. A prospective cohort study of newly diagnosed T2DM participants from 96 primary care practices, comparing demographic and biomedical variables between those with diagnostic HbA1c < 48 mmol/mol or HbA1c ≥ 48 mmol/mol at recruitment and after one year. Results. Of 1488 participants, 22.8% had diagnostic HbA1c < 48 mmol/mol. They were older and more likely to be white (p < 0.05). At recruitment and one year, there were no between-group differences in the prevalence of diabetic complications, except that those diagnosed with HbA1c < 48 mmol/mol had more sensory neuropathy at recruitment (p = 0.039) and, at one year, had new myocardial infarction (p = 0.012) but less microalbuminuria (p = 0.012). Conclusions. Use of HbA1c ≥ 48 mmol/mol as the sole T2DM diagnostic criterion may miss almost a quarter of those previously diagnosed in South London yet HbA1c < 48 mmol/mol may not exclude clinically important diabetes. PMID:26090473

[Analysis of monosaccharides and uronic acids in polysaccharides by pre-column derivatization with p-aminobenzoic acid and high performance liquid chromatography].

PubMed

Hao, Guitang; Chen, Shangwei; Zhu, Song; Yin, Hongping; Dai, Jun; Cao, Yuhua

2007-01-01

An ion-pair reversed-phase high performance liquid chromatographic (RP-HPLC) method for the simultaneous determination of carbohydrate and uronic acids was developed. p-Aminobenzoic acid (p-AMBA) was used for pre-column derivatization of the analytes, enabling fluorescence (lambda(ex) = 313 nm, lambda(em) = 358 nm) or ultraviolet (UV at 303 nm) detection. Reaction conditions such as reaction temperature and reaction time were optimized. Atlantis dC18 column with hydrophilic end capping was selected for the separation of derivatives. Effects of mobile phase compositions such as ion pairs and their concentrations and pH on the retention behaviors and separation results of 9 monosaccharides and 2 uronic acids were investigated. Derivatives of fructose, galactose, glucose, mannose, xylose, arabinose, ribose, galacturonic acid, fucose, glucuronic acid and rhamnose were separated within 42 min, applying tetrabutyl ammonium hydrogen bisulfate (TBAHSO4) as the ion pair reagent. The detection limits were between 3.38 x 10(-8) mol/L and 176 x 10(-8) mol/L for fluorescence detection and between 2.55 x 10(-7) mol/L and 13.4 x 10(-7) mol/L for UV detection. Good linearities were obtained with correlation coefficients (r2) above 0.99. The relative standard deviations (RSDs) of the peak area of the derivatives in 12 - 51 h after derivatization were from 2.5% to 3.9%. This method has been applied for the determination of mono-/disaccharides and uronic acids in spirulina polysaccharide after dissolved in trifluoroacetic acid solution (2 mol/L). The results showed this method is suitable for the analysis of monosaccharide compositions in polysaccharides.

Characterization of ultrahigh-molecular weight cationic polyacrylamide using frit-inlet asymmetrical flow field-flow fractionation and multi-angle light scattering.

PubMed

Woo, Sohee; Lee, Ju Yong; Choi, Woonjin; Moon, Myeong Hee

2016-01-15

In this study, frit inlet asymmetrical flow field-flow fractionation (FlFFF) with multi-angle light scattering (MALS) and differential refractive index (DRI) detection is utilized for size separation, determination of molecular weight (MW), and conformation of ultrahigh-MW (10(7)-10(9) g/mol) cationic polyacrylamides (C-PAMs), a class of water-soluble copolymers based on acrylamide and vinyl-type comonomers with quaternary ammonium cations that are widely used in wastewater treatment and in paper industries. Linear and branched C-PAM copolymers prepared in two different polymerization methods (solution and emulsion) from varying amounts of crosslinking agent and initiator were size fractionated by FlFFF with field-programming. It was found experimentally that the linear copolymers from both polymerization methods were less than 10(8) g/mol in MW with compact, nearly spherical structures, while the branched C-PAM copolymers from the emulsion polymerization showed a significant increase in average MW up to ∼ 10(9)g/mol, which was about 20-fold greater than those from the solution method, and the branched copolymers had more compact or shrunken conformations. While both linear and branched copolymers less than 10(8) g/mol MW were well resolved in an increasing order of MW (normal mode), it was noted that branched copolymers prepared through emulsion polymerization exhibited significantly larger MWs of 10(8-)10(9) g/mol and eluted in the steric/hyperlayer mode, in which the elution order is reversed in an extreme run condition (strong initial field strength followed by a fast field decay during programming). Copyright © 2015 Elsevier B.V. All rights reserved.

Commercial Molecular Tests for Fungal Diagnosis from a Practical Point of View.

PubMed

Lackner, Michaela; Lass-Flörl, Cornelia

2017-01-01

The increasing interest in molecular diagnostics is a result of tremendously improved knowledge on fungal infections in the past 20 years and the rapid development of new methods, in particular polymerase chain reaction. High expectations have been placed on molecular diagnostics, and the number of laboratories now using the relevant technology is rapidly increasing-resulting in an obvious need for standardization and definition of laboratory organization. In the past 10 years, multiple new molecular tools were marketed for the detection of DNA, antibodies, cell wall components, or other antigens. In contrast to classical culture methods, molecular methods do not detect a viable organisms, but only molecules which indicate its presence; this can be nucleic acids, cell components (antigens), or antibodies (Fig. 1). In this chapter, an overview is provided on commercially available detection tools, their strength and how to use them. A main focus is laid on providing tips and tricks that make daily life easier. We try to focus and mention methodical details which are not highlighted in the manufacturer's instructions of these test kits, but are based on our personal experience in the laboratory. Important to keep in mind is that molecular tools cannot replace culture, microscopy, or a critical view on patients' clinical history, signs, and symptoms, but provide a valuable add on tool. Diagnosis should not be based solely on a molecular test, but molecular tools might deliver an important piece of information that helps matching the diagnostic puzzle to a diagnosis, in particular as few tests are in vitro diagnostic tests (IVD) or only part of the whole test carries the IVD certificate (e.g., DNA extraction is often not included). Please be aware that the authors do not claim to provide a complete overview on all commercially available diagnostic assays being currently marketed for fungal detection, as those are subject to constant change. A main focus is put on commonly used panfungal assays and pathogen-specific assays, including Aspergillus-specific, Candida-specific, Cryptococcus specific, Histoplasma-specific, and Pneumocystis-specific assays. Assays are categorized according to their underlying principle in either antigen-detecting or antibody-detecting or DNA-detecting (Fig. 1). Other non-DNA-detecting nucleic acid methods such as FISH and PNA FISH are not summarized in this chapter and an overview on test performance, common false positives, and the clinical evaluation of commercial tests in studies is provided already in a previous book series by Javier Yugueros Marcos and David H. Pincus (Marcos and Pincus, Methods Mol Biol 968:25-54, 2013).

G4CEP: A G4 theory modification by including pseudopotential for molecules containing first-, second- and third-row representative elements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Silva, Cleuton de Souza; Instituto de Ciências Exatas e Tecnologia, Universidade Federal do Amazonas, Campus de Itacoatiara, 69100-021 Itacoatiara, Amazonas; Pereira, Douglas Henrique

2016-05-28

The G4CEP composite method was developed from the respective G4 all-electron version by considering the implementation of compact effective pseudopotential (CEP). The G3/05 test set was used as reference to benchmark the adaptation by treating in this work atoms and compounds from the first and second periods of the periodic table, as well as representative elements of the third period, comprising 440 thermochemical data. G4CEP has not reached a so high level of accuracy as the G4 all-electron theory. G4CEP presented a mean absolute error around 1.09 kcal mol{sup −1}, while the original method presents a deviation corresponding to 0.83more » kcal mol{sup −1}. The similarity of the optimized molecular geometries between G4 and G4CEP indicates that the core-electron effects and basis set adjustments may be pointed out as a significant factor responsible for the large discrepancies between the pseudopotential results and the experimental data, or even that the all-electron calculations are more efficient either in its formulation or in the cancellation of errors. When the G4CEP mean absolute error (1.09 kcal mol{sup −1}) is compared to 1.29 kcal mol{sup −1} from G3CEP, it does not seem so efficient. However, while the G3CEP uncertainty is ±4.06 kcal mol{sup −1}, the G4CEP deviation is ±2.72 kcal mol{sup −1}. Therefore, the G4CEP theory is considerably more reliable than any previous combination of composite theory and pseudopotential, particularly for enthalpies of formation and electron affinities.« less

Immobilised histidine tagged β2-adrenoceptor oriented by a diazonium salt reaction and its application in exploring drug-protein interaction using ephedrine and pseudoephedrine as probes.

PubMed

Li, Qian; Bian, Liujiao; Zhao, Xinfeng; Gao, Xiaokang; Zheng, Jianbin; Li, Zijian; Zhang, Youyi; Jiang, Ru; Zheng, Xiaohui

2014-01-01

A new oriented method using a diazonium salt reaction was developed for linking β2-adrenoceptor (β2-AR) on the surface of macroporous silica gel. Stationary phase containing the immobilised receptor was used to investigate the interaction between β2-AR and ephedrine plus pseudoephedrine by zonal elution. The isotherms of the two drugs best fit the Langmuir model. Only one type of binding site was found for ephedrine and pseudoephedrine targeting β2-AR. At 37 °C, the association constants during the binding were (5.94±0.05)×103/M for ephedrine and (3.80±0.02) ×103/M for pseudoephedrine, with the binding sites of (8.92±0.06) ×10-4 M. Thermodynamic studies showed that the binding of the two compounds to β2-AR was a spontaneous reaction with exothermal processes. The ΔGθ, ΔHθ and ΔSθ for the interaction between ephedrine and β2-AR were -(22.33±0.04) kJ/mol, -(6.51±0.69) kJ/mol and 50.94±0.31 J/mol·K, respectively. For the binding of pseudoephedrine to the receptor, these values were -(21.17±0.02) kJ/mol, -(7.48±0.56) kJ/mol and 44.13±0.01 J/mol·K. Electrostatic interaction proved to be the driving force during the binding of the two drugs to β2-AR. The proposed immobilised method will have great potential for attaching protein to solid substrates and realizing the interactions between proteins and drugs.

Immobilised Histidine Tagged β 2-Adrenoceptor Oriented by a Diazonium Salt Reaction and Its Application in Exploring Drug-Protein Interaction Using Ephedrine and Pseudoephedrine as Probes

PubMed Central

Li, Qian; Bian, Liujiao; Zhao, Xinfeng; Gao, Xiaokang; Zheng, Jianbin; Li, Zijian; Zhang, Youyi; Jiang, Ru; Zheng, Xiaohui

2014-01-01

A new oriented method using a diazonium salt reaction was developed for linking β 2-adrenoceptor (β 2-AR) on the surface of macroporous silica gel. Stationary phase containing the immobilised receptor was used to investigate the interaction between β 2-AR and ephedrine plus pseudoephedrine by zonal elution. The isotherms of the two drugs best fit the Langmuir model. Only one type of binding site was found for ephedrine and pseudoephedrine targeting β 2-AR. At 37 °C, the association constants during the binding were (5.94±0.05)×103/M for ephedrine and (3.80±0.02) ×103/M for pseudoephedrine, with the binding sites of (8.92±0.06) ×10−4 M. Thermodynamic studies showed that the binding of the two compounds to β 2-AR was a spontaneous reaction with exothermal processes. The ΔGθ, ΔHθ and ΔSθ for the interaction between ephedrine and β 2-AR were −(22.33±0.04) kJ/mol, −(6.51±0.69) kJ/mol and 50.94±0.31 J/mol·K, respectively. For the binding of pseudoephedrine to the receptor, these values were −(21.17±0.02) kJ/mol, −(7.48±0.56) kJ/mol and 44.13±0.01 J/mol·K. Electrostatic interaction proved to be the driving force during the binding of the two drugs to β 2-AR. The proposed immobilised method will have great potential for attaching protein to solid substrates and realizing the interactions between proteins and drugs. PMID:24747442

G4CEP: A G4 theory modification by including pseudopotential for molecules containing first-, second- and third-row representative elements.

PubMed

Silva, Cleuton de Souza; Pereira, Douglas Henrique; Custodio, Rogério

2016-05-28

The G4CEP composite method was developed from the respective G4 all-electron version by considering the implementation of compact effective pseudopotential (CEP). The G3/05 test set was used as reference to benchmark the adaptation by treating in this work atoms and compounds from the first and second periods of the periodic table, as well as representative elements of the third period, comprising 440 thermochemical data. G4CEP has not reached a so high level of accuracy as the G4 all-electron theory. G4CEP presented a mean absolute error around 1.09 kcal mol(-1), while the original method presents a deviation corresponding to 0.83 kcal mol(-1). The similarity of the optimized molecular geometries between G4 and G4CEP indicates that the core-electron effects and basis set adjustments may be pointed out as a significant factor responsible for the large discrepancies between the pseudopotential results and the experimental data, or even that the all-electron calculations are more efficient either in its formulation or in the cancellation of errors. When the G4CEP mean absolute error (1.09 kcal mol(-1)) is compared to 1.29 kcal mol(-1) from G3CEP, it does not seem so efficient. However, while the G3CEP uncertainty is ±4.06 kcal mol(-1), the G4CEP deviation is ±2.72 kcal mol(-1). Therefore, the G4CEP theory is considerably more reliable than any previous combination of composite theory and pseudopotential, particularly for enthalpies of formation and electron affinities.

Determination of low-molecular-weight organic acids in non-small cell lung cancer with a new liquid chromatography-tandem mass spectrometry method.

PubMed

Klupczynska, Agnieszka; Plewa, Szymon; Dyszkiewicz, Wojciech; Kasprzyk, Mariusz; Sytek, Natalia; Kokot, Zenon J

2016-09-10

As compared to other classes of metabolites, determination of organic acids is an underrepresented field in cancer research and till now there has been a lack of appropriate analytical procedure for determination of serum levels of organic acids potentially associated with cancer development. The aim of the study was to develop a new rapid liquid chromatography-tandem mass spectrometry method for the quantification of six low-molecular-weight organic acids in human serum and to apply this method in an analysis of samples collected from non-small cell lung cancer (NSCLC) patients and a matched control group. The samples were prepared by solid phase extraction (Clean-up CUQAX, UCT). Chromatography was conducted on a Synergi Hydro-RP column (Phenomenex) and a gradient run of 15min. Detection was performed using a negative multiple reaction monitoring mode. The calibration ranges were as follows: 0.24-38.42μmol/L for 2-hydroxybutyric acid, 0.09-17.23μmol/L for fumaric acid, 0.08-15.13μmol/L for glutaric acid, 0.11-2.22mmol/L for lactic acid, 0.39-30.98μmol/L for pyroglutamic acid, and 0.08-16.93μmol/L for succinic acid. Mean relative recovery range was 85.99-114.42% and the determined intra- and inter day coefficients of variation were ≤14%. Among the studied acids, pyroglutamic acid showed the best discriminating potential and enabled to identify accurately NSCLC patients and control subjects regardless of the cancer stage. Further investigations of serum organic acids may allow us to better understand the underlying mechanisms involved in NSCLC and develop novel means of its detection and treatment. The developed method may be also a valuable tool to study metabolic changes associated with other types of cancer. Copyright © 2016 Elsevier B.V. All rights reserved.

Computational and Experimental Study of Thermodynamics of the Reaction of Titania and Water at High Temperatures.

PubMed

Nguyen, Q N; Bauschlicher, C W; Myers, D L; Jacobson, N S; Opila, E J

2017-12-14

Gaseous titanium hydroxide and oxyhydroxide species were studied with quantum chemical methods. The results are used in conjunction with an experimental transpiration study of titanium dioxide (TiO 2 ) in water vapor-containing environments at elevated temperatures to provide a thermodynamic description of the Ti(OH) 4 (g) and TiO(OH) 2 (g) species. The geometry and harmonic vibrational frequencies of these species were computed using the coupled-cluster singles and doubles method with a perturbative correction for connected triple substitutions [CCSD(T)]. For the OH bending and rotation, the B3LYP density functional theory was used to compute corrections to the harmonic approximations. These results were combined to determine the enthalpy of formation. Experimentally, the transpiration method was used with water contents from 0 to 76 mol % in oxygen or argon carrier gases for 20-250 h exposure times at 1473-1673 K. Results indicate that oxygen is not a key contributor to volatilization, and the primary reaction for volatilization in this temperature range is TiO 2 (s) + H 2 O(g) = TiO(OH) 2 (g). Data were analyzed with both the second and third law methods using the thermal functions derived from the theoretical calculations. The third law enthalpy of formation at 298.15 K for TiO(OH) 2 (g) at 298 K was -838.9 ± 6.5 kJ/mol, which compares favorably to the theoretical calculation of -838.7 ± 25 kJ/mol. We recommend the experimentally derived third law enthalpy of formation at 298.15 K for TiO(OH) 2 , the computed entropy of 320.67 J/mol·K, and the computed heat capacity [149.192 + (-0.02539)T + (8.28697 × 10 -6 )T 2 + (-15614.05)/T + (-5.2182 × 10 -11 )/T 2 ] J/mol-K, where T is the temperature in K.

Identification of the Transformational Properties and Transcriptional Targets of the Oncogenic SRY Transcription Factor SOX4

DTIC Science & Technology

2008-01-01

oncogenic properties of the transcription factor SOX4 and to determine its role in murine prostate development. Our lab has previously shown SOX4...mRNA and protein to be overexpressed in prostate cancer, and this expression is correlated with increasing Gleason score. Other labs have shown SOX4...D. Lieb, Genome Biol 6, R97 (2005). 2. M. van Beest et al., J Biol Chem 275, 27266 (Sep 1, 2000). 3. M. van de Wetering, M. Oosterwegel, K. van

Intramembraneous Particle Cluster and Cytoplasmic Vesicles in Mice with Nephrogenic Defects of Urinary Concentration.

DTIC Science & Technology

1987-01-01

DiBona , D.R., M.M. Civan, and A. Leaf. The cellular specificity of the effect of vasopressin on toad urinary bladder. J. Membr. Biol. 1:79-91, 1969. 30...Chem. 240:4524-4526, 1965. 62. Hardy, M.A., and D.R. DiBona . Microfilaments and the hydrosmotic action of vasopressin in toad urinary bladder. Am. J... DiBona , D.R., M.M. Civan, and A. Leaf. The cellular specificity of the effect of vasopressin on toad urinary bladder. J. Membr. Biol. 1:79-91, 1969. 30

External anal sphincter fatigue is not improved by N-acetylcysteine in an animal model.

PubMed

Healy, C F; McMorrow, C; O'Herlihy, C; O'Connell, P R; Jones, J F X

2008-06-01

Oxidative stress is associated with skeletal muscle fatigue. This study tests the hypotheses that N-acetylcysteine (NAC) reduces fatigue and accelerates recovery of the rat external anal sphincter (EAS). Fifteen female Wistar rats were killed humanely. The EAS was mounted as a ring preparation and electrically stimulated with 50 Hz trains of 200 ms in duration every 4 s for three and a half minutes. Three groups were analysed: a control group (n = 5), a group pretreated with NAC (10(-4) mol L(-1); n = 5) and a group pretreated with NAC (10(-3) mol L(-1); n = 5). A novel fatigue index was formulated and was compared to a conventional method of expressing fatigue. There was no significant difference at concentrations of NAC (10(-4) mol L(-1); P > 0.05). At high concentrations of NAC (10(-3) mol L(-1)) there was a significant depression in peak twitch amplitude before fatigue (P = 0.04). N-acetylcysteine in both concentrations used, did not alter fatigue or recovery of the rat EAS. There was a significant positive correlation between the two methods of expressing fatigue but the conventional method produced a higher fatigue index (22.4% on average). N-acetylcysteine does not ameliorate fatigue or accelerate recovery of the EAS and may not be a useful medical therapy for faecal incontinence.

Moringa oleifera Lam.: Protease activity against blood coagulation cascade

PubMed Central

Satish, A; Sairam, Sudha; Ahmed, Faiyaz; Urooj, Asna

2012-01-01

Background: The present study evaluated the protease activity of aqueous extracts of Moringa oleifera (Moringaceae) leaf (MOL) and root (MOR). Materials and Methods: Protease activity was assayed using casein, human plasma clot and human fibrinogen as substrates. Results: Caseinolytic activity of MOL was significantly higher (P ≤ 0.05) than that of MOR. Similar observations were found in case of human plasma clot hydrolyzing activity, wherein MOL caused significantly higher (P ≤ 0.05) plasma clot hydrolysis than MOR. Zymographic techniques were used to detect proteolytic enzymes following electrophoretic separation in gels. Further, both the extracts exhibited significant procoagulant activity as reflected by a significant decrease (P ≤ 0.05) in recalcification time, accompanied by fibrinogenolytic and fibrinolytic activities; clotting time was decreased from 180 ± 10 sec to 119 ± 8 sec and 143 ± 10 sec by MOL and MOR, respectively, at a concentration of 2.5 mg/mL. Fibrinogenolytic (human fibrinogen) and fibrinolytic activity (human plasma clot) was determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), plate method and colorimetric method. Zymographic profile indicated that both the extracts exerted their procoagulant activity by selectively hydrolyzing Aα and Bβ subunits of fibrinogen to form fibrin clot, thereby exhibiting fibrinogenolytic activity. However, prolonged incubation resulted in degradation of the formed fibrin clot, suggesting fibrinolytic like activity. Conclusions: These findings support the traditional usage of M. oleifera extracts for wound healing. PMID:22224061

Post-chemiluminescence determination of chloramphenicol based on luminol-potassium periodate system.

PubMed

Yang, Xiao Feng; Li, Nian Bing; Luo, Hong Qun

2012-01-01

A post-chemiluminescence (PCL) phenomenon was observed when chloramphenicol was injected into a mixture of luminol and potassium periodate after the chemiluminescence (CL) reaction of luminol-potassium periodate had finished. The possible reaction mechanism was proposed based on studies of the CL kinetic characteristics, the CL spectra, the fluorescence spectra and the UV-vis absorption spectra of the related substances. Based on the PCL reaction, a rapid and sensitive method for the determination of chloramphenicol was established. The linear response range was 6.0 × 10(-7) -1.0 × 10(-5) mol/L, with a correlation coefficient of 0.9986. The relative standard deviation (RSD) for 5.0 × 10(-6) mol/L chloramphenicol was 2.3% (n = 11). The detection limit was 1.6 × 10(-7) mol/L. The method has been applied to the determination of chloramphenicol in pharmaceutical samples with satisfactory results. Copyright © 2011 John Wiley & Sons, Ltd.

[Effects of elevated ozone concentrations on reactive oxygen metabolism and related gene expression in Ginkgo biloba leaves].

PubMed

Ruan, Ya Nan; Xu, Sheng; Guo, Long; Zhu, Ming Zhu; Wang, Cong; Li, Shu Yuan; Wang, Hong Yan

2017-11-01

By using the open top chambers (OTCs) fumigation method, this paper investigated the changes of foliar injury, level of reactive oxygen species (ROS), activities and gene expression of antioxidant enzymes in Ginkgo biloba leaves under different ozone (ambient ozone≈40, 80, 160, 200 nmol·mol -1 ) concentrations, in order to study the effects of elevated ozone (O 3 ) concentrations on reactive metabolism. The results showed that the obvious foliar injuries were observed in 160 and 200 nmol·mol -1 O 3 treatments, while no visible injury was observed in 80 nmol·mol -1 O 3 and ambient O 3 treatments. After 20 d, a significant increase in O 2 -· generation rate was observed in G. biloba leaves exposed to 160, 200 nmol·mol -1 O 3 , compared with ambient ozone and 80 nmol·mol -1 O 3 , and there were no significant differences between ambient O 3 and 80 nmol·mol -1 treatments. After 40 d, H 2 O 2 content of G. biloba leaves in 160 and 200 nmol·mol -1 O 3 was significantly higher than that in 80 nmol·mol -1 and ambient ozone, respectively. The activities of catalase (CAT) in 160 and 200 nmol·mol -1 treatments were also significantly higher than that in 80 nmol·mol -1 and ambient O 3 treatments. The ascorbate peroxidase (APX) activity of leaves for each elevated O 3 treatment was lower than that of ambient ozone. The level of CAT and APX expression increased progressively after 40 d O 3 treatment. The expression intensity of GbD was conspicuously strengthened along with the increase of ozone concentration and fumigation time. Le-vel of reactive oxygen increased, activities of antioxidant enzyme decreased, level of gene expression down-regulated, and foliar visible injury was observed in leaves of G. biloba in elevated ozone stress.

Dissociation of Rac1(GDP)·RhoGDI Complexes by the Cooperative Action of Anionic Liposomes Containing Phosphatidylinositol 3,4,5-Trisphosphate, Rac Guanine Nucleotide Exchange Factor, and GTP*

PubMed Central

Ugolev, Yelena; Berdichevsky, Yevgeny; Weinbaum, Carolyn; Pick, Edgar

2008-01-01

Rac plays a pivotal role in the assembly of the superoxide-generating NADPH oxidase of phagocytes. In resting cells, Rac is found in the cytosol in complex with Rho GDP dissociation inhibitor (RhoGDI). NADPH oxidase assembly involves dissociation of the Rac·RhoGDI complex and translocation of Rac to the membrane. We reported that liposomes containing high concentrations of monovalent anionic phospholipids cause Rac·RhoGDI complex dissociation (Ugolev, Y., Molshanski-Mor, S., Weinbaum, C., and Pick, E. (2006) J. Biol. Chem.281 ,19204 -1921916702219). We now designed an in vitro model mimicking membrane phospholipid remodeling during phagocyte stimulation in vivo. We showed that liposomes of “resting cell membrane” composition (less than 20 mol % monovalent anionic phospholipids), supplemented with 1 mol % of polyvalent anionic phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) in conjunction with constitutively active forms of the guanine nucleotide exchange factors (GEFs) for Rac, Trio, or Tiam1 and a non-hydrolyzable GTP analogue, cause dissociation of Rac1(GDP)·RhoGDI complexes, GDP to GTP exchange on Rac1, and binding of Rac1(GTP) to the liposomes. Complexes were not dissociated in the absence of GEF and GTP, and optimal dissociation required the presence of PtdIns(3,4,5)P3 in the liposomes. Dissociation of Rac1(GDP)·RhoGDI complexes was correlated with the affinity of particular GEF constructs, via the N-terminal pleckstrin homology domain, for PtdIns(3,4,5)P3 and involved GEF-mediated GDP to GTP exchange on Rac1. Phagocyte membranes enriched in PtdIns(3,4,5)P3 responded by NADPH oxidase activation upon exposure in vitro to Rac1(GDP)·RhoGDI complexes, p67phox, GTP, and Rac GEF constructs with affinity for PtdIns(3,4,5)P3 at a level superior to that of native membranes. PMID:18505730

Two-strain competition in quasineutral stochastic disease dynamics.

PubMed

Kogan, Oleg; Khasin, Michael; Meerson, Baruch; Schneider, David; Myers, Christopher R

2014-10-01

We develop a perturbation method for studying quasineutral competition in a broad class of stochastic competition models and apply it to the analysis of fixation of competing strains in two epidemic models. The first model is a two-strain generalization of the stochastic susceptible-infected-susceptible (SIS) model. Here we extend previous results due to Parsons and Quince [Theor. Popul. Biol. 72, 468 (2007)], Parsons et al. [Theor. Popul. Biol. 74, 302 (2008)], and Lin, Kim, and Doering [J. Stat. Phys. 148, 646 (2012)]. The second model, a two-strain generalization of the stochastic susceptible-infected-recovered (SIR) model with population turnover, has not been studied previously. In each of the two models, when the basic reproduction numbers of the two strains are identical, a system with an infinite population size approaches a point on the deterministic coexistence line (CL): a straight line of fixed points in the phase space of subpopulation sizes. Shot noise drives one of the strain populations to fixation, and the other to extinction, on a time scale proportional to the total population size. Our perturbation method explicitly tracks the dynamics of the probability distribution of the subpopulations in the vicinity of the CL. We argue that, whereas the slow strain has a competitive advantage for mathematically "typical" initial conditions, it is the fast strain that is more likely to win in the important situation when a few infectives of both strains are introduced into a susceptible population.

Simple flow injection analysis system for simultaneous determination of phenolic antioxidants with multiple pulse amperometric detection at a boron-doped diamond electrode.

PubMed

Medeiros, Roberta Antigo; Lourenção, Bruna Cláudia; Rocha-Filho, Romeu Cardozo; Fatibello-Filho, Orlando

2010-10-15

A method for simultaneous determination of butylated hydroxyanisole (BHA) and butylated hydroxytoluene (BHT) in food was developed that uses multiple pulse amperometry (MPA) with flow injection analysis (FIA). Determination of these phenolic antioxidants was carried out with a cathodically pretreated boron-doped diamond electrode and an aqueous ethanolic (30% ethanol, v/v) 10 mmol L⁻¹ KNO₃ solution (pH(cond) = 1.5) as supporting electrolyte. A dual-potential waveform, at E(det1) = 850 mV/200 ms and E(det2) = 1150 mV/200 ms versus Ag/AgCl (3.0 mol L⁻¹ KCl), was employed. The use of E(det1) or E(det2) caused the oxidation of BHA or of BHA and BHT, respectively; hence, concentration subtraction could be used to determine both species. The respective analytical curves presented good linearity in the investigated concentration range (0.050-3.0 μmol L⁻¹ for BHA and 0.70-70 μmol L⁻¹ for BHT), and the detection limits were 0.030 μmol L⁻¹ for BHA and 0.40 μmol L⁻¹ for BHT. The proposed method, which is simple, quick, and presents good precision and accuracy, was successfully applied in the simultaneous determination of BHA and BHT in commercial mayonnaise samples, with results similar to those obtained by HPLC, at a 95% confidence level.

