Duvelisib treatment is associated with altered expression of apoptotic regulators that helps in sensitization of chronic lymphocytic leukemia cells to venetoclax (ABT-199)

PubMed Central

Patel, Viralkumar M.; Balakrishnan, Kumudha; Douglas, Mark; Tibbitts, Thomas; Xu, Ethan Y.; Kutok, Jeffery L.; Ayers, Mary; Sarkar, Aloke; Guerrieri, Renato; Wierda, William G.; O’Brien, Susan; Jain, Nitin; Stern, Howard M.; Gandhi, Varsha

2017-01-01

Duvelisib, an oral dual inhibitor of PI3K-δ and PI3K-γ, is in phase III trials for the treatment of chronic lymphocytic leukemia (CLL) and indolent non-Hodgkin’s lymphoma (iNHL). In CLL, duvelisib monotherapy is associated with high iwCLL and nodal response rates, but complete remissions are rare. To characterize the molecular effect of duvelisib, we obtained samples from CLL patients on the duvelisib phase I trial. Gene-expression studies (RNA seq, Nanostring, Affymetrix array, and real time RT-PCR) demonstrated increased expression of BCL2 along with several BH3-only pro-apoptotic genes. In concert with induction of transcript levels, reverse phase protein arrays and immunoblots confirmed increase at the protein level. The BCL2 inhibitor venetoclax induced greater apoptosis in ex-vivo cultured CLL cells obtained from patients on duvelisib compared to pre-treatment CLL cells from the same patients. In vitro combination of duvelisib and venetoclax resulted in enhanced apoptosis even in CLL cells cultured under conditions that simulate the tumor microenvironment. These data provide a mechanistic rationale for testing the combination of duvelisib and venetoclax in the clinic. Such combination regimen (NCT02640833) is being evaluated for patients with B-cell malignancies including CLL. PMID:28017967

Duvelisib treatment is associated with altered expression of apoptotic regulators that helps in sensitization of chronic lymphocytic leukemia cells to venetoclax (ABT-199).

PubMed

Patel, V M; Balakrishnan, K; Douglas, M; Tibbitts, T; Xu, E Y; Kutok, J L; Ayers, M; Sarkar, A; Guerrieri, R; Wierda, W G; O'Brien, S; Jain, N; Stern, H M; Gandhi, V

2017-09-01

Duvelisib, an oral dual inhibitor of PI3K-δ and PI3K-γ, is in phase III trials for the treatment of chronic lymphocytic leukemia (CLL) and indolent non-Hodgkin's lymphoma. In CLL, duvelisib monotherapy is associated with high iwCLL (International Workshop on Chronic Lymphocytic Leukemia) and nodal response rates, but complete remissions are rare. To characterize the molecular effect of duvelisib, we obtained samples from CLL patients on the duvelisib phase I trial. Gene expression studies (RNAseq, Nanostring, Affymetrix array and real-time RT-PCR) demonstrated increased expression of BCL2 along with several BH3-only pro-apoptotic genes. In concert with induction of transcript levels, reverse phase protein arrays and immunoblots confirmed increase at the protein level. The BCL2 inhibitor venetoclax induced greater apoptosis in ex vivo-cultured CLL cells obtained from patients on duvelisib compared with pre-treatment CLL cells from the same patients. In vitro combination of duvelisib and venetoclax resulted in enhanced apoptosis even in CLL cells cultured under conditions that simulate the tumor microenvironment. These data provide a mechanistic rationale for testing the combination of duvelisib and venetoclax in the clinic. Such combination regimen (NCT02640833) is being evaluated for patients with B-cell malignancies including CLL.

Comparison of Orthogonal Transforms for Teleseismic Data

DTIC Science & Technology

1974-10-31

inverse transform Because the computations are done in-plaee( Y is both input and output arrays; X is a complex buffer array. The program generates...the forward transform the FFT is done first, then the array is phase-shifted; for the inverse transform the reverse procedure is followed. Each

Reverse-phase protein array profiling of oropharyngeal cancer and significance of PIK3CA mutations in HPV-associated head and neck cancer.

PubMed

Sewell, Andrew; Brown, Brandee; Biktasova, Asel; Mills, Gordon B; Lu, Yiling; Tyson, Darren R; Issaeva, Natalia; Yarbrough, Wendell G

2014-05-01

Human papilloma virus (HPV)-associated (HPV+) oropharyngeal squamous cell carcinomas (OPSCC) have different molecular and biologic characteristics and clinical behavior compared with HPV-negative (HPV-) OPSCC. PIK3CA mutations are more common in HPV(+) OPSCC. To define molecular differences and tumor subsets, protein expression and phosphorylation were compared between HPV(+) and HPV(-) OPSCC and between tumors with and without PIK3CA mutations. Expression of 137 total and phosphorylated proteins was evaluated by reverse-phase protein array in 29 HPV(+) and 13 HPV(-) prospectively collected OPSCCs. Forty-seven OPSCCs were tested for hotspot-activating mutations in PIK3CA and AKT. Activation of PIK3CA downstream targets and sensitivity to pathway inhibitors were determined in HPV(+) head and neck cancer cells overexpressing wild-type or mutant PIK3CA. Analyses revealed 41 differentially expressed proteins between HPV(+) and HPV(-) OPSCC categorized into functional groups: DNA repair, cell cycle, apoptosis, phosphoinositide 3-kinase (PI3K)/AKT/mTOR, and receptor kinase pathways. All queried DNA repair proteins were significantly upregulated in HPV(+) samples. A total of 8 of 33 HPV(+) and 0 of 14 HPV(-) tumors contained activating PIK3CA mutations. Despite all activating PIK3CA mutations occurring in HPV(+) samples, HPV(+) tumors had lower mean levels of activated AKT and downstream AKT target phosphorylation. Ectopic expression of mutant PIK3CA in HPV(+) cells increased mTOR, but not AKT activity. HPV E6/E7 overexpression inhibited AKT phosphorylation in HPV-negative cells. Mutant PIK3CA overexpressing cells were more sensitive to a dual PI3K/mTOR inhibitor compared with an AKT inhibitor. Protein expression analyses suggest that HPV(+) and HPV(-) OPSCC differentially activate DNA repair, cell cycle, apoptosis, PI3K/AKT/mTOR, and receptor kinase pathways. PIK3CA mutations are more common in HPV(+) OPSCC and are associated with activation of mTOR, but not AKT. These data suggest that inhibitors for mTOR may have activity against HPV(+) PIK3CA mutant oropharyngeal cancers. ©2014 AACR.

Advances in organic polymer-based monolithic column technology for high-resolution liquid chromatography-mass spectrometry profiling of antibodies, intact proteins, oligonucleotides, and peptides.

PubMed

Eeltink, Sebastiaan; Wouters, Sam; Dores-Sousa, José Luís; Svec, Frantisek

2017-05-19

This review focuses on the preparation of organic polymer-based monolithic stationary phases and their application in the separation of biomolecules, including antibodies, intact proteins and protein isoforms, oligonucleotides, and protein digests. Column and material properties, and the optimization of the macropore structure towards kinetic performance are also discussed. State-of-the-art liquid chromatography-mass spectrometry biomolecule separations are reviewed and practical aspects such as ion-pairing agent selection and carryover are presented. Finally, advances in comprehensive two-dimensional LC separations using monolithic columns, in particular ion-exchange×reversed-phase and reversed-phase×reversed-phase LC separations conducted at high and low pH, are shown. Copyright © 2017 Elsevier B.V. All rights reserved.

Implementation of a Multiplex and Quantitative Proteomics Platform for Assessing Protein Lysates Using DNA-Barcoded Antibodies.

PubMed

Lee, Jinho; Geiss, Gary K; Demirkan, Gokhan; Vellano, Christopher P; Filanoski, Brian; Lu, Yiling; Ju, Zhenlin; Yu, Shuangxing; Guo, Huifang; Bogatzki, Lisa Y; Carter, Warren; Meredith, Rhonda K; Krishnamurthy, Savitri; Ding, Zhiyong; Beechem, Joseph M; Mills, Gordon B

2018-06-01

Molecular analysis of tumors forms the basis for personalized cancer medicine and increasingly guides patient selection for targeted therapy. Future opportunities for personalized medicine are highlighted by the measurement of protein expression levels via immunohistochemistry, protein arrays, and other approaches; however, sample type, sample quantity, batch effects, and "time to result" are limiting factors for clinical application. Here, we present a development pipeline for a novel multiplexed DNA-labeled antibody platform which digitally quantifies protein expression from lysate samples. We implemented a rigorous validation process for each antibody and show that the platform is amenable to multiple protocols covering nitrocellulose and plate-based methods. Results are highly reproducible across technical and biological replicates, and there are no observed "batch effects" which are common for most multiplex molecular assays. Tests from basal and perturbed cancer cell lines indicate that this platform is comparable to orthogonal proteomic assays such as Reverse-Phase Protein Array, and applicable to measuring the pharmacodynamic effects of clinically-relevant cancer therapeutics. Furthermore, we demonstrate the potential clinical utility of the platform with protein profiling from breast cancer patient samples to identify molecular subtypes. Together, these findings highlight the potential of this platform for enhancing our understanding of cancer biology in a clinical translation setting. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Expression and Production of SH2 Domain Proteins.

PubMed

Liu, Bernard A; Ogiue-Ikeda, Mari; Machida, Kazuya

2017-01-01

The Src Homology 2 (SH2) domain lies at the heart of phosphotyrosine signaling, coordinating signaling events downstream of receptor tyrosine kinases (RTKs), adaptors, and scaffolds. Over a hundred SH2 domains are present in mammals, each having a unique specificity which determines its interactions with multiple binding partners. One of the essential tools necessary for studying and determining the role of SH2 domains in phosphotyrosine signaling is a set of soluble recombinant SH2 proteins. Here we describe methods, based on a broad experience with purification of all SH2 domains, for the production of SH2 domain proteins needed for proteomic and biochemical-based studies such as peptide arrays, mass-spectrometry, protein microarrays, reverse-phase microarrays, and high-throughput fluorescence polarization (HTP-FP). We describe stepwise protocols for expression and purification of SH2 domains using GST or poly His-tags, two widely adopted affinity tags. In addition, we address alternative approaches, challenges, and validation studies for assessing protein quality and provide general characteristics of purified human SH2 domains.