Protective role of Osthole on myocardial cell apoptosis induced by doxorubicin in rats

PubMed Central

Xu, Hongdang; Han, Yu; Zhang, Mengwei; Yan, Min; Gao, Chuanyu

2015-01-01

Objective: To explore the effect of Osthole on protecting myocardial cell apoptosis induced by doxorubicin during cardiac failure in rats. Methods: Myocardial cells isolated from the newborn SD rats were separated into three groups: cells treated with 1 μmol doxorubicin, cells treated with Osthole at three concentrations of 10, 20, and 40 μmol, cells treated neither with Osthole nor with doxorubicin were the control groups. Consequently, cell apoptosis of myocardial cells in each group was analyzed using TUNEL assay. Also, expressions of oxidase, NADPH, and ROS in myocardial cells were analyzed using different biological methods. Moreover, expressions of cell apoptosis associated proteins were analyzed using Western blotting. Results: Compared with the controls, the results showed that cells received Osthole and doxorubicin treatments performed high percentage of cell apoptosis, suggesting that Osthole could anesis myocardial cell apoptosis induced by doxorubicin (P<0.05). Osthole of 10 μmol depressed the expressions of cell apoptosis associated proteins including Caspase-3 and Cytc, and enhancing expression of Bcl-XL expression (P<0.05). Osthole of 20 μmol significantly decreased the generation of intracellar superoxidase, NADPH, and NADPH activity in myocardial cells treated with doxorubicin (P<0.05). Moreover, Osthole of 20 μmol could significantly increase phosphorylated elF2α level in cells. Conclusion: Our study suggested that Osthole may play a protective role in suppressing myocardial apoptosis induced by doxorubicin through inhibiting NADPH and superoxidase production and downstream phosphorylated elF2α. PMID:26617794

Anodic stripping voltammetric determination of mercury using multi-walled carbon nanotubes film coated glassy carbon electrode.

PubMed

Yi, Hongchao

2003-10-01

An electrochemical method for the determination of trace levels of mercury based on a multi-walled carbon nanotubes (MWNT) film coated glassy carbon electrode (GCE) is described. In 0.1 mol L(-1) HCl solution containing 0.02 mol L(-1) KI, Hg(2+) was firstly preconcentrated at the MWNT film and then reduced at -0.60 V. During the anodic potential sweep, reduced mercury was oxidized, and then a sensitive and well-defined stripping peak at about -0.20 V appeared. Under identical conditions, a MWNT film coated GCE greatly enhances the stripping peak current of mercury in contrast to a bare GCE. Low concentrations of I(-) remarkably improve the determining sensitivity, since this increases the accumulation efficiency of Hg(2+) at the MWNT film coated GCE. The stripping peak current is proportional to the concentration of Hg(2+) over the range 8 x 10(-10)-5 x 10(-7) mol L(-1). The lowest detectable concentration of Hg(2+) is 2 x 10(-10) mol L(-1) at 5 min accumulation. The relative standard deviation (RSD) at 1 x 10(-8) mol L(-1) Hg(2+) was about 6% ( n=10). By using this proposed method, Hg(2+) in some water samples was determined, and the results were compared with those obtained by atomic absorption spectrometry (AAS). The two results are similar, suggesting that the MWNT-film coated GCE has great potential in practical analysis.

Sol-Gel synthesis of MgO-SiO2 glass compositions having stable liquid-liquid immiscibility

NASA Technical Reports Server (NTRS)

Bansal, Narottam P.

1987-01-01

MgO-SiO2 glasses containing up to 15 mol % MgO, which could not have been prepared by the conventional glass melting method due to the presence of stable liquid-liquid immiscibility, were synthesized by the sol-gel technique. Clear and transparent gels were obtained from the hydrolysis and polycondensation of silicon tetraethoxide (TEOS) and magnesium nitrate hexahydrate when the water/TEOS mole ratio was four or more. The gelling time decreased with increase in magnesium content, water/TEOS ratio, and reaction temperature. Magnesium nitrate hexahydrate crystallized out of the gels containing 15 and 20 mol % MgO on slow drying. This problem was partially alleviated by drying the gels quickly at higher temperatures. Monolithic gel samples were prepared using glycerol as the drying control additive. The gels were subjected to various thermal treatments and characterized by several methods. No organic groups could be detected in the glasses after heat treatments to approx. 800 C, but trace amounts of hydroxyl groups were still present. No crystalline phase was found from X-ray diffraction in the gel samples to approx. 890 C. At higher temperatures, alpha quartz precipitated out as the crystalline phase in gels containing up to 10 mol % MgO. The overall activation energy for gel formation in 10MgO-90SiO2 (mol %) system for water/TEOS mole ratio of 7.5 was calculated to be 58.7 kJ/mol.

Sol-gel synthesis of magnesium oxide-silicon dioxide glass compositions

NASA Technical Reports Server (NTRS)

Bansal, Narottam P.

1988-01-01

MgO-SiO2 glasses containing up to 15 mol pct MgO, which could not have been prepared by the conventional glass melting method due to the presence of stable liquid-liquid immiscibility, were synthesized by the sol-gel technique. Clear and transparent gels were obtained from the hydrolysis and polycondensation of silicon tetraethoxide (TEOS) and magnesium nitrate hexahydrate when the water/TEOS mole ratio was four or more. The gelling time decreased with increase in magnesium content, water/TEOS ratio, and reaction temperature. Magnesium nitrate hexahydrate crystallized out of the gels containing 15 and 20 mol pct MgO on slow drying. This problem was partially alleviated by drying the gels quickly at higher temperatures. Monolithic gel samples were prepared using glycerol as the drying control additive. The gels were subjected to various thermal treatments and characterized by several methods. No organic groups could be detected in the glasses after heat treatments to approx. 800 C, but trace amounts of hydroxyl groups were still present. No crystalline phase was found from X-ray diffraction in the gel samples to approx. 890 C. At higher temperatures, alpha quartz precipitated out as the crystalline phase in gels containing up to 10 mol pct MgO. The overall activation energy for gel formation in 10MgO-90SiO2 (mol pct) system for water/TEOS mole ratio of 7.5 was calculated to be 58.7 kJ/mol.

Coevolutionary modeling of protein sequences: Predicting structure, function, and mutational landscapes

NASA Astrophysics Data System (ADS)

Weigt, Martin

Over the last years, biological research has been revolutionized by experimental high-throughput techniques, in particular by next-generation sequencing technology. Unprecedented amounts of data are accumulating, and there is a growing request for computational methods unveiling the information hidden in raw data, thereby increasing our understanding of complex biological systems. Statistical-physics models based on the maximum-entropy principle have, in the last few years, played an important role in this context. To give a specific example, proteins and many non-coding RNA show a remarkable degree of structural and functional conservation in the course of evolution, despite a large variability in amino acid sequences. We have developed a statistical-mechanics inspired inference approach - called Direct-Coupling Analysis - to link this sequence variability (easy to observe in sequence alignments, which are available in public sequence databases) to bio-molecular structure and function. In my presentation I will show, how this methodology can be used (i) to infer contacts between residues and thus to guide tertiary and quaternary protein structure prediction and RNA structure prediction, (ii) to discriminate interacting from non-interacting protein families, and thus to infer conserved protein-protein interaction networks, and (iii) to reconstruct mutational landscapes and thus to predict the phenotypic effect of mutations. References [1] M. Figliuzzi, H. Jacquier, A. Schug, O. Tenaillon and M. Weigt ''Coevolutionary landscape inference and the context-dependence of mutations in beta-lactamase TEM-1'', Mol. Biol. Evol. (2015), doi: 10.1093/molbev/msv211 [2] E. De Leonardis, B. Lutz, S. Ratz, S. Cocco, R. Monasson, A. Schug, M. Weigt ''Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction'', Nucleic Acids Research (2015), doi: 10.1093/nar/gkv932 [3] F. Morcos, A. Pagnani, B. Lunt, A. Bertolino, D. Marks, C. Sander, R. Zecchina, J.N. Onuchic, T. Hwa, M. Weigt, ''Direct-coupling analysis of residue co-evolution captures native contacts across many protein families'', Proc. Natl. Acad. Sci. 108, E1293-E1301 (2011).

A comparison of somatic mutational spectra in healthy study populations from Russia, Sweden and USA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noori, P; Hou, S; Jones, I M

Comparison of mutation spectra at the hypoxanthine-phosphoribosyl transferase (HPRT) gene of peripheral blood T lymphocytes may provide insight into the aetiology of somatic mutation contributing to carcinogenesis and other diseases. To increase knowledge of mutation spectra in healthy people, we have analyzed HPRT mutant T-cells of 50 healthy Russians originally recruited as controls for a study of Chernobyl clean-up workers (Jones et al. Radiation Res. 158, 2002, 424). Reverse transcriptase polymerase chain reactions and DNA sequencing identified 161 independent mutations among 176 thioguanine resistant mutants. Forty (40) mutations affected splicing mechanisms and 27 deletions or insertions of 1 to 60more » nucleotides were identified. Ninety four (94) single base substitutions were identified, including 62 different mutations at 55 different nucleotide positions, of which 19 had not previously been reported in human T-cells. Comparison of this base substitution spectrum with mutation spectra in a USA (Burkhart-Schultz et al. Carcinogenesis 17, 1996, 1871) and two Swedish populations (Podlutsky et al, Carcinogenesis 19, 1998, 557, Podlutsky et al. Mutation Res. 431, 1999, 325) revealed similarity in the type, frequency and distribution of mutations in the four spectra, consistent with aetiologies inherent in human metabolism. There were 15-19 identical mutations in the three pair-wise comparisons of Russian with USA and Swedish spectra. Intriguingly, there were 21 mutations unique to the Russian spectrum, and comparison by the Monte Carlo method of Adams and Skopek (J. Mol. Biol. 194, 1987, 391) indicated that the Russian spectrum was different from both Swedish spectra (P=0.007, 0.002) but not different from the USA spectrum (P=0.07), when Bonferroni correction for multiple comparisons was made (p < 0.008 required for significance). Age and smoking did not account for these differences. Other factors causing mutational differences need to be explored.« less

Speciation on a conveyor belt: sequential colonization of the hawaiian islands by Orsonwelles spiders (Araneae, Linyphiidae).

PubMed

Hormiga, Gustavo; Arnedo, Miquel; Gillespie, Rosemary G

2003-02-01

Spiders of the recently described linyphiid genus Orsonwelles (Araneae, Linyphiidae) are one of the most conspicuous groups of terrestrial arthropods of Hawaiian native forests. There are 13 known Orsonwelles species, and all are single- island endemics. This radiation provides an excellent example of insular gigantism. We reconstructed the cladistic relationships of Orsonwelles species using a combination of morphological and molecular characters (both mitochondrial and nuclear sequences) within a parsimony framework. We explored and quantified the contribution of different character partitions and their sensitivity to changes in the traditional parameters (gap, transition, and transversion costs). The character data show a strong phylogenetic signal, robust to parameter changes. The monophyly of the genus Orsonwelles is strongly supported. The parsimony analysis of all character evidence combined recovered a clade with of all the non-Kauai Orsonwelles species; the species from Kauai form a paraphyletic assemblage with respect to the latter former clade. The biogeographic pattern of the Hawaiian Orsonwelles species is consistent with colonization by island progression, but alternative explanations for our data exist. Although the geographic origin of the radiation remains unknown, it appears that the ancestral colonizing species arrived first on Kauai (or an older island). The ambiguity in the area cladogram (i.e., post-Oahu colonization) is not derived from conflicting or unresolved phylogenetic signal among Orsonwelles species but rather from the number of taxa on the youngest islands. Speciation in Orsonwelles occurred more often within islands (8 of the 12 cladogenic events) than between islands. A molecular clock was rejected for the sequence data. Divergence times were estimated by using the nonparametric rate smoothing method of Sanderson (1997, Mol. Biol. Evol. 14:1218-1231) and the available geological data for calibration. The results suggest that the oldest divergences of Orsonwelles spiders (on Kauai) go back about 4 million years.

High resolution analysis of trace elements in corals by laser ablation ICP-MS

NASA Astrophysics Data System (ADS)

Sinclair, Daniel J.; Kinsley, Leslie P. J.; McCulloch, Malcolm T.

1998-06-01

A method has been developed using laser ablation inductively-coupled plasma mass spectrometry (LA-ICP-MS) for rapid high resolution analysis of B, Mg, Sr, Ba, and U in corals. Corals represent a challenge for a microbeam technique due to their compositional and structural heterogeneity, their nonsilicate matrix, and their unusual range of trace element compositions relative to available standards. The method employs an argon-fluoride excimer laser (λ = 193 nm), masked to produce a beam 600 μm wide by 20 μm across to average ablation sampling over a range of structural features. Coral sections are scanned at a constant rate beneath the laser to produce a continuous sampling of the coral surface. Sensitivity drift is controlled by careful preconditioning of the ICP-MS to carbonate material, and standardisation is carried out by bracketing each traverse down the coral sample by analyses of a CaSiO 3 glass synthesised from coral powder. The method demonstrates excellent reproducibility of both the shape and magnitude of coralline trace element profiles, with typical precisions of between 1.0 and 3.7% based on analysis of the synthetic standard. Accuracy varies between 3.8% for B and 31% for U. Discrepancies are attributed to heterogeneities in the synthetic standard, and matrix differences between the silicate standard and carbonate sample. The method is demonstrated by analysis of a coral collected from Australia's Great Barrier Reef near a weather station recording in-situ sea-surface-temperature (SST). The elements B, Mg, Sr, and U show seasonal compositional cycles, and tentative calibrations against SST have been derived. Using independent ICP-MS solution estimates of the coral composition to correct for standardisation uncertainties, the following calibrations have been derived: B/Ca (μmol/mol)= 1000 (±20)- 20.6 (±0.8)× SSTMg/Ca (mmol/mol)= 0.0 (±0.3)+ 0.16 (±0.01)× SSTSr/Ca (mmol/mol)= 10.8 (±0.1)- 0.070 (±0.004)× SSTU/Ca (μmol/mol)= 2.24 (±0.07)- 0.046 (±0.003)× SSTl These calibrations agree with literature within experimental errors, except for Mg which displays a 35% greater temperature dependence than reported previously. None of the elements in the coral appear to be sensitive to decreases in salinity associated with heavy rainfall in the summer of 1991/1992.

Spectrophotometric determination of fluoxetine hydrochloride in bulk and in pharmaceutical formulations.

PubMed

Prabhakar, A H; Patel, V B; Giridhar, R

1999-07-01

Two new rapid, sensitive and economical spectrophotometric methods are described for the determination of fluoxetine hydrochloride in bulk and in pharmaceutical formulations. Both methods are based on the formation of a yellow ion-pair complex due to the action of methyl orange (MO) and thymol blue (TM) on fluoxetine in acidic (pH 4.0) and basic (pH 8.0) medium, respectively. Under optimised conditions they show an absorption maxima at 433 nm (MO) and 410 nm (TB), with molar absorptivities of 2.12 x 10(-4) and 4.207 x 10(-3) l mol(-1) cm(-1) and Sandell's Sensitivities of 1.64 x 10(-2) and 0.082 microg cm(-2) per 0.001 absorbance unit for MO and TB, respectively. The colour is stable for 5 min after extraction. In both cases Beer's Law is obeyed at 1-20 microg mol(-1) with MO and 4-24 microg mol(-1) with TB. The proposal method was successfully extended to pharmaceutical preparations capsules. The results obtained by both the agreement and E.P. (3rd edition) were in good agreement and statistical comparison by Student's t-test and variance ratio F-test showed no significant difference in the three methods.

Characterization of gold kiwifruit pectin from fruit of different maturities and extraction methods.

PubMed

Yuliarti, Oni; Matia-Merino, Lara; Goh, Kelvin K T; Mawson, John; Williams, Martin A K; Brennan, Charles

2015-01-01

Studies on gold kiwifruit pectins are limited. In this work, the characterization of pectin isolated from two different stages of maturity of gold kiwifruit, namely early harvested fruit (EHF) and main harvested fruit (MHF) isolated by three methods (acid, water, enzymatic) was carried out. Pectins isolated from MHF were higher in galacturonic acid content (52-59% w/w) and weight-average molecular weights (Mw, 1.7-3.8 × 10(6)g/mol) compared with EHF pectins (29-49% w/w and 0.2-1.7 × 10(6)g/mol respectively). Enzymatic treatment gave the highest yield but lowest in Mw, viscosity and mechanical spectra for both maturities. The pectin of both maturities was classified as high-methoxyl pectin with the degree of esterification ranged from 82% to 90%. Water-extracted MHF pectin molecules had the highest RMS radius (182.7 nm) and Mw (3.75 × 10(6)g/mol). The water extraction method appeared to retain the native state of pectin molecules compared with acid and enzymatic extraction methods based on the Mw and viscosity data. Copyright © 2014 Elsevier Ltd. All rights reserved.

Extraction and characterisation of pomace pectin from gold kiwifruit (Actinidia chinensis).

PubMed

Yuliarti, Oni; Goh, Kelvin K T; Matia-Merino, Lara; Mawson, John; Brennan, Charles

2015-11-15

Gold kiwifruit pomace extracted using citric acid, water and enzyme (Celluclast 1.5L) were studied in terms of pectin yield, protein, ash, non-starch polysaccharide, galacturonic acid (GalA), neutral sugar composition, molar mass (Mw), viscosity and degree of branching. Water-extracted pectin was considered closest to its native form. Enzyme extracted pectin showed the highest yield (∼ 4.5%w/w) as compared with the acid and water extraction methods (∼ 3.6-3.8%w/w). Pectin obtained from different extraction methods showed different degree of branching. The Mw and root mean square (RMS) radius varied with the extraction methods with values of 8.4 × 10(5) g/mol and 92 nm, 8.5 × 10(5)g/mol and 102 nm, 6.7 × 10(5) g/mol and 52 nm for acid, water and enzymatic extraction methods, respectively. Similar trend was observed for pectin viscosity, with water-extracted pectin giving a slightly higher viscosity followed by acid and enzyme-extracted pectin. This study showed that gold kiwifruit pomace pectin has potential application in food products. Copyright © 2015 Elsevier Ltd. All rights reserved.

Calorimetric determination of the enthalpy of 1-butyl-3-methylimidazolium bromide synthesis: a key quantity in thermodynamics of ionic liquids.

PubMed

Paulechka, Yauheni U; Kabo, Andrey G; Blokhin, Andrey V

2009-11-05

The enthalpy of the 1-butyl-3-methylimidazolium bromide [C(4)mim]Br ionic liquid synthesis reaction 1-methylimidazole (liq) + 1-bromobutane (liq) --> [C(4)mim]Br (liq) was determined in a homemade small-volume isoperibol calorimeter to be Delta(r)H degrees (298) = -87.7 +/- 1.6 kJ x mol(-1). The activation energy for this reaction in a homogeneous system E(A) = 73 +/- 4 kJ x mol(-1) was found from the results of calorimetric measurements. The formation enthalpies for the crystalline and liquid [C(4)mim]Br were determined from the calorimetric data: Delta(f)H degrees (298)(cr) = -178 +/- 5 kJ x mol(-1) and Delta(f)H degrees (298)(liq) = -158 +/- 5 kJ x mol(-1). The ideal-gas formation enthalpy of this compound Delta(f)H degrees (298)(g) = 16 +/- 7 kJ x mol(-1) was calculated using the methods of quantum chemistry and statistical thermodynamics. The vaporization enthalpy of [C(4)mim]Br, Delta(vap)H degrees (298) = 174 +/- 9 kJ x mol(-1), was estimated from the experimental and calculated formation enthalpies. It was demonstrated that vapor pressure of this ionic liquid cannot be experimentally determined.

Kinetics of non-isothermal decomposition of cinnamic acid

NASA Astrophysics Data System (ADS)

Zhao, Ming-rui; Qi, Zhen-li; Chen, Fei-xiong; Yue, Xia-xin

2014-07-01

The thermal stability and kinetics of decomposition of cinnamic acid were investigated by thermogravimetry and differential scanning calorimetry at four heating rates. The activation energies of this process were calculated from analysis of TG curves by methods of Flynn-Wall-Ozawa, Doyle, Distributed Activation Energy Model, Šatava-Šesták and Kissinger, respectively. There are only one stage of thermal decomposition process in TG and two endothermic peaks in DSC. For this decomposition process of cinnamic acid, E and log A[s-1] were determined to be 81.74 kJ mol-1 and 8.67, respectively. The mechanism was Mampel Power law (the reaction order, n = 1), with integral form G(α) = α (α = 0.1-0.9). Moreover, thermodynamic properties of Δ H ≠, Δ S ≠, Δ G ≠ were 77.96 kJ mol-1, -90.71 J mol-1 K-1, 119.41 kJ mol-1.

Poly(N-vinyl-2-pyrrolidone)-stabilized palladium-platinum nanoparticles-catalyzed hydrolysis of ammonia borane for hydrogen generation

NASA Astrophysics Data System (ADS)

Rakap, Murat

2015-02-01

The catalytic use of highly efficient poly(N-vinyl-2-pyrrolidone)-stabilized palladium-platinum nanoparticles (4.2 ± 1.9 nm) in the hydrolysis of ammonia-borane is reported. The catalyst is prepared by co-reduction of two metal ions in ethanol/water mixture by an alcohol reduction method and characterized by transmission electron microscopy, X-ray photoelectron spectroscopy and UV-Vis spectroscopy. They are recyclable and highly active for hydrogen generation from the hydrolysis of ammonia-borane even at very low concentrations and temperature, providing a record numbers of average turnover frequency value (125 mol H2/mol cat.min-1) and maximum hydrogen generation rate (3468 L H2 min-1 (mol cat)-1). They also provide activation energy of 51.7 ± 2 kJ/mol for the hydrolysis of ammonia borane.

Chiral recognition of naproxen enantiomers based on fluorescence quenching of bovine serum albumin-stabilized gold nanoclusters

NASA Astrophysics Data System (ADS)

Jafari, Marzieh; Tashkhourian, Javad; Absalan, Ghodratollah

2017-10-01

A simple, fast and green method for chiral recognition of S- and R-naproxen has been introduced. The method was based on quenching of the fluorescence intensity of bovine serum albumin-stabilized gold nanoclusters in the presence of naproxen enantiomers. The quenching intensity in the presence of S-naproxen was higher than R-naproxen when phosphate buffer solution at pH 7.0 was used. The chiral recognition occurred due to steric effect between bovine serum albumin conformation and naproxen enantiomers. Two linear determination range were established as 7.4 × 10-7-9.1 × 10-6 and 9.1 × 10-6-3.1 × 10-5 mol L-1 for both enantiomers and detection limits of 7.4 × 10-8 mol L- 1 and 9.5 × 10-8 mol L-1 were obtained for S- and R-naproxen, respectively. The developed method showed good repeatability and reproducibility for the analysis of a synthetic sample. To make the procedure applicable to biological samples, the removal of heavy metals from the sample is suggested before any analytical attempt.

Enrichment of omega-3 fatty acids in cod liver oil via alternate solvent winterization and enzymatic interesterification.

PubMed

Lei, Qiong; Ba, Sai; Zhang, Hao; Wei, Yanyan; Lee, Jasmine Yiqin; Li, Tianhu

2016-05-15

Enrichment of omega-3 fatty acids in cod liver oil via alternate operation of solvent winterization and enzymatic interesterification was attempted. Variables including separation method, solvent, oil concentration, time and temperature were optimized for the winterization. Meanwhile, Novozyme 435, Lipozyme RM IM and Lipozyme TL IM were screened for interesterification efficiency under different system air condition, time and temperature. In optimized method, alternate winterization (0.1g/mL oil/acetone, 24h, -80°C, precooled Büchner filtration) and interesterification (Lipozyme TL IM, N2 flow, 2.5h, 40°C) successfully doubled the omega-3 fatty acid content to 43.20 mol%. (1)H NMR was used to determine omega-3 fatty acid content, and GC-MS to characterize oil product, which mainly contained DHA (15.81 mol%) and EPA (20.23 mol%). The proposed method offers considerable efficiency and reduce production cost drastically. Oil produced thereof is with high quality and of particular importance for the development of omega-3 based active pharmaceutical ingredients. Copyright © 2015 Elsevier Ltd. All rights reserved.

Thickness Dependence of Failure in Ultra-thin Glassy Polymer Films

NASA Astrophysics Data System (ADS)

Bay, Reed; Shimomura, Shinichiro; Liu, Yujie; Ilton, Mark; Crosby, Alfred

The physical properties of polymer thin films change as the polymer chains become confined. Similar changes in mechanical properties have been observed, though these critical properties have only been explored a limited extent and with indirect methods. Here, we use a recently developed method to measure the complete uniaxial stress strain relationship of polymer thin films of polystyrene films (PS, Mw =130kg/mol, 490kg/mol, and 853kg/mol) as a function of thickness (20 nm-220nm). In this method, we hold a `dog-bone' shaped film on water between a flexible cantilever and a movable rigid boundary, measuring force-displacement from the cantilever deflection. From our measurements, we find that the modulus decreases as the PS chains become confined. The PS thin films exhibit ``ideal perfectly plastic'' behavior due to crazing, which differs from the typical brittle response of bulk PS. The draw stress due to crazing decreases with film thickness. These results provide new fundamental insight into how polymer behavior is altered due to structural changes in the entangled polymer network upon confinement. NSF DMR 1608614.

Vildagliptin vs sulfonylurea in Indian Muslim diabetes patients fasting during Ramadan

PubMed Central

Shete, Abhijit; Shaikh, Aheson; Nayeem, K Javeed; Rodrigues, Lily; Ali, Mohamed Sheikamunadeen Sadiq; Shah, Parag; Khanna, Rajiv; Majid, Sarfaraj; Rasheed, Sabeer A; Shaikh, Shehla; Rahman, Tawfiqur

2013-01-01

AIM: To compare the use of vildagliptin and sulfonylurea with or without metformin in Indian Muslim patients with type 2 diabetes mellitus, fasting during Ramadan. METHODS: This was a 4-wk, multicenter, non-interventional, open-label, observational study. Incidence of hypoglycemic events (HEs), adverse events, and changes in glycosylated hemoglobin A1c (HbA1c), fasting plasma glucose, postprandial plasma glucose and body weight were measured pre- and post-Ramadan. RESULTS: Totally, 97 patients were recruited and all completed the study (vildagliptin group, n = 55; sulfonylurea group, n = 42). HEs were reported in low frequencies in both the vildagliptin and the sulfonylurea groups [0 vs 2 (4.8%) patients, respectively]. Interestingly, HbA1c reduced by -0.43% (-4.71 mmol/mol) in the vildagliptin group [8.75% (72.10 mmol/mol) to 8.32% (67.38 mmol/mol), P = 0.009] while in the sulfonylurea group there was a small increase by 0.01% [0.08 mmol/mol; 8.64% (70.92 mmol/mol) to 8.65% (71.00 mmol/mol), P = 0.958]. Higher percentage of vildagliptin-treated patients achieved HbA1c < 7.0% (< 53 mmol/mol) compared with sulfonylurea (16.4% vs 4.8%). Mean decrease in the body weight was 1.2 kg and 0.03 kg, respectively (P < 0.001). Both treatment groups were well tolerated during Ramadan. CONCLUSION: Vildagliptin is an attractive treatment option for Indian patients with type 2 diabetes mellitus who are fasting during Ramadan. PMID:24379927

Multiscale Persistent Functions for Biomolecular Structure Characterization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xia, Kelin; Li, Zhiming; Mu, Lin

Here in this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions (MRFs) with persistent homology analysis, so as to construct a series of multiscale persistent functions, particularly multiscale persistent entropies, for structure characterization. To clarify the fundamental idea of our method, the multiscale persistent entropy (MPE) model is discussed in great detail. Mathematically, unlike the previous persistent entropy (Chintakunta et al. in Pattern Recognit 48(2):391–401, 2015; Merelli et al. in Entropy 17(10):6872–6892, 2015; Rucco et al. in: Proceedings of ECCS 2014, Springer, pp 117–128, 2016), a special resolutionmore » parameter is incorporated into our model. Various scales can be achieved by tuning its value. Physically, our MPE can be used in conformational entropy evaluation. More specifically, it is found that our method incorporates in it a natural classification scheme. This is achieved through a density filtration of an MRF built from angular distributions. To further validate our model, a systematical comparison with the traditional entropy evaluation model is done. Additionally, it is found that our model is able to preserve the intrinsic topological features of biomolecular data much better than traditional approaches, particularly for resolutions in the intermediate range. Moreover, by comparing with traditional entropies from various grid sizes, bond angle-based methods and a persistent homology-based support vector machine method (Cang et al. in Mol Based Math Biol 3:140–162, 2015), we find that our MPE method gives the best results in terms of average true positive rate in a classic protein structure classification test. More interestingly, all-alpha and all-beta protein classes can be clearly separated from each other with zero error only in our model. Finally, a special protein structure index (PSI) is proposed, for the first time, to describe the “regularity” of protein structures. Basically, a protein structure is deemed as regular if it has a consistent and orderly configuration. Our PSI model is tested on a database of 110 proteins; we find that structures with larger portions of loops and intrinsically disorder regions are always associated with larger PSI, meaning an irregular configuration, while proteins with larger portions of secondary structures, i.e., alpha-helix or beta-sheet, have smaller PSI. Essentially, PSI can be used to describe the “regularity” information in any systems.« less

A simple fluorescence quenching method for berberine determination using water-soluble CdTe quantum dots as probes

NASA Astrophysics Data System (ADS)

Cao, Ming; Liu, Meigui; Cao, Chun; Xia, Yunsheng; Bao, Linjun; Jin, Yingqiong; Yang, Song; Zhu, Changqing

2010-03-01

A novel method for the determination of berberine has been developed based on quenching of the fluorescence of thioglycolic acid-capped CdTe quantum dots (TGA-CdTe QDs) by berberine in aqueous solutions. Under optimum conditions, the relative fluorescence intensity was linearly proportional to the concentration of berberine between 2.5 × 10 -8 and 8.0 × 10 -6 mol L -1 with a detection limit of 6.0 × 10 -9 mol L -1. The method has been applied to the determination of berberine in real samples, and satisfactory results were obtained. The mechanism of the proposed reaction was also discussed.

The Role of a Novel Nucleolar Protein in Regulation of E2F1 in Breast Cancer

DTIC Science & Technology

2009-09-01

publication and successful defense of a PhD. 8 References 1. Paik JC, Wang B, Liu K, Lue J , Lin WC. Regulation of E2F1-induced apoptosis by...the nucleolar protein RRP1B. J Biol Chem. 2009 Dec 29. [E-pub ahead of print] 2. Hsieh SM, Look MP, Sieuwerts AM, Foekens JA, Hunter KW. Distinct...factor. J Biol Chem. 2009 Oct 16;284(42):28660-73. 4. Crawford NP, Walker RC, Lukes L, Officewala JS, Williams RW, Hunter KW. The Diasporin Pathway: a

Development of Pantothenate Analogs That Can Treat Combat-Related Infections

DTIC Science & Technology

2012-01-01

are as follows (Fig. 6): the MIC for E . faecalis was determined as 156 g/ml for N5-Pan and 29 g/ml for N7-Pan, respectively. In the case of S...Crystallogr.D.Biol.Crystallogr. 60, 2126-2132 (2004). 7. G. N. Murshudov, A. A. Vagin , E . J. Dodson, Acta Crystallogr.D.Biol.Crystallogr. 53, 240-255 (1997). 8. I. W...CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER E -Mail: 5f. WORK UNIT

INT6 May Influence Breast Cancer Formation by Regulating the 26S Proteasome

DTIC Science & Technology

2007-04-01

to res- cue the growth defects were discarded. The final cDNA clones were sequenced u s i n g t w o p r i m e r s : 5 ’ - CAATCTCATTCTCACTTTCTGAC-3...polyclonal rab- b i t a n t i b o d y u s i n g CIVKEIQDEKEAEAARKKGR as a pep- tide antigen. The confirmation of this an- tibody (1: 2,000) is shown...J. W. (1997) J. Biol. Chem. 272, 23477- 23480 12. Bandyopadhyay, A., Lakshmanan, V., Matsumoto, T ., Chang, E. C., and Maitra, U. (2002) J. Biol. Chem

A new irreversible enzyme-aided esterification method in organic solvents.

PubMed

Jeromin, Günter E; Zoor, Annegreth

2008-05-01

A new irreversible esterification method for carboxylic acids catalyzed by a lipase from Candida antarctica (Novozyme 435) in organic solvents has been developed. The water produced during the process is chemically destroyed by a corresponding ester of acetoacetate, which acts as a sacrificial substrate in this reaction. The flavour esters isobutyl acetate, methyl butyrate, ethyl butyrate and benzyl butyrate were synthesized either in small scale (0.05 mol) or large scale (1 mol). The yields range from 82 to 92% within 24 h at 52 degrees C. Optimal molar ratios of reactants were 1:1:1 (carboxylic acid:alcohol:acetoacetate).

Determination of β-blockers in pharmaceutical and human urine by capillary electrophoresis with electrochemiluminescence detection and studies on the pharmacokinetics.

PubMed

Wang, Yuanchao; Wu, Qiong; Cheng, Meirong; Cai, Cheng

2011-04-15

A novel method for simultaneous determination of atenolol, metoprolol and esmolol was proposed by capillary electrophoresis (CE) separation and electrochemiluminescence (ECL) detection. Poly-β-cyclodextrin (Poly-β-CD) was used as an additive in the running buffer to improve the separation of three analytes. The conditions for CE separation, ECL detection and effect of Poly-β-CD were investigated in detail. The three β-blockers with very similar structures were well separated and detected under the optimum conditions. The linear ranges of the standard solution for atenolol and esmolol were 2.5-125 μmol/L with a detection limit (S/N=3) of 0.5 μmol/L, and for metoprolol was 0.5-25 μmol/L with a detection limit of 0.1 μmol/L. For three β-blockers from spiked aqueous and urine samples, the accuracy and precision including intraday and interday experiments were performed by calculating the recovery, the relative standard deviations of the ECL intensity and the migration time, respectively. The developed method was applied to the determination of metoprolol content in commercial pharmaceutical, and the analytical results are in good agreement with the nominal value with recoveries in the range of 98.7-105%. The proposed method was also applied to the monitoring of pharmacokinetics for metoprolol in human body. Crown Copyright © 2011. Published by Elsevier B.V. All rights reserved.

Cell Signaling by a Novel SH2 Domain Protein that is Overexpressed with Her2 in Breast Cancer

DTIC Science & Technology

1998-01-01

1990) Methods Enzymol. 185, 51. Wary, K. K, Mainiero, F ., Isakoff, S. J., Marcantonio , E. E., and Giancotti 527-537 F . G. (1996) Cell 87, 733-743...family of SH2 domain proteins and acts cell nonautonomously in excretory canal development. Dev. Biol. 184:150-164. 3. Pelicci, G., L. Lanfrancone, F ...Grignani, J. McGlade, F . Cavallo, G. Forni, I. Nicoletti, T. Pawson, and P. G. Pelicci. 1992. A novel transforming protein (SHC) with an SH2

Comment on 'Imaging of prompt gamma rays emitted during delivery of clinical proton beams with a Compton camera: feasibility studies for range verification'.

PubMed

Sitek, Arkadiusz

2016-12-21

The origin ensemble (OE) algorithm is a new method used for image reconstruction from nuclear tomographic data. The main advantage of this algorithm is the ease of implementation for complex tomographic models and the sound statistical theory. In this comment, the author provides the basics of the statistical interpretation of OE and gives suggestions for the improvement of the algorithm in the application to prompt gamma imaging as described in Polf et al (2015 Phys. Med. Biol. 60 7085).

Comment on ‘Imaging of prompt gamma rays emitted during delivery of clinical proton beams with a Compton camera: feasibility studies for range verification’

NASA Astrophysics Data System (ADS)

Sitek, Arkadiusz

2016-12-01

The origin ensemble (OE) algorithm is a new method used for image reconstruction from nuclear tomographic data. The main advantage of this algorithm is the ease of implementation for complex tomographic models and the sound statistical theory. In this comment, the author provides the basics of the statistical interpretation of OE and gives suggestions for the improvement of the algorithm in the application to prompt gamma imaging as described in Polf et al (2015 Phys. Med. Biol. 60 7085).

Effect of preparation methods on the activity of titanium dioxide-carbon nitride composites for photocatalytic degradation of salicylic acid

NASA Astrophysics Data System (ADS)

Yuliati, L.; Salleh, A. M.; Hatta, M. H. M.; Lintang, H. O.

2018-04-01

In this study, titanium dioxide-carbon nitride (TiO2-CN) composites were prepared by three methods, which were one pot oxidation, impregnation, and physical mixing. Each series of the photocatalysts was prepared with different ratios of titanium to carbon (Ti/C), i.e., 1, 5, 10, 20, and 50 mol%. All samples were characterized by X-ray diffraction (XRD) and diffuse reflectance ultraviolet-visible (DR UV-Vis) spectroscopies. The characterization results confirmed the successful preparation of TiO2, CN, and the TiO2-CN composites. Photocatalytic activity tests were carried out for degradation of salicylic acid at room temperature for 6 h under UV and visible light irradiations. It was confirmed that all the prepared TiO2-CN composites showed better photocatalytic activities than the bare TiO2 and the bare CN. Under UV light irradiation, 90.6% of salicylic acid degradation was achieved on the best composite prepared by one pot oxidation with 5 mol% of titanium to carbon (Ti/C) ratio. On the other hand, the highest degradation under visible light irradiation was 94.3%, observed on the composite that was prepared also by one pot oxidation method with the Ti/C ratio of 10 mol%. Therefore, among the investigated methods, the best method to prepare the titanium dioxide-carbon nitride composites with high photocatalytic activity was one pot oxidation method.

Selective sensing of submicromolar iron(III) with 3,3‧,5,5‧-tetramethylbenzidine as a chromogenic probe

NASA Astrophysics Data System (ADS)

Zhang, Lufeng; Du, Jianxiu

2016-04-01

The development of highly selective and sensitive method for iron(III) detection is of great importance both from human health as well as environmental point of view. We herein reported a simple, selective and sensitive colorimetric method for the detection of Fe(III) at submicromolar level with 3,3,‧5,5‧-tetramethylbenzidine (TMB) as a chromogenic probe. It was observed that Fe(III) could directly oxidize TMB to form a blue solution without adding any extra oxidants. The reaction has a stoichiometric ratio of 1:1 (Fe(III)/TMB) as determined by a molar ratio method. The resultant color change can be perceived by the naked eye or monitored the absorbance change at 652 nm. The method allowed the measurement of Fe(III) in the range 1.0 × 10- 7-1.5 × 10- 4 mol L- 1 with a detection limit of 5.5 × 10- 8 mol L- 1. The relative standard deviation was 0.9% for eleven replicate measurements of 2.5 × 10- 5 mol L- 1 Fe(III) solution. The chemistry showed high selectivity for Fe(III) in contrast to other common cation ions. The practically of the method was evaluated by the determination of Fe in milk samples; good consistency was obtained between the results of this method and atomic absorption spectrophotometry as indicated by statistical analysis.

Fast simultaneous determination of trimethoprim and sulfamethoxazole by capillary zone electrophoresis with capacitively coupled contactless conductivity detection.

PubMed

da Silva, Iranaldo Santos; Vidal, Denis Tadeu Rajh; do Lago, Claudimir Lucio; Angnes, Lúcio

2013-04-01

The association of trimethoprim and sulfamethoxazole is a very effective with antibiotic properties, and commonly used in the treatment of a variety of infections. Due to the importance in diseases treatment of humans and also of animals, the development of methods for their quantification in commercial formulations is highly desirable. In the present study, a rapid method for simultaneous determination of these compounds using CE with capacitively coupled contactless conductivity detection was developed. A favorable working region for both analytes was from 12.5 to 200 μmol/L (linear responses with R > 0.999 for N = 5). Other parameters calculated were sensitivity (1.28 ± 0.10/1.45 ± 0.11) min/(μmol L), RSD (4.5%/2.0%), and LOD (1.1/3.3) μmol/L for trimethoprim and sulfamethoxazole, respectively. Under this condition, the total run time was only 2.6 min. The proposed method was applied to the determination of trimethoprim and sulfamethoxazole in commercial samples and the results were compared to those obtained by using a HPLC pharmacopoeia method. This new method is advantageous for quality-control analyses of trimethoprim and sulfamethoxazole in pharmaceuticals samples, because it is rapid and precise. Moreover, it is less laborious and demands minimum amounts of reagents in comparison to the recommended method. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The fluorescence and resonance Rayleigh scattering spectra study on the interactions of palladium (II)-Nootropic chelate with Congo red and their analytical applications

NASA Astrophysics Data System (ADS)

Chen, Fang; Peng, Jingdong; Liu, Shaopu; Peng, Huanjun; Pan, Ziyu; Bu, Lingli; Xiao, Huan; Zhang, Ruiwen

2017-04-01

A highly sensitive detection approach of resonance Rayleigh scattering spectra (RRS) is firstly applied to analyzing nootropic drugs including piracetam (PIR) and oxiracetam (OXI). In HCl-NaAc buffer solution (pH = 3.0), the OXI chelated with palladium (II) to form the chelate cation [Pd2·OXI]2 +, and then reacted with Congo red (CGR) by virtue of electrostatic attraction and hydrophobic force to form binary complex [Pd2·OXI]. CGR2, which could result in the great enhancement of RRS. The resonance Rayleigh scattering signal was recorded at λex = λem = 375 nm. This mixture complex not only has higher RRS, but also makes contribution to significant increase of fluorescence, and the same phenomena also were discovered in PIR. The enhanced RRS intensity is in proportion to the PIR and OXI concentration in the range of 0.03-3.0 μg mL- 1, and the detection limit (DL) of RRS method for PIR and OXI is 2.3 ng mL- 1 and 9.7 ng mL- 1. In addition, the DL of fluorescence method for PIR and OXI is 8.4 μg mL- 1 and 19.5 μg mL- 1. Obviously, the RRS is the highly sensitive method, and the recoveries of the two kinds of nootropic drugs were range from 100.4% to 101.8.0% with RSD (n = 5) from 1.1% to 3.1% by RRS method. This paper not only investigated the optimum conditions for detecting nootropics with using RRS method, but also focused on the reasons for enhancing RRS intensity and the reaction mechanism, which in order to firm and contract the resultant. Finally, The RRS method has been applied to detect nootropic drugs in human urine samples with satisfactory results. Fig. S2. The effect of ionic strength: Pd (II)-CGR system (curve a); Pd (II)-OXI-CGR system (curve b); Pd (II)-PIR- CGR system (curve c). Pd (II): 2.0 × 10- 4 mol L- 1; CGR: 1.0 × 10- 5 mol L- 1; OXI: 1.5 μg mL- 1; PIR: 2 μg mL- 1; NaCl: 1 mol L- 1. Fig. S3. The effect of time: Pd (II)-OXI-CGR system (curve a); Pd (II)-PIR-CGR system (curve b). Pd (II): 2.0 × 10- 4 mol L- 1; CGR: 1.0 × 10- 5 mol L- 1; OXI: 1.5 μg mL- 1. Fig. S4 Absorption spectra for Pd (II)-Nootropic-CGR system. Measured using a water blank: (1) OXI; (2) GIR; (3) OXI-CGR; (4) Pd (II); (5) Pd(II)-OXI; (6) PIR-OXI-CGR, OXI: 1.0 μg mL- 1; Pd (II) concentration: 3.0 × 10- 4 mol L- 1; CGR concentration: 1.0 × 10- 5 mol L- 1; HCl-NaAc: pH 3.0.

Hydrothermal Synthesis of PbTiO3 Nanocrystals with a pH-Adjusting Agent of Ammonia Solution

NASA Astrophysics Data System (ADS)

Li, Xinyi; Huang, Zhixiong; Zhang, Lianmeng; Guo, Dongyun

2018-05-01

The PbTiO3 nanocrystals were synthesized by a hydrothermal method, and ammonia solution was firstly used as a pH-adjusting agent. The effect of ammonia concentration on formation and morphologies of PbTiO3 nanocrystals was investigated. At low ammonia concentration (0-2.2 mol/L), no perovskite PbTiO3 phase was formed. When the ammonia concentration was 4.4 mol/L, the rod-like PbTiO3 nanocrystals with highly crystalline were successfully synthesized. As the ammonia concentration further increased to 13.2 mol/L, the flake-like PbTiO3 nanocrystals were formed.

Pathways for the OH + Br2 → HOBr + Br and HOBr + Br → HBr + BrO Reactions.

PubMed

Wang, Hongyan; Qiu, Yudong; Schaefer, Henry F

2016-02-11

The OH radical reaction with Br2 and the subsequent reaction HOBr + Br are of exceptional importance to atmospheric chemistry and environmental chemistry. The entrance complex, transition state, and exit complex for both reactions have been determined using the coupled-cluster method with single, double, and perturbative triple excitations CCSD(T) with correlation consistent basis sets up to size cc-pV5Z and cc-pV5Z-PP. Coupled cluster effects with full triples (CCSDT) and full quadruples (CCSDTQ) are explicitly investigated. Scalar relativistic effects, spin-orbit coupling, and zero-point vibrational energy corrections are evaluated. The results from the all-electron basis sets are compared with those from the effective core potential (ECP) pseudopotential (PP) basis sets. The results are consistent. The OH + Br2 reaction is predicted to be exothermic 4.1 ± 0.5 kcal/mol, compared to experiment, 3.9 ± 0.2 kcal/mol. The entrance complex HO···BrBr is bound by 2.2 ± 0.2 kcal/mol. The transition state lies similarly well below the reactants OH + Br2. The exit complex HOBr···Br is bound by 2.7 ± 0.6 kcal/mol relative to separated HOBr + Br. The endothermicity of the reaction HOBr + Br → HBr + BrO is 9.6 ± 0.7 kcal/mol, compared with experiment 8.7 ± 0.3 kcal/mol. For the more important reverse (exothermic) HBr + BrO reaction, the entrance complex BrO···HBr is bound by 1.8 ± 0.6 kcal/mol. The barrier for the HBr + BrO reaction is 6.8 ± 0.9 kcal/mol. The exit complex (Br···HOBr) for the HBr + BrO reaction is bound by 1.9 ± 0.2 kcal/mol with respect to the products HOBr + Br.

Vasorelaxant and antihypertensive effects of formononetin through endothelium-dependent and -independent mechanisms.

PubMed

Sun, Tao; Liu, Rui; Cao, Yong-xiao

2011-08-01

To investigate the mechanisms underlying the vasorelaxant effect of formononetin, an O-methylated isoflavone, in isolated arteries, and its antihypertensive activity in vivo. Arterial rings of superior mesenteric arteries, renal arteries, cerebral basilar arteries, coronary arteries and abdominal aortas were prepared from SD rats. Isometric tension of the arterial rings was recorded using a myograph system. Arterial pressure was measured using tail-cuff method in spontaneously hypertensive rats. Formononetin (1-300 μmol/L) elicited relaxation in arteries of the five regions that were pre-contracted by KCl (60 mmol/L), U46619 (1 μmol/L) or phenylephrine (10 μmol/L). The formononetin-induced relaxation was reduced by removal of endothelium or by pretreatment with L-NAME (100 μmol/L). Under conditions of endothelium denudation, formononetin (10, 30, and 100 μmol/L) inhibited the contraction induced by KCl and that induced by CaCl(2) in Ca(2+)-free depolarized medium. In the absence of extracellular Ca(2+), formononetin (10, 30, and 100 μmol/L) depressed the constriction caused by phenylephrine (10 μmol/L), but did not inhibit the tonic contraction in response to the addition of CaCl(2) (2 mmol/L). The contraction caused by caffeine (30 mmol/L) was not inhibited by formononetin (100 μmol/L). Formononetin (10 and 100 μmol/L) reduced the change rate of Ca(2+)-fluorescence intensity in response to KCl (50 mmol/L). In spontaneously hypertensive rats, formononetin (5, 10, and 20 mg/kg) slowly lowered the systolic, diastolic and mean arterial pressure. Formononetin causes vasodilatation via two pathways: (1) endothelium-independent pathway, probably due to inhibition of voltage-dependent Ca(2+) channels and intracellular Ca(2+) release; and (2) endothelium-dependent pathway by releasing NO. Both the pathways may contribute to its antihypertensive effect.

Toxicity Profile and Pharmacokinetic Study of A Phase I Low-Dose Schedule-Dependent Radiosensitizing Paclitaxel Chemoradiation Regimen for Inoperable Non-Small-Cell Lung Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Yuhchyau; Pandya, Kishan J.; Feins, Richard

Purpose: We report the toxicity profile and pharmacokinetic data of a schedule-dependent chemoradiation regimen using pulsed low-dose paclitaxel for radiosensitization in a Phase I study for inoperable non-small-cell lung cancer. Methods and Materials: Paclitaxel at escalating doses of 15 mg/m{sup 2}, 20 mg/m{sup 2}, and 25 mg/m{sup 2} were infused on Monday, Wednesday, and Friday with daily chest radiation in cohorts of 6 patients. Daily radiation was delayed for maximal G2/M arrest and apoptotic effect, an observation from preclinical investigations. Plasma paclitaxel concentration was determined by high-performance liquid chromatography. Results: Dose-limiting toxicities included 3 of 18 patients with Grade 3more » pneumonitis and 3 of 18 patients with Grade 3 esophagitis. There was no Grade 4 or 5 pneumonitis or esophagitis. There was also no Grade 3 or 4 neutropenia, thrombocytopenia, anemia or neuropathy. For Dose Levels I (15 mg/m{sup 2}), II (20 mg/m{sup 2}), and III (25 mg/m{sup 2}), the mean peak plasma level was 0.23 {+-} 0.06 {mu}mol/l, 0.32 {+-} 0.05 {mu}mol/l, and 0.52 {+-} 0.14 {mu}mol/l, respectively; AUC was 0.44 {+-} 0.09 {mu}mol/l, 0.61 {+-} 0.1 {mu}mol/l, and 0.96 {+-} 0.23 {mu}mol/l, respectively; and duration of drug concentration >0.05 {mu}mol/l (t > 0.05 {mu}mol/l) was 1.6 {+-} 0.3 h, 1.9 {+-} 0.2 h, and 3.0 {+-} 0.9 h, respectively. Conclusion: Pulsed low-dose paclitaxel chemoradiation is associated with low toxicity. Pharmacokinetic data showed that plasma paclitaxel concentration >0.05 {mu}mol/l for a minimum of 1.6 h was sufficient for effective radiosensitization.« less

Removal of toxic metals from vanadium-contaminated soils using a washing method: Reagent selection and parameter optimization.

PubMed

Jiang, Jianguo; Yang, Meng; Gao, Yuchen; Wang, Jiaming; Li, Dean; Li, Tianran

2017-08-01

Vanadium (V) contamination in soils is an increasing worldwide concern facing human health and environmental conservation. The fractionation of a metal influences its mobility and biological toxicity. We analyzed the fractionations of V and several other metals using the BCR three-step sequential extraction procedure. Among methods for removing metal contamination, soil washing is an effective permanent treatment. We conducted experiments to select the proper reagents and to optimize extraction conditions. Citric acid, tartaric acid, oxalic acid, and Na 2 EDTA all exhibited high removal rates of the extractable state of V. With a liquid-to-solid ratio of 10, washing with 0.4 mol/L citric acid, 0.4 mol/L tartaric acid, 0.4 mol/L oxalic acid, and 0.12 mol/L Na 2 EDTA led to removal rates of 91%, 88%, 88%, and 61%, respectively. The effect of multiple washing on removal rate was also explored. According to the changes observed in metal fractionations, differences in removal rates among reagents is likely associated with their pK a value, pH in solution, and chemical structure. We concluded that treating with appropriate washing reagents under optimal conditions can greatly enhance the remediation of vanadium-contaminated soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

Functionalized Multiwalled Carbon Nanotube Electrochemical Sensor for Determination of Anticancer Drug Flutamide

NASA Astrophysics Data System (ADS)

Farias, Julianna Santos; Zanin, Hudson; Caldas, Adriana Silva; dos Santos, Clenilton Costa; Damos, Flavio Santos; de Cássia Silva Luz, Rita

2017-10-01

An electrochemical sensor based on functionalized multiwalled carbon nanotubes (MWCNTf) has been developed and applied for determination of anticancer drug flutamide in pharmaceutical and artificial urine samples. The electrode was prepared by modifying a glassy carbon electrode with MWCNTf, denoted herein as MWCNTf/GCE. The MWCNTf/GCE electrode exhibited high catalytic activity, high sensitivity, and high stability and was applicable over a wide concentration range for flutamide. The effects of the scan rate, pH, and nature of the electrolyte on the electrochemical behavior of flutamide on the MWCNTf/GCE were investigated. The results showed that this electrode presented the best square-wave voltammetric response to flutamide in Britton-Robinson buffer solution at pH 5.0 at frequency of 50 Hz and amplitude of 0.06 V. The proposed sensor presents a wide linear response range from concentration of 0.1 μmol L-1 up to 1000 μmol L-1 (or 27.6 μg L-1 up to 0.27 g L-1), with limit of detection, limit of quantification, and sensitivity of 0.03 μmol L-1, 0.1 μmol L-1, and 0.30 μA μmol-1 L, respectively. The MWCNTf/GCE electrode was successfully applied for determination of flutamide in pharmaceutical formulations and artificial urine samples, giving results in agreement with those obtained by a comparative method described in literature. A paired Student's t-test revealed no statistical difference between the reference and proposed method at 95% confidence level. The average recovery for fortified samples was 101 ± 1%.

Low cost estimation of the contribution of post-CCSD excitations to the total atomization energy using density functional theory calculations

NASA Astrophysics Data System (ADS)

Sánchez, H. R.; Pis Diez, R.

2016-04-01

Based on the Aλ diagnostic for multireference effects recently proposed [U.R. Fogueri, S. Kozuch, A. Karton, J.M. Martin, Theor. Chem. Acc. 132 (2013) 1], a simple method for improving total atomization energies and reaction energies calculated at the CCSD level of theory is proposed. The method requires a CCSD calculation and two additional density functional theory calculations for the molecule. Two sets containing 139 and 51 molecules are used as training and validation sets, respectively, for total atomization energies. An appreciable decrease in the mean absolute error from 7-10 kcal mol-1 for CCSD to about 2 kcal mol-1 for the present method is observed. The present method provides atomization energies and reaction energies that compare favorably with relatively recent scaled CCSD methods.

H2O and CO2 fluxes at the floor of a boreal pine forest

NASA Astrophysics Data System (ADS)

Kulmala, Liisa; Launiainen, Samuli; Pumpanen, Jukka; Lankreijer, Harry; Lindroth, Anders; Hari, Pertti; Vesala, Timo

2008-04-01

We measured H2O and CO2 fluxes at a boreal forest floor using eddy covariance (EC) and chamber methods. Maximum evapotranspiration measured with EC ranged from 1.5 to 2.0mmol m-2 s-1 while chamber estimates depended substantially on the location and the vegetation inside the chamber. The daytime net CO2 exchange measured with EC (0-2μmol m-2 s-1) was of the same order as measured with the chambers. The nocturnal net CO2 exchange measured with the chambers ranged from 4 to 7μmol m-2 s-1 and with EC from ~4 to ~5μmol m-2 s-1 when turbulent mixing below the canopy was sufficient and the measurements were reliable. We studied gross photosynthesis by measuring the light response curves of the most common forest floor species and found the saturated rates of photosynthesis (Pmax) to range from 0.008 (mosses) to 0.184μmol g-1 s-1 (blueberry). The estimated gross photosynthesis at the study site based on average leaf masses and the light response curves of individual plant species was 2-3μmol m-2 s-1. At the same time, we measured a whole community with another chamber and found maximum gross photosynthesis rates from 4 to 7μmol m-2 s-1.

Phase stability and photocatalytic activity of Zr-doped anatase synthesized in miniemulsion

NASA Astrophysics Data System (ADS)

Schiller, Renate; Weiss, Clemens K.; Landfester, Katharina

2010-10-01

A series of mesoporous anatase-type TiO2 doped with zirconium (0-50 mol% Zr) was synthesized by combining the sol-gel process with the inverse miniemulsion technique. Nanoparticles between 100 and 300 nm were directly prepared from acidic precursor solutions of titanium glycolate (EGMT) and zirconium isopropoxide. The miniemulsion technique is a simple and convenient method to synthesize nanoparticles of homogeneous size because the reactions (here hydrolysis and condensation) take place in the confined space of nanodroplets (several hundreds of nanometres) and therefore in a highly controlled manner. For low doping levels (0-7.1 mol% Zr), ZrxTi1 - xO2 solid solutions were formed where Zr was uniformly dispersed into the anatase framework. For higher amounts of zirconium (Zr >= 7.1 mol%), the crystallization of zirconium titanate (ZrTiO4) occurred at a low temperature of 650 °C and it was obtained as a pure material for 47.4 mol% <= Zr <= 50 mol%. The influence of the amount of zirconium on the crystallinity, crystallite size, phase composition and stability, morphology and specific surface area was investigated. For the characterization transmission electron microscopy (TEM), x-ray diffraction (XRD), nitrogen sorption (BET) and inductively coupled plasma-optical emission spectrometry (ICP-OES) were used. The photocatalytic activity of the crystalline mixed oxides (0-9.4 mol% Zr) was examined for the degradation of methylene blue under UV irradiation.

Sensitive determination of 2-methoxyestradiol in pharmaceutical preparations and serum samples using flow injection chemiluminescence.

PubMed

Yao, Hanchun; Zhang, Min; Zeng, Wenyuan; Zeng, Xiaoying; Zhang, Zhenzhong

2014-05-01

A rapid and sensitive flow injection chemiluminescence (FI-CL) method is described for the determination of 2-methoxyestradiol (2ME) based on enhancement of the CL intensity from a potassium ferricyanide-calcein system in sodium hydroxide medium. The optimum conditions for the CL emission were investigated. Under optimized conditions, a linear calibration graph was obtained over the range 1.0 × 10(-8) to 1.0 × 10(-6) mol/L (r = 0.998) 2ME with a detection limit (3σ) of 5.4 × 10(-9) mol/L. The relative standard deviation (RSD) for 5.0 × 10(-7) mol/L 2ME was 1.7%. As a preliminary application, the proposed method was successfully applied to the determination of 2ME in injection solutions and serum samples. The possible CL mechanism was also proposed. Copyright © 2013 John Wiley & Sons, Ltd.

Determination of volatile corrosion inhibitors by capillary electrophoresis.