Solid-phase extraction method for the isolation of plant thionins from European mistletoe, wheat and barley using zirconium silicate embedded in poly(styrene-co-divinylbenzene) hollow-monoliths.

PubMed

Hussain, Shah; Güzel, Yüksel; Schönbichler, Stefan A; Rainer, Matthias; Huck, Christian W; Bonn, Günther K

2013-09-01

Thionins are cysteine-rich, biologically active small (∼5 kDa) and basic proteins occurring ubiquitously in the plant kingdom. This study describes an efficient solid-phase extraction (SPE) method for the selective isolation of these pharmacologically active proteins. Hollow-monolithic extraction tips based on poly(styrene-co-divinylbenzene) with embedded zirconium silicate nano-powder were designed, which showed an excellent selectivity for sulphur-rich proteins owing to strong co-ordination between zirconium and the sulphur atoms from the thiol-group of cysteine. The sorbent provides a combination of strong hydrophobic and electrostatic interactions which may help in targeted separation of certain classes of proteins in a complex mixture based upon the binding strength of different proteins. European mistletoe, wheat and barley samples were used for selective isolation of viscotoxins, purothionins and hordothionins, respectively. The enriched fractions were subjected to analysis by matrix-assisted laser desorption/ionisation-time-of-flight mass spectrometer to prove the selectivity of the SPE method towards thionins. For peptide mass-fingerprint analysis, tryptic digests of SPE eluates were examined. Reversed-phase high-performance liquid chromatography hyphenated to diode-array detection was employed for the purification of individual isoforms. The developed method was found to be highly specific for the isolation and purification of thionins.

Protein-surface interactions on stimuli-responsive polymeric biomaterials.

PubMed

Cross, Michael C; Toomey, Ryan G; Gallant, Nathan D

2016-03-04

Responsive surfaces: a review of the dependence of protein adsorption on the reversible volume phase transition in stimuli-responsive polymers. Specifically addressed are a widely studied subset: thermoresponsive polymers. Findings are also generalizable to other materials which undergo a similarly reversible volume phase transition. As of 2015, over 100,000 articles have been published on stimuli-responsive polymers and many more on protein-biomaterial interactions. Significantly, fewer than 100 of these have focused specifically on protein interactions with stimuli-responsive polymers. These report a clear trend of increased protein adsorption in the collapsed state compared to the swollen state. This control over protein interactions makes stimuli-responsive polymers highly useful in biomedical applications such as wound repair scaffolds, on-demand drug delivery, and antifouling surfaces. Outstanding questions are whether the protein adsorption is reversible with the volume phase transition and whether there is a time-dependence. A clear understanding of protein interactions with stimuli-responsive polymers will advance theoretical models, experimental results, and biomedical applications.

Similarities of prosurvival signals in Bcl-2-positive and Bcl-2-negative follicular lymphomas identified by reverse phase protein microarray.

PubMed

Zha, Hongbin; Raffeld, Mark; Charboneau, Lu; Pittaluga, Stefania; Kwak, Larry W; Petricoin, Emanuel; Liotta, Lance A; Jaffe, Elaine S

2004-02-01

Overexpression of Bcl-2 protein has been known to play a role in the pathogenesis of follicular lymphoma (FL). However, 10-15% of FLs are negative for Bcl-2 by immunohistochemistry, raising the possibility that another gene product(s) may provide prosurvival signal(s). We used reverse phase protein microarray to analyze lysates of follicle center cells isolated by laser capture microdissection from: Bcl-2+ FL, Bcl-2- FL and reactive follicular hyperplasia (FH) (nine cases each group). TUNEL assay confirmed similar and reduced levels of apoptosis in Bcl-2+ FL and Bcl-2- FL, indicating the likelihood of Bcl-2-independent inhibition of apoptosis. Arrays were quantitatively analyzed with antibodies to proteins involved in the apoptotic pathway. As expected, Bcl-2 levels were up to eight-fold higher in Bcl-2+ FL than in FH and Bcl-2- FL. However, there was no difference in levels of Mcl-1 and survivin among these three groups. Bcl-X(L) showed a trend for increased expression in Bcl-2- FL as compared with Bcl-2+ FL, although the differences did not reach statistical significance (P>0.1). The increase in Bcl-X(L) may provide an alternative antiapoptotic signal in FL negative for Bcl-2 protein. Interestingly, Bax expression was higher in FL (Bcl-2+ or -) than in FH (P=0.001). Notably, phospho-Akt (Ser-473) was increased in FL (Bcl-2+ or -) (P<0.03) with increased phospho-Bad (Ser-136), as compared with levels in FH. The activation of the Akt/Bad pathway provides further evidence of prosurvival signals in FL, independent of Bcl-2 alone. These data suggest that nodal FL represents a single disease with a final common biochemical pathway.

Modeling Protein Expression and Protein Signaling Pathways

PubMed Central

Telesca, Donatello; Müller, Peter; Kornblau, Steven M.; Suchard, Marc A.; Ji, Yuan

2015-01-01

High-throughput functional proteomic technologies provide a way to quantify the expression of proteins of interest. Statistical inference centers on identifying the activation state of proteins and their patterns of molecular interaction formalized as dependence structure. Inference on dependence structure is particularly important when proteins are selected because they are part of a common molecular pathway. In that case, inference on dependence structure reveals properties of the underlying pathway. We propose a probability model that represents molecular interactions at the level of hidden binary latent variables that can be interpreted as indicators for active versus inactive states of the proteins. The proposed approach exploits available expert knowledge about the target pathway to define an informative prior on the hidden conditional dependence structure. An important feature of this prior is that it provides an instrument to explicitly anchor the model space to a set of interactions of interest, favoring a local search approach to model determination. We apply our model to reverse-phase protein array data from a study on acute myeloid leukemia. Our inference identifies relevant subpathways in relation to the unfolding of the biological process under study. PMID:26246646

DETERMINATION OF CARBENDAZIM IN WATER BY HIGH-PERFORMANCE IMMUNOAFFINITY CHROMATOGRAPHY ON-LINE WITH HIGH-PERFORMANCE LIQUID CHROMATOGRAPHY WITH DIODE-ARRAY OR MASS SPECTROMETRIC DETECTION

EPA Science Inventory

An automated method for the determination of carbendazim in water that combines high-performance immunoaffinity chromatography (HPIAC), high-performance liquid chromatography (HPLC) in the reversed-phase mode, and detection by either UV-Vis diode array detector (DAD) spectroscopy...

How may targeted proteomics complement genomic data in breast cancer?

PubMed

Guerin, Mathilde; Gonçalves, Anthony; Toiron, Yves; Baudelet, Emilie; Audebert, Stéphane; Boyer, Jean-Baptiste; Borg, Jean-Paul; Camoin, Luc

2017-01-01

Breast cancer (BC) is the most common female cancer in the world and was recently deconstructed in different molecular entities. Although most of the recent assays to characterize tumors at the molecular level are genomic-based, proteins are the actual executors of cellular functions and represent the vast majority of targets for anticancer drugs. Accumulated data has demonstrated an important level of quantitative and qualitative discrepancies between genomic/transcriptomic alterations and their protein counterparts, mostly related to the large number of post-translational modifications. Areas covered: This review will present novel proteomics technologies such as Reverse Phase Protein Array (RPPA) or mass-spectrometry (MS) based approaches that have emerged and that could progressively replace old-fashioned methods (e.g. immunohistochemistry, ELISA, etc.) to validate proteins as diagnostic, prognostic or predictive biomarkers, and eventually monitor them in the routine practice. Expert commentary: These different targeted proteomic approaches, able to complement genomic data in BC and characterize tumors more precisely, will permit to go through a more personalized treatment for each patient and tumor.

Determination of 4-nonylphenol and 4-octylphenol in human blood samples by high-performance liquid chromatography with multi-electrode electrochemical coulometric-array detection.

PubMed

Inoue, K; Yoshimura, Y; Makino, T; Nakazawa, H

2000-11-01

Alkylphenols can affect human health because they disrupt the endocrine system. In this study, an analytical method for determining trace amounts of 4-nonylphenol (NP) and 4-octylphenol (OP) in human blood samples was developed. Reversed-phase HPLC with multi-electrode electrochemical coulometric-array detection was used for the determination of NP and OP in plasma and serum samples prepared with a solid-phase extraction method. The separation was achieved using an isocratic mobile phase of 0.7% phosphoric acid-acetonitrile with a C18 reversed phase column. The detection limits of NP and OP were 1.0 and 0.5 ng ml-1, respectively. The recoveries of NP and OP added to human plasma samples were above 70.0% with a relative standard deviation of less than 15.5%. The method was found to be applicable to the determination of NP and OP in various human blood samples such as serum and plasma.

Separation and quantitation of colour pigments of chili powder (Capsicum frutescens) by high-performance liquid chromatography-diode array detection.

PubMed

Cserháti, T; Forgács, E; Morais, M H; Mota, T; Ramos, A

2000-10-27

The performance of reversed-phase thin-layer (RP-TLC) and reversed-phase high-performance liquid chromatography (RP-HPLC) was compared for the separation and determination of the colour pigments of chili (Capsicum frutescens) powder using a wide variety of eluent systems. No separation of pigments was achieved in RP-TLC, however, it was established that tetrahydrofuran shows an unusually high solvent strength. RP-HPLC using water-methanol-acetonitrile gradient elution separated the chili pigments in many fractions. Diode array detection (DAD) indicated that yellow pigments are eluted earlier than the red ones and chili powder contains more yellow pigments than common paprika powders. It was established that the very different absorption spectra of pigments make the use of DAD necessary.

The physiological and pathological biophysics of phase separation and gelation of RNA binding proteins in amyotrophic lateral sclerosis and fronto-temporal lobar degeneration.

PubMed

St George-Hyslop, Peter; Lin, Julie Qiaojin; Miyashita, Akinori; Phillips, Emma C; Qamar, Seema; Randle, Suzanne J; Wang, GuoZhen

2018-04-30

Many RNA binding proteins, including FUS, contain moderately repetitive, low complexity, intrinsically disordered domains. These sequence motifs have recently been found to underpin reversible liquid: liquid phase separation and gelation of these proteins, permitting them to reversibly transition from a monodispersed state to liquid droplet- or hydrogel-like states. This function allows the proteins to serve as scaffolds for the formation of reversible membraneless intracellular organelles such as nucleoli, stress granules and neuronal transport granules. Using FUS as an example, this review examines the biophysics of this physiological process, and reports on how mutations and changes in post-translational state alter phase behaviour, and lead to neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Copyright © 2018. Published by Elsevier B.V.