PubMed

Pereira, Elisabete A; Tavares, Marina F M

2004-10-08

In this work, a capillary electrophoresis (CE) method using indirect UV detection (214nm) for the simultaneous determination of monoethanolamine (MEA), diethanolamine (DEA), triethanolamine (TEA), diethylethanolamine (DEEA), monocyclohexylamine (MCHA) and dicyclohexylamine (DCHA) in water/ethanol extracts of wrapping materials containing volatile corrosion inhibitors (VCIs) was described. A running buffer consisting of 0.010 molL(-1) imidazole, 0.010 molL(-1) 2-hydroxyisobutyric acid (HIBA) and 0.010 molL(-1) 18-crown-6 ether enabled separation of the analytes in less than 7 min. A few method validation parameters were determined revealing good migration time repeatability (<0.7% RSD) and area repeatability (< 1.8% RSD). Limits of detection were in the range of 0.52-1.54 mg L(-1). Recovery values were in the range of 94.8-100.9%. The methodology was successfully applied to the analysis of three commercial products (VCI treated paper, foam and plastic). The concentration of amines in these materials varied from 0.050 to 22.3% (w/w).

Up-conversion green emission of Yb3+/Er3+ ions doped YVO4 nanocrystals obtained via modified Pechini's method

NASA Astrophysics Data System (ADS)

Szczeszak, Agata; Runowski, Marcin; Wiglusz, Rafal J.; Grzyb, Tomasz; Lis, Stefan

2017-12-01

A series of lanthanide doped yttrium vanadates were prepared by Pechini's method (sol-gel process). The as-prepared precursors, in the presence of citric acid, were calcined in the temperature range of 600-900 °C. The obtained products were composed of small nanoparticles, in the size range of 20-50 nm, depending on the annealing temperature, exhibiting a bright green up-conversion emission, under NIR laser irradiation, and emission lifetimes in the range of 4.7-18.3 μs. Their structural, morphological and spectroscopic properties were investigated in detail by XRD, HR-TEM including FFT analysis, EDX and spectroscopic techniques (emission, power dependence and emission kinetics). The luminescence quenching phenomenon, manifested in a decrease of up-conversion intensity and shortening of emission lifetime, was observed with increasing of the Yb3+ ion concentration and decreasing the particle size. The optimal concentration of the Yb3+ ions was found to be 15 mol% (YVO4: Yb3+ 15 mol%, Er3+ 2 mol%).

Magnetic, Electric and Optical Properties of Mg-Substituted Ni-Cu-Zn Ferrites

NASA Astrophysics Data System (ADS)

Kabbur, S. M.; Ghodake, U. R.; Kambale, Rahul C.; Sartale, S. D.; Chikhale, L. P.; Suryavanshi, S. S.

2017-10-01

The Ni0.25- x Mg x Cu0.30Zn0.45Fe2O4 ( x = 0.00 mol, 0.05 mol, 0.10 mol, 0.15 mol, 0.20 mol and 0.25 mol) magnetic oxide system was prepared by a sol-gel auto-combustion method using glycine as a fuel. X-ray diffraction study reveals the formation of pure spinel lattice symmetry along with the presence of a small fraction of unreacted Fe2O3 phase as a secondary phase due to incomplete combustion reaction between fuel and oxidizer. The lattice constant ( a) was found to decrease with the increase of Mg2+ content; the average crystallite size ( D) is observed in the range of 26.78-33.14 nm. At room temperature, all the samples show typical magnetic hysteresis loops with the decrease of magnetic moment ( n B) of Ni-Cu-Zn ferrites with the increase of Mg2+ content. The intrinsic vibrational absorption bands for the tetrahedral and octahedral sites of the spinel structure were confirmed by infrared (IR) spectroscopy. The optical parameters such as refractive index ( η), velocity of IR waves ( v) and jump rates ( J 1, J 2, J) were studied and found to be dependent on the variation of the lattice constant. The Curie temperature ( T c) of Ni-Cu-Zn mixed ferrite was found to decrease with Mg2+ addition. The composition x = 0.15 mol.% with a low dielectric loss tangent of 2% seems to have potential for multilayer chip inductor applications at a wide range of frequencies.

[The establishment of the immortalized mouse brain microvascular pericytes model and its preliminary application in screening of cerebrovascular toxicants].

PubMed

Zhao, H P; Gao, Y F; Xia, D; Zhao, Z Q; Wu, S; Wang, X H; Liu, H X; Xiao, C; Xing, X M; He, Y

2018-05-06

Objective: To establish the immortalized mouse brain microvascular pericytes model and to apply to the cerebrovascular toxicants screening study. Methods: Brain pericytes were isolated from 3 weeks of mice by tissue digestion. Immortalized pericyte cell line was constructed by infecting with LT retrovirus. Monoclone was selected to purify the immortalized pericyte cell line. The pericyte characteristics and purity were explored by immunocytochemistry. Cell proliferation was measured by using the Pomega MTS cell Proliferation Colorimetric Assay Kit. Pericytes were treated with 0, 160, 320, 640, 1 280, 2 560 μmol/L lead acetate, 0, 5, 10, 20, 40, 80 μmol/L cadmium chloride and 0, 5, 10, 20, 40, 80 μmol/L sodium arsenite in 24 hours. Cell toxicity of each group was determined by MTS assay, median lethal dose (LD(50)) was calculated in linear regression. Results: Mouse brain pericytes were successfully isolated by tissue separation and enzyme digestion method. After immortalized by LT retroviruses, monoclone was selected and expanded to establish pericyte cell line. The brain pericytes exhibited typical long spindle morphology and positive staining for α-SMA and Vimentin. The proliferation of brain pericytes cell lines was very slowly, and the doubling time was about 48 hours. The proliferation of immortalized brain pericytes cell lines was very quickly, and the doubling time was about 24 hours. After lead acetate, cadmium chloride and sodium arsenite treatment for 24 hours respectively, gradual declines in cell viability were observed. The LD(50) of lead acetate was 2 025.0 μmol/L, the LD(50) of cadmium chloride was 36.6 μmol/L, and the LD(50) of sodium arsenite was 33.2 μmol/L. Conclusion: The immortalized mouse brain microvascular pericyte model is established successfully by infecting with LT retrovirus, and can be applied to screen cerebrovascular toxicants. The toxicity of these toxicants to immortalized mouse brain microvascular pericyte is in sequence: sodium arsenite,cadmium chloride, lead acetate.

Structure and properties of Li 2S-P 2S 5-P 2S 3 glass and glass-ceramic electrolytes

NASA Astrophysics Data System (ADS)

Minami, Keiichi; Hayashi, Akitoshi; Ujiie, Satoshi; Tatsumisago, Masahiro

High lithium ion conducting 70Li 2S·(30 - x)P 2S 5· xP 2S 3 (mol%) glasses and glass-ceramics were prepared by the mechanical milling method. Glasses were obtained in the composition range of 0 ≦ x ≦ 10. The substitution of P 2S 3 for P 2S 5 promoted the formation of the P 2S 6 4- units in the glasses. The conductivity of the glass increased with an increase in P 2S 3 contents up to 5 mol% and the glass with 5 mol% of P 2S 3 showed the conductivity of 1 × 10 -4 S cm -1 at room temperature. In the case of glass-ceramics, the conductivity increased with an increase in P 2S 3 contents up to 1 mol%, and the superionic conducting Li 7P 3S 11 crystal was precipitated in the glass-ceramic. The glass-ceramic with 1 mol% of P 2S 3 showed the highest conductivity of 3.9 × 10 -3 S cm -1 at room temperature.

[6]-Shogaol inhibits melanogenesis in B16 mouse melanoma cells through activation of the ERK pathway

PubMed Central

Yao, Cheng; Oh, Jang-hee; Oh, Inn Gyung; Park, Chi-hyun; Chung, Jin Ho

2013-01-01

Aim: To investigate the effect of [6]-shogaol, an active ingredient in ginger, on melanogenesis and the underlying mechanisms. Methods: B16F10 mouse melanoma cells were tested. Cell viability was determined with the MTT assay. Melanin content and tyrosinase activity were analyzed with a spectrophotometer. The protein expression of tyrosinase and microphthalmia associated transcription factor (MITF), as well as phosphorylated or total ERK1/2 and Akt were measured using Western blot. Results: Treatment of the cells with [6]-shogaol (1, 5, 10 μmol/L) reduced the melanin content in a concentration-dependent manner. [6]-Shogaol (5 and 10 μmol/L) significantly decreased the intracellular tyrosinase activity, and markedly suppressed the expression levels of tyrosinase and MITF proteins in the cells. Furthermore, [6]-shogaol (10 μmol/L) activated ERK, which was known to negatively regulate melanin synthesis in these cells. Pretreatment with the specific ERK pathway inhibitor PD98059 (20 μmol/L) greatly attenuated the inhibition of melanin synthesis by [6]-shogaol (10 μmol/L). Conclusion: The results demonstrate that [6]-shogaol inhibits melanogenesis in B16F10 mouse melanoma cells via activating the ERK pathway. PMID:23123645

Mass Spectrometric Analysis of a Cyclic 7,8-Butanoguanine Adduct of N-Nitrosopyrrolidine: Comparison to other N-Nitrosopyrrolidine Adducts in Rat Hepatic DNA

PubMed Central

Loureiro, Ana Paula M.; Zhang, Wenbing; Kassie, Fekadu; Zhang, Siyi; Villalta, Peter W.; Wang, Mingyao; Hecht, Stephen S.

2009-01-01

The well established rat hepatocarcinogen N-nitrosopyrrolidine (NPYR, 1) requires metabolic activation to DNA adducts to express its carcinogenic activity. Among the NPYR-DNA adducts that have been identified, the cyclic 7,8-butanoguanine adduct 2-amino-6,7,8,9-tetrahydro-9-hydroxypyrido[2,1-f]purine-4(3H)-one (6), has been quantified using moderately sensitive methods, but its levels have never been compared to those of other DNA adducts of NPYR in rat hepatic DNA. Therefore, in this study, we developed a sensitive new LC-ESI-MS/MS-SRM method for quantitation of adduct 6, and compared its levels to those of several other NPYR-DNA adducts formed by different mechanisms. The new method was shown to be accurate and precise, with good recoveries and low fmol detection limits. Rats were treated with NPYR by gavage at doses of 46, 92, or 184 mg/kg body weight and sacrificed 16 h later. Hepatic DNA was isolated and analyzed for NPYR-DNA adducts. Adduct 6 was by far the most prevalent, with levels ranging from about 900 – 3000 μmol/mol Gua and responsive to dose. Levels of adducts formed from crotonaldehyde, a metabolite of NPYR, were about 0.2 – 0.9 Pmol/mol dGuo, while those of adducts resulting from reaction with DNA of tetrahydrofuranyl- like intermediates were in the range of 0.01 – 4 μmol/mol deoxyribonucleoside. The results of this study demonstrate that, among typical NPYR-DNA adducts, adduct 6 is easily the most abundant in hepatic DNA. Since previous studies have shown that it can be detected in the urine of NPYR-treated rats, the results suggest that it is a potential candidate as a biomarker for assessing human exposure to and metabolic activation of NPYR. PMID:19761253

Flow injection analysis of ethyl xanthate by gas diffusion and UV detection as CS2 for process monitoring of sulfide ore flotation.

PubMed

Cordeiro, Thiago G; Hidalgo, Pilar; Gutz, Ivano G R; Pedrotti, Jairo J

2010-07-15

A sensitive and robust analytical method for spectrophotometric determination of ethyl xanthate, CH(3)CH(2)OCS(2)(-) at trace concentrations in pulp solutions from froth flotation process is proposed. The analytical method is based on the decomposition of ethyl xanthate, EtX(-), with 2.0 mol L(-1) HCl generating ethanol and carbon disulfide, CS(2). A gas diffusion cell assures that only the volatile compounds diffuse through a PTFE membrane towards an acceptor stream of deionized water, thus avoiding the interferences of non-volatile compounds and suspended particles. The CS(2) is selectively detected by UV absorbance at 206 nm (epsilon=65,000 L mol(-1) cm(-1)). The measured absorbance is directly proportional to EtX(-) concentration present in the sample solutions. The Beer's law is obeyed in a 1x10(-6) to 2x10(-4) mol L(-1) concentration range of ethyl xanthate in the pulp with an excellent correlation coefficient (r=0.999) and a detection limit of 3.1x10(-7) mol L(-1), corresponding to 38 microg L(-1). At flow rates of 200 microL min(-1) of the donor stream and 100 microL min(-1) of the acceptor channel a sampling rate of 15 injections per hour could be achieved with RSD<2.3% (n=10, 300 microL injections of 1x10(-5) mol L(-1) EtX(-)). Two practical applications demonstrate the versatility of the FIA method: (i) evaluation the free EtX(-) concentration during a laboratory study of the EtX(-) adsorption capacity on pulverized sulfide ore (pyrite) and (ii) monitoring of EtX(-) at different stages (from starting load to washing effluents) of a flotation pilot plant processing a Cu-Zn sulfide ore. Copyright 2010 Elsevier B.V. All rights reserved.

DFT study of gases adsorption on sharp tip nano-catalysts surface for green fertilizer synthesis

NASA Astrophysics Data System (ADS)

Yahya, Noorhana; Irfan, Muhammad; Shafie, Afza; Soleimani, Hassan; Alqasem, Bilal; Rehman, Zia Ur; Qureshi, Saima

2016-11-01

The energy minimization and spin modifications of sorbates with sorbents in magnetic induction method (MIM) play a vital role in yield of fertilizer. Hence, in this article the focus of study is the interaction of sorbates/reactants (H2, N2 and CO2) in term of average total adsorption energies, average isosteric heats of adsorption energies, magnetic moments, band gaps energies and spin modifications over identical cone tips nanocatalyst (sorbents) of Fe2O3, Fe3O4 (magnetic), CuO and Al2O3 (non-magnetic) for green nano-fertilizer synthesis. Study of adsorption energy, band structures and density of states of reactants with sorbents are purely classical and quantum mechanical based concepts that are vividly illustrated and supported by ADSORPTION LOCATOR and Cambridge Seriel Total Energy Package (CASTEP) modules following classical and first principle DFT simulation study respectively. Maximum values of total average energies, total average adsorption energies and average adsorption energies of H2, N2 and CO2 molecules are reported as -14.688 kcal/mol, -13.444 kcal/mol, -3.130 kcal/mol, - kcal/mol and -6.348 kcal/mol over Al2O3 cone tips respectively and minimum over magnetic cone tips. Whereas, the maximum and average minimum values of average isosteric heats of adsorption energies of H2, N2 and CO2 molecules are figured out to be 3.081 kcal/mol, 4.842 kcal/mol and 6.848 kcal/mol, 0.988 kcal/mol, 1.554 kcal/mol and 2.236 kcal/mol over aluminum oxide and Fe3O4 cone tips respectively. In addition to the adsorption of reactants over identical cone sorbents the maximum and minimum values of net spin, electrons and number of bands for magnetite and aluminum oxide cone structures are attributed to 82 and zero, 260 and 196, 206 and 118 for Fe3O4 and Al2O3 cones respectively. Maximum and least observed values of band gap energies are figured out to be 0.188 eV and 0.018 eV with Al2O3 and Fe3O4 cone structures respectively. Ultimately, with the adsorption of reactants an identical increment of 14 electrons each in up and down spins is resulted.

[The role of transforming growth factor-β1/connective tissue growth factor signaling pathway in paraquat-induced pulmonary fibrosis].

PubMed

Li, H H; Cai, Q; Wang, Y P; Liu, H R; Huang, M

2016-07-20

Objective: To investigate the effects of Paraquat on human embryonic lung fibroblasts (MRC5) and explore the role of transforming growth factor-β 1 /connective tissue growth factor signaling pathway in paraquat-induced pulmonary fibrosis. Methods: MRC5 cells were cultured with different concentration of PQ (0, 12.5, 25, 50, 100, 200, 400 μmol/L) for 24 h. The viability of cells was measured by MTT. The protein level of TGF-β 1 were analyzed by ELISA after PQ treatment (0, 25, 50, 100 μmol/L) . To examine whether TGF-β 1 /CTGF signaling pathway was involved in paraquat-induced cytotoxicity, cells was divided into 6 groups: (1) control; (2) 25 μmol/L PQ group; (3) 50 μmol/L PQ group; (4) 100 μmol/L PQ group; (5) TGF-β 1 positive control group (50 μmol/L rhTGF-β 1 ) ; (6) stimulate group (100 μmol/L PQ+50 μmol/L TGF-β 1 ) . The protein levels of p-Smad2, p-Smad3 and CTGF were assayed by western blot. The mRNA level of CTGF was assayed by real time RT-PCR. Results: MTT showed that cell viability decreased with increasing PQ concentration ( P <0.05) . The protein expression of TGF-β 1 treated with PQ (25, 50, 100 μmol/L) significantly increased compared with control in a dose-independent manner ( P <0.05) . Exposure to PQ (25, 50, 100 μmol/L) induced increase of protein levels of p-Smad2 and p-Smad3. Noteworthy, the expression of p-Smad2 and p-Smad3 were dramatically increased following PQ plus TGF-β 1 stimulation ( P <0.05) . Exposure to PQ (50, 100μmol/L) induced increase of CTGF protein expression and similar greatly increase following PQ plus TGF-β 1 stimulation ( P <0.05) . Real time RT-PCR showed CTGF mRNA in all groups also significantly up-regulated compared with control ( P <0.05) . Conclusion: TGF-β 1 regulates the expression of target gene CTGF to exhibit its pro-fibrogenic effects by activating TGF-β 1 /Smad signaling pathway in PQ-induced pulmonary fibrosis.

Differential electrolytic potentiometric titration method for the determination of ciprofloxacin in drug formulations.

PubMed

Abulkibash, Abdalla M; Sultan, Salah M; Al-Olyan, Abeer M; Al-Ghannam, Sheikha M

2003-10-17

A simple and rapid differential electrolytic potentiometric titration method for the determination of ciprofloxacin was developed. The work is based on the fast complexation reaction between iron(III) and ciprofloxacin in a ratio of 1:3, respectively, in sulfuric acid media of 0.09 mol dm(-3). Among the electrodes tested silver amalgam electrodes were found to be a suitable indicating system. By applying a current density of 0.5 muA cm(-2) to these electrodes and using iron(III) solution of 0.097 mol dm(-3) as a titrant, normal titration curves were obtained. The method was successfully applied for the determination of ciprofloxacin in drug formulations as low as 4.0 ppm.

The protonation of N2O reexamined - A case study on the reliability of various electron correlation methods for minima and transition states

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.

1993-01-01

The protonation of N2O and the intramolecular proton transfer in N2OH(+) are studied using various basis sets and a variety of methods, including second-order many-body perturbation theory (MP2), singles and doubles coupled cluster (CCSD), the augmented coupled cluster (CCSD/T/), and complete active space self-consistent field (CASSCF) methods. For geometries, MP2 leads to serious errors even for HNNO(+); for the transition state, only CCSD/T/ produces a reliable geometry due to serious nondynamical correlation effects. The proton affinity at 298.15 K is estimated at 137.6 kcal/mol, in close agreement with recent experimental determinations of 137.3 +/- 1 kcal/mol.

Chemical and spectral behavior of nitric acid in aqueous sulfuric acid solutions: Absorption spectrum and molar absorption coefficient of nitronium ion

NASA Astrophysics Data System (ADS)

Ershov, Boris G.; Panich, Nadezhda M.

2018-01-01

The chemical species formed from nitric acid in aqueous solutions of sulfuric acid (up to 18.0 mol L- 1) were studied by optical spectroscopy method. The concentration region of nitronium ion formation was identified and NO2+ ion absorption spectrum was measured (λmax ≤ 190 nm and ε190 = 1040 ± 50 mol- 1 L cm- 1).

Inhibitory effects of patchouli alcohol on stress-induced diarrhea-predominant irritable bowel syndrome

PubMed Central

Zhou, Tian-Ran; Huang, Jing-Jing; Huang, Zi-Tong; Cao, Hong-Ying; Tan, Bo

2018-01-01

AIM To elucidate the mechanism of patchouli alcohol (PA) in treatment of rat models of diarrhea-predominant irritable bowel syndrome (IBS-D). METHODS We studied the effects of PA on colonic spontaneous motility using its cumulative log concentration (3 × 10−7 mol/L to 1 × 10−4 mol/L). We then determined the responses of the proximal and distal colon segments of rats to the following stimuli: (1) carbachol (1 × 10−9 mol/L to 1 × 10−5 mol/L); (2) neurotransmitter antagonists including Nω-nitro-L-arginine methyl ester hydrochloride (10 μmol/L) and (1R*, 2S*)-4-[2-Iodo-6-(methylamino)-9H-purin-9-yl]-2-(phosphonooxy)bicyclo[3.1.0]hexane-1-methanol dihydrogen phosphate ester tetraammonium salt (1 μmol/L); (3) agonist α,β-methyleneadenosine 5′-triphosphate trisodium salt (100 μmol/L); and (4) single KCl doses (120 mmol/L). The effects of blockers against antagonist responses were also assessed by pretreatment with PA (100 μmol/L) for 1 min. Electrical-field stimulation (40 V, 2-30 Hz, 0.5 ms pulse duration, and 10 s) was performed to observe nonadrenergic, noncholinergic neurotransmitter release in IBS-D rat colon. The ATP level of Kreb’s solution was also determined. RESULTS PA exerted a concentration-dependent inhibitory effect on the spontaneous contraction of the colonic longitudinal smooth muscle, and the half maximal effective concentration (EC50) was 41.9 μmol/L. In comparison with the KCl-treated IBS-D group, the contractile response (mg contractions) in the PA + KCl-treated IBS-D group (11.87 ± 3.34) was significantly decreased in the peak tension (P < 0.01). Compared with CCh-treated IBS-D rat colon, the cholinergic contractile response of IBS-D rat colonic smooth muscle (EC50 = 0.94 μmol/L) was significantly decreased by PA (EC50 = 37.43 μmol/L) (P < 0.05). Lack of nitrergic neurotransmitter release in stress-induced IBS-D rats showed contraction effects on colonic smooth muscle. Pretreatment with PA resulted in inhibitory effect on L-NAME-induced (10 μmol/L) contraction (P < 0.05). ATP might not be the main neurotransmitter involved in inhibitory effects of PA in the colonic relaxation of stress-induced IBS-D rats. CONCLUSION PA application may serve as a new therapeutic approach for IBS-D. PMID:29456408

The plastoquinol-plastoquinone exchange mechanism in photosystem II: insight from molecular dynamics simulations.

PubMed

Zobnina, Veranika; Lambreva, Maya D; Rea, Giuseppina; Campi, Gaetano; Antonacci, Amina; Scognamiglio, Viviana; Giardi, Maria Teresa; Polticelli, Fabio

2017-01-01

In the photosystem II (PSII) of oxygenic photosynthetic organisms, the reaction center (RC) core mediates the light-induced electron transfer leading to water splitting and production of reduced plastoquinone molecules. The reduction of plastoquinone to plastoquinol lowers PSII affinity for the latter and leads to its release. However, little is known about the role of protein dynamics in this process. Here, molecular dynamics simulations of the complete PSII complex embedded in a lipid bilayer have been used to investigate the plastoquinol release mechanism. A distinct dynamic behavior of PSII in the presence of plastoquinol is observed which, coupled to changes in charge distribution and electrostatic interactions, causes disruption of the interactions seen in the PSII-plastoquinone complex and leads to the "squeezing out" of plastoquinol from the binding pocket. Displacement of plastoquinol closes the second water channel, recently described in a 2.9 Å resolution PSII structure (Guskov et al. in Nat Struct Mol Biol 16:334-342, 2009), allowing to rule out the proposed "alternating" mechanism of plastoquinol-plastoquinone exchange, while giving support to the "single-channel" one. The performed simulations indicated a pivotal role of D 1 -Ser264 in modulating the dynamics of the plastoquinone binding pocket and plastoquinol-plastoquinone exchange via its interaction with D 1 -His252 residue. The effects of the disruption of this hydrogen bond network on the PSII redox reactions were experimentally assessed in the D 1 site-directed mutant Ser264Lys.

Alteration of pyruvate metabolism in African trypanosomes during differentiation from bloodstream into insect forms.

PubMed

Barnard, J P; Pedersen, P L

1994-08-15

In the presence of glucose and ample oxygen, insect form African trypanosomes release pyruvate more than 100-fold more slowly than do bloodstream forms. This rate decrease could not be accounted for simply by an increased mitochondrial pyruvate oxidation rate as inhibiting mitochondrial respiration increases pyruvate efflux to rates only 2-3% of that observed for bloodstream form trypanosomes. Alternatively, decreased pyruvate efflux from insect form trypanosomes could not be accounted for by decreased pyruvate transporter activity, which, surprisingly, was nearly as high in insect form trypanosomes as reported by us earlier for bloodstream forms (J.P. Barnard, B. Reynafarje, and P.L. Pedersen (1993) J. Biol. Chem. 268, 3654-3661). Rather, the low pyruvate efflux rate appears to be due primarily to reduced levels of the enzyme pyruvate kinase, which, in contrast to conclusions of an earlier study, is readily detected in insect form trypanosomes in the absence of added activators at an activity level about 4% of that found in bloodstream forms. Insect form pyruvate kinase seems to be located in the cytosol and exhibits kinetic profiles and constants nearly identical to those reported by us earlier for the bloodstream form enzyme (J.P. Barnard, and P.L. Pedersen (1988) Mol. Biochem. Parasitol. 31, 141-148). It is suggested that the reduced levels of pyruvate kinase, and hence the reduced pyruvate efflux rates, in insect form trypanosomes result from down regulation of the gene encoding the cytosolic enzyme.

Coexpression of alpha and beta subunits of the rod cyclic GMP-gated channel restores native sensitivity to cyclic AMP: role of D604/N1201.

PubMed Central

Pagès, F; Ildefonse, M; Ragno, M; Crouzy, S; Bennett, N

2000-01-01

Coexpression of the betawt and alphawt subunits of the bovine rod channel restores two characteristics of the native channels: higher sensitivity to cAMP and potentiation of cGMP-induced currents by low cAMP concentrations. To test whether the increased sensitivity to cAMP is due to the uncharged nature of the asparagine residue (N1201) situated in place of aspartate D604 in the beta subunit as previously suggested (, Neuron. 15:619-625), we compared currents from wild-type (alphawt and alphawt/betawt) and from mutated channels (alphaD604N, alphaD604N/betawt, and alphawt/betaN1201D). The results show that the sensitivity to cAMP and cAMP potentiation is partly but not entirely determined by the charge of residue 1201 in the beta subunit. The D604N mutation in the alpha subunit and, to a lesser extent, coexpression of the betawt subunit with the alphawt subunit reduce the open probability for cGMP compared to that of the alphawt channel. Interpretation of the data with the MWC allosteric model (model of Monod, Wyman, Changeux;, J. Mol. Biol. 12:88-118) suggests that the D604N mutation in the alpha subunits and coassembly of alpha and beta subunits alter the free energy of gating by cAMP more than that of cAMP binding. PMID:10692312

Structural studies on Desulfovibrio gigas cytochrome c3 by two-dimensional 1H-nuclear-magnetic-resonance spectroscopy.

PubMed Central

Piçarra-Pereira, M A; Turner, D L; LeGall, J; Xavier, A V

1993-01-01

Several aromatic amino acid residues and haem resonances in the fully reduced form of Desulfovibrio gigas cytochrome c3 are assigned, using two-dimensional 1H n.m.r., on the basis of the interactions between the protons of the aromatic amino acids and the haem protons as well as the intrahaem distances known from the X-ray structure [Kissinger (1989) Ph.D. Thesis, Washington State University]. The interhaem interactions observed in the n.m.r. spectra are in full agreement with the D. gigas X-ray structure and also with the n.m.r. data from Desulfovibrio vulgaris (Hildenborough) [Turner, Salgueiro, LeGall and Xavier (1992) Eur. J. Biochem. 210, 931-936]. The good correlation between the calculated ring-current shifts and the observed chemical shifts strongly supports the present assignments. Observation of the two-dimensional nuclear-Overhauser-enhancement spectra of the protein in the reduced, intermediate and fully oxidized stages led to the ordering of the haems in terms of their midpoint redox potentials and their identification in the X-ray structure. The first haem to oxidize is haem I, followed by haems II, III and IV, numbered according to the Cys ligand positions in the amino acid sequences [Mathews (1985) Prog. Biophys. Mol. Biol. 54, 1-56]. Although the haem core architecture is the same for the different Desulfovibrio cytochromes c3, the order of redox potentials is different. PMID:8397514

Intracellular modifications induced by poliovirus reduce the requirement for structural motifs in the 5' noncoding region of the genome involved in internal initiation of protein synthesis.

PubMed Central

Percy, N; Belsham, G J; Brangwyn, J K; Sullivan, M; Stone, D M; Almond, J W

1992-01-01

A series of genetic deletions based partly on two RNA secondary structure models (M. A. Skinner, V. R. Racaniello, G. Dunn, J. Cooper, P. D. Minor, and J. W. Almond, J. Mol. Biol. 207:379-392, 1989; E. V. Pilipenko, V. M. Blinov, L. I. Romanova, A. N. Sinyakov, S. V. Maslova, and V. I. Agol, Virology 168:201-209, 1989) was made in the cDNA encoding the 5' noncoding region (5' NCR) of the poliovirus genome in order to study the sequences that direct the internal entry of ribosomes. The modified cDNAs were placed between two open reading frames in a single transcriptional unit and used to transfect cells in culture. Internal entry of ribosomes was detected by measuring translation from the second open reading frame in the bicistronic mRNA. When assayed alone, a large proportion of the poliovirus 5' NCR superstructure including several well-defined stem-loops was required for ribosome entry and efficient translation. However, in cells cotransfected with a complete infectious poliovirus cDNA, the requirement for the stem-loops in this large superstructure was reduced. The results suggest that virus infection modifies the cellular translational machinery, so that shortened forms of the 5' NCR are sufficient for cap-independent translation, and that the internal entry of ribosomes occurs by two distinct modes during the virus replication cycle. Images PMID:1310772

Negative regulation of prophenoloxidase (proPO) activation by a clip-domain serine proteinase homolog (SPH) from endoparasitoid venom.

PubMed

Zhang, Guangmei; Lu, Zhi-Qiang; Jiang, Haobo; Asgari, Sassan

2004-05-01

Most parasitic wasps inject maternal factors into the host hemocoel to suppress the host immune system and ensure successful development of their progeny. Melanization is one of the insect defence mechanisms against intruding pathogens or parasites. We previously isolated from the venom of Cotesia rubecula a 50 kDa protein that blocked melanization in the hemolymph of its host, Pieris rapae [Insect Biochem. Mol. Biol. 33 (2003) 1017]. This protein, designated Vn50, is a serine proteinase homolog (SPH) containing an amino-terminal clip domain. In this work, we demonstrated that recombinant Vn50 bound P. rapae hemolymph components that were recognized by antisera to Tenebrio molitor prophenoloxidase (proPO) and Manduca sexta proPO-activating proteinase (PAP). Vn50 is stable in the host hemolymph-it remained intact for at least 72 h after parasitization. Using M. sexta as a model system, we found that Vn50 efficiently down-regulated proPO activation mediated by M. sexta PAP-1, SPH-1, and SPH-2. Vn50 did not inhibit active phenoloxidase (PO) or PAP-1, but it significantly reduced the proteolysis of proPO. If recombinant Vn50 binds P. rapae proPO and PAP (as suggested by the antibody reactions), it is likely that the molecular interactions among M. sexta proPO, PAP-1, and SPHs were impaired by this venom protein. A similar strategy might be employed by C. rubecula to negatively impact the proPO activation reaction in its natural host.

Enantiomeric analysis of overlapped chromatographic profiles in the presence of interferences. Determination of ibuprofen in a pharmaceutical formulation containing homatropine.

PubMed

Padró, J M; Osorio-Grisales, J; Arancibia, J A; Olivieri, A C; Castells, C B

2016-10-07

In this work, we studied the combination of chemometric methods with chromatographic separations as a strategy applied to the analysis of enantiomers when complete enantioseparation is difficult or requires long analysis times and, in addition, the target signals have interference from the matrix. We present the determination of ibuprofen enantiomers in pharmaceutical formulations containing homatropine as interference by chiral HPLC-DAD detection in combination with partial least-squares algorithms. The method has been applied to samples containing enantiomeric ratios from 95:5 to 99.5:0.5 and coelution of interferents. The results were validated using univariate calibration and without homatropine. Relative error of the method was less than 4.0%, for both enantiomers. Limits of detection (LOD) and quantification (LOQ) for (S)-(+)-ibuprofen were 4.96×10 -10 and 1.50×10 -9 mol, respectively. LOD and LOQ for the R-(-)-ibuprofen were LOD=1.60×10 -11 mol and LOQ=4.85×10 -11 mol, respectively. Finally, the chemometric method was applied to the determination of enantiomeric purity of commercial pharmaceuticals. The ultimate goal of this research was the development of rapid, reliable, and robust methods for assessing enantiomeric purity by conventional diode array detector assisted by chemometric tools. Copyright © 2016 Elsevier B.V. All rights reserved.

Long-branch attraction and the phylogeny of true water bugs (Hemiptera: Nepomorpha) as estimated from mitochondrial genomes

PubMed Central

2014-01-01

Background Most previous studies of morphological and molecular data have consistently supported the monophyly of the true water bugs (Hemiptera: Nepomorpha). An exception is a recent study by Hua et al. (BMC Evol Biol 9: 134, 2009) based on nine nepomorphan mitochondrial genomes. In the analysis of Hua et al. (BMC Evol Biol 9: 134, 2009), the water bugs in the group Pleoidea formed the sister group to a clade that consisted of Nepomorpha (the remaining true water bugs) + Leptopodomorpha (shore bugs) + Cimicomorpha (assassin bugs and relatives) + Pentatomomorpha (stink bugs and relatives), thereby suggesting that fully aquatic hemipterans evolved independently at least twice. Based on these results, Hua et al. (BMC Evol Biol 9: 134, 2009) elevated the Pleoidea to a new infraorder, the Plemorpha. Results Our reanalysis suggests that the lack of support for the monophyly of the true water bugs (including Pleoidea) by Hua et al. (BMC Evol Biol 9: 134, 2009) likely resulted from inadequate taxon sampling. In particular, long-branch attraction (LBA) between the distant outgroup taxa and Pleoidea, as well as LBA among taxa in the ingroup, made Nepomorpha appear to be polyphyletic. We used three complementary strategies to test and alleviate the effects of LBA: (1) the removal of distant outgroups from the analysis; (2) the addition of closely related outgroups; and (3) the addition of a mitochondrial genome from a second family of Pleoidea. We also performed likelihood-ratio tests to examine the support for monophyly of Nepomorpha with different combinations of taxa included in the analysis. Furthermore, we found that specimens of Helotrephes sp. were misidentified as Paraplea frontalis (Fieber, 1844) by Hua et al. (BMC Evol Biol 9: 134, 2009). Conclusions All analyses that included the addition of more taxa significantly and consistently supported the placement of Pleoidea within the Nepomorpha (i.e., supported the monophyly of the traditional true water bugs). Our analyses further support a close relationship between Notonectoidea and Pleoidea within Nepomorpha, and the superfamilies Nepoidea, Ochteroidea, Naucoroidea, and Pleoidea are resolved as monophyletic in all trees with strong support. Our results also confirmed that monophyly of Nepomorpha clearly is not refuted by the mitochondrial genome data. PMID:24884699

Dependence of the kinetic and thermodynamic parameters on hydrophilic-lipophilic character of alprazolam, clonazepam, diazepam, doxepin and haloperidol in alkaline environment.

PubMed

Maślanka, Anna; Krzek, Jan; Szlósarczyk, Marek; Żmudzki, Paweł; Wach, Katarzyna

2013-10-15

Examination of the stability of clonazepam, diazepam, alprazolam, haloperidol, and doxepin in basic solutions was performed, together with an assessment of the kinetic (k, t0.1i t0.5) and thermodynamic (Ea, ΔH(++)i ΔS(++)) stability-indicating parameters, which were compared with the lipophilicity (logP) of the studied drugs. It was observed that the calculated values of Ea, ΔH(++) and ΔS(++) for the studied drugs increased from 41.04 kJ/mol to 125.50 kJ/mol, from 37.82 kJ/mol to 122.24 kJ/mol and from -167.09 J/Kmol to 53.02 J/Kmol, respectively, along with an increase of lipophilicity (logP) from 2.12 to 4.30 for the most hydrophilic alprazolam to the most lipophilic haloperidol. The degradation products were identified using UPLC/MS/MS method. Copyright © 2013 Elsevier B.V. All rights reserved.

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers.

PubMed

Reimers, Jeffrey R; Panduwinata, Dwi; Visser, Johan; Chin, Yiing; Tang, Chunguang; Goerigk, Lars; Ford, Michael J; Sintic, Maxine; Sum, Tze-Jing; Coenen, Michiel J J; Hendriksen, Bas L M; Elemans, Johannes A A W; Hush, Noel S; Crossley, Maxwell J

2015-11-10

Modern quantum chemical electronic structure methods typically applied to localized chemical bonding are developed to predict atomic structures and free energies for meso-tetraalkylporphyrin self-assembled monolayer (SAM) polymorph formation from organic solution on highly ordered pyrolytic graphite surfaces. Large polymorph-dependent dispersion-induced substrate-molecule interactions (e.g., -100 kcal mol(-1) to -150 kcal mol(-1) for tetratrisdecylporphyrin) are found to drive SAM formation, opposed nearly completely by large polymorph-dependent dispersion-induced solvent interactions (70-110 kcal mol(-1)) and entropy effects (25-40 kcal mol(-1) at 298 K) favoring dissolution. Dielectric continuum models of the solvent are used, facilitating consideration of many possible SAM polymorphs, along with quantum mechanical/molecular mechanical and dispersion-corrected density functional theory calculations. These predict and interpret newly measured and existing high-resolution scanning tunnelling microscopy images of SAM structure, rationalizing polymorph formation conditions. A wide range of molecular condensed matter properties at room temperature now appear suitable for prediction and analysis using electronic structure calculations.

Characterization of polysaccharides extracted from spent coffee grounds by alkali pretreatment.

PubMed

Ballesteros, Lina F; Cerqueira, Miguel A; Teixeira, José A; Mussatto, Solange I

2015-01-01

Spent coffee grounds (SCG), obtained during the processing of coffee powder with hot water to make soluble coffee, are the main coffee industry residues and retain approximately seventy percent of the polysaccharides present in the roasted coffee beans. The purpose of this study was to extract polysaccharides from SCG by using an alkali pretreatment with sodium hydroxide at 25°C, and determine the chemical composition, as well as the antioxidant and antimicrobial properties of the extracted polysaccharides. Galactose (60.27%mol) was the dominant sugar in the recovered polysaccharides, followed by arabinose (19.93%mol), glucose (15.37%mol) and mannose (4.43%mol). SCG polysaccharides were thermostable, and presented a typical carbohydrate pattern. Additionally, they showed good antioxidant activity through different methods and presented high antimicrobial percent inhibition against Phoma violacea and Cladosporium cladosporioides (41.27% and 54.60%, respectively). These findings allow identifying possible applications for these polysaccharides in the food industry. Copyright © 2015 Elsevier Ltd. All rights reserved.

Crystal phase analysis of SnO{sub 2}-based varistor ceramic using the Rietveld method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moreira, M.L.; Pianaro, S.A.; Andrade, A.V.C.

2006-09-15

A second addition of l mol% of CoO to a pre calcined SnO{sub 2}-based ceramic doped with 1.0 mol% of CoO, 0.05 mol% of Nb{sub 2}O{sub 5} and 0.05 mol% of Cr{sub 2}O{sub 3} promotes the appearance of a secondary phase, Co{sub 2}SnO{sub 4}, besides the SnO{sub 2} cassiterite phase, when the ceramic was sintered at 1350 deg. C/2 h. This was observed using X-ray powder diffraction, scanning electron microscopy and energy dispersive X-ray techniques. Rietveld refinement was carried out to quantify the phases present in the ceramic system. The results of the quantitative analysis were 97 wt.% SnO{sub 2}more » and 3 wt.% Co{sub 2}SnO{sub 4}. The microstructural analysis showed that a certain amount of cobalt ion remains into cassiterite grains.« less

Facile synthesis of antimony-doped tin oxide nanoparticles by a polymer-pyrolysis method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yuan-Qing, E-mail: yqli@mail.ipc.ac.cn; Wang, Jian-Lei; Fu, Shao-Yun, E-mail: syfu@mail.ipc.ac.cn

2010-06-15

In this article, antimony-doped tin oxide (ATO) nanoparticles was synthesized by a facile polymer-pyrolysis method. The pyrolysis behaviors of the polymer precursors prepared via in situ polymerization of metal salts and acrylic acid were analyzed by simultaneous thermogravimetric and differential scanning calorimetry (TG-DSC). The structural and morphological characteristics of the products were studied by powder X-ray diffraction (XRD) and transmission electron microscope (TEM). The results reveal that the ATO nanoparticles calcined at 600 {sup o}C show good crystallinity with the cassiterite structure and cubic-spherical like morphology. The average particle size of ATO decreases from 200 to 15 nm as themore » Sb doping content increases from 5 mol% to 15 mol%. Electrical resistivity measurement shows that the resistivity for the 10-13 mol% Sb-doped SnO{sub 2} nanoparticles is reduced by more than three orders compared with the pure SnO{sub 2} nanoparticles. In addition, due to its versatility this polymer-pyrolysis method can be extended to facile synthesis of other doped n-type semiconductor, such as In, Ga, Al doped ZnO, Sn doped In{sub 2}O{sub 3}.« less

Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal-Organic Frameworks.

PubMed

Kundu, Arpan; Piccini, GiovanniMaria; Sillar, Kaido; Sauer, Joachim

2016-10-26

For CO and N 2 on Mg 2+ sites of the metal-organic framework CPO-27-Mg (Mg-MOF-74), ab initio calculations of Gibbs free energies of adsorption have been performed. Combined with the Bragg-Williams/Langmuir model and taking into account the experimental site availability (76.5%), we obtained adsorption isotherms in close agreement with those in experiment. The remaining deviations in the Gibbs free energy (about 1 kJ/mol) are significantly smaller than the "chemical accuracy" limit of about 4 kJ/mol. The presented approach uses (i) a DFT dispersion method (PBE+D2) to optimize the structure and to calculate anharmonic frequencies for vibrational partition functions and (ii) a "hybrid MP2:(PBE+D2)+ΔCCSD(T)" method to determine electronic energies. With the achieved accuracy (estimated uncertainty ±1.4 kJ/mol), the ab initio energies become useful benchmarks for assessing different DFT + dispersion methods (PBE+D2, B3LYP+D*, and vdW-D2), whereas the ab initio heats, entropies, and Gibbs free energies of adsorption are used to assess the reliability of experimental values derived from fitting isotherms or from variable-temperature IR studies.

One-Step Fabrication of a Multifunctional Magnetic Nickel Ferrite/Multi-walled Carbon Nanotubes Nanohybrid-Modified Electrode for the Determination of Benomyl in Food.

PubMed

Wang, Qiong; Yang, Jichun; Dong, Yuanyuan; Zhang, Lei

2015-05-20

Benomyl, as one kind of agricultural pesticide, has adverse impact on human health and the environment. It is urgent to develop effective and rapid methods for quantitative determination of benomyl. A simple and sensitive electroanalytical method for determination of benomyl using a magnetic nickel ferrite (NiFe2O4)/multi-walled carbon nanotubes (MWCNTs) nanohybrid-modified glassy carbon electrode (GCE) was presented. The electrocatalytic properties and electroanalysis of benomyl on the modified electrode were investigated by cyclic voltammetry (CV) and differential pulse voltammetry (DPV). In the phosphate-buffered saline (PBS) of pH 6.0, this constructed biosensor exhibited two linear relationships with the benomyl concentration range from 1.00 × 10(-7) to 5.00 × 10(-7) mol/L and from 5.00 × 10(-7) to 1.00 × 10(-5) mol/L, respectively. The detection limit was 2.51 × 10(-8) mol/L (S/N = 3). Moreover, the proposed method was successfully applied to determine benomyl in real samples with satisfactory results. The NiFe2O4/MWCNTs/GCE showed good reproducibility and stability, excellent catalytic activity, and anti-interference.

DFT study on the isomerization and tautomerism in vitamins B3 (niacin), B5 (pantothenic acid) and B7 (biotin)

NASA Astrophysics Data System (ADS)

Valadbeigi, Younes; Farrokhpour, Hossein; Tabrizchi, Mahmoud

2014-05-01

Isomerization and tautomerism of the three water soluble vitamins including B3, B5 and B7 were studied applying density functional theory using B3LYP method in gas and aqueous phases. Activation energies (Ea), Gibbs free energies of activation (ΔG#), and imaginary frequencies of the transition state structures were calculated for all the isomerization and tautomerism reactions. Activation energies of the neutral → zwitterion (amine-enamine) tautomerism in vitamin B3 were 310-360 kJ/mol where these values for the keto-enol tautomerism were 100-130 kJ/mol. It was found that water molecule catalyzes the tautomerism and decreases the activation energies about 90-160 kJ/mol.

Study on fluorescence characteristics of duloxetine hydrochloride

NASA Astrophysics Data System (ADS)

Liu, Xiangping; Du, Yingxiang; Wu, Xiulan

2008-12-01

The fluorescence characteristics of duloxetine hydrochloride are studied in this paper. The fluorescence emission spectra of duloxetine demonstrate that intramolecular charge-transfer takes place between thiophene ring and napthalenyloxy group upon irradiation. The effects of excitation light, solvent system, variation of solution pH value, metal ions and vitamin C on the fluorescence spectra of duloxetine hydrochloride are elucidated, respectively. A spectrofluorometric method of quantitative determination of duloxetine in dosage form is reported for the first time, the linear range is 7.14 × 10 -8 mol/L to 1.43 × 10 -5 mol/L, the linear correlation coefficient r is equal to 0.9997, and the detection limit is 3.5 × 10 -8 mol/L. The accuracy and the precision are satisfactory.

The nonchromatin substructures of the nucleus: the ribonucleoprotein (RNP)-containing and RNP-depleted matrices analyzed by sequential fractionation and resinless section electron microscopy

PubMed Central

1986-01-01

The nonchromatin structure or matrix of the nucleus has been studied using an improved fractionation in concert with resinless section electron microscopy. The resinless sections show the nucleus of the intact cell to be filled with a dense network or lattice composed of soluble proteins and chromatin in addition to the structural nuclear constituents. In the first fractionation step, soluble proteins are removed by extraction with Triton X-100, and the dense nuclear lattice largely disappears. Chromatin and nonchromatin nuclear fibers are now sharply imaged. Nuclear constituents are further separated into three well-defined, distinct protein fractions. Chromatin proteins are those that require intact DNA for their association with the nucleus and are released by 0.25 M ammonium sulfate after internucleosomal DNA is cut with DNAase I. The resulting structure retains most heterogeneous nuclear ribonucleoprotein (hnRNP) and is designated the RNP-containing nuclear matrix. The proteins of hnRNP are those associated with the nucleus only if RNA is intact. These are released when nuclear RNA is briefly digested with RNAase A. Ribonuclease digestion releases 97% of the hnRNA and its associated proteins. These proteins correspond to the hnRNP described by Pederson (Pederson, T., 1974, J. Mol. Biol., 83:163- 184) and are distinct from the proteins that remain in the ribonucleoprotein (RNP)-depleted nuclear matrix. The RNP-depleted nuclear matrix is a core structure that retains lamins A and C, the intermediate filaments, and a unique set of nuclear matrix proteins (Fey, E. G., K. M. Wan, and S. Penman, 1984, J. Cell Biol. 98:1973- 1984). This core had been previously designated the nuclear matrix- intermediate filament scaffold and its proteins are a third, distinct, and nonoverlapping subset of the nuclear nonhistone proteins. Visualizing the nuclear matrix using resinless sections shows that nuclear RNA plays an important role in matrix organization. Conventional Epon-embedded electron microscopy sections show comparatively little of the RNP-containing and RNP-depleted nuclear matrix structure. In contrast, resinless sections show matrix interior to be a three-dimensional network of thick filaments bounded by the nuclear lamina. The filaments are covered with 20-30-nm electron dense particles which may contain the hnRNA. The large electron dense bodies, enmeshed in the interior matrix fibers, have the characteristic morphology of nucleoli. Treatment of the nuclear matrix with RNAase results in the aggregation of the interior fibers and the extensive loss of the 20-30-nm particles.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:3700470

Nonspecific microvascular vasodilation during iontophoresis is attenuated by application of hyperosmolar saline.

PubMed

Asberg, A; Holm, T; Vassbotn, T; Andreassen, A K; Hartmann, A

1999-07-01

Iontophoretic administration of acetylcholine chloride (ACh) and sodium nitroprusside (SNP) combined with laser Doppler skin blood perfusion measurements are used for determination of endothelial-dependent and -independent vasodilation. However, the method is biased by nonspecific vasodilation. The primary aim of this study was to investigate if iontophoresis-induced nonspecific vasodilation may be attenuated by addition of high molar concentrations of NaCl to the iontophoresis solutions. Secondary we investigated the applicability of 5 mol/liter NaCl solution as vehicle for ACh and SNP in this method. Skin perfusion changes were determined for iontophoresis of pure vehicles, deionized water and 5 mol/liter NaCl solution, in 12 healthy volunteers. Responses in skin perfusion to iontophoresis of ACh and SNP dissolved in both vehicles were also investigated. Addition of 5 mol/liter NaCl to deionized water significantly attenuated the nonspecific vasodilation and lowered the potential applied over the skin. The inter- and intraindividual coefficients of variation to ACh and SNP responses became, however, higher using hyperosmolar vehicle. During iontophoresis of SNP (in deionized water) we were unable to distinguish between SNP and vehicle effects. This study shows that the nonspecific vasodilation induced by iontophoresis can be attenuated by addition of 5 mol/liter NaCl, possibly due to lower electrical potential over the skin. However, the variability of the method was not improved. When deionized water was used as vehicle the effect of SNP could not be differentiated from that of the vehicle. This was not the case for ACh. Copyright 1999 Academic Press.

Development of capillary electrophoresis methods for quantitative determination of taurine in vehicle system and biological media.

PubMed

da Silva, Dayse L P; Rüttinger, Hans H; Mrestani, Yahia; Baum, Walter F; Neubert, Reinhard H H

2006-06-01

CE methods have been developed for the determination of taurine in pharmaceutical formulation (microemulsion) and in biological media such as sweat. The CE system with end-column pulsed amperometric detection has been found to be an interesting method in comparison with UV and fluorescence detection for its simplicity and rapidity. A gold-disk electrode of 100 mm diameter was used as the working electrode. The effects of a field decoupler at the end of the capillary, separation voltage, injection and pressure times were investigated. A detection limit of 4 x 10(-5) mol/L was reached using integrated pulsed amperometric detection, a method successfully applied to taurine analysis of the biological samples such as sweat. For taurine analysis of oil-in-water microemulsion, fluorescence detector was the favored method, the detection limit of which was 4 x 10(-11) mol/L.

DFT-based method for more accurate adsorption energies: An adaptive sum of energies from RPBE and vdW density functionals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hensley, Alyssa J. R.; Ghale, Kushal; Rieg, Carolin

In recent years, the popularity of density functional theory with periodic boundary conditions (DFT) has surged for the design and optimization of functional materials. However, no single DFT exchange–correlation functional currently available gives accurate adsorption energies on transition metals both when bonding to the surface is dominated by strong covalent or ionic bonding and when it has strong contributions from van der Waals interactions (i.e., dispersion forces). Here we present a new, simple method for accurately predicting adsorption energies on transition-metal surfaces based on DFT calculations, using an adaptively weighted sum of energies from RPBE and optB86b-vdW (or optB88-vdW) densitymore » functionals. This method has been benchmarked against a set of 39 reliable experimental energies for adsorption reactions. Our results show that this method has a mean absolute error and root mean squared error relative to experiments of 13.4 and 19.3 kJ/mol, respectively, compared to 20.4 and 26.4 kJ/mol for the BEEF-vdW functional. For systems with large van der Waals contributions, this method decreases these errors to 11.6 and 17.5 kJ/mol. Furthermore, this method provides predictions of adsorption energies both for processes dominated by strong covalent or ionic bonding and for those dominated by dispersion forces that are more accurate than those of any current standard DFT functional alone.« less

DFT-based method for more accurate adsorption energies: An adaptive sum of energies from RPBE and vdW density functionals

DOE PAGES

Hensley, Alyssa J. R.; Ghale, Kushal; Rieg, Carolin; ...

2017-01-26

In recent years, the popularity of density functional theory with periodic boundary conditions (DFT) has surged for the design and optimization of functional materials. However, no single DFT exchange–correlation functional currently available gives accurate adsorption energies on transition metals both when bonding to the surface is dominated by strong covalent or ionic bonding and when it has strong contributions from van der Waals interactions (i.e., dispersion forces). Here we present a new, simple method for accurately predicting adsorption energies on transition-metal surfaces based on DFT calculations, using an adaptively weighted sum of energies from RPBE and optB86b-vdW (or optB88-vdW) densitymore » functionals. This method has been benchmarked against a set of 39 reliable experimental energies for adsorption reactions. Our results show that this method has a mean absolute error and root mean squared error relative to experiments of 13.4 and 19.3 kJ/mol, respectively, compared to 20.4 and 26.4 kJ/mol for the BEEF-vdW functional. For systems with large van der Waals contributions, this method decreases these errors to 11.6 and 17.5 kJ/mol. Furthermore, this method provides predictions of adsorption energies both for processes dominated by strong covalent or ionic bonding and for those dominated by dispersion forces that are more accurate than those of any current standard DFT functional alone.« less

Intermolecular dissociation energies of dispersively bound complexes of aromatics with noble gases and nitrogen

NASA Astrophysics Data System (ADS)

Knochenmuss, Richard; Sinha, Rajeev K.; Leutwyler, Samuel

2018-04-01

We measured accurate intermolecular dissociation energies D0 of the supersonic jet-cooled complexes of 1-naphthol (1NpOH) with the noble gases Ne, Ar, Kr, and Xe and with N2, using the stimulated-emission pumping resonant two-photon ionization method. The ground-state values D0(S0) for the 1NpOHṡS complexes with S= Ar, Kr, Xe, and N2 were bracketed to be within ±3.5%; they are 5.67 ± 0.05 kJ/mol for S = Ar, 7.34 ± 0.07 kJ/mol for S = Kr, 10.8 ± 0.28 kJ/mol for S = Xe, 6.67 ± 0.08 kJ/mol for isomer 1 of the 1NpOHṡN2 complex, and 6.62 ± 0.22 kJ/mol for the corresponding isomer 2. For S = Ne, the upper limit is D0 < 3.36 kJ/mol. The dissociation energies increase by 1%-5% upon S0 → S1 excitation of the complexes. Three dispersion-corrected density functional theory (DFT-D) methods (B97-D3, B3LYP-D3, and ωB97X-D) predict that the most stable form of these complexes involves dispersive binding to the naphthalene "face." A more weakly bound edge isomer is predicted in which the S moiety is H-bonded to the OH group of 1NpOH; however, no edge isomers were observed experimentally. The B97-D3 calculated dissociation energies D0(S0) of the face complexes with Ar, Kr, and N2 agree with the experimental values within <5%, but the D0(S0) for Xe is 12% too low. The B3LYP-D3 and ωB97X-D calculated D0(S0) values exhibit larger deviations to both larger and smaller dissociation energies. For comparison to 1-naphthol, we calculated the D0(S0) of the carbazole complexes with S = Ne, Ar, Kr, Xe, and N2 using the same DFT-D methods. The respective experimental values have been previously determined to be within <2%. Again, the B97-D3 results are in the best overall agreement with experiment.

Accurate ab initio potential energy surface, thermochemistry, and dynamics of the F(-) + CH3F SN2 and proton-abstraction reactions.

PubMed

Szabó, István; Telekes, Hajnalka; Czakó, Gábor

2015-06-28

We develop a full-dimensional global analytical potential energy surface (PES) for the F(-) + CH3F reaction by fitting about 50 000 energy points obtained by an explicitly correlated composite method based on the second-order Møller-Plesset perturbation-F12 and coupled-cluster singles, doubles, and perturbative triples-F12a methods and the cc-pVnZ-F12 [n = D, T] basis sets. The PES accurately describes the (a) back-side attack Walden inversion mechanism involving the pre- and post-reaction (b) ion-dipole and (c) hydrogen-bonded complexes, the configuration-retaining (d) front-side attack and (e) double-inversion substitution pathways, as well as (f) the proton-abstraction channel. The benchmark quality relative energies of all the important stationary points are computed using the focal-point analysis (FPA) approach considering electron correlation up to coupled-cluster singles, doubles, triples, and perturbative quadruples method, extrapolation to the complete basis set limit, core-valence correlation, and scalar relativistic effects. The FPA classical(adiabatic) barrier heights of (a), (d), and (e) are -0.45(-0.61), 46.07(45.16), and 29.18(26.07) kcal mol(-1), respectively, the dissociation energies of (b) and (c) are 13.81(13.56) and 13.73(13.52) kcal mol(-1), respectively, and the endothermicity of (f) is 42.54(38.11) kcal mol(-1). Quasiclassical trajectory computations of cross sections, scattering (θ) and initial attack (α) angle distributions, as well as translational and internal energy distributions are performed for the F(-) + CH3F(v = 0) reaction using the new PES. Apart from low collision energies (Ecoll), the SN2 excitation function is nearly constant, the abstraction cross sections rapidly increase with Ecoll from a threshold of ∼40 kcal mol(-1), and retention trajectories via double inversion are found above Ecoll = ∼ 30 kcal mol(-1), and at Ecoll = ∼ 50 kcal mol(-1), the front-side attack cross sections start to increase very rapidly. At low Ecoll, the indirect mechanism dominates (mainly isotropic backward-forward symmetric θ distribution and translationally cold products) and significant long-range orientation effects (isotropic α distribution) and barrier recrossings are found. At higher Ecoll, the SN2 reaction mainly proceeds with direct rebound mechanism (backward scattering and hot product translation).

Accurate ab initio potential energy surface, thermochemistry, and dynamics of the F- + CH3F SN2 and proton-abstraction reactions

NASA Astrophysics Data System (ADS)

Szabó, István; Telekes, Hajnalka; Czakó, Gábor

2015-06-01

We develop a full-dimensional global analytical potential energy surface (PES) for the F- + CH3F reaction by fitting about 50 000 energy points obtained by an explicitly correlated composite method based on the second-order Møller-Plesset perturbation-F12 and coupled-cluster singles, doubles, and perturbative triples-F12a methods and the cc-pVnZ-F12 [n = D, T] basis sets. The PES accurately describes the (a) back-side attack Walden inversion mechanism involving the pre- and post-reaction (b) ion-dipole and (c) hydrogen-bonded complexes, the configuration-retaining (d) front-side attack and (e) double-inversion substitution pathways, as well as (f) the proton-abstraction channel. The benchmark quality relative energies of all the important stationary points are computed using the focal-point analysis (FPA) approach considering electron correlation up to coupled-cluster singles, doubles, triples, and perturbative quadruples method, extrapolation to the complete basis set limit, core-valence correlation, and scalar relativistic effects. The FPA classical(adiabatic) barrier heights of (a), (d), and (e) are -0.45(-0.61), 46.07(45.16), and 29.18(26.07) kcal mol-1, respectively, the dissociation energies of (b) and (c) are 13.81(13.56) and 13.73(13.52) kcal mol-1, respectively, and the endothermicity of (f) is 42.54(38.11) kcal mol-1. Quasiclassical trajectory computations of cross sections, scattering (θ) and initial attack (α) angle distributions, as well as translational and internal energy distributions are performed for the F- + CH3F(v = 0) reaction using the new PES. Apart from low collision energies (Ecoll), the SN2 excitation function is nearly constant, the abstraction cross sections rapidly increase with Ecoll from a threshold of ˜40 kcal mol-1, and retention trajectories via double inversion are found above Ecoll = ˜ 30 kcal mol-1, and at Ecoll = ˜ 50 kcal mol-1, the front-side attack cross sections start to increase very rapidly. At low Ecoll, the indirect mechanism dominates (mainly isotropic backward-forward symmetric θ distribution and translationally cold products) and significant long-range orientation effects (isotropic α distribution) and barrier recrossings are found. At higher Ecoll, the SN2 reaction mainly proceeds with direct rebound mechanism (backward scattering and hot product translation).