Neisseria meningitidis causes cell cycle arrest of human brain microvascular endothelial cells at S phase via p21 and cyclin G2.

PubMed

Oosthuysen, Wilhelm F; Mueller, Tobias; Dittrich, Marcus T; Schubert-Unkmeir, Alexandra

2016-01-01

Microbial pathogens have developed several mechanisms to modulate and interfere with host cell cycle progression. In this study, we analysed the effect of the human pathogen Neisseria meningitidis on cell cycle in a brain endothelial cell line as well as in primary brain endothelial cells. We found that N.  Meningitidis causes an accumulation of cells in the S phase early at 3 and at 24 h post-infection that was paralleled by a decrease of cells in G2/M phase. Importantly, the outer membrane proteins of the colony opacity-associated (Opa) protein family as well as the Opc protein proved to trigger the accumulation of cells in the S phase. A focused cell cycle reverse transcription quantitative polymerase chain reaction-based array and integrated network analysis revealed changes in the abundance of several cell cycle regulatory mRNAs, including the cell cycle inhibitors p21(WAF1/CIP1) and cyclin G2. These alterations were reflected in changes in protein expression levels and/or relocalization in N. meningitidis-infected cells. Moreover, an increase in p21(WAF1/CIP1) expression was found to be p53 independent. Genetic ablation of p21(WAF1/CIP1) and cyclin G2 abrogated N. meningitidis-induced S phase accumulation. Finally, by measuring the levels of the biomarker 8-hydroxydeoxyguanosine and phosphorylation of the histone variant H2AX, we provide evidence that N. meningitidis induces oxidative DNA damage in infected cells. © 2015 John Wiley & Sons Ltd.

Forward and reverse control system for induction motors

DOEpatents

Wright, J.T.

1987-09-15

A control system for controlling the direction of rotation of a rotor of an induction motor includes an array of five triacs with one of the triacs applying a current of fixed phase to the windings of the rotor and four of the triacs being switchable to apply either hot ac current or return ac current to the stator windings so as to reverse the phase of current in the stator relative to that of the rotor and thereby reverse the direction of rotation of the rotor. Switching current phase in the stator is accomplished by operating the gates of pairs of the triacs so as to connect either hot ac current or return ac current to the input winding of the stator. 1 fig.

Direct CRISPR spacer acquisition from RNA by a natural reverse-transcriptase-Cas1 fusion protein

PubMed Central

Sidote, David J.; Markham, Laura M.; Sanchez-Amat, Antonio; Bhaya, Devaki; Lambowitz, Alan M.; Fire, Andrew Z.

2016-01-01

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) systems mediate adaptive immunity in diverse prokaryotes. CRISPR-associated Cas1 and Cas2 proteins have been shown to enable adaptation to new threats in Type I and II CRISPR systems by the acquisition of short segments of DNA (“spacers”) from invasive elements. In several Type III CRISPR systems, Cas1 is naturally fused to a reverse transcriptase (RT). In the marine bacterium Marinomonas mediterranea (MMB-1), we show that an RT-Cas1 fusion enables the acquisition of RNA spacers in vivo in an RT-dependent manner. In vitro, the MMB-1 RT-Cas1 and Cas2 proteins catalyze ligation of RNA segments into the CRISPR array, followed by reverse transcription. These observations outline a host-mediated mechanism for reverse information flow from RNA to DNA. PMID:26917774

Elevated NIBP/TRAPPC9 mediates tumorigenesis of cancer cells through NFκB signaling

PubMed Central

Wang, Hong; Yang, Wensheng; Li, Fang; Yang, Fan; Yu, Daohai; Ramsey, Frederick V.; Tuszyski, George P.; Hu, Wenhui

2015-01-01

Regulatory mechanisms underlying constitutive and inducible NFκB activation in cancer remain largely unknown. Here we investigated whether a novel NIK- and IKK2-binding protein (NIBP) is required for maintaining malignancy of cancer cells in an NFκB-dependent manner. Real-time polymerase chain reaction analysis of a human cancer survey tissue-scan cDNA array, immunostaining of a human frozen tumor tissue array and immunoblotting of a high-density reverse-phase cancer protein lysate array showed that NIBP is extensively expressed in most tumor tissues, particularly in breast and colon cancer. Lentivirus-mediated NIBP shRNA knockdown significantly inhibited the growth/proliferation, invasion/migration, colony formation and xenograft tumorigenesis of breast (MDA-MB-231) or colon (HCT116) cancer cells. NIBP overexpression in HCT116 cells promoted cell proliferation, migration and colony formation. Mechanistically, NIBP knockdown in cancer cells inhibited cytokine-induced activation of NFκB luciferase reporter, thus sensitizing the cells to TNFα-induced apoptosis. Endogenous NIBP bound specifically to the phosphorylated IKK2 in a TNFα-dependent manner. NIBP knockdown transiently attenuated TNFα-stimulated phosphorylation of IKK2/p65 and degradation of IκBα. In contrast, NIBP overexpression enhanced TNFα-induced NFκB activation, thus inhibiting constitutive and TNFα-induced apoptosis. Collectively, our data identified important roles of NIBP in promoting tumorigenesis via NFκΒ signaling, spotlighting NIBP as a promising target in cancer therapeutic intervention. PMID:25704885

Quantifying Kinase-Specific Phosphorylation Stoichiometry Using Stable Isotope Labeling In a Reverse In-Gel Kinase Assay

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

Li, Xiang; Cox, Jonathan T.; Huang, Weiliang

2016-12-06

Reversible protein phosphorylation regulates essentially all cellular activities. Aberrant protein phosphorylation is an etiological factor in a wide array of diseases, including cancer1, diabetes2, and Alzheimer’s3. Given the broad impact of protein phosphorylation on cellular biology and organismal health, understanding how protein phosphorylation is regulated and the consequences of gain and loss of phosphoryl moieties from proteins is of primary importance. Advances in instrumentation, particularly in mass spectrometry, coupled with high throughput approaches have recently yielded large datasets cataloging tens of thousands of protein phosphorylation sites in multiple organisms4-6. While these studies are seminal in term of data collection, ourmore » understanding of protein phosphorylation regulation remains largely one-dimensional.« less

Applications of reversible covalent chemistry in analytical sample preparation.

PubMed

Siegel, David

2012-12-07

Reversible covalent chemistry (RCC) adds another dimension to commonly used sample preparation techniques like solid-phase extraction (SPE), solid-phase microextraction (SPME), molecular imprinted polymers (MIPs) or immuno-affinity cleanup (IAC): chemical selectivity. By selecting analytes according to their covalent reactivity, sample complexity can be reduced significantly, resulting in enhanced analytical performance for low-abundance target analytes. This review gives a comprehensive overview of the applications of RCC in analytical sample preparation. The major reactions covered include reversible boronic ester formation, thiol-disulfide exchange and reversible hydrazone formation, targeting analyte groups like diols (sugars, glycoproteins and glycopeptides, catechols), thiols (cysteinyl-proteins and cysteinyl-peptides) and carbonyls (carbonylated proteins, mycotoxins). Their applications range from low abundance proteomics to reversible protein/peptide labelling to antibody chromatography to quantitative and qualitative food analysis. In discussing the potential of RCC, a special focus is on the conditions and restrictions of the utilized reaction chemistry.

Optimization of the β-Elimination/Michael Addition Chemistry on Reversed-Phase Supports for Mass Spectrometry Analysis of O-Linked Protein Modifications

PubMed Central

Nika, Heinz; Nieves, Edward; Hawke, David H.; Angeletti, Ruth Hogue

2013-01-01

We previously adapted the β-elimination/Michael addition chemistry to solid-phase derivatization on reversed-phase supports, and demonstrated the utility of this reaction format to prepare phosphoseryl peptides in unfractionated protein digests for mass spectrometric identification and facile phosphorylation-site determination. Here, we have expanded the use of this technique to β-N-acetylglucosamine peptides, modified at serine/threonine, phosphothreonyl peptides, and phosphoseryl/phosphothreonyl peptides, followed in sequence by proline. The consecutive β-elimination with Michael addition was adapted to optimize the solid-phase reaction conditions for throughput and completeness of derivatization. The analyte remained intact during derivatization and was recovered efficiently from the silica-based, reversed-phase support with minimal sample loss. The general use of the solid-phase approach for enzymatic dephosphorylation was demonstrated with phosphoseryl and phosphothreonyl peptides and was used as an orthogonal method to confirm the identity of phosphopeptides in proteolytic mixtures. The solid-phase approach proved highly suitable to prepare substrates from low-level amounts of protein digests for phosphorylation-site determination by chemical-targeted proteolysis. The solid-phase protocol provides for a simple, robust, and efficient tool to prepare samples for phosphopeptide identification in MALDI mass maps of unfractionated protein digests, using standard equipment available in most biological laboratories. The use of a solid-phase analytical platform is expected to be readily expanded to prepare digest from O-glycosylated- and O-sulfonated proteins for mass spectrometry-based structural characterization. PMID:23997661

[Determination of canthaxanthin and astaxanthin in egg yolks by reversed phase high performance liquid chromatography with diode array detection].

PubMed

He, Kang-Hao; Zou, Xiao-Li; Liu, Xiang; Zeng, Hong-Yan

2012-01-01

A method using reversed phase high performance liquid chromatography (RP-HPLC) coupled with diode array detector (DAD) was developed for the simultaneous determination of canthaxanthin and astaxanthin in egg yolks. Samples were extracted with acetonitrile in ultrasonic bath for 20 minutes and then purified by freezing-lipid filtration and solid phase extraction (SPE). After being vaporized to dryness by nitrogen blowing and made up to volume with methanol, the extract solution was chromatographically separated in C18 column with a unitary mobile phase consisting of acetonitrile. The proposed method was validated in terms of linearity, precision, accuracy, and limit of detection (LOD). Regression analysis revealed a good linearity between peak area of each analyte and its concentration (r > or = 0.998). The intra- and inter-day relative standard deviations (RSDs) were less than 3.6% and 5.2%, respectively. LODs of canthaxanthin and astaxanthin were 0.035 and 0.027 microg/mL (S/N = 3). The average recoveries of canthaxanthin and astaxanthin were 91.5% and 88.7%. The proposed method is simple, fast and easy to apply.

Examination of time-reversal acoustics in shallow water and applications to noncoherent underwater communications.

PubMed

Smith, Kevin B; Abrantes, Antonio A M; Larraza, Andres

2003-06-01

The shallow water acoustic communication channel is characterized by strong signal degradation caused by multipath propagation and high spatial and temporal variability of the channel conditions. At the receiver, multipath propagation causes intersymbol interference and is considered the most important of the channel distortions. This paper examines the application of time-reversal acoustic (TRA) arrays, i.e., phase-conjugated arrays (PCAs), that generate a spatio-temporal focus of acoustic energy at the receiver location, eliminating distortions introduced by channel propagation. This technique is self-adaptive and automatically compensates for environmental effects and array imperfections without the need to explicitly characterize the environment. An attempt is made to characterize the influences of a PCA design on its focusing properties with particular attention given to applications in noncoherent underwater acoustic communication systems. Due to the PCA spatial diversity focusing properties, PC arrays may have an important role in an acoustic local area network. Each array is able to simultaneously transmit different messages that will focus only at the destination receiver node.

The Quorum-Sensing Regulon of Vibriofischeri: Novel Components of the Autoinducer/LuxR Regulatory Circuit

DTIC Science & Technology

1999-06-01

cpdP, from the marine symbiotic bacterium Vibrio fische ri 160 Table of abbreviations 30C6-HSL AI-1 AI-2 C8-HSL CHAPS CNP EDTA FMN GFP HPLC ...using a Zorbax C18 1.0 mm by 150 mm reverse-phase column on a Hewlett-Packard 1090 HPLC /1040 diode array detector at the Harvard Microchemistry...separated by reversed-phase HPLC , and sequenced (Table 2; 10-PK12, 10-PK39, and 10-PK51). From two of the three peptide sequences (Materials and

Simplified biased random walk model for RecA-protein-mediated homology recognition offers rapid and accurate self-assembly of long linear arrays of binding sites

NASA Astrophysics Data System (ADS)

Kates-Harbeck, Julian; Tilloy, Antoine; Prentiss, Mara

2013-07-01

Inspired by RecA-protein-based homology recognition, we consider the pairing of two long linear arrays of binding sites. We propose a fully reversible, physically realizable biased random walk model for rapid and accurate self-assembly due to the spontaneous pairing of matching binding sites, where the statistics of the searched sample are included. In the model, there are two bound conformations, and the free energy for each conformation is a weakly nonlinear function of the number of contiguous matched bound sites.

Solid-phase synthesis of protein-polymers on reversible immobilization supports.

PubMed

Murata, Hironobu; Carmali, Sheiliza; Baker, Stefanie L; Matyjaszewski, Krzysztof; Russell, Alan J

2018-02-27

Facile automated biomacromolecule synthesis is at the heart of blending synthetic and biologic worlds. Full access to abiotic/biotic synthetic diversity first occurred when chemistry was developed to grow nucleic acids and peptides from reversibly immobilized precursors. Protein-polymer conjugates, however, have always been synthesized in solution in multi-step, multi-day processes that couple innovative chemistry with challenging purification. Here we report the generation of protein-polymer hybrids synthesized by protein-ATRP on reversible immobilization supports (PARIS). We utilized modified agarose beads to covalently and reversibly couple to proteins in amino-specific reactions. We then modified reversibly immobilized proteins with protein-reactive ATRP initiators and, after ATRP, we released and analyzed the protein polymers. The activity and stability of PARIS-synthesized and solution-synthesized conjugates demonstrated that PARIS was an effective, rapid, and simple method to generate protein-polymer conjugates. Automation of PARIS significantly reduced synthesis/purification timelines, thereby opening a path to changing how to generate protein-polymer conjugates.

AbMiner: a bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies.

PubMed

Major, Sylvia M; Nishizuka, Satoshi; Morita, Daisaku; Rowland, Rick; Sunshine, Margot; Shankavaram, Uma; Washburn, Frank; Asin, Daniel; Kouros-Mehr, Hosein; Kane, David; Weinstein, John N

2006-04-06

Monoclonal antibodies are used extensively throughout the biomedical sciences for detection of antigens, either in vitro or in vivo. We, for example, have used them for quantitation of proteins on "reverse-phase" protein lysate arrays. For those studies, we quality-controlled > 600 available monoclonal antibodies and also needed to develop precise information on the genes that encode their antigens. Translation among the various protein and gene identifier types proved non-trivial because of one-to-many and many-to-one relationships. To organize the antibody, protein, and gene information, we initially developed a relational database in Filemaker for our own use. When it became apparent that the information would be useful to many other researchers faced with the need to choose or characterize antibodies, we developed it further as AbMiner, a fully relational web-based database under MySQL, programmed in Java. AbMiner is a user-friendly, web-based relational database of information on > 600 commercially available antibodies that we validated by Western blot for protein microarray studies. It includes many types of information on the antibody, the immunogen, the vendor, the antigen, and the antigen's gene. Multiple gene and protein identifier types provide links to corresponding entries in a variety of other public databases, including resources for phosphorylation-specific antibodies. AbMiner also includes our quality-control data against a pool of 60 diverse cancer cell types (the NCI-60) and also protein expression levels for the NCI-60 cells measured using our high-density "reverse-phase" protein lysate microarrays for a selection of the listed antibodies. Some other available database resources give information on antibody specificity for one or a couple of cell types. In contrast, the data in AbMiner indicate specificity with respect to the antigens in a pool of 60 diverse cell types from nine different tissues of origin. AbMiner is a relational database that provides extensive information from our own laboratory and other sources on more than 600 available antibodies and the genes that encode the antibodies' antigens. The data will be made freely available at http://discover.nci.nih.gov/abminer.

A New Method, "Reverse Yeast Two-Hybrid Array" (RYTHA), Identifies Mutants that Dissociate the Physical Interaction Between Elg1 and Slx5.

PubMed

Lev, Ifat; Shemesh, Keren; Volpe, Marina; Sau, Soumitra; Levinton, Nelly; Molco, Maya; Singh, Shivani; Liefshitz, Batia; Ben Aroya, Shay; Kupiec, Martin

2017-07-01

The vast majority of processes within the cell are carried out by proteins working in conjunction. The Yeast Two-Hybrid (Y2H) methodology allows the detection of physical interactions between any two interacting proteins. Here, we describe a novel systematic genetic methodology, "Reverse Yeast Two-Hybrid Array" (RYTHA), that allows the identification of proteins required for modulating the physical interaction between two given proteins. Our assay starts with a yeast strain in which the physical interaction of interest can be detected by growth on media lacking histidine, in the context of the Y2H methodology. By combining the synthetic genetic array technology, we can systematically screen mutant libraries of the yeast Saccharomyces cerevisiae to identify trans -acting mutations that disrupt the physical interaction of interest. We apply this novel method in a screen for mutants that disrupt the interaction between the N-terminus of Elg1 and the Slx5 protein. Elg1 is part of an alternative replication factor C-like complex that unloads PCNA during DNA replication and repair. Slx5 forms, together with Slx8, a SUMO-targeted ubiquitin ligase (STUbL) believed to send proteins to degradation. Our results show that the interaction requires both the STUbL activity and the PCNA unloading by Elg1, and identify topoisomerase I DNA-protein cross-links as a major factor in separating the two activities. Thus, we demonstrate that RYTHA can be applied to gain insights about particular pathways in yeast, by uncovering the connection between the proteasomal ubiquitin-dependent degradation pathway, DNA replication, and repair machinery, which can be separated by the topoisomerase-mediated cross-links to DNA. Copyright © 2017 by the Genetics Society of America.

Plasma-gun-assisted field-reversed configuration formation in a conical θ-pinch

NASA Astrophysics Data System (ADS)

Weber, T. E.; Intrator, T. P.; Smith, R. J.

2015-04-01

Injection of plasma via an annular array of coaxial plasma guns during the pre-ionization phase of field-reversed configuration (FRC) formation is shown to catalyze the bulk ionization of a neutral gas prefill in the presence of a strong axial magnetic field and change the character of outward flux flow during field-reversal from a convective process to a much slower resistive diffusion process. This approach has been found to significantly improve FRC formation in a conical θ-pinch, resulting in a ˜350% increase in trapped flux at typical operating conditions, an expansion of accessible formation parameter space to lower densities and higher temperatures, and a reduction or elimination of several deleterious effects associated with the pre-ionization phase.

Atypical Diabetic Foot Ulcer Keratinocyte Protein Signaling Correlates with Impaired Wound Healing.

PubMed

Hoke, Glenn D; Ramos, Corrine; Hoke, Nicholas N; Crossland, Mary C; Shawler, Lisa G; Boykin, Joseph V

2016-01-01

Diabetes mellitus is associated with chronic diabetic foot ulcers (DFUs) and wound infections often resulting in lower extremity amputations. The protein signaling architecture of the mechanisms responsible for impaired DFU healing has not been characterized. In this preliminary clinical study, the intracellular levels of proteins involved in signal transduction networks relevant to wound healing were non-biasedly measured using reverse-phase protein arrays (RPPA) in keratinocytes isolated from DFU wound biopsies. RPPA allows for the simultaneous documentation and assessment of the signaling pathways active in each DFU. Thus, RPPA provides for the accurate mapping of wound healing pathways associated with apoptosis, proliferation, senescence, survival, and angiogenesis. From the study data, we have identified potential diagnostic, or predictive, biomarkers for DFU wound healing derived from the ratios of quantified signaling protein expressions within interconnected pathways. These biomarkers may allow physicians to personalize therapeutic strategies for DFU management on an individual basis based upon the signaling architecture present in each wound. Additionally, we have identified altered, interconnected signaling pathways within DFU keratinocytes that may help guide the development of therapeutics to modulate these dysregulated pathways, many of which parallel the therapeutic targets which are the hallmarks of molecular therapies for treating cancer.