A promising tool to achieve chemical accuracy for density functional theory calculations on Y-NO homolysis bond dissociation energies.

PubMed

Li, Hong Zhi; Hu, Li Hong; Tao, Wei; Gao, Ting; Li, Hui; Lu, Ying Hua; Su, Zhong Min

2012-01-01

A DFT-SOFM-RBFNN method is proposed to improve the accuracy of DFT calculations on Y-NO (Y = C, N, O, S) homolysis bond dissociation energies (BDE) by combining density functional theory (DFT) and artificial intelligence/machine learning methods, which consist of self-organizing feature mapping neural networks (SOFMNN) and radial basis function neural networks (RBFNN). A descriptor refinement step including SOFMNN clustering analysis and correlation analysis is implemented. The SOFMNN clustering analysis is applied to classify descriptors, and the representative descriptors in the groups are selected as neural network inputs according to their closeness to the experimental values through correlation analysis. Redundant descriptors and intuitively biased choices of descriptors can be avoided by this newly introduced step. Using RBFNN calculation with the selected descriptors, chemical accuracy (≤1 kcal·mol(-1)) is achieved for all 92 calculated organic Y-NO homolysis BDE calculated by DFT-B3LYP, and the mean absolute deviations (MADs) of the B3LYP/6-31G(d) and B3LYP/STO-3G methods are reduced from 4.45 and 10.53 kcal·mol(-1) to 0.15 and 0.18 kcal·mol(-1), respectively. The improved results for the minimal basis set STO-3G reach the same accuracy as those of 6-31G(d), and thus B3LYP calculation with the minimal basis set is recommended to be used for minimizing the computational cost and to expand the applications to large molecular systems. Further extrapolation tests are performed with six molecules (two containing Si-NO bonds and two containing fluorine), and the accuracy of the tests was within 1 kcal·mol(-1). This study shows that DFT-SOFM-RBFNN is an efficient and highly accurate method for Y-NO homolysis BDE. The method may be used as a tool to design new NO carrier molecules.

Development and validation of a 2nd tier test for identification of purine nucleoside phosphorylase deficiency patients during expanded newborn screening by liquid chromatography-tandem mass spectrometry.

PubMed

la Marca, Giancarlo; Giocaliere, Elisa; Malvagia, Sabrina; Villanelli, Fabio; Funghini, Silvia; Ombrone, Daniela; Della Bona, Maria; Forni, Giulia; Canessa, Clementina; Ricci, Silvia; Romano, Francesca; Guerrini, Renzo; Resti, Massimo; Azzari, Chiara

2016-04-01

Purine nucleoside phosphorylase (PNP) deficiency has been recently introduced in the newborn screening program in Tuscany. In order to improve the PNP screening efficiency, we developed a 2nd tier test to quantify PNP primary markers deoxyguanosine (dGuo) and deoxyinosine (dIno). Dried blood spots (DBS) samples were extracted with 200 μL of methanol and 100 μL of water (by two steps). Internal standards were added at a final concentration of 10 μmol/L. After extraction, samples were analysed by LC-MS/MS. The chromatographic run was performed in gradient mode by using a Synergi Fusion column. The assay was linear over a concentration range of 0.05-50 μmol/L (R2>0.999) for dGuo and 0.5-50 μmol/L (R2>0.998) for dIno. Intra- and interassay imprecision (mean CVs) for dIno and dGuo ranged from 2.9% to 12%. Limit of quantitaion (LOQ) were found to be 0.05 μmol/L and 0.5 μmol/L for dGuo and dIno, respectively. The reference ranges, obtained by measuring dGuo and dIno concentrations on DBS, were close to zero for both biomarkers. Moreover, DBS samples from seven patients with confirmed PNP were retrospectively evaluated and correctly identified. The LC-MS/MS method can reliably measure dIno and dGuo in DBS for the diagnosis of PNP. Validation data confirm the present method is characterised by good reproducibility, accuracy and imprecision for the quantitation of dIno and dGuo. The assay also appears suitable for use in monitoring treatment of PNP patients.

Theoretical studies of mechanisms of cycloaddition reaction between difluoromethylene carbene and acetone

NASA Astrophysics Data System (ADS)

Lu, Xiu Hui; Yu, Hai Bin; Wu, Wei Rong; Xu, Yue Hua

Mechanisms of the cycloaddition reaction between singlet difluoromethylene carbene and acetone have been investigated with the second-order Møller-Plesset (MP2)/6-31G* method, including geometry optimization and vibrational analysis. Energies for the involved stationary points on the potential energy surface (PES) are corrected by zero-point energy (ZPE) and CCSD(T)/6-31G* single-point calculations. From the PES obtained with the CCSD(T)//MP2/6-31G* method for the cycloaddition reaction between singlet difluoromethylene carbene and acetone, it can be predicted that path B of reactions 2 and 3 should be two competitive leading channels of the cycloaddition reaction between difluoromethylene carbene and acetone. The former consists of two steps: (i) the two reactants first form a four-membered ring intermediate, INT2, which is a barrier-free exothermic reaction of 97.8 kJ/mol; (ii) the intermediate INT2 isomerizes to a four-membered product P2b via a transition state TS2b with an energy barrier of 24.9 kJ/mol, which results from the methyl group transfer. The latter proceeds in three steps: (i) the two reactants first form an intermediate, INT1c, through a barrier-free exothermic reaction of 199.4 kJ/mol; (ii) the intermediate INT1c further reacts with acetone to form a polycyclic intermediate, INT3, which is also a barrier-free exothermic reaction of 27.4 kJ/mol; and (iii) INT3 isomerizes to a polycyclic product P3 via a transition state TS3 with an energy barrier of 25.8 kJ/mol.

Raman spectroscopy study and first-principles calculations of the interaction between nucleic acid bases and carbon nanotubes.

PubMed

Stepanian, Stepan G; Karachevtsev, Maksym V; Glamazda, Alexander Yu; Karachevtsev, Victor A; Adamowicz, L

2009-04-16

In this work, we have used Raman spectroscopy and quantum chemical methods (MP2 and DFT) to study the interactions between nucleic acid bases (NABs) and single-walled carbon nanotubes (SWCNT). We found that the appearance of the interaction between the nanotubes and the NABs is accompanied by a spectral shift of the high-frequency component of the SWCNT G band in the Raman spectrum to a lower frequency region. The value of this shift varies from 0.7 to 1.3 cm(-1) for the metallic nanotubes and from 2.1 to 3.2 cm(-1) for the semiconducting nanotubes. Calculations of the interaction energies between the NABs and a fragment of the zigzag(10,0) carbon nanotube performed at the MP2/6-31++G(d,p)[NABs atoms]|6-31G(d)[nanotube atoms] level of theory while accounting for the basis set superposition error during geometry optimization allowed us to order the NABs according to the increasing interaction energy value. The order is: guanine (-67.1 kJ mol(-1)) > adenine (-59.0 kJ mol(-1)) > cytosine (-50.3 kJ mol(-1)) approximately = thymine (-50.2 kJ mol(-1)) > uracil (-44.2 kJ mol(-1)). The MP2 equilibrium structures and the interaction energies were used as reference points in the evaluation of the ability of various functionals in the DFT method to predict those structures and energies. We showed that the M05, MPWB1K, and MPW1B95 density functionals are capable of correctly predicting the SWCNT-NAB geometries but not the interaction energies, while the M05-2X functional is capable of correctly predicting both the geometries and the interaction energies.

A quantum chemical calculation of the potential energy surface in the formation of HOSO 2 from OH + SO 2

NASA Astrophysics Data System (ADS)

Sitha, Sanyasi; Jewell, Linda L.; Piketh, Stuart J.; Fourie, Gerhard

2011-01-01

The formation of HOSO 2 from OH and SO 2 has been thoroughly investigated using several different methods (MP2=Full, MP2=FC, B3LYP, HF and composite G∗ methods) and basis sets (6-31G(d,p), 6-31++G(d,p), 6-31++G(2d,2p), 6-31++G(2df,2p) and aug-cc-pVnZ). We have found two different possible transition state structures, one of which is a true transition state since it has a higher energy than the reactants and products (MP2=Full, MP2=FC and HF), while the other is not a true transition state since it has an energy which lies between that of the reactants and products (B3LYP and B3LYP based methods). The transition state structure (from MP2) has a twist angle of the OH fragment relative to the SO bond of the SO 2 fragment of -50.0°, whereas this angle is 26.7° in the product molecule. Examination of the displacement vectors confirms that this is a true transition state structure. The MP2=Full method with a larger basis set (MP2=Full/6-31++G(2df,2p)) predicts the enthalpy of reaction to be -112.8 kJ mol -1 which is close to the experimental value of -113.3 ± 6 kJ mol -1, and predicts a rather high barrier of 20.0 kJ mol -1. When the TS structure obtained by the MP2 method is used as the input for calculating the energetics using the QCISD/6-31++G(2df,2p) method, a barrier of 4.1 kJ mol -1 is obtained (ZPE corrected). The rate constant calculated from this barrier is 1.3 × 10 -13 cm 3 molecule -1 s -1. We conclude that while the MP2 methods correctly predict the TS from a structural point of view, higher level energy corrections are needed for estimation of exact barrier height.

Moringa oleifera Lam.: Protease activity against blood coagulation cascade.

PubMed

Satish, A; Sairam, Sudha; Ahmed, Faiyaz; Urooj, Asna

2012-01-01

The present study evaluated the protease activity of aqueous extracts of Moringa oleifera (Moringaceae) leaf (MOL) and root (MOR). Protease activity was assayed using casein, human plasma clot and human fibrinogen as substrates. Caseinolytic activity of MOL was significantly higher (P ≤ 0.05) than that of MOR. Similar observations were found in case of human plasma clot hydrolyzing activity, wherein MOL caused significantly higher (P ≤ 0.05) plasma clot hydrolysis than MOR. Zymographic techniques were used to detect proteolytic enzymes following electrophoretic separation in gels. Further, both the extracts exhibited significant procoagulant activity as reflected by a significant decrease (P ≤ 0.05) in recalcification time, accompanied by fibrinogenolytic and fibrinolytic activities; clotting time was decreased from 180 ± 10 sec to 119 ± 8 sec and 143 ± 10 sec by MOL and MOR, respectively, at a concentration of 2.5 mg/mL. Fibrinogenolytic (human fibrinogen) and fibrinolytic activity (human plasma clot) was determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), plate method and colorimetric method. Zymographic profile indicated that both the extracts exerted their procoagulant activity by selectively hydrolyzing Aα and Bβ subunits of fibrinogen to form fibrin clot, thereby exhibiting fibrinogenolytic activity. However, prolonged incubation resulted in degradation of the formed fibrin clot, suggesting fibrinolytic like activity. These findings support the traditional usage of M. oleifera extracts for wound healing.

Pyroglutamate (5-oxoproline) measured with hydrophilic interaction chromatography (HILIC) tandem mass spectrometry in acutely ill patients.

PubMed

Pretorius, Carel J; Reade, Michael C; Warnholtz, Chris; McWhinney, Brett; Phua, Meng Mei; Lipman, Jeffrey; Ungerer, Jacobus P J

2017-03-01

Pyroglutamic acid (PGA) is challenging to quantify in plasma and is a rare cause of metabolic acidosis that is associated with inherited disorders or acquired after exposure to drugs. We developed a hydrophilic interaction liquid chromatography tandem mass spectrometry method with a short analysis time. We established a reference interval and then measured PGA in acutely ill patients to investigate associations with clinical, pharmaceutical and laboratory parameters. The assay limit of the blank was 0.14μmol/L and was linear to 5000μmol/L with good precision. In-source formation of PGA from glutamate and glutamine was avoided by chromatographic separation. The PGA in controls had a reference interval of 22.6 to 47.8μmol/L. The median PGA concentration in acutely ill patients was similar (P=0.21), but 18 individuals were above the reference interval with concentrations up to 250μmol/L. We detected an association between PGA concentration and antibiotic and acetaminophen administration as well as renal impairment and severity of illness. Elevations of PGA in this unselected cohort were small compared to those reported in patients with pyroglutamic acidosis. The method is suitable for routine clinical use. We confirmed several expected associations with PGA in an acutely ill population. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Dielectric properties and microstructures for various MLCCs coated with additives

NASA Astrophysics Data System (ADS)

Oh, Min Wook; Yeo, Dong Hun; Shin, Hyo Soon; Jeong, Dae Yong

2013-12-01

As electronic devices become smaller and have higher capacity, dielectric thin films are being used in the development of multilayer ceramic capacitors (MLCCs). Smaller BaTiO3 dielectric particles should be used to obtain the thickness of low dielectric layers. Further, MLCC properties are achieved through the uniform addition of various additives, but the existing method of adding nano additives has limitations. As such, this study evaluated the dielectric properties of BaTiO3 pellets after using the liquid coating method to add additives such as Dy, Mg, Mn, Cr, and Si to 150 nm BaTiO3 dielectric powder. Mn, Cr, and Si ions were each fixed at 0.1, 0.1, and 0.65 mol-%. Sintering was performed in a reducing atmosphere, and the microstructure and the dielectric properties were evaluated while varying Dy from 0.5 to 1.0 mol-% and Mg from 1.0 to 2.0 mol-%. Grain growth was observed for higher amounts of Dy, but were suppressed for higher amounts of Mg. With regards to changes in particle size, both the permittivity and the temperature coefficient of capacitance (TCC) increased with increasing particle size. The permittivity was highest for Si=0.65, Mn=0.1, Cr=0.1 Dy=0.75, and Mg=2.0 mol-%. These levels also satisfied the TCC properties of X7R. In the microstructure, the core-shell was the most developed.

Sequential Proton Loss Electron Transfer in Deactivation of Iron(IV) Binding Protein by Tyrosine Based Food Components.

PubMed

Tang, Ning; Skibsted, Leif H

2017-08-02

The iron(IV) binding protein ferrylmyoglobin, MbFe(IV)═O, was found to be reduced by tyrosine based food components in aqueous solution through a sequential proton loss electron transfer reaction mechanism without binding to the protein as confirmed by isothermal titration calorimetry. Dopamine and epinephrine are the most efficient food components reducing ferrylmyoglobin to oxymyoglobin, MbFe(II)O 2 , and metmyoglobin, MbFe(III), as revealed by multivariate curve resolution alternating least-squares with second order rate constants of 33.6 ± 2.3 L/mol/s (ΔH ⧧ of 19 ± 5 kJ/mol, ΔS ⧧ of -136 ± 18 J/mol K) and 228.9 ± 13.3 L/mol/s (ΔH ⧧ of 110 ± 7 kJ/mol, ΔS ⧧ of 131 ± 25 J/mol K), respectively, at pH 7.4 and 25 °C. The other tyrosine based food components were found to reduce ferrylmyoglobin to metmyoglobin with similar reduction rates at pH 7.4 and 25 °C. These reduction reactions were enhanced by protonation of ferrylmyoglobin and facilitated proton transfer at acidic conditions. Enthalpy-entropy compensation effects were observed for the activation parameters (ΔH ⧧ and ΔS ⧧ ), indicating the common reaction mechanism. Moreover, principal component analysis combined with heat map were performed to understand the relationship between density functional theory calculated molecular descriptors and kinetic data, which was further modeled by partial least squares for quantitative structure-activity relationship analysis. In addition, a three tyrosine residue containing protein, lysozyme, was also found to be able to reduce ferrylmyoglobin with a second order rate constant of 66 ± 28 L/mol/s as determined by a competitive kinetic method.

Water dissociative adsorption on NiO(111): Energetics and structure of the hydroxylated surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Wei; Bajdich, Michal; Carey, Spencer

The energetics of the reactions of water with metal oxide surfaces are of tremendous interest for catalysis, electrocatalysis, and geochemistry, yet the energy for the dissociative adsorption of water was only previously measured on one well-defined oxide surface, iron oxide. In the present paper, the enthalpy of the dissociative adsorption of water is measured on NiO(111)-2 × 2 at 300 K using single-crystal adsorption calorimetry. The differential heat of dissociative adsorption decreases with coverage from 170 to 117 kJ/mol in the first 0.25 ML of coverage. Water adsorbs molecularly on top of that, with a heat of ~92 kJ/mol. Densitymore » functional theory (DFT) calculations reproduce the measured energies well (all within 17 kJ/mol) and provide insight into the atomic-level structure of the surfaces studied experimentally. They show that the oxygen-terminated O-octo(2 × 2) structure is the most stable NiO(111)-2 × 2 termination and gives reaction energies with water that are more consistent with the calorimetry results than the metal-terminated surface. They show that water adsorbs dissociatively on this (2 × 2)-O-octo surface to produce a hydroxyl-covered surface with a heat of adsorption of 171 ± 5 kJ/mol in the low-coverage limit (very close to 170 kJ/mol experimentally) and an integral heat that decreases by 14 kJ/mol up to saturation (compared to ~30 kJ/mol experimentally). As a result, sensitivity of this reaction’s energy to choice of DFT method is tested using a variety of different exchange correlation functionals, including HSE06, and found to be quite weak.« less

Water dissociative adsorption on NiO(111): Energetics and structure of the hydroxylated surface

DOE PAGES

Zhao, Wei; Bajdich, Michal; Carey, Spencer; ...

2016-09-19

The energetics of the reactions of water with metal oxide surfaces are of tremendous interest for catalysis, electrocatalysis, and geochemistry, yet the energy for the dissociative adsorption of water was only previously measured on one well-defined oxide surface, iron oxide. In the present paper, the enthalpy of the dissociative adsorption of water is measured on NiO(111)-2 × 2 at 300 K using single-crystal adsorption calorimetry. The differential heat of dissociative adsorption decreases with coverage from 170 to 117 kJ/mol in the first 0.25 ML of coverage. Water adsorbs molecularly on top of that, with a heat of ~92 kJ/mol. Densitymore » functional theory (DFT) calculations reproduce the measured energies well (all within 17 kJ/mol) and provide insight into the atomic-level structure of the surfaces studied experimentally. They show that the oxygen-terminated O-octo(2 × 2) structure is the most stable NiO(111)-2 × 2 termination and gives reaction energies with water that are more consistent with the calorimetry results than the metal-terminated surface. They show that water adsorbs dissociatively on this (2 × 2)-O-octo surface to produce a hydroxyl-covered surface with a heat of adsorption of 171 ± 5 kJ/mol in the low-coverage limit (very close to 170 kJ/mol experimentally) and an integral heat that decreases by 14 kJ/mol up to saturation (compared to ~30 kJ/mol experimentally). As a result, sensitivity of this reaction’s energy to choice of DFT method is tested using a variety of different exchange correlation functionals, including HSE06, and found to be quite weak.« less

A computational study on the energetics and mechanisms for the dissociative adsorption of SiHx(x = 1-4) on W(1 1 1) surface

NASA Astrophysics Data System (ADS)

Lin, Y. H.; Raghunath, P.; Lin, M. C.

2016-01-01

The adsorption and dissociation mechanisms of SiHx(x = 1-4) species on W(1 1 1) surface have been investigated by using the periodic density functional theory with the projector-augmented wave approach. The adsorption of all the species on four surface sites: top (T), bridge (B), shallow (S), and deep (D) sites have been analyzed. For SiH4 on a top site, T-SiH4(a), it is more stable with an adsorption energy of 2.6 kcal/mol. For SiH3, the 3-fold shallow site is most favorable with adsorption energy of 46.0 kcal/mol. For SiH2, its adsorption on a bridge site is most stable with 73.0 kcal/mol binding energy, whereas for SiH and Si the most stable adsorption configurations are on 3-fold deep sites with very high adsorption energies, 111.8 and 134.7 kcal/mol, respectively. The potential energy surfaces for the dissociative adsorption of all SiHx species on the W(1 1 1) surface have been constructed using the CINEB method. The barriers for H-atom migration from SiHx(a) to its neighboring W atoms, preferentially on B-sites, were predicted to be 0.4, 1.0, 4.5 and, 8.0 kcal/mol, respectively, for x = 4, 3, 2, and 1, respectively. The adsorption energy of the H atom on a bridge site on the clean W(1 1 1) surface was predicted to be 65.9 kcal/mol, which was found to be slightly affected by the co-adsorption of SiHx-1 within ± 1 kcal/mol.

Effect of increasing concentration of Na2O on structural, elastic and optical properties of (90  -  x)GeO2-xNa2O-10PbO glass system in the germanate anomaly region

NASA Astrophysics Data System (ADS)

Zainudin, C. N.; Hisam, R.; Yusof, M. I. M.; Yahya, A. K.; Halimah, M. K.

2017-10-01

Ternary germanate glasses (90  -  x)GeO2-xNa2O-10PbO (x  =  10-30 mol%) have been prepared by the melt-quenching method. Density, ρ increased with Na2O content up to maxima at 20 mol% while molar volume, V a showed an opposite trend to the density, with a minima at 20 mol% of Na2O content indicating the presence of the germanate anomaly. Ultrasonic velocity measurements showed both longitudinal, v l and shear, v s velocities increased up to 20 mol% before decreasing with further addition of Na2O. Independent longitudinal, L and shear, G moduli along with Young’s modulus, Y, mean sound velocity, v m, Debye temperature, θ D, and hardness, H recorded maximum values at 20 mol% of Na2O content which were suggested to be related to the germanate anomaly. Structural modification occurring due to conversion of six-membered GeO4 rings to three-membered rings of GeO4 changed bond density and compactness of the glass systems and caused the increase in rigidity and stiffness of the glasses. Beyond 20 mol% of Na2O, the decrease in the elastic moduli was due to depolymerization of the glass network. Meanwhile, optical energy gap, E opt exhibited a minima at 20 mol% whereas Urbach energy, E U and refractive index, n showed a maxima at the same concentration, thereby indicating variation in polarizability due to changes in concentration of bridging and non-bridging oxygen.

Search for β2 Adrenergic Receptor Ligands by Virtual Screening via Grid Computing and Investigation of Binding Modes by Docking and Molecular Dynamics Simulations

PubMed Central

Bai, Qifeng; Shao, Yonghua; Pan, Dabo; Zhang, Yang; Liu, Huanxiang; Yao, Xiaojun

2014-01-01

We designed a program called MolGridCal that can be used to screen small molecule database in grid computing on basis of JPPF grid environment. Based on MolGridCal program, we proposed an integrated strategy for virtual screening and binding mode investigation by combining molecular docking, molecular dynamics (MD) simulations and free energy calculations. To test the effectiveness of MolGridCal, we screened potential ligands for β2 adrenergic receptor (β2AR) from a database containing 50,000 small molecules. MolGridCal can not only send tasks to the grid server automatically, but also can distribute tasks using the screensaver function. As for the results of virtual screening, the known agonist BI-167107 of β2AR is ranked among the top 2% of the screened candidates, indicating MolGridCal program can give reasonable results. To further study the binding mode and refine the results of MolGridCal, more accurate docking and scoring methods are used to estimate the binding affinity for the top three molecules (agonist BI-167107, neutral antagonist alprenolol and inverse agonist ICI 118,551). The results indicate agonist BI-167107 has the best binding affinity. MD simulation and free energy calculation are employed to investigate the dynamic interaction mechanism between the ligands and β2AR. The results show that the agonist BI-167107 also has the lowest binding free energy. This study can provide a new way to perform virtual screening effectively through integrating molecular docking based on grid computing, MD simulations and free energy calculations. The source codes of MolGridCal are freely available at http://molgridcal.codeplex.com. PMID:25229694

Poly (3-hydroxybutyrate-co-15 mol% 3hydroxyhexanoate)/ZnO nanocomposites by solvent casting method: a study of optical, surface, and thermal properties

NASA Astrophysics Data System (ADS)

Vishnu Chandar, J.; Shanmugan, S.; Mutharasu, D.; Azlan, A. A.

2017-01-01

Biopolymer nanocomposites are gaining interest due to their biodegradable and biocompatible nature, with exceptional properties which are superior to those of pure polymer and that can be used as a replacement for petroleum-based plastics. Pure poly (3-hydroxybutyrate-co-15 mol% 3hydroxyhexanoate) [P(3HB-co-15 mol% 3HHx)] and ZnO nanoparticles (NPs) reinforced P(3HB-co-15 mol% 3HHx) composite films were prepared and their morphological, optical, and thermal analyses were carried out to study the effect of ZnO NPs on P(3HB-co-15 mol% 3HHx) copolymer. From optical analysis, a strong absorbance peak at ˜358 nm with high intensity for 5%ZnO NPs reinforced P(3HB-co-15 mol% 3HHx) composite sample was observed. Nano-sized particles and their increased trend with increased ZnO NPs concentration were confirmed by UV-Vis spectral analysis. In addition to that, ZnO NPs reduced the reflectance behaviour of P(3HB-co-15 mol% 3HHx) copolymer in the UV region. Field emission scanning electron microscopy analysis evidenced that the pore numbers and their size in the composite matrix was decreased with increased ZnO NPs concentration. Improved thermal stability and melting temperature of the copolymer matrix was confirmed by thermogravimetric analysis and differential scanning calorimetry analysis, respectively. ZnO NPs acted as a retarding agent and showed a low degree of crystallinity (X c ) and enthalpy of melting (ΔH M ). From these observations, ZnO NPs reinforced P(3HB-co-15 mol% 3HHx) composites can be integrated with suitable resin and can be used as an LED encapsulant to block UV rays. They can also be used as a UV blocking coating material in the glass, plastic, and textile industries, for NIR shielding and food packaging applications.

Thermochemical properties for isooctane and carbon radicals: computational study.

PubMed

Snitsiriwat, Suarwee; Bozzelli, Joseph W

2013-01-17

Thermochemical properties for isooctane, its internal rotation conformers, and radicals with corresponding bond energies are determined by use of computational chemistry. Enthalpies of formation are determined using isodesmic reactions with B3LYP density function theory and composite CBS-QB3 methods. Application of group additivity with comparison to calculated values is illustrated. Entropy and heat capacities are determined using geometric parameters, internal rotor potentials, and frequencies from B3LYP/6-31G(d,p) calculations for the lowest energy conformer. Internal rotor potentials are determined for the isooctane parent and for the primary, secondary, and tertiary radicals in order to identify isomer energies. Intramolecular interactions are shown to have a significant effect on the enthalpy of formation of the isooctane parent and its radicals. The computed standard enthalpy of formation for the lowest energy conformers of isooctane from this study is -54.40 ± 1.60 kcal mol(-1), which is 0.8 kcal mol(-1) lower than the evaluated experimental value -53.54 ± 0.36 kcal mol(-1). The standard enthalpy of formation for the primary radical for a methyl on the quaternary carbon is -5.00 ± 1.69 kcal mol(-1), for the primary radical on the tertiary carbon is -5.18 ± 1.69 kcal mol(-1), for the secondary isooctane radical is -9.03 ± 1.84 kcal mol(-1), and for the tertiary isooctane radical is -12.30 ± 2.02 kcal mol(-1). Bond energy values for the isooctane radicals are 100.64 ± 1.73, 100.46 ± 1.73, 96.41 ± 1.88 and 93.14 ± 2.05 kcal mol(-1) for C3•CCCC2, C3CCCC2•, C3CC•CC2, and C3CCC•C2, respectively. Entropy and heat capacity values are reported for the lowest energy homologues.

[Mixture Leaching Remediation Technology of Arsenic Contaminated Soil].

PubMed

Chen, Xun-feng; Li, Xiao-ming; Chen, Can; Yang, Qi; Deng, Lin-jing; Xie, Wei-qiang; Zhong, Yui; Huang, Bin; Yang, Wei-qiang; Zhang, Zhi-bei

2016-03-15

Soil contamination of arsenic pollution has become a severely environmental issue, while soil leaching is an efficient method for remediation of arsenic-contaminated soil. In this study, batch tests were primarily conducted to select optimal mixture leaching combination. Firstly, five conventional reagents were selected and combined with each other. Secondly, the fractions were analyzed before and after the tests. Finally, to explore the feasibility of mixed leaching, three soils with different arsenic pollution levels were used to compare the leaching effect. Comparing with one-step washing, the two-step sequential washing with different reagents increased the arsenic removal efficiency. These results showed that the mixture of 4 h 0.5 mol · L⁻¹ NaOH + 4 h 0.1 mol · L⁻¹ EDTA was found to be practicable, which could enhance the removal rate of arsenic from 66.67% to 91.83%, and the concentration of arsenic in soil was decreased from 186 mg · kg⁻¹ to 15.2 mg · kg⁻¹. Furthermore, the results indicated that the distribution of fractions of arsenic in soil changed apparently after mixture leaching. Leaching process could significantly reduce the available contents of arsenic in soil. Moreover, the mixture of 0.5 mol · L⁻¹ NaOH + 0.1 mol L⁻¹ EDTA could well decrease the arsenic concentration in aluminum-type soils, while the mixture of 0.5 mol · L⁻¹ OX + 0.5 mol · L⁻¹ NaOH could well decrease the arsenic concentration in iron-type soils.