Protein Profiling Identifies mTOR Pathway Modulation and Cytostatic Effects of Pim Kinase Inhibitor, AZD1208, in Acute Myeloid Leukemia

PubMed Central

Chen, Lisa S.; Yang, Ji-Yeon; Liang, Han; Cortes, Jorge E.; Gandhi, Varsha

2017-01-01

Pim kinases phosphorylate and regulate a number of key AML cell survival proteins, and Pim inhibitors have recently entered clinical trial for hematological malignancies. AZD1208 is a small molecule pan-Pim kinase inhibitor and AZD1208 treatment resulted in growth inhibition and cell size reduction in AML cell lines including FLT3-WT (OCI-AML-3, KG-1a, MOLM-16) and FLT3-ITD mutated (MOLM-13, MV-4-11). There was limited apoptosis induction (<10% increase) in the AML cell lines evaluated with up to 3 μM AZD1208 for 24h, suggesting that growth inhibition is not through apoptosis induction. Using reverse phase protein array (RPPA) and immunoblot analysis, we identified that AZD1208 resulted in suppression of mTOR signaling, including inhibition of protein phosphorylation of mTOR(Ser2448), p70S6K(Thr389), S6(Ser235/236) and 4E-BP1(Ser65). Consistent with mTOR inhibition, there was also a reduction in protein synthesis that correlated with cell size reduction and growth inhibition with AZD1208; our study provide insights into the mechanism of AZD1208. PMID:27054578

Atypical Diabetic Foot Ulcer Keratinocyte Protein Signaling Correlates with Impaired Wound Healing

PubMed Central

Hoke, Glenn D.; Ramos, Corrine; Hoke, Nicholas N.; Crossland, Mary C.; Shawler, Lisa G.

2016-01-01

Diabetes mellitus is associated with chronic diabetic foot ulcers (DFUs) and wound infections often resulting in lower extremity amputations. The protein signaling architecture of the mechanisms responsible for impaired DFU healing has not been characterized. In this preliminary clinical study, the intracellular levels of proteins involved in signal transduction networks relevant to wound healing were non-biasedly measured using reverse-phase protein arrays (RPPA) in keratinocytes isolated from DFU wound biopsies. RPPA allows for the simultaneous documentation and assessment of the signaling pathways active in each DFU. Thus, RPPA provides for the accurate mapping of wound healing pathways associated with apoptosis, proliferation, senescence, survival, and angiogenesis. From the study data, we have identified potential diagnostic, or predictive, biomarkers for DFU wound healing derived from the ratios of quantified signaling protein expressions within interconnected pathways. These biomarkers may allow physicians to personalize therapeutic strategies for DFU management on an individual basis based upon the signaling architecture present in each wound. Additionally, we have identified altered, interconnected signaling pathways within DFU keratinocytes that may help guide the development of therapeutics to modulate these dysregulated pathways, many of which parallel the therapeutic targets which are the hallmarks of molecular therapies for treating cancer. PMID:27840833

Simultaneous determination of ascorbic acid and caffeine in commercial soft drinks using reversed-phase ultraperformance liquid chromatography.

PubMed

Turak, Fatma; Güzel, Remziye; Dinç, Erdal

2017-04-01

A new reversed-phase ultraperformance liquid chromatography method with a photodiode array detector was developed for the quantification of ascorbic acid (AA) and caffeine (CAF) in 11 different commercial drinks consisting of one energy drink and 10 ice tea drinks. Separation of the analyzed AA and CAF with an internal standard, caffeic acid, was performed on a Waters BEH C 18 column (100 mm × 2.1 mm, 1.7 μm i.d.), using a mobile phase consisting of acetonitrile and 0.2M H 3 PO 4 (11:89, v/v) with a flow rate of 0.25 mL/min and an injection volume of 1.0 μL. Calibration graphs for AA and CAF were computed from the peak area ratio of AA/internal standard and CAF/internal standard detected at 244.0 nm and 273.6 nm, respectively. The developed reversed-phase ultraperformance liquid chromatography method was validated by analyzing standard addition samples. The proposed reversed-phase ultraperformance liquid chromatography method gave us successful results for the quantitative analysis of commercial drinks containing AA and CAF substances. Copyright © 2016. Published by Elsevier B.V.

Improved image reconstruction of low-resolution multichannel phase contrast angiography

PubMed Central

P. Krishnan, Akshara; Joy, Ajin; Paul, Joseph Suresh

2016-01-01

Abstract. In low-resolution phase contrast magnetic resonance angiography, the maximum intensity projected channel images will be blurred with consequent loss of vascular details. The channel images are enhanced using a stabilized deblurring filter, applied to each channel prior to combining the individual channel images. The stabilized deblurring is obtained by the addition of a nonlocal regularization term to the reverse heat equation, referred to as nonlocally stabilized reverse diffusion filter. Unlike reverse diffusion filter, which is highly unstable and blows up noise, nonlocal stabilization enhances intensity projected parallel images uniformly. Application to multichannel vessel enhancement is illustrated using both volunteer data and simulated multichannel angiograms. Robustness of the filter applied to volunteer datasets is shown using statistically validated improvement in flow quantification. Improved performance in terms of preserving vascular structures and phased array reconstruction in both simulated and real data is demonstrated using structureness measure and contrast ratio. PMID:26835501

High-rate synthetic aperture communications in shallow water.

PubMed

Song, H C; Hodgkiss, W S; Kuperman, W A; Akal, T; Stevenson, M

2009-12-01

Time reversal communication exploits spatial diversity to achieve spatial and temporal focusing in complex ocean environments. Spatial diversity can be provided easily by a vertical array in a waveguide. Alternatively, spatial diversity can be obtained from a virtual horizontal array generated by two elements, a transmitter and a receiver, due to relative motion between them, referred to as a synthetic aperture. This paper presents coherent synthetic aperture communication results from at-sea experiments conducted in two different frequency bands: (1) 2-4 kHz and (2) 8-20 kHz. Case (1) employs binary-phase shift-keying modulation, while case (2) involves up to eight-phase shift keying modulation with a data rate of 30 kbits/s divided by the number of transmissions (diversity) to be accumulated. The receiver utilizes time reversal diversity combining followed by a single channel equalizer, with frequent channel updates to accommodate the time-varying channel due to coupling of space and time in the presence of motion. Two to five consecutive transmissions from a source moving at 4 kts over 3-6 km range in shallow water are combined successfully after Doppler compensation, confirming the feasibility of coherent synthetic aperture communications using time reversal.

Phosphoproteomic analysis reveals Smad protein family activation following Rift Valley fever virus infection.

PubMed

de la Fuente, Cynthia; Pinkham, Chelsea; Dabbagh, Deemah; Beitzel, Brett; Garrison, Aura; Palacios, Gustavo; Hodge, Kimberley Alex; Petricoin, Emanuel F; Schmaljohn, Connie; Campbell, Catherine E; Narayanan, Aarthi; Kehn-Hall, Kylene

2018-01-01

Rift Valley fever virus (RVFV) infects both ruminants and humans leading to a wide variance of pathologies dependent on host background and age. Utilizing a targeted reverse phase protein array (RPPA) to define changes in signaling cascades after in vitro infection of human cells with virulent and attenuated RVFV strains, we observed high phosphorylation of Smad transcription factors. This evolutionarily conserved family is phosphorylated by and transduces the activation of TGF-β superfamily receptors. Moreover, we observed that phosphorylation of Smad proteins required active RVFV replication and loss of NSs impaired this activation, further corroborating the RPPA results. Gene promoter analysis of transcripts altered after RVFV infection identified 913 genes that contained a Smad-response element. Functional annotation of these potential Smad-regulated genes clustered in axonal guidance, hepatic fibrosis and cell signaling pathways involved in cellular adhesion/migration, calcium influx, and cytoskeletal reorganization. Furthermore, chromatin immunoprecipitation confirmed the presence of a Smad complex on the interleukin 1 receptor type 2 (IL1R2) promoter, which acts as a decoy receptor for IL-1 activation.

Plasma-gun-assisted field-reversed configuration formation in a conical θ-pinch

DOE PAGES

Weber, T. E.; Intrator, T. P.; Smith, R. J.

2015-04-29

We show through injection of plasma via an annular array of coaxial plasma guns, during the pre-ionization phase of field-reversed configuration (FRC) formation how to catalyze the bulk ionization of a neutral gas prefill in the presence of a strong axial magnetic field and change the character of outward flux flow during field-reversal from a convective process to a much slower resistive diffusion process. Our approach has been found to significantly improve FRC formation in a conical θ-pinch, resulting in a ~350% increase in trapped flux at typical operating conditions, an expansion of accessible formation parameter space to lower densitiesmore » and higher temperatures, and a reduction or elimination of several deleterious effects associated with the pre-ionization phase.« less

Plasma-gun-assisted field-reversed configuration formation in a conical θ-pinch

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

Weber, T. E., E-mail: tweber@lanl.gov; Intrator, T. P.; Smith, R. J.

2015-04-15

Injection of plasma via an annular array of coaxial plasma guns during the pre-ionization phase of field-reversed configuration (FRC) formation is shown to catalyze the bulk ionization of a neutral gas prefill in the presence of a strong axial magnetic field and change the character of outward flux flow during field-reversal from a convective process to a much slower resistive diffusion process. This approach has been found to significantly improve FRC formation in a conical θ-pinch, resulting in a ∼350% increase in trapped flux at typical operating conditions, an expansion of accessible formation parameter space to lower densities and highermore » temperatures, and a reduction or elimination of several deleterious effects associated with the pre-ionization phase.« less

Transglutaminase 2 expression in acute myeloid leukemia: Association with adhesion molecule expression and leukemic blast motility

PubMed Central

Meyer, Stefan; Ravandi-Kashani, Farhad; Borthakur, Gautam; Coombes, Kevin R.; Zhang, Nianxiang; Kornblau, Steven

2016-01-01

Acute myeloid leukemia (AML) is a heterogenous disease with differential oncogene association, outcome and treatment regimens. Treatment strategies for AML have improved outcome but despite increased molecular biological information AML is still associated with poor prognosis. Proteomic analysis on the effects of a range of leukemogenic oncogenes showed that the protein transglutaminase 2 (TG2) is expressed at greater levels as a consequence of oncogenic transformation. Further analysis of this observation was performed with 511 AML samples using reverse phase proteomic arrays, demonstrating that TG2 expression was higher at relapse than diagnosis in many cases. In addition elevated TG2 expression correlated with increased expression of numerous adhesion proteins and many apoptosis regulating proteins, two processes related to leukemogenesis. TG2 has previously been linked to drug resistance in cancer and given the negative correlation between TG2 levels and peripheral blasts observed increased TG2 levels may lead to the protection of the leukemic stem cell due to increased adhesion/reduced motility. TG2 may therefore form part of a network of proteins that define poor outcome in AML patients and potentially offer a target to sensitize AML stem cells to drug treatment. PMID:23576428

Online combination of reversed-phase/reversed-phase and porous graphitic carbon liquid chromatography for multicomponent separation of proteomics and glycoproteomics samples.

PubMed

Lam, Maggie P Y; Lau, Edward; Siu, S O; Ng, Dominic C M; Kong, Ricky P W; Chiu, Philip C N; Yeung, William S B; Lo, Clive; Chu, Ivan K

2011-11-01

In this paper, we describe an online combination of reversed-phase/reversed-phase (RP-RP) and porous graphitic carbon (PGC) liquid chromatography (LC) for multicomponent analysis of proteomics and glycoproteomics samples. The online RP-RP portion of this system provides comprehensive 2-D peptide separation based on sequence hydrophobicity at pH 2 and 10. Hydrophilic components (e.g. glycans, glycopeptides) that are not retained by RP are automatically diverted downstream to a PGC column for further trapping and separation. Furthermore, the RP-RP/PGC system can provide simultaneous extension of the hydropathy range and peak capacity for analysis. Using an 11-protein mixture, we found that the system could efficiently separate native peptides and released N-glycans from a single sample. We evaluated the applicability of the system to the analysis of complex biological samples using 25 μg of the lysate of a human choriocarcinoma cell line (BeWo), confidently identifying a total of 1449 proteins from a single experiment and up to 1909 distinct proteins from technical triplicates. The PGC fraction increased the sequence coverage through the inclusion of additional hydrophilic sequences that accounted for up to 6.9% of the total identified peptides from the BeWo lysate, with apparent preference for the detection of hydrophilic motifs and proteins. In addition, RP-RP/PGC is applicable to the analysis of complex glycomics samples, as demonstrated by our analysis of a concanavalin A-extracted glycoproteome from human serum; in total, 134 potentially N-glycosylated serum proteins, 151 possible N-glycosylation sites, and more than 40 possible N-glycan structures recognized by concanavalin A were simultaneously detected. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atomic Force Microscopy of Photosystem II and Its Unit Cell Clustering Quantitatively Delineate the Mesoscale Variability in Arabidopsis Thylakoids

PubMed Central

Onoa, Bibiana; Schneider, Anna R.; Brooks, Matthew D.; Grob, Patricia; Nogales, Eva; Geissler, Phillip L.; Niyogi, Krishna K.; Bustamante, Carlos

2014-01-01

Photoautotrophic organisms efficiently regulate absorption of light energy to sustain photochemistry while promoting photoprotection. Photoprotection is achieved in part by triggering a series of dissipative processes termed non-photochemical quenching (NPQ), which depend on the re-organization of photosystem (PS) II supercomplexes in thylakoid membranes. Using atomic force microscopy, we characterized the structural attributes of grana thylakoids from Arabidopsis thaliana to correlate differences in PSII organization with the role of SOQ1, a recently discovered thylakoid protein that prevents formation of a slowly reversible NPQ state. We developed a statistical image analysis suite to discriminate disordered from crystalline particles and classify crystalline arrays according to their unit cell properties. Through detailed analysis of the local organization of PSII supercomplexes in ordered and disordered phases, we found evidence that interactions among light-harvesting antenna complexes are weakened in the absence of SOQ1, inducing protein rearrangements that favor larger separations between PSII complexes in the majority (disordered) phase and reshaping the PSII crystallization landscape. The features we observe are distinct from known protein rearrangements associated with NPQ, providing further support for a role of SOQ1 in a novel NPQ pathway. The particle clustering and unit cell methodology developed here is generalizable to multiple types of microscopy and will enable unbiased analysis and comparison of large data sets. PMID:25007326

Adaptive spatial combining for passive time-reversed communications.

PubMed

Gomes, João; Silva, António; Jesus, Sérgio

2008-08-01

Passive time reversal has aroused considerable interest in underwater communications as a computationally inexpensive means of mitigating the intersymbol interference introduced by the channel using a receiver array. In this paper the basic technique is extended by adaptively weighting sensor contributions to partially compensate for degraded focusing due to mismatch between the assumed and actual medium impulse responses. Two algorithms are proposed, one of which restores constructive interference between sensors, and the other one minimizes the output residual as in widely used equalization schemes. These are compared with plain time reversal and variants that employ postequalization and channel tracking. They are shown to improve the residual error and temporal stability of basic time reversal with very little added complexity. Results are presented for data collected in a passive time-reversal experiment that was conducted during the MREA'04 sea trial. In that experiment a single acoustic projector generated a 24-PSK (phase-shift keyed) stream at 200400 baud, modulated at 3.6 kHz, and received at a range of about 2 km on a sparse vertical array with eight hydrophones. The data were found to exhibit significant Doppler scaling, and a resampling-based preprocessing method is also proposed here to compensate for that scaling.

Surface plasmon resonance imaging system with Mach-Zehnder phase-shift interferometry for DNA micro-array hybridization

NASA Astrophysics Data System (ADS)

Hsiu, Feng-Ming; Chen, Shean-Jen; Tsai, Chien-Hung; Tsou, Chia-Yuan; Su, Y.-D.; Lin, G.-Y.; Huang, K.-T.; Chyou, Jin-Jung; Ku, Wei-Chih; Chiu, S.-K.; Tzeng, C.-M.

2002-09-01

Surface plasmon resonance (SPR) imaging system is presented as a novel technique based on modified Mach-Zehnder phase-shifting interferometry (PSI) for biomolecular interaction analysis (BIA), which measures the spatial phase variation of a resonantly reflected light in biomolecular interaction. In this technique, the micro-array SPR biosensors with over a thousand probe NDA spots can be detected simultaneously. Owing to the feasible and swift measurements, the micro-array SPR biosensors can be extensively applied to the nonspecific adsorption of protein, the membrane/protein interactions, and DNA hybridization. The detection sensitivity of the SPR PSI imaging system is improved to about 1 pg/mm2 for each spot over the conventional SPR imaging systems. The SPR PSI imaging system and its SPR sensors have been successfully used to observe slightly index change in consequence of argon gas flow through the nitrogen in real time, with high sensitivity, and at high-throughout screening rates.

Theory of nematic order with aggregate dehydration for reversibly assembling proteins in concentrated solutions: Application to sickle-cell hemoglobin polymers

NASA Astrophysics Data System (ADS)

Hentschke, Reinhard; Herzfeld, Judith

1991-06-01

The reversible association of globular protein molecules in concentrated solution leads to highly polydisperse fibers, e.g., actin filaments, microtubules, and sickle-cell hemoglobin fibers. At high concentrations, excluded-volume interactions between the fibers lead to spontaneous alignment analogous to that in simple lyotropic liquid crystals. However, the phase behavior of reversibly associating proteins is complicated by the threefold coupling between the growth, alignment, and hydration of the fibers. In protein systems aggregates contain substantial solvent, which may cause them to swell or shrink, depending on osmotic stress. Extending previous work, we present a model for the equilibrium phase behavior of the above-noted protein systems in terms of simple intra- and interaggregate interactions, combined with equilibration of fiber-incorporated solvent with the bulk solvent. Specifically, we compare our model results to recent osmotic pressure data for sickle-cell hemoglobin and find excellent agreement. This comparison shows that particle interactions sufficient to cause alignment are also sufficient to squeeze significant amounts of solvent out of protein fibers. In addition, the model is in accord with findings from independent sedimentation and birefringence studies on sickle-cell hemoglobin.

Method of achieving ultra-wideband true-time-delay beam steering for active electronically scanned arrays

DOEpatents

Loui, Hung; Brock, Billy C.

2016-10-25

The various embodiments presented herein relate to beam steering an array antenna by modifying intermediate frequency (IF) waveforms prior to conversion to RF signals. For each channel, a direct digital synthesis (DDS) component can be utilized to generate a waveform or modify amplitude, timing and phase of a waveform relative to another waveform, whereby the generation/modification can be performed prior to the IF input port of a mixer on each channel. A local oscillator (LO) signal can be utilized to commonly drive each of the mixers. After conversion at the RF output port of each of the mixers, each RF signal can be transmitted by a respective antenna element in the antenna array. Initiation of transmission of each RF signal can be performed simultaneously at each antenna. The process can be reversed during receive whereby timing, amplitude, and phase of the received can be modified digitally post ADC conversion.

Simulation study of a chaotic cavity transducer based virtual phased array used for focusing in the bulk of a solid material.

PubMed

Delrue, Steven; Van Den Abeele, Koen; Bou Matar, Olivier

2016-04-01

In acoustic and ultrasonic non-destructive testing techniques, it is sometimes beneficial to concentrate sound energy at a chosen location in space and at a specific instance in time, for example to improve the signal-to-noise ratio or activate the nonlinearity of damage features. Time Reversal (TR) techniques, taking advantage of the reversible character of the wave equation, are particularly suited to focus ultrasonic waves in time and space. The characteristics of the energy focusing in solid media using principles of time reversed acoustics are highly influenced by the nature and dimensions of the medium, the number of transducers and the length of the received signals. Usually, a large number of transducers enclosing the domain of interest is needed to improve the quality of the focusing. However, in the case of highly reverberant media, the number of transducers can be reduced to only one (single-channel TR). For focusing in a non-reverberant medium, which is impossible when using only one source, an adaptation of the single-channel reciprocal TR procedure has been recently suggested by means of a Chaotic Cavity Transducer (CCT), a single element transducer glued on a cavity of chaotic shape. In this paper, a CCT is used to focus elastic energy, at different times, in different points along a predefined line on the upper surface of a thick solid sample. Doing so, all focusing points can act as a virtual phased array transducer, allowing to focus in any point along the depth direction of the sample. This is impossible using conventional reciprocal TR, as you need to have access to all points in the bulk of the material for detecting signals to be used in the TR process. To asses and provide a better understanding of this concept, a numerical study has been developed, allowing to verify the basic concepts of the virtual phased array and to illustrate multi-component time reversal focusing in the bulk of a solid material. Copyright © 2016 Elsevier B.V. All rights reserved.

Synchronization in monkey visual cortex analyzed with an information-theoretic measure

NASA Astrophysics Data System (ADS)

Manyakov, Nikolay V.; Van Hulle, Marc M.