Thermodynamic changes in mechanochemically synthesized magnesium hydride nanoparticles.

PubMed

Paskevicius, Mark; Sheppard, Drew A; Buckley, Craig E

2010-04-14

The thermodynamic properties of magnesium hydride nanoparticles have been investigated by hydrogen decomposition pressure measurements using the Sieverts technique. A mechanochemical method was used to synthesize MgH(2) nanoparticles (down to approximately 7 nm in size) embedded in a LiCl salt matrix. In comparison to bulk MgH(2), the mechanochemically produced MgH(2) with the smallest particle size showed a small but measurable decrease in the decomposition reaction enthalpy (DeltaH decrease of 2.84 kJ/mol H(2) from DeltaH(bulk) = 74.06 +/- 0.42 kJ/mol H(2) to DeltaH(nano) = 71.22 +/- 0.49 kJ/mol H(2)). The reduction in DeltaH matches theoretical predictions and was also coupled with a similar reduction in reaction entropy (DeltaS decrease of 3.8 J/mol H(2)/K from DeltaS(bulk) = 133.4 +/- 0.7 J/mol H(2)/K to DeltaS(nano) = 129.6 +/- 0.8 J/mol H(2)/K). The thermodynamic changes in the MgH(2) nanoparticle system correspond to a drop in the 1 bar hydrogen equilibrium temperature (T(1 bar)) by approximately 6 degrees C to 276.2 +/- 2.4 degrees C in contrast to the bulk MgH(2) system at 281.8 +/- 2.2 degrees C. The reduction in the desorption temperature is less than that expected from theoretical studies due to the decrease in DeltaS that acts to partially counteract the effect from the change in DeltaH.

Efficient enzymatic production of hydroxy fatty acids by linoleic acid Δ9 hydratase from Lactobacillus plantarum AKU 1009a.

PubMed

Takeuchi, M; Kishino, S; Park, S-B; Hirata, A; Kitamura, N; Saika, A; Ogawa, J

2016-05-01

This study aims to produce hydroxy fatty acids efficiently. Escherichia coli overexpressing linoleic acid Δ9 hydratase from Lactobacillus plantarum AKU 1009a was employed to produce hydroxy fatty acids with industrial potential. We found that 280 g l(-1) of linoleic acid (1 mol l(-1)) was converted into (S)-10-hydoxy-cis-12-octadecenoic acid (HYA) with a high conversion rate of 98% (mol/mol) and more than 99·9% enantiomeric excess (e.e.) by recombinant E. coli cells in the presence of FAD and NADH. In the same way, many kinds of C18 unsaturated fatty acids with Δ9 carbon double bond (280 g l(-1)) were converted into corresponding 10-hydroxy fatty acids with the conversion rates over 95% (mol/mol). We also produced HYA at a high rate of accumulation (289 g l(-1) ) with a high yield (97 mol%) in a reaction mixture that contained glucose instead of NADH. We developed a process for producing several types of hydroxy fatty acids with high accumulation rates and high yields. Hydroxy fatty acids are important materials for the chemical, food, cosmetic and pharmaceutical industries, and thus they have recently attracted much interest in a variety of research fields. However, the mass production of hydroxy fatty acids has been limited. This method of hydroxy fatty acids production will facilitate the widespread application of hydroxy fatty acids in various industries. © 2016 The Society for Applied Microbiology.

Exploration of the Visual System: Part 2: In Vivo Analysis Methods: Virtual-Reality Optomotor System, Fundus Examination, and Fluorescent Angiography.

PubMed

Marcelli, Fabienne; Escher, Pascal; Schorderet, Daniel F

2012-09-01

The mouse has emerged as an animal model for many diseases. At IRO, we have used this animal to understand the development of many eye diseases and treatment of some of them. Precise evaluation of vision is a prerequisite for both these approaches. In this unit we describe three ways to measure vision: testing the optokinetic response, and evaluating the fundus by direct observation and by fluorescent angiography. Curr. Protoc. Mouse Biol. 2:207-218 © 2012 by John Wiley & Sons, Inc. Copyright © 2012 John Wiley & Sons, Inc.

The lowest-lying electronic singlet and triplet potential energy surfaces for the HNO-NOH system: energetics, unimolecular rate constants, tunneling and kinetic isotope effects for the isomerization and dissociation reactions.

PubMed

Bozkaya, Uğur; Turney, Justin M; Yamaguchi, Yukio; Schaefer, Henry F

2012-04-28

The lowest-lying electronic singlet and triplet potential energy surfaces (PES) for the HNO-NOH system have been investigated employing high level ab initio quantum chemical methods. The reaction energies and barriers have been predicted for two isomerization and four dissociation reactions. Total energies are extrapolated to the complete basis set limit applying focal point analyses. Anharmonic zero-point vibrational energies, diagonal Born-Oppenheimer corrections, relativistic effects, and core correlation corrections are also taken into account. On the singlet PES, the (1)HNO → (1)NOH endothermicity including all corrections is predicted to be 42.23 ± 0.2 kcal mol(-1). For the barrierless decomposition of (1)HNO to H + NO, the dissociation energy is estimated to be 47.48 ± 0.2 kcal mol(-1). For (1)NOH → H + NO, the reaction endothermicity and barrier are 5.25 ± 0.2 and 7.88 ± 0.2 kcal mol(-1). On the triplet PES the reaction energy and barrier including all corrections are predicted to be 7.73 ± 0.2 and 39.31 ± 0.2 kcal mol(-1) for the isomerization reaction (3)HNO → (3)NOH. For the triplet dissociation reaction (to H + NO) the corresponding results are 29.03 ± 0.2 and 32.41 ± 0.2 kcal mol(-1). Analogous results are 21.30 ± 0.2 and 33.67 ± 0.2 kcal mol(-1) for the dissociation reaction of (3)NOH (to H + NO). Unimolecular rate constants for the isomerization and dissociation reactions were obtained utilizing kinetic modeling methods. The tunneling and kinetic isotope effects are also investigated for these reactions. The adiabatic singlet-triplet energy splittings are predicted to be 18.45 ± 0.2 and 16.05 ± 0.2 kcal mol(-1) for HNO and NOH, respectively. Kinetic analyses based on solution of simultaneous first-order ordinary-differential rate equations demonstrate that the singlet NOH molecule will be difficult to prepare at room temperature, while the triplet NOH molecule is viable with respect to isomerization and dissociation reactions up to 400 K. Hence, our theoretical findings clearly explain why (1)NOH has not yet been observed experimentally.

The ethane + oxygen(,2) reaction mechanism: High-level ab initio characterizations

NASA Astrophysics Data System (ADS)

Rienstra-Kiracofe, Jonathan C.

The C2H˙5+O2 reaction, central to ethane oxidation and thus of fundamental importance to hydrocarbon combustion chemistry, has been examined in detail via highly sophisticated electronic structure methods. The geometries, energies, and harmonic vibrational frequencies of the reactants, transition states, intermediates, and products for the reaction of the ethyl radical (X~ 2A ') with O2 (X S-g3 , a 1Δg) have been investigated using the CCSD and CCSD(T) ab initio methods with basis sets ranging in quality from double-zeta plus polarization (DZP) to triple-zeta plus double polarization with f functions (TZ2Pf). Five mechanisms (M1-M5) involving the ground-state from the ethyl radical by O2 to give ethylene + HO˙2 with an overall 0 K activation energy, Ea(0 K) = +15.1 kcal mol-1 with CCSD(T)/TZ2Pf//CCSD(T)/TZ2P. (M2) Ethylperoxy β- hydrogen transfer with O-O bond rupture to yield oxirane + .OH Ea(0 K) = +5.3 kcal mol-1 with CCSD(T)/TZ2Pf//CCSD(T)/TZ2P. (M3) Ethylperoxy α- hydrogen transfer with O-O bond rupture to yield acetaldehyde + .OH Ea(0 K) = +11.5 kcal mol-1 with CCSD(T)/TZ2P//CCSD(T)/DZP. (M4) Ethylperoxy β- hydrogen transfer with C-O bond rupture to yield ethylene + HO˙2 ; Ea(0 K) = +5.3 kcal mol-1 with CCSD(T)/TZ2Pf//CCSD(T)/TZ2P, the C-O bond rupture barrier lying 1.2 kcal mol-1 above the O-O bond rupture barrier of M2 at the CCSD(T)/TZ2P//CCSD(T)/DZP level. (M5) Concerted elimination of HO˙2 from the ethylperoxy radical to give ethylene + HO˙2 ; Ea(0 K) = -0.9 kcal mol -1 with CCSD(T)/TZPf//CCSD(T)/TZ2P. We show that M5 is energetically preferred and is also the only mechanism consistent with experimental observations of a negative temperature coefficient. The reverse reaction (C2H 4 + HO˙2 --> .C2H4OOH) has a zero-point corrected barrier of 14.4 kcal mol-1 with CCSD(T)/TZ2P//CCSD(T)/DZP.

EDITORIAL: Roberts Prize for the best paper published in 2011 Roberts Prize for the best paper published in 2011

NASA Astrophysics Data System (ADS)

Cherry, Simon; Ruffle, Jon

2012-08-01

The publishers of Physics in Medicine and Biology (PMB), IOP Publishing, in association with the journal owners, the Institute of Physics and Engineering in Medicine (IPEM), jointly award an annual prize for the best paper published in PMB during the previous year. The procedure for deciding the winner is a two-stage process. First, a shortlist of contenders is drawn up based on those papers that had the best referees' quality assessments, with a further quality check and endorsement by the Editorial Board. The papers on the shortlist are then reviewed by a specially convened IPEM committee consisting of members with fellow status. This committee reads the shortlisted papers and selects the winner. We have much pleasure in advising readers that the Roberts Prize for the best paper published in 2011 is awarded to Matthew Hough et al from the University of Florida, the Francis Marion University and the National Cancer Institute, USA for their paper on a comprehensive electron dosimetry model of skeletal tissues in the adult male: An image-based skeletal dosimetry model for the ICRP reference adult male—internal electron sources 2011 Phys. Med. Biol. 56 2309 Matthew Hough1, Perry Johnson1, Didier Rajon2, Derek Jokisch3, Choonsik Lee4 and Wesley Bolch1,5 1Department of Nuclear and Radiological Engineering, University of Florida, Gainesville, FL, USA 2Department of Neurosurgery, University of Florida, Gainesville, FL, USA 3Department of Physics and Astronomy, Francis Marion University, Florence, SC, USA 4Radiation Epidemiology Branch, National Cancer Institute, Bethesda, MD, USA 5Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA Bone marrow is one of the more radiosensitive tissues in the human body and is housed within a complex structure of bone. This paper describes a comprehensive model of energy deposition by internal electron or beta particle emitters for the ICRP reference adult male based upon ex vivo CT and microCT images of bone from a male cadaver. This work will be important for both the assessment of skeletal doses in radiation protection and nuclear medicine, and also for following external photon irradiation in medical imaging and radiotherapy. Our congratulations go to these authors. Of course all of the shortlisted papers were of an extremely high standard, and they are listed below in alphabetical order. We also would like to thank the IPEM Committee members for their hard work in reading the papers and making what must have been a difficult decision. Simon R Cherry Editor-in-Chief Jon Ruffle Publisher References Hough M, Johnson P, Rajon D, Jokisch D, Lee C and Bolch W 2011 An image-based skeletal dosimetry model for the ICRP reference adult male—internal electron sources Phys. Med. Biol. 56 2309 Jan S 2011 GATE V6: a major enhancement of the GATE simulation platform enabling modelling of CT and radiotherapy Phys. Med. Biol. 56 881 Jing H, Yang Y, and Nishikawa R M 2011 Detection of clustered microcalcifications using spatial point process modeling Phys. Med. Biol. 56 1 Li T, Thongphiew D, Zhu X, Lee W R, Vujaskovic Z, Yin F-F, Wu Q J A 2011 Adaptive prostate IGRT combining online re-optimization and re-positioning: a feasibility study Phys. Med. Biol. 56 1243 Kitchen M J, Paganin D M, Uesugi K, Allison B J, Lewis R A, Hooper S B, Pavlov K M 2011 Phase contrast image segmentation using a Laue analyser crystal Phys. Med. Biol. 56 515 Yamaya T, Mitsuhashi T, Matsumoto T, Inadama N, Nishikido F, Yoshida E, Murayama H, Kawai H, Suga M and Watanabe M 2011 A SiPM-based isotropic-3D PET detector X'tal cube with a three-dimensional array of 1 mm3 crystals Phys. Med. Biol. 56 6793 Yu Z, Wunderlich A, Dennerlein F, Lauritsch G and Noo F 2011 Line plus arc source trajectories and their R-line coverage for long-object cone-beam imaging with a C-arm system Phys. Med. Biol. 56 3447

Optical properties of Nd3+ doped bismuth zinc borate glasses

NASA Astrophysics Data System (ADS)

Shanmugavelu, B.; Venkatramu, V.; Ravi Kanth Kumar, V. V.

2014-03-01

Glasses with compositions of (100-x) (Bi2ZnOB2O6) - x Nd2O3 (where x = 0.1, 0.3, 0.5, 1 and 2 mol%) were prepared by melt quenching method and characterized through optical absorption, emission and decay curve measurements. Optical absorption spectra have been analyzed using Judd-Ofelt theory. The emission spectra exhibit three peaks at 919, 1063 and 1337 nm corresponding to 4F3/2 to 4I9/2, 4I11/2 and 4I13/2 transitions in the near infrared region. The emission intensity of the 4F3/2 to 4I11/2 transition increases with increase of Nd3+ concentration up to 1 mol% and then concentration quenching is observed for 2 mol% of Nd3+ concentration. The lifetimes for the 4F3/2 level are found to decrease with increase in Nd2O3 concentration in the glasses. The decay curves of the glass up to 0.3 mol% of Nd3+ exhibit single exponential nature and thereafter the curves become nonexponential nature (0.5, 1 and 2 mol%). The nonexponential curve has been fitted to the Inokuti-Hirayama model to understand the nature of energy transfer process.

Interactions on External MOF Surfaces: Desorption of Water and Ethanol from CuBDC Nanosheets.

PubMed

Elder, Alexander C; Aleksandrov, Alexandr B; Nair, Sankar; Orlando, Thomas M

2017-10-03

The external surfaces of metal-organic framework (MOF) materials are difficult to experimentally isolate due to the high porosities of these materials. MOF surface surrogates in the form of copper benzenedicarboxylate (CuBDC) nanosheets were synthesized using a bottom-up approach, and the surface interactions of water and ethanol were investigated by temperature-programmed desorption (TPD). A method of analysis of diffusion-influenced TPD was developed to measure the desorption properties of these porous materials. This approach also allows the extraction of diffusion coefficients from TPD data. The transmission Fourier transform infrared spectra, powder X-ray diffraction patterns, and TPD data indicate that water desorbs from CuBDC nanosheets with activation energies of 44 ± 2 kJ/mol at edge sites and 58 ± 1 kJ/mol at external surface and internal and pore sites. Ethanol desorbs with activation energies of 58 ± 1 kJ/mol at internal pore sites and 66 ± 0.4 kJ/mol at external surface sites. Co-adsorption of water and ethanol was also investigated. The presence of ethanol was found to inhibit the desorption of water, resulting in a water desorption process with an activation energy of 68 ± 0.7 kJ/mol.

Optical properties of Nd3+ doped bismuth zinc borate glasses.

PubMed

Shanmugavelu, B; Venkatramu, V; Ravi Kanth Kumar, V V

2014-03-25

Glasses with compositions of (100-x) (Bi2ZnOB2O6) -x Nd2O3 (where x=0.1, 0.3, 0.5, 1 and 2 mol%) were prepared by melt quenching method and characterized through optical absorption, emission and decay curve measurements. Optical absorption spectra have been analyzed using Judd-Ofelt theory. The emission spectra exhibit three peaks at 919, 1063 and 1337 nm corresponding to (4)F3/2 to (4)I9/2, (4)I11/2 and (4)I13/2 transitions in the near infrared region. The emission intensity of the (4)F3/2 to (4)I11/2 transition increases with increase of Nd(3+) concentration up to 1 mol% and then concentration quenching is observed for 2 mol% of Nd(3+) concentration. The lifetimes for the (4)F3/2 level are found to decrease with increase in Nd2O3 concentration in the glasses. The decay curves of the glass up to 0.3 mol% of Nd(3+) exhibit single exponential nature and thereafter the curves become nonexponential nature (0.5, 1 and 2 mol%). The nonexponential curve has been fitted to the Inokuti-Hirayama model to understand the nature of energy transfer process. Copyright © 2013 Elsevier B.V. All rights reserved.

A 300,000-mol-wt intermediate filament-associated protein in baby hamster kidney (BHK-21) cells.

PubMed

Yang, H Y; Lieska, N; Goldman, A E; Goldman, R D

1985-02-01

Native intermediate filament (IF) preparations from the baby hamster kidney fibroblastic cell line (BHK-21) contain a number of minor polypeptides in addition to the IF structural subunit proteins desmin, a 54,000-mol-wt protein, and vimentin, a 55,000-mol-wt protein. A monoclonal antibody was produced that reached exclusively with a high molecular weight (300,000) protein representative of these minor proteins. Immunological methods and comparative peptide mapping techniques demonstrated that the 300,000-mol-wt species was biochemically distinct from the 54,000- and 55,000-mol-wt proteins. Double-label immunofluorescence observations on spread BHK cells using this monoclonal antibody and a rabbit polyclonal antibody directed against the 54,000- and 55,000-mol-wt proteins showed that the 300,000-mol-wt species co-distributed with IF in a fibrous pattern. In cells treated with colchicine or those in the early stages of spreading, double-labeling with these antibodies revealed the co-existence of the respective antigens in the juxtanuclear cap of IF that is characteristic of cells in these physiological states. After colchicine removal, or in the late stages of cell spreading, the 300,00-mol-wt species and the IF subunits redistributed to their normal, highly coincident cytoplasmic patterns. Ultrastructural localization by the immunogold technique using the monoclonal antibody supported the light microscopic findings in that the 300,000-mol-wt species was associated with IF in the several physiological and morphological cell states investigated. The gold particle pattern was less intimately associated with IF than that defined by anti-54/55 and was one of non-uniform distribution along IF, being clustered primarily at points of proximity between IF, where an amorphous, proteinaceous material was often the labeled element. Occasionally, "bridges" of label were seen extending outward from such clusters on IF. Gold particles were infrequently bound to microtubules, microfilaments, or other cellular organelles, and when so, IF were usually contiguous. During multiple cycles of in vitro disassembly/assembly of the IF from native preparations, the 300,000-mol-wt protein remained in the fraction containing the 54,000- and 55,000-mol-wt structural subunits, whether the latter were in the soluble state or pelleted as formed filaments. In keeping with the nomenclature developed for the microtubule-associated proteins (MAPs), the acronym IFAP-300K (intermediate filament associated protein) is proposed for this molecule.

Thermoluminescence glow curve analysis and CGCD method for erbium doped CaZrO{sub 3} phosphor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tiwari, Ratnesh, E-mail: 31rati@gmail.com; Chopra, Seema

2016-05-06

The manuscript report the synthesis, thermoluminescence study at fixed concentration of Er{sup 3+} (1 mol%) doped CaZrO{sub 3} phosphor. The phosphors were prepared by modified solid state reaction method. The powder sample was characterized by thermoluminescence (TL) glow curve analysis. In TL glow curve the optimized concentration in 1mol% for UV irradiated sample. The kinetic parameters were calculated by computerized glow curve deconvolution (CGCD) techniaue. Trapping parameters gives the information of dosimetry loss in prepared phosphor and its usability in environmental monitoring and for personal monitoring. CGCD is the advance tool for analysis of complicated TL glow curves.

[A study on europium sensitized chemiluminescence of pipemidic acid].

PubMed

Li, Xia; Qiang, Hong; Wang, Xiao-li; Chen, Shi-lü; Zhao, Hui-chun

2004-12-01

A flow injection chemiluminescence method for the determination of Pipemidic acid (PPA) was developed. It is based on luminescence produced with KMnO4-Na2S2O4 CL system sensitized by Eu3+-PPA. The familar excipients such as starch and dextrine do not cause interference. The several kinds of affect on chemiluminescence were studied. The linear range and detection limit for PPA are 7.00 x 10(-9)-9.00 x 10(-7) mol x L(-1) and 4.09 x 10(-9) mol x L(-1), respectively. This method have successfully been applied to the determination of PPA in tablet and urine. And the mechanism of chemiluminescence is proposed.

Application of Purpald® for determination of 3-cyclohexene-1-carboxaldehyde and hydroxyisohexyl 3-cyclohexene carboxaldehyde.

PubMed

Zakrzewski, Robert; Skowron, Monika; Rembisz, Zaneta; Ciesielski, Witold

2013-01-01

A spectrophotometric method for determination of 3-cyclohexene-1-carboxaldehyde and hydroxyisohexyl 3-cyclohexene carboxaldehyde was developed. This procedure is based on the reaction of carbonyl compounds with the selective derivatization reagent Purpald® in alkaline solution. The product of reaction is a colored compound with maximum absorption at 538 nm. The linear relationship is in the range of (2.5-30) × 10-5 mol·l-1 for 3-cyclohexene-1-carboxaldehyde and (2.0-20) × 10-5 mol·l-1 for hydroxyisohexyl 3-cyclohexene carboxaldehyde. The proposed method was successfully used for determination of hydroxyisohexyl 3-cyclohexene carboxaldehyde in a cosmetic product.

Evaluation of Haemoglobin and Cytochrome Responses During Forearm Ischaemia Using Multi-wavelength Time Domain NIRS.

PubMed

Lange, Frédéric; Dunne, Luke; Tachtsidis, Ilias

2017-01-01

We demonstrate the ability of a 16-wavelength time domain near-infrared spectroscopy system to monitor changes in oxy- and deoxy haemoglobin ([HbO 2 ] [HHb]) and the oxidation of cytochrome-c-oxidase ([oxCCO]), during forearm ischaemia. We tested two methods to retrieve the concentration changes. The first uses the measured changes in light attenuation and the modified Beer-Lambert law, and the second uses the absorption and scattering estimated by the measured time-point spread function. The system is able to retrieve the concentration changes with both methods, giving similar results. At the end of forearm ischaemia (t = 5 min), we measured an increase in [HHb] of 16.77 ± 2.52 and 16.37 ± 2.33 μMol, and a decrease in [HbO 2 ] of -6.12 ± 1.62 and -5.57 ± 2.02 μMol for method 1 and 2, respectively. At that same time, the changes in [oxCCO] were -0.36 ± 0.33 and -1.40 ± 1.20 μMol, for method 1 and 2, respectively. These small changes in [oxCCO], despite a huge change in haemoglobin, demonstrate the absence of crosstalk and are comparable to previous measurements using broadband NIRS.

Determination of total phthalate in cosmetics using a simple three-phase sample preparation method.

PubMed

Liu, Laping; Wang, Zhengmeng; Zhao, Sihan; Duan, Jiahui; Tao, Hu; Wang, Wenji; Liu, Shuhui

2018-02-01

A simple sample preparation method requiring minimal organic solvents is proposed for the determination of the total phthalate content in cosmetics by high-performance liquid chromatography-tandem mass spectrometry. The hydrolysis of phthalates and purification of interfering substances were performed in a three-phase system that included an upper n-hexane phase, a middle ethanol phase, and a lower aqueous alkali solution. This three-phase system utilized an incremental purification strategy. The apolar ingredients were extracted with n-hexane, the polar pigments accumulated in the ethanol phase, and the hydrolysis product, phthalic acid, remained in the hydrolysate. Under the optimized conditions, the correlation coefficients (r) for the calibration curves were 0.998-0.999 in the range 0.60-12 mol L -1 . The limit of detection was 5.1 μmol kg -1 , and the limit of quantification was 9.2 μmol kg -1 . The recoveries varied from 84 to 97% with RSDs equal to or lower than 11%. The intra-day and inter-day repeatability values, expressed as the relative standard deviation, were less than 8.7 and 9.8, respectively. No obvious matrix effect existed in the different cosmetics matrices. The validated method was applied for the analysis of 57 commercial cosmetic samples. Graphical abstract Analysis of phthalates in cosmetics using a three-phase preparation method.

Enhanced Albumin Synthesis in Severely Burned Adults

DTIC Science & Technology

2010-10-01

changes in albumin syn- thesis in relation to changes in albumin levels. MATERIALS AND METHODS Sterile stable isotope ring-d5- phenylalanine (d5... phenylalanine ) and 5,5,5- d3-ketoisocaproic acid (d3-KIC, potassium salt) were purchased from Cam- bridge Isotope Laboratories (Andover, Mass). Sterile...hypermetabolic state. Stable isotope solutions of d5- phenylalanine (80 2mol I mL j1) and d3-KIC (120 2mol I mLj1) were prepared at the Pharmacy

Holographic Methods for the Investigation of Photophysical Properties.

DTIC Science & Technology

1983-04-22

terphenyl doped with 10- 3 mol/mol of pentacene . Obtaining k from decay curves as in * A -Fig. 14a and plotting k as a function of 02 (see Fig. 14b...translation diffusion of molecules in liquid solvents can be used to probe solute conformations, solvent-solute interactions and local solvent structure...eiion of 1.7omoAr WauW by TrArWAOn GFarinP So far, local heating by the absorption of the two interfering light pulses has not been taken into

Isothermal reduction kinetics of Panzhihua ilmenite concentrate under 30vol% CO-70vol% N2 atmosphere

NASA Astrophysics Data System (ADS)

Zhang, Ying-yi; Lü, Wei; Lü, Xue-wei; Li, Sheng-ping; Bai, Chen-guang; Song, Bing; Han, Ke-xi

2017-03-01

The reduction of ilmenite concentrate in 30vol% CO-70vol% N2 atmosphere was characterized by thermogravimetric and differential thermogravimetric (TG-DTG) analysis methods at temperatures from 1073 to 1223 K. The isothermal reduction results show that the reduction process comprised two stages; the corresponding apparent activation energy was obtained by the iso-conversional and model-fitting methods. For the first stage, the effect of temperature on the conversion degree was not obvious, the phase boundary chemical reaction was the controlling step, with an apparent activation energy of 15.55-40.71 kJ·mol-1. For the second stage, when the temperatures was greater than 1123 K, the reaction rate and the conversion degree increased sharply with increasing temperature, and random nucleation and subsequent growth were the controlling steps, with an apparent activation energy ranging from 182.33 to 195.95 kJ·mol-1. For the whole reduction process, the average activation energy and pre-exponential factor were 98.94-118.33 kJ·mol-1 and 1.820-1.816 min-1, respectively.

Investigation on the co-luminescence effect of europium (III)-lanthanum(III)-dopamine-sodium dodecylbenzene sulfonate system and its application.

PubMed

Si, Hailin; Zhao, Fang; Cai, Huan

2013-01-01

A novel luminescence, enhancement phenomenon in the europium(III)-dopamine-sodium dodecylbenzene sulfonate system was observed when lanthanum(III) was added. Based on this, a sensitive co-luminescence method was established for the determination of dopamine. The luminescence signal for the europium (III)-lanthanum(III)-dopamine-sodium dodecylbenzene sulfonate system was monitored at λ(ex) = 300 nm, λ(em) = 618 nm and pH 8.3. Under optimized conditions, the enhanced luminescence signal responded linearly to the concentration of dopamine in the range 1.0 × 10(-10)-5.0 × 10(-7) mol/L with a correlation coefficient of 0.9993 (n = 11). The detection limit (3σ) was 2.7 × 10(-11) mol/L and the relative standard deviation for 11 parallel measurements of 3.0 × 10(-8) mol/L dopamine was 1.9%. The presented method was successfully applied for the estimation of dopamine in samples of pharmaceutical preparations, human serum and urine. The possible luminescence enhancement mechanism of the system is discussed briefly. Copyright © 2013 John Wiley & Sons, Ltd.

Cryopreservation of gametophytes of Laminaria japonica (Phaeophyta) using encapsulation-dehydration with two-step cooling method

NASA Astrophysics Data System (ADS)

Zhang, Quansheng; Cong, Yizhou; Qu, Shancun; Luo, Shiju; Yang, Guanpin

2008-02-01

Gametophytes of Laminaria japonica were cryopreserved in liquid nitrogen using encapsulation-dehydration with two-step cooling method. Gametophytes cultured at 10°C and under continuous irradiance of 30 μmol m-2 s-1 for 3 weeks were encapsulated in calcium alginate beads. The beads were dehydrated in 0.4 molL-1 sucrose prepared with seawater for 6 h, desiccated in an incubator set at 10°C and 70% relative humidity for 4 h, pre-frozen at either -40°C or -60°C for 30 min, and stored in liquid nitrogen for >24 h. As high as 43% of survival rate was observed when gametophytes were thawed by placing the beads in 40°C seawater and re-hydrated in 0.05 molL-1 citrate sodium prepared using 30‰ NaCl 7 d later. More cells of male gametophytes survived the whole procedure in comparison with female gametophytes. The cells of gametophytes surviving the preservation were able to grow asexually and produce morphologically normal sporophytes.

Antioxidant Activity of Brazilian Vegetables and Its Relation with Phenolic Composition

PubMed Central

Tiveron, Ana P.; Melo, Priscilla S.; Bergamaschi, Keityane B.; Vieira, Thais M. F. S.; Regitano-d’Arce, Marisa A. B.; Alencar, Severino M.