2008-09-01

We apply an information-theoretic measure for phase synchrony to local field potentials recorded with a multi-electrode array implanted in area V4 of the monkey visual cortex during a reinforcement pairing experiment. We show for the first time that (1) the phase synchrony is significantly higher for the rewarded stimulus than the unrewarded one, after training the monkey; (2) just after the stimuli reversal, the difference in phase synchronization is due to the stimuli, not the reward; (3) the difference between reward and no reward is most clear in two disconnected time intervals between stimuli onset and the expected delivery of the reward; and (4) synchronous activity appears in waves running over the array, and their timing correlates well with the time intervals where the difference between reward and no reward is most prominent.

Performance of an underwater acoustic volume array using time-reversal focusing.

PubMed

Root, Joseph A; Rogers, Peter H

2002-11-01

Time reversal permits acoustic focusing and beam forming in inhomogeneous and/or high-scattering environments. A volumetric array geometry can suppress back lobes and can fit a large, powerful array of elements into small spaces, like the free-water spaces on submarines. This research investigates applying the time-reversal method to an underwater acoustic volume array. The experiments evaluate the focusing performance of a 27-element volume array when different scattering structures are present within the volume of the array. The array is arranged in a 3x3x3 cubic matrix configuration with 18.75-cm vertical and horizontal element spacing. The system utilizes second-derivative Gaussian pulses to focus on a point 30 cm from the array. Results include a comparison between time-reversal focusing and standard focusing, an evaluation of the volume array's ability to suppress back lobes, and an analysis of how different scattering environments affect focal region size. Potential underwater applications for a volume array using time reversal include acoustic imaging, naval mine hunting, sonar, and underwater communications.

Performance of an underwater acoustic volume array using time-reversal focusing

NASA Astrophysics Data System (ADS)

Root, Joseph A.; Rogers, Peter H.

2002-11-01

Time reversal permits acoustic focusing and beam forming in inhomogeneous and/or high-scattering environments. A volumetric array geometry can suppress back lobes and can fit a large, powerful array of elements into small spaces, like the free-water spaces on submarines. This research investigates applying the time-reversal method to an underwater acoustic volume array. The experiments evaluate the focusing performance of a 27-element volume array when different scattering structures are present within the volume of the array. The array is arranged in a 3 x3 x3 cubic matrix configuration with 18.75-cm vertical and horizontal element spacing. The system utilizes second-derivative Gaussian pulses to focus on a point 30 cm from the array. Results include a comparison between time-reversal focusing and standard focusing, an evaluation of the volume array's ability to suppress back lobes, and an analysis of how different scattering environments affect focal region size. Potential underwater applications for a volume array using time reversal include acoustic imaging, naval mine hunting, sonar, and underwater communications. copyright 2002 Acoustical Society of America.

Quantitative ultrasonic testing of acoustically anisotropic materials with verification on austenitic and dissimilar weld joints

NASA Astrophysics Data System (ADS)

Boller, C.; Pudovikov, S.; Bulavinov, A.

2012-05-01

Austenitic stainless steel materials are widely used in a variety of industry sectors. In particular, the material is qualified to meet the design criteria of high quality in safety related applications. For example, the primary loop of the most of the nuclear power plants in the world, due to high durability and corrosion resistance, is made of this material. Certain operating conditions may cause a range of changes in the integrity of the component, and therefore require nondestructive testing at reasonable intervals. These in-service inspections are often performed using ultrasonic techniques, in particular when cracking is of specific concern. However, the coarse, dendritic grain structure of the weld material, formed during the welding process, is extreme and unpredictably anisotropic. Such structure is no longer direction-independent to the ultrasonic wave propagation; therefore, the ultrasonic beam deflects and redirects and the wave front becomes distorted. Thus, the use of conventional ultrasonic testing techniques using fixed beam angles is very limited and the application of ultrasonic Phased Array techniques becomes desirable. The "Sampling Phased Array" technique, invented and developed by Fraunhofer IZFP, allows the acquisition of time signals (A-scans) for each individual transducer element of the array along with fast image reconstruction techniques based on synthetic focusing algorithms. The reconstruction considers the sound propagation from each image pixel to the individual sensor element. For anisotropic media, where the sound beam is deflected and the sound path is not known a-priori, a novel phase adjustment technique called "Reverse Phase Matching" is implemented. By taking into account the anisotropy and inhomogeneity of the weld structure, a ray tracing algorithm for modeling the acoustic wave propagation and calculating the sound propagation time is applied. This technique can be utilized for 2D and 3D real time image reconstruction. The "Gradient Constant Descent Method" (GECDM), an iterative algorithm, is implemented, which is essential for examination of inhomogeneous anisotropic media having unknown properties (elastic constants). The Sampling Phased Array technique with Reverse Phase Matching extended by GECDM-technique determines unknown elastic constants and provides reliable and efficient quantitative flaw detection in the austenitic welds. The validation of ray-tracing algorithm and GECDM-method is performed by number of experiments on test specimens with artificial as well as natural material flaws. A mechanized system for ultrasonic testing of stainless steel and dissimilar welds is developed. The system works on both conventional and Sampling Phased Array techniques. The new frontend ultrasonic unit with optical data link allows the 3D visualization of the inspection results in real time.

Late Protein Synthesis-Dependent Phases in CTA Long-Term Memory: BDNF Requirement

PubMed Central

Martínez-Moreno, Araceli; Rodríguez-Durán, Luis F.; Escobar, Martha L.

2011-01-01

It has been proposed that long-term memory (LTM) persistence requires a late protein synthesis-dependent phase, even many hours after memory acquisition. Brain-derived neurotrophic factor (BDNF) is an essential protein synthesis product that has emerged as one of the most potent molecular mediators for long-term synaptic plasticity. Studies in the rat hippocampus have been shown that BDNF is capable to rescue the late-phase of long-term potentiation as well as the hippocampus-related LTM when protein synthesis was inhibited. Our previous studies on the insular cortex (IC), a region of the temporal cortex implicated in the acquisition and storage of conditioned taste aversion (CTA), have demonstrated that intracortical delivery of BDNF reverses the deficit in CTA memory caused by the inhibition of IC protein synthesis due to anisomycin administration during early acquisition. In this work, we first analyze whether CTA memory storage is protein synthesis-dependent in different time windows. We observed that CTA memory become sensible to protein synthesis inhibition 5 and 7 h after acquisition. Then, we explore the effect of BDNF delivery (2 μg/2 μl per side) in the IC during those late protein synthesis-dependent phases. Our results show that BDNF reverses the CTA memory deficit produced by protein synthesis inhibition in both phases. These findings support the notion that recurrent rounds of consolidation-like events take place in the neocortex for maintenance of CTA memory trace and that BDNF is an essential component of these processes. PMID:21960964

The Physiology of Protein S-acylation

PubMed Central

Chamberlain, Luke H.; Shipston, Michael J.

2015-01-01

Protein S-acylation, the only fully reversible posttranslational lipid modification of proteins, is emerging as a ubiquitous mechanism to control the properties and function of a diverse array of proteins and consequently physiological processes. S-acylation results from the enzymatic addition of long-chain lipids, most typically palmitate, onto intracellular cysteine residues of soluble and transmembrane proteins via a labile thioester linkage. Addition of lipid results in increases in protein hydrophobicity that can impact on protein structure, assembly, maturation, trafficking, and function. The recent explosion in global S-acylation (palmitoyl) proteomic profiling as a result of improved biochemical tools to assay S-acylation, in conjunction with the recent identification of enzymes that control protein S-acylation and de-acylation, has opened a new vista into the physiological function of S-acylation. This review introduces key features of S-acylation and tools to interrogate this process, and highlights the eclectic array of proteins regulated including membrane receptors, ion channels and transporters, enzymes and kinases, signaling adapters and chaperones, cell adhesion, and structural proteins. We highlight recent findings correlating disruption of S-acylation to pathophysiology and disease and discuss some of the major challenges and opportunities in this rapidly expanding field. PMID:25834228

The retrotransposon Tf1 assembles virus-like particles that contain excess Gag relative to integrase because of a regulated degradation process.

PubMed

Atwood, A; Lin, J H; Levin, H L

1996-01-01

The retrotransposon Tf1, isolated from Schizosaccharomyces pombe, contains a single open reading frame with sequences encoding Gag, protease, reverse transcriptase, and integrase (IN). Tf1 has previously been shown to possess significant transposition activity. Although Tf1 proteins do assemble into virus-like particles, the assembly does not require readthrough of a translational reading frame shift or stop codon, common mechanisms used by retroelements to express Gag in molar excess of the polymerase proteins. This study was designed to determine if Tf1 particles contain equal amounts of Gag and polymerase proteins or whether they contain the typical molar excess of Gag. After using two separate methods to calibrate the strength of our antibodies, we found that both S. pombe extracts and partially purified Tf1 particles contained a 26-fold molar excess of Gag relative to IN. Knowing that Gag and IN are derived from the same Tf1 primary translation product, we concluded that the excess Gag most likely resulted from specific degradation of IN. We obtained evidence of regulated IN degradation in comparisons of Tf1 protein extracted from log-phase cells and that extracted from stationary-phase cells. The log-phase cells contained equal molar amounts of Gag and IN, whereas cells approaching stationary phase rapidly degraded IN, leaving an excess of Gag. Analysis of the reverse transcripts indicated that the bulk of reverse transcription occurred within the particles that possess a molar excess of Gag.

Increased expression of resistin in ectopic endometrial tissue of women with endometriosis.