2012-01-01

Vegetables are widely consumed in Brazil and exported to several countries. This study was performed to evaluate the phenolic content and antioxidant activity of vegetables commonly consumed in Brazil using five different methods, namely DPPH and ABTS free radical, β-carotene bleaching, reduction of Fe3+ (FRAP), oxidative stability in Rancimat, and the chemical composition using gas chromatography-mass spectrometry (GC-MS). The content of phenolic compounds ranged from 1.2 mg GA/g (carrot) to 16.9 mg GA/g (lettuce). Vegetables presenting the highest antioxidant activity were lettuce (77.2 μmol Trolox/g DPPH•; 447.1 μmol F2+/g FRAP), turmeric (118.6 μmol Trolox/g ABTS•+; 92.8% β-carotene), watercress and broccoli (protective factor 1.29—Rancimat method). Artichoke, spinach, broccoli, and asparagus also showed considerable antioxidant activity. The most frequent phenolic compounds identified by GC-MS were ferulic, caffeic, p-coumaric, 2-dihydroxybenzoic, 2,5-dihydroxybenzoic acids, and quercetin. We observed antioxidant activity in several vegetables and our results point out their importance in the diet. PMID:22942744

Photo-induced self-cleaning and sterilizing activity of Sm3+ doped ZnO nanomaterials.

PubMed

Saif, M; Hafez, H; Nabeel, A I

2013-01-01

Highly active samarium doped zinc oxide self-cleaning and biocidal surfaces (x mol% Sm(3+)/ZnO where x=0, 1, 2 and 4 mol%) with crystalline porous structures were synthesized by hydrothermal method. Sm(3+)/ZnO thin films were characterized by X-ray diffraction (XRD), transmission electron microscope (TEM), scanning electron microscope (SEM), energy dispersive spectroscopic (EDS), UV-visible diffuse reflectance and fluorescence (FL) spectroscopy. The combination between doping and hydrothermal treatments significantly altered the morphology of ZnO into rod and plate-like nanoshapes structure and enhanced its absorption and emission of ultraviolet radiation. The photo-activity in term of quantitative determination of the active oxidative species (()OH) produced on the thin film surfaces was evaluated using fluorescent probe method. The results showed that, the hydrothermally treated 2.0 mol% Sm(3+)/ZnO film (S2) is the highly active one. The optical, structural, morphology and photo-activity properties of the highly active thin film (S2) make it promising surface for self-cleaning and sterilizing applications. Copyright © 2012 Elsevier Ltd. All rights reserved.

Impact of steam explosion on the wheat straw lignin structure studied by solution-state nuclear magnetic resonance and density functional methods.

PubMed

Heikkinen, Harri; Elder, Thomas; Maaheimo, Hannu; Rovio, Stella; Rahikainen, Jenni; Kruus, Kristiina; Tamminen, Tarja

2014-10-29

Chemical changes of lignin induced by the steam explosion (SE) process were elucidated. Wheat straw was studied as the raw material, and lignins were isolated by the enzymatic mild acidolysis lignin (EMAL) procedure before and after the SE treatment for analyses mainly by two-dimensional (2D) [heteronuclear single-quantum coherence (HSQC) and heteronuclear multiple-bond correlation (HMBC)] and (31)P nuclear magnetic resonance (NMR). The β-O-4 structures were found to be homolytically cleaved, followed by recoupling to β-5 linkages. The homolytic cleavage/recoupling reactions were also studied by computational methods, which verified their thermodynamic feasibility. The presence of the tricin bound to wheat straw lignin was confirmed, and it was shown to participate in lignin reactions during the SE treatment. The preferred homolytic β-O-4 cleavage reaction was calculated to follow bond dissociation energies: G-O-G (guaiacyl) (69.7 kcal/mol) > G-O-S (syringyl) (68.4 kcal/mol) > G-O-T (tricin) (67.0 kcal/mol).

Spectrofluorimetric study on the inclusion interaction between vitamin K 3 with p-( p-sulfonated benzeneazo)calix[6]arene and determination of VK 3

NASA Astrophysics Data System (ADS)

Zhou, Yunyou; Xu, Hongwei; Wu, Lian; Liu, Chun; Lu, Qin; Wang, Lun

2008-11-01

The characteristics of host-guest complexation between p-( p-sulfonated benzeneazo) calix[6]arene (SBC6A) and vitamin K 3 (VK 3) were investigated by fluorescence spectrometry. A 1:1 stoichiometry for the complexation was established and was verified by Job's plot. An association constant of 4.95 × 10 3 L mol -1 at 20 °C was calculated by applying a deduced equation. The interaction mechanism of the inclusion complex was discussed. It was found that the fluorescence of SBC6A could be remarkably quenched by an appropriate amount of VK 3 especially when non-ionic surfactant Triton X-100 existed. According to the obtained results, a novel sensitive spectrofluorimetric method for the determination of VK 3 based on supramolecular complex was developed with a linear range of 5.0 × 10 -7-3.0 × 10 -5 mol L -1 and a detection limit of 2.0 × 10 -7 mol L -1. The proposed method was used to determine VK 3 in commercial preparations with satisfactory results.

Spectrofluorimetric study on the inclusion interaction between vitamin K3 with p-(p-sulfonated benzeneazo)calix[6]arene and determination of VK3.

PubMed

Zhou, Yunyou; Xu, Hongwei; Wu, Lian; Liu, Chun; Lu, Qin; Wang, Lun

2008-11-15

The characteristics of host-guest complexation between p-(p-sulfonated benzeneazo) calix[6]arene (SBC6A) and vitamin K3 (VK3) were investigated by fluorescence spectrometry. A 1:1 stoichiometry for the complexation was established and was verified by Job's plot. An association constant of 4.95 x 10(3)L mol(-1) at 20 degrees C was calculated by applying a deduced equation. The interaction mechanism of the inclusion complex was discussed. It was found that the fluorescence of SBC6A could be remarkably quenched by an appropriate amount of VK3 especially when non-ionic surfactant Triton X-100 existed. According to the obtained results, a novel sensitive spectrofluorimetric method for the determination of VK3 based on supramolecular complex was developed with a linear range of 5.0 x 10(-7) -3.0 x 10(-5)mol L(-1) and a detection limit of 2.0 x 10(-7)mol L(-1). The proposed method was used to determine VK3 in commercial preparations with satisfactory results.

[Determination of terbium (III) with EHPG-Tb (III) system by fluorescence spectroscopy].

PubMed

Zhao, Chun-gui; Li, Xiao-li; Yang, Bin-sheng

2007-12-01

The fluorescence of terbium was sensitized after addition of terbium to the ethylene-N, N'-bis (o-hydioxyphenylglycine) (EHPG) solution. A novel and simple method used for the determination of Tb (III) was developed by means of fluorescence spectroscopy in the presence of EHPG. It was showed that the relative fluorescence intensity is proportional to the concentration of terbium ions, while the molar ratio of terbium to EHPG is less than 1.0 in the system. The maximum wavelengths of excitation and emission are 295 and 547 nm respectively. The optimal range of pH is 7-9. The linear range of detection of the concentration of terbium is from 1.0 x 10(-8) mol x L(-1) to 1.0 x 10(-5) mol x L(-1), with a detection limit of 1.18 x 10(-9) mol x L(-1). The relative standard deviation is still within +/-3% in the presence of other lanthanide ions. The method was applied to the determination of the recoveries of synthetic samples and a rare earth sample with satisfactory results.

New Method for Measuring the Anchoring Energy of Strongly-Bound Membrane-Associated Proteins [Method for measuring the anchoring energy of strongly-bound membrane-associated proteins].

DOE PAGES

Kent, Michael S.; La Bauve, Elisa; Vernon, Briana C.; ...

2016-02-01

Here, we describe a new method to measure the activation energy required to remove a strongly-bound membrane-associated protein from a lipid membrane (anchoring energy). It is based on measuring the rate of release of a liposome-bound protein during centrifugation on a sucrose gradient as a function of time and temperature. The method was used to determine anchoring energy for the soluble dengue virus envelope protein (sE) strongly bound to 80:20 POPC:POPG liposomes at pH 5.5. We also measured the binding energy of sE at the same pH for the initial, predominantly reversible, phase of binding to a 70:30 PC:PG lipidmore » bilayer. The anchoring energy (37 +/- 1.7 kcal/mol, 20% PG) was found to be much larger than the binding energy (7.8 +/- 0.3 kcal/mol for 30% PG, or est. 7.0 kcal/mol for 20% PG). This is consistent with data showing that free sE is a monomer at pH 5.5, but assembles into trimers after associating with membranes. But, trimerization alone is insufficient to account for the observed difference in energies, and we conclude that some energy dissipation occurs during the release process. This new method to determine anchoring energy should be useful to understand the complex interactions of integral monotopic proteins and strongly-bound peripheral membrane proteins with lipid membranes.« less

New Method for Measuring the Anchoring Energy of Strongly-Bound Membrane-Associated Proteins [Method for measuring the anchoring energy of strongly-bound membrane-associated proteins].

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kent, Michael S.; La Bauve, Elisa; Vernon, Briana C.

Here, we describe a new method to measure the activation energy required to remove a strongly-bound membrane-associated protein from a lipid membrane (anchoring energy). It is based on measuring the rate of release of a liposome-bound protein during centrifugation on a sucrose gradient as a function of time and temperature. The method was used to determine anchoring energy for the soluble dengue virus envelope protein (sE) strongly bound to 80:20 POPC:POPG liposomes at pH 5.5. We also measured the binding energy of sE at the same pH for the initial, predominantly reversible, phase of binding to a 70:30 PC:PG lipidmore » bilayer. The anchoring energy (37 +/- 1.7 kcal/mol, 20% PG) was found to be much larger than the binding energy (7.8 +/- 0.3 kcal/mol for 30% PG, or est. 7.0 kcal/mol for 20% PG). This is consistent with data showing that free sE is a monomer at pH 5.5, but assembles into trimers after associating with membranes. But, trimerization alone is insufficient to account for the observed difference in energies, and we conclude that some energy dissipation occurs during the release process. This new method to determine anchoring energy should be useful to understand the complex interactions of integral monotopic proteins and strongly-bound peripheral membrane proteins with lipid membranes.« less

4D analysis of influence of patient movement and anatomy alteration on the quality of 3D U/S-based prostate HDR brachytherapy treatment delivery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Milickovic, Natasa; Mavroidis, Panayiotis; Tselis, Nikolaos

2011-09-15

Purpose: Modern HDR brachytherapy treatment for prostate cancer based on the 3D ultrasound (U/S) plays increasingly important role. The purpose of this study is to investigate possible patient movement and anatomy alteration between the clinical image set acquisition, made after the needle implantation, and the patient irradiation and their influence on the quality of treatment. Methods: The authors used 3D U/S image sets and the corresponding treatment plans based on a 4D-treatment planning procedure: plans of 25 patients are obtained right after the needle implantation (clinical plan is based on this 3D image set) and just before and after themore » treatment delivery. The authors notice the slight decrease of treatment quality with increase of time gap between the clinical image set acquisition and the patient irradiation. 4D analysis of dose-volume-histograms (DVHs) for prostate: CTV1 = PTV, and urethra, rectum, and bladder as organs at risk (OARs) and conformity index (COIN) is presented, demonstrating the effect of prostate, OARs, and needles displacement. Results: The authors show that in the case that the patient body movement/anatomy alteration takes place, this results in modification of DVHs and radiobiological parameters, hence the plan quality. The observed average displacement of needles (1 mm) and of prostate (0.57 mm) is quite small as compared with the average displacement noted in several other reports [A. A. Martinez et al., Int. J. Radiat. Oncol., Biol., Phys. 49(1), 61-69 (2001); S. J. Damore et al., Int. J. Radiat. Oncol., Biol., Phys. 46(5), 1205-1211 (2000); P. J. Hoskin et al., Radiotherm. Oncol. 68(3), 285-288 (2003); E. Mullokandov et al., Int. J. Radiat. Oncol., Biol., Phys. 58(4), 1063-1071 (2004)] in the literature. Conclusions: Although the decrease of quality of dosimetric and radiobiological parameters occurs, this does not cause clinically unacceptable changes to the 3D dose distribution, according to our clinical protocol.« less

Machine learning methods in chemoinformatics

PubMed Central

Mitchell, John B O

2014-01-01

Machine learning algorithms are generally developed in computer science or adjacent disciplines and find their way into chemical modeling by a process of diffusion. Though particular machine learning methods are popular in chemoinformatics and quantitative structure–activity relationships (QSAR), many others exist in the technical literature. This discussion is methods-based and focused on some algorithms that chemoinformatics researchers frequently use. It makes no claim to be exhaustive. We concentrate on methods for supervised learning, predicting the unknown property values of a test set of instances, usually molecules, based on the known values for a training set. Particularly relevant approaches include Artificial Neural Networks, Random Forest, Support Vector Machine, k-Nearest Neighbors and naïve Bayes classifiers. WIREs Comput Mol Sci 2014, 4:468–481. How to cite this article: WIREs Comput Mol Sci 2014, 4:468–481. doi:10.1002/wcms.1183 PMID:25285160

Effect of gingerol on colonic motility via inhibition of calcium channel currents in rats

PubMed Central

Cai, Zheng-Xu; Tang, Xu-Dong; Wang, Feng-Yun; Duan, Zhi-Jun; Li, Yu-Chun; Qiu, Juan-Juan; Guo, Hui-Shu

2015-01-01

AIM: To investigate the effect of gingerol on colonic motility and the action of L-type calcium channel currents in this process. METHODS: The distal colon was cut along the mesenteric border and cleaned with Ca2+-free physiological saline solution. Muscle strips were removed and placed in Ca2+-free physiological saline solution, which was oxygenated continuously. Longitudinal smooth muscle samples were prepared by cutting along the muscle strips and were then placed in a chamber. Mechanical contractile activities of isolated colonic segments in rats were recorded by a 4-channel physiograph. Colon smooth muscle cells were dissociated by enzymatic digestion. L-type calcium currents were recorded using the conventional whole-cell patch-clamp technique. RESULTS: Gingerol inhibited the spontaneous contraction of colonic longitudinal smooth muscle in a dose-dependent manner with inhibition percentages of 13.3% ± 4.1%, 43.4% ± 3.9%, 78.2% ± 3.6% and 80.5% ± 4.5% at 25 μmol/L, 50 μmol/L, 75 μmol/L and 100 μmol/L, respectively (P < 0.01). Nifedipine, an L-type calcium channel blocker, diminished the inhibition of colonic motility by gingerol. Gingerol inhibited L-type calcium channel currents in colonic longitudinal myocytes of rats. At a 75 μmol/L concentration of gingerol, the percentage of gingerol-induced inhibition was diminished by nifedipine from 77.1% ± 4.2% to 42.6% ± 3.6% (P < 0.01). Gingerol suppressed IBa in a dose-dependent manner, and the inhibition rates were 22.7% ± 2.38%, 35.77% ± 3.14%, 49.78% ± 3.48% and 53.78% ± 4.16% of control at 0 mV, respectively, at concentrations of 25 μmol/L, 50 μmol/L, 75 μmol/L and 100 μmol/L (P < 0.01). The steady-state activation curve was shifted to the right by treatment with gingerol. The value of half activation was -14.23 ± 1.12 mV in the control group and -10.56 ± 1.04 mV in the 75 μmol/L group (P < 0.05) with slope factors, Ks, of 7.16 ± 0.84 and 7.02 ± 0.93 (P < 0.05) in the control and 75 μmol/L groups, respectively. However, the steady-state inactivation curve was not changed, with a half-inactivation voltage, 0.5 V, of -27.43 ± 1.26 mV in the control group and -26.56 ± 1.53 mV in the 75 μmol/L gingerol group (P > 0.05), and a slope factor, K, of 13.24 ± 1.62 in the control group and 13.45 ± 1.68 (P > 0.05) in the 75 μmol/L gingerol group. CONCLUSION: Gingerol inhibits colonic motility by preventing Ca2+ influx through L-type calcium channels. PMID:26730157

Reply to Comment: 'A novel method for fast and robust estimation of fluorescence decay dynamics using constrained least-square deconvolution with Laguerre expansion'.

PubMed

Ma, Dinglong; Liu, Jing; Qi, Jinyi; Marcu, Laura

2017-02-21

In this response we underscore that the instrumentation described in the original publication (Liu et al 2012 Phys. Med. Biol. 57 843-65) was based on pulse-sampling technique, while the comment by Zhang et al is based on the assumption that a time-correlated single photon counting (TCSPC) instrumentation was used. Therefore the arguments made in the comment are not applicable to the noise model reported by Liu et al. As reported in the literature (Lakowicz 2006 Principles of Fluorescence Spectroscopy (New York: Springer)), while in the TCSPC the experimental noise can be estimated from Poisson statistics, such an assumption is not valid for pulse-sampling (transient recording) techniques. To further clarify this aspect, we present here a comprehensive noise model describing the signal and noise propagation of the pulse sampling time-resolved fluorescence detection. Experimental data recorded in various conditions are analyzed as a case study to demonstrate the noise model of our instrumental system. In addition, regarding the statement of correcting equation (3) in Liu et al (2012 Phys. Med. Biol. 57 843-65), the notation of discrete time Laguerre function in the original publication was clear and consistent with literature conventions (Marmarelis 1993 Ann. Biomed. Eng. 21 573-89, Westwick and Kearney 2003 Identification of Nonlinear Physiological Systems (Hoboken, NJ: Wiley)). Thus, it does not require revision.

Reply to Comment: ‘A novel method for fast and robust estimation of fluorescence decay dynamics using constrained least-square deconvolution with Laguerre expansion’

NASA Astrophysics Data System (ADS)

Ma, Dinglong; Liu, Jing; Qi, Jinyi; Marcu, Laura

2017-02-01

In this response we underscore that the instrumentation described in the original publication (Liu et al 2012 Phys. Med. Biol. 57 843-65) was based on pulse-sampling technique, while the comment by Zhang et al is based on the assumption that a time-correlated single photon counting (TCSPC) instrumentation was used. Therefore the arguments made in the comment are not applicable to the noise model reported by Liu et al. As reported in the literature (Lakowicz 2006 Principles of Fluorescence Spectroscopy (New York: Springer)), while in the TCSPC the experimental noise can be estimated from Poisson statistics, such an assumption is not valid for pulse-sampling (transient recording) techniques. To further clarify this aspect, we present here a comprehensive noise model describing the signal and noise propagation of the pulse sampling time-resolved fluorescence detection. Experimental data recorded in various conditions are analyzed as a case study to demonstrate the noise model of our instrumental system. In addition, regarding the statement of correcting equation (3) in Liu et al (2012 Phys. Med. Biol. 57 843-65), the notation of discrete time Laguerre function in the original publication was clear and consistent with literature conventions (Marmarelis 1993 Ann. Biomed. Eng. 21 573-89, Westwick and Kearney 2003 Identification of Nonlinear Physiological Systems (Hoboken, NJ: Wiley)). Thus, it does not require revision.

Fast batch injection analysis of H(2)O(2) using an array of Pt-modified gold microelectrodes obtained from split electronic chips.

PubMed

Pacheco, Bruno D; Valério, Jaqueline; Angnes, Lúcio; Pedrotti, Jairo J

2011-06-24

A fast and robust analytical method for amperometric determination of hydrogen peroxide (H(2)O(2)) based on batch injection analysis (BIA) on an array of gold microelectrodes modified with platinum is proposed. The gold microelectrode array (n=14) was obtained from electronic chips developed for surface mounted device technology (SMD), whose size offers advantages to adapt them in batch cells. The effect of the dispensing rate, volume injected, distance between the platinum microelectrodes and the pipette tip, as well as the volume of solution in the cell on the analytical response were evaluated. The method allows the H(2)O(2) amperometric determination in the concentration range from 0.8 μmolL(-1) to 100 μmolL(-1). The analytical frequency can attain 300 determinations per hour and the detection limit was estimated in 0.34 μmolL(-1) (3σ). The anodic current peaks obtained after a series of 23 successive injections of 50 μL of 25 μmolL(-1) H(2)O(2) showed an RSD<0.9%. To ensure the good selectivity to detect H(2)O(2), its determination was performed in a differential mode, with selective destruction of the H(2)O(2) with catalase in 10 mmolL(-1) phosphate buffer solution. Practical application of the analytical procedure involved H(2)O(2) determination in rainwater of São Paulo City. A comparison of the results obtained by the proposed amperometric method with another one which combines flow injection analysis (FIA) with spectrophotometric detection showed good agreement. Copyright © 2011 Elsevier B.V. All rights reserved.

Mechanised flow system for on-line microwave digestion of food samples with off-line catalytic spectrophotometric determination of cobalt at ng l-1 levels.

PubMed

Pereira-Filho, E R; Arruda, M A

1999-12-01

A mechanised system for on-line slurry food sample digestion was developed and an off-line cobalt determination was performed. The stabilised slurry sample was introduced into an air carrier stream until reaching the digestion coils located inside a household microwave oven. Software written in Visual Basic 3.0 was developed to permit the transport of the slurry samples and the programming of the microwave oven and also the control of the mineralization valve. The proposed system was optimized for determination of cobalt in certified samples such as mussels, bovine liver and fish and also uncertified fish samples. The digestion parameters were established as 3 mol l-1 HNO3 for mussels, 3 mol l-1 HNO3 plus 0.16% v/v H2O2 for bovine liver and 12 mol l-1 HNO3 for fish employing maximum power for 5 min of microwave actuation. In the subsequent spectrophotometric method for the catalytic determination of cobalt, the Tiron and hydrogen peroxide concentrations were 1.8 x 10(-3) and 3.0 x 10(-4) mol l-1, respectively, and the sample residence time was 300 s as determined by an optimisation process. The proposed method features a linear range from 10 to 200 ng l-1 Co (r > 0.996) with detection and quantification limits of 1.7 and 5.5 ng l-1 Co, respectively. The precision, expressed as RSD, was 2.4% (n = 12) for repeatability and 5.2% (n = 10) for reproducibility and the accuracy of the proposed method was assessed by using certified samples and an alternative technique (ETAAS).

[Inventive activity of the Departments of Chemistry and Biochemistry of Enzymes, and Protein Structure and Function of the Palladin Institute of Biochemistry of NAS of Ukraine. Part III. Diagnostic test-systems for analysis of fibrinolysis blood system and novel approaches to thrombosis treatment].

PubMed

Danilova, V M; Vynogradova, R P; Chernysh, I Yu

2016-01-01

This article continues analysis of scientific achievements of the Institute of Biochemistry in the study of hemostasis system. Two previous articles were focused on the studies of blood coagulation proteins and development of the immune-enzyme test-systems for evaluation of the risk of thrombosis upon various pathologies. This article highlights the research on the blood fibrinolysis system and new approaches to thrombosis treatment, which were developed (and are under development) in the Palladin Institute of Biochemistry of the NAS of Ukraine, in particular, in the Department of Chemistry and Biochemistry of Enzymes headed previously by Dr.Sci.(Biol.) S. O. Kudinov and now by Dr.Sci.(Biol.) T .V. Grinenko, and also in the Department of Protein Structure and Function headed by Dr.Biol.Sci. E. M. Makogonenko. The fundamental knowledge of protein molecule functions and mechanisms of regulation of blood coagulation and fibrinolysis opens up new opportunities to diagnose hemostasis disorders and control the effectiveness of the cardiovascular disease treatment and also contributes to development of new techniques for isolation of new proteins – promising therapeutic agents.

Calculation of Five Thermodynamic Molecular Descriptors by Means of a General Computer Algorithm Based on the Group-Additivity Method: Standard Enthalpies of Vaporization, Sublimation and Solvation, and Entropy of Fusion of Ordinary Organic Molecules and Total Phase-Change Entropy of Liquid Crystals.

PubMed

Naef, Rudolf; Acree, William E

2017-06-25

The calculation of the standard enthalpies of vaporization, sublimation and solvation of organic molecules is presented using a common computer algorithm on the basis of a group-additivity method. The same algorithm is also shown to enable the calculation of their entropy of fusion as well as the total phase-change entropy of liquid crystals. The present method is based on the complete breakdown of the molecules into their constituting atoms and their immediate neighbourhood; the respective calculations of the contribution of the atomic groups by means of the Gauss-Seidel fitting method is based on experimental data collected from literature. The feasibility of the calculations for each of the mentioned descriptors was verified by means of a 10-fold cross-validation procedure proving the good to high quality of the predicted values for the three mentioned enthalpies and for the entropy of fusion, whereas the predictive quality for the total phase-change entropy of liquid crystals was poor. The goodness of fit ( Q ²) and the standard deviation (σ) of the cross-validation calculations for the five descriptors was as follows: 0.9641 and 4.56 kJ/mol ( N = 3386 test molecules) for the enthalpy of vaporization, 0.8657 and 11.39 kJ/mol ( N = 1791) for the enthalpy of sublimation, 0.9546 and 4.34 kJ/mol ( N = 373) for the enthalpy of solvation, 0.8727 and 17.93 J/mol/K ( N = 2637) for the entropy of fusion and 0.5804 and 32.79 J/mol/K ( N = 2643) for the total phase-change entropy of liquid crystals. The large discrepancy between the results of the two closely related entropies is discussed in detail. Molecules for which both the standard enthalpies of vaporization and sublimation were calculable, enabled the estimation of their standard enthalpy of fusion by simple subtraction of the former from the latter enthalpy. For 990 of them the experimental enthalpy-of-fusion values are also known, allowing their comparison with predictions, yielding a correlation coefficient R ² of 0.6066.

Flow-injection chemiluminescence method for the determination of chloramphenicol based on luminol-sodium periodate order-transform second-chemiluminescence reaction.

PubMed

Zhuang, Ya-Feng; Zhu, Sheng-Nan; Wei, Wei; Li, Jie-Li

2011-01-01

A new chemiluminescence (CL) reaction was observed when chloramphenicol solution was injected into the mixture after the end of the reaction of alkaline luminol and sodium periodate or sodium periodate was injected into the reaction mixture of chloramphenicol and alkaline luminol. This reaction is described as an order-transform second-chemiluminescence (OTSCL) reaction. The OTSCL method combined with a flow-injection technique was applied to the determination of chloramphenicol. The optimum conditions for the order-transform second-chemiluminescence emission were investigated. A mechanism for OTSCL has been proposed on the basis of the chemiluminescence kinetic characteristics, the UV-visible spectra and the chemiluminescent spectra. Under optimal experimental conditions, the CL response is proportional to the concentration of chloramphenicol over the range 5.0 × 10(-7)-5.0 × 10(-5) mol/L with a correlation coefficient of 0.9969 and a detection limit of 6.0 × 10(-8) mol/L (3σ). The relative standard deviation (RSD) for 11 repeated determinations of 5.0 × 10(-6) mol/L chloramphenicol is 1.7%. The method has been applied to the determination of chloramphenicol in pharmaceutical samples with satisfactory results. Copyright © 2011 John Wiley & Sons, Ltd.

Extracting electron transfer coupling elements from constrained density functional theory

NASA Astrophysics Data System (ADS)

Wu, Qin; Van Voorhis, Troy

2006-10-01

Constrained density functional theory (DFT) is a useful tool for studying electron transfer (ET) reactions. It can straightforwardly construct the charge-localized diabatic states and give a direct measure of the inner-sphere reorganization energy. In this work, a method is presented for calculating the electronic coupling matrix element (Hab) based on constrained DFT. This method completely avoids the use of ground-state DFT energies because they are known to irrationally predict fractional electron transfer in many cases. Instead it makes use of the constrained DFT energies and the Kohn-Sham wave functions for the diabatic states in a careful way. Test calculations on the Zn2+ and the benzene-Cl atom systems show that the new prescription yields reasonable agreement with the standard generalized Mulliken-Hush method. We then proceed to produce the diabatic and adiabatic potential energy curves along the reaction pathway for intervalence ET in the tetrathiafulvalene-diquinone (Q-TTF-Q) anion. While the unconstrained DFT curve has no reaction barrier and gives Hab≈17kcal /mol, which qualitatively disagrees with experimental results, the Hab calculated from constrained DFT is about 3kcal /mol and the generated ground state has a barrier height of 1.70kcal/mol, successfully predicting (Q-TTF-Q)- to be a class II mixed-valence compound.

Simultaneous detection of morphine and codeine in urine samples of heroin addicts using multi-walled carbon nanotubes modified SnO2-Zn2SnO4 nanocomposites paste electrode

NASA Astrophysics Data System (ADS)

Taei, M.; Hasanpour, F.; Hajhashemi, V.; Movahedi, M.; Baghlani, H.

2016-02-01

The SnO2-Zn2SnO4 nanocomposite was successfully prepared via a simple solid state method. Then, a chemically modified electrode based on incorporating SnO2-Zn2SnO4 into multi-walled carbon nanotube paste matrix (MWCNTs/SnO2-Zn2SnO4/CPE) was prepared for the simultaneous determination of morphine(MO) and codeine (CO). The measurements were carried out by application of differential pulse voltammetry (DPV), cyclic voltammetry, and chronoamperometry. The MWCNTs/SnO2-Zn2SnO4/CPE showed an efficient electrocatalytic activity for the oxidation of MO and CO. The separation of the oxidation peak potential for MO-CO was about 550 mV. The calibration curves obtained for MO and CO were in the ranges of 0.1-310 μmol L-1 and 0.1-600.0 μmol L-1, respectively. The detection limits (S/N = 3) were 0.009 μmol L-1 for both drugs. The method also successfully employed as a selective, simple, and precise method for the determination of MO and CO in pharmaceutical and biological samples.