PubMed

Oh, Yoon Kyung; Ha, Young Ran; Yi, Kyong Wook; Park, Hyun Tae; Shin, Jung-Ho; Kim, Tak; Hur, Jun-Young

2017-11-01

Inflammation is a key process in the establishment and progression of endometriosis. Resistin, an adipocytokine, has biological properties linked to immunologic functions, but its role in endometriosis is unclear. Resistin gene expression was examined in eutopic and ectopic endometrial tissues from women with (n=25) or without (n=25) endometriosis. Resistin mRNA and protein levels were determined in endometrial tissue using quantitative real-time reverse transcription PCR and Western blotting, following adipokine profiling arrays. Resistin protein was detected in human endometrial tissues using an adipokine array test. Resistin mRNA and protein levels were significantly higher in ectopic endometrial tissue of patients with endometriosis than in normal eutopic endometrial tissue. Our results indicate that resistin is differentially expressed in endometrial tissues from women with endometriosis and imply a role for resistin in endometriosis-associated pelvic inflammation. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

TTK/hMPS1 Is an Attractive Therapeutic Target for Triple-Negative Breast Cancer

PubMed Central

Maire, Virginie; Baldeyron, Céline; Richardson, Marion; Tesson, Bruno; Vincent-Salomon, Anne; Gravier, Eléonore; Marty-Prouvost, Bérengère; De Koning, Leanne; Rigaill, Guillem; Dumont, Aurélie; Gentien, David; Barillot, Emmanuel; Roman-Roman, Sergio; Depil, Stéphane; Cruzalegui, Francisco; Pierré, Alain; Tucker, Gordon C.; Dubois, Thierry

2013-01-01

Triple-negative breast cancer (TNBC) represents a subgroup of breast cancers (BC) associated with the most aggressive clinical behavior. No targeted therapy is currently available for the treatment of patients with TNBC. In order to discover potential therapeutic targets, we searched for protein kinases that are overexpressed in human TNBC biopsies and whose silencing in TNBC cell lines causes cell death. A cohort including human BC biopsies obtained at Institut Curie as well as normal tissues has been analyzed at a gene-expression level. The data revealed that the human protein kinase monopolar spindle 1 (hMPS1), also known as TTK and involved in mitotic checkpoint, is specifically overexpressed in TNBC, compared to the other BC subgroups and healthy tissues. We confirmed by immunohistochemistry and reverse phase protein array that TNBC expressed higher levels of TTK protein compared to the other BC subgroups. We then determined the biological effects of TTK depletion by RNA interference, through analyses of tumorigenic capacity and cell viability in different human TNBC cell lines. We found that RNAi-mediated depletion of TTK in various TNBC cell lines severely compromised their viability and their ability to form colonies in an anchorage-independent manner. Moreover, we observed that TTK silencing led to an increase in H2AX phosphorylation, activation of caspases 3/7, sub-G1 cell population accumulation and high annexin V staining, as well as to a decrease in G1 phase cell population and an increased aneuploidy. Altogether, these data indicate that TTK depletion in TNBC cells induces apoptosis. These results point out TTK as a protein kinase overexpressed in TNBC that may represent an attractive therapeutic target specifically for this poor prognosis associated subgroup of breast cancer. PMID:23700430

Proceedings of the Conference on Emerging Technologies in Optical Sciences (ETOS 2004) held at University College Cork, Ireland on July 26-29, 2004

DTIC Science & Technology

2004-07-29

coherent coupling in large element arrays . 16 Characterisation of Picosecond Pulses Propagating through a Semiconductor Optical Amplifier...Effect is used. QSCE is widely used in optical intensity and phase modula- Oiz et • to tors [i]. The speed of reverse-biased devices is po- tentially...such devices generally have poor beam quality . The out-of- phase mode is In fact typically favoured in these devices because of the better

Proteomic Screening and Lasso Regression Reveal Differential Signaling in Insulin and Insulin-like Growth Factor I (IGF1) Pathways *

PubMed Central

Erdem, Cemal; Nagle, Alison M.; Casa, Angelo J.; Litzenburger, Beate C.; Wang, Yu-fen; Taylor, D. Lansing; Lee, Adrian V.; Lezon, Timothy R.

2016-01-01

Insulin and insulin-like growth factor I (IGF1) influence cancer risk and progression through poorly understood mechanisms. To better understand the roles of insulin and IGF1 signaling in breast cancer, we combined proteomic screening with computational network inference to uncover differences in IGF1 and insulin induced signaling. Using reverse phase protein array, we measured the levels of 134 proteins in 21 breast cancer cell lines stimulated with IGF1 or insulin for up to 48 h. We then constructed directed protein expression networks using three separate methods: (i) lasso regression, (ii) conventional matrix inversion, and (iii) entropy maximization. These networks, named here as the time translation models, were analyzed and the inferred interactions were ranked by differential magnitude to identify pathway differences. The two top candidates, chosen for experimental validation, were shown to regulate IGF1/insulin induced phosphorylation events. First, acetyl-CoA carboxylase (ACC) knock-down was shown to increase the level of mitogen-activated protein kinase (MAPK) phosphorylation. Second, stable knock-down of E-Cadherin increased the phospho-Akt protein levels. Both of the knock-down perturbations incurred phosphorylation responses stronger in IGF1 stimulated cells compared with insulin. Overall, the time-translation modeling coupled to wet-lab experiments has proven to be powerful in inferring differential interactions downstream of IGF1 and insulin signaling, in vitro. PMID:27364358

One-pot synthesized functionalized mesoporous silica as a reversed-phase sorbent for solid-phase extraction of endocrine disrupting compounds in milks.

PubMed

Gañán, Judith; Morante-Zarcero, Sonia; Pérez-Quintanilla, Damián; Marina, María Luisa; Sierra, Isabel

2016-01-08

A new procedure for the determination of 12 naturally occurring hormones and some related synthetic chemicals in milk, commonly used as growth promoters in cattle, is reported. The method is based on liquid-liquid extraction followed by solid-phase extraction (SPE) using a new one-pot synthesized ordered mesoporous silica (of the SBA-15 type) functionalized with octadecyl groups (denoted as SBA-15-C18-CO) as reversed-phase sorbent. The analytes were eluted with methanol and then submitted to HPLC with diode array detection. Under optimal conditions, the method quantification limit for the analytes ranged from 0.023 to 1.36μg/mL. The sorbent affored the extraction of estrone, 17β-estradiol, estriol, progesterone, hexestrol, diethylstilbestrol, 4-androstene-3,17-dione, ethinylestradiol, 17α-methyltestosterone, nandrolone, prednisolone and testosterone with mean recoveries ranging from 72% to 105% (except for diethylstilbestrol) with RSD<11%. These results were comparable and, in some cases, even better than those obtained with other extraction methods, therefore SBA-15-C18-CO mesoporous silica possess a high potential as a reversed-phase sorbent for SPE of the 12 mentioned endocrine disrupting compounds in milk samples. Copyright © 2015 Elsevier B.V. All rights reserved.

Multiple chimeric antigen receptors successfully target chondroitin sulfate proteoglycan 4 in several different cancer histologies and cancer stem cells

PubMed Central

2014-01-01

Background The development of immunotherapy has led to significant progress in the treatment of metastatic cancer, including the development of genetic engineering technologies that redirect lymphocytes to recognize and target a wide variety of tumor antigens. Chimeric antigen receptors (CARs) are hybrid proteins combining antibody recognition domains linked to T cell signaling elements. Clinical trials of CAR-transduced peripheral blood lymphocytes (PBL) have induced remission of both solid organ and hematologic malignancies. Chondroitin sulfate proteoglycan 4 (CSPG4) is a promising target antigen that is overexpressed in multiple cancer histologies including melanoma, triple-negative breast cancer, glioblastoma, mesothelioma and sarcoma. Methods CSPG4 expression in cancer cell lines was assayed using flow cytometry (FACS) and reverse-transcription PCR (RT-PCR). Immunohistochemistry was utilized to assay resected melanomas and normal human tissues (n = 30) for CSPG4 expression and a reverse-phase protein array comprising 94 normal tissue samples was also interrogated for CSPG4 expression. CARs were successfully constructed from multiple murine antibodies (225.28S, TP41.2, 149.53) using second generation (CD28.CD3ζ) signaling domains. CAR sequences were cloned into a gamma-retroviral vector with subsequent successful production of retroviral supernatant and PBL transduction. CAR efficacy was assayed by cytokine release and cytolysis following coculture with target cell lines. Additionally, glioblastoma stem cells were generated from resected human tumors, and CSPG4 expression was determined by RT-PCR and FACS. Results Immunohistochemistry demonstrated prominent CSPG4 expression in melanoma tumors, but failed to demonstrate expression in any of the 30 normal human tissues studied. Two of 94 normal tissue protein lysates were positive by protein array. CAR constructs demonstrated cytokine secretion and cytolytic function after co-culture with tumor cell lines from multiple different histologies, including melanoma, breast cancer, mesothelioma, glioblastoma and osteosarcoma. Furthermore, we report for the first time that CSPG4 is expressed on glioblastoma cancer stem cells (GSC) and demonstrate that anti-CSPG4 CAR-transduced T cells recognize and kill these GSC. Conclusions The functionality of multiple different CARs, with the widespread expression of CSPG4 on multiple malignancies, suggests that CSPG4 may be an attractive candidate tumor antigen for CAR-based immunotherapies using appropriate technology to limit possible off-tumor toxicity. PMID:25197555

Therapeutic targeting of sunitinib-induced AR phosphorylation in renal cell carcinoma.

PubMed

Adelaiye-Ogala, Remi; Damayanti, Nur P; Orillion, Ashley R; Arisa, Sreevani; Chintala, Sreenivasulu; Titus, Mark A; Kao, Chinghai; Pili, Roberto

2018-03-23

Androgen receptor (AR) plays a crucial role in the development and progression of prostate cancer. AR expression has also been reported in other solid tumors, including renal cell carcinoma (RCC), but its biological role here remains unclear. Through integrative analysis of a reverse phase protein array (RPPA), we discovered increased expression of AR in an RCC patient-derived xenograft model of acquired resistance to the receptor tyrosine kinase inhibitor (RTKi) sunitinib. AR expression was increased in RCC cell lines with either acquired or intrinsic sunitinib resistance in vitro. An AR signaling gene array profiler indicated elevated levels of AR target genes in sunitinib-resistant cells. Sunitinib-induced AR transcriptional activity was associated with increased phosphorylation of serine 81 (pS81) on AR. Additionally, AR overexpression resulted in acquired sunitinib resistance, and the AR antagonist enzalutamide-induced AR degradation and attenuated AR downstream activity in sunitinib-resistant cells, also indicated by decreased secretion of human kallikrein 2 (KLK2). Enzalutamide-induced AR degradation was rescued by either proteasome inhibition or by knockdown of the AR ubiquitin ligase speckle-type POZ protein (SPOP). In vivo treatment with enzalutamide and sunitinib demonstrated that this combination efficiently induced tumor regression in an RCC model following acquired sunitinib resistance. Overall, our results suggest the potential role of AR as a target for therapeutic interventions, in combination with RTKi, to overcome drug resistance in RCC. Copyright ©2018, American Association for Cancer Research.

Coherent and Noncoherent Joint Processing of Sonar for Detection of Small Targets in Shallow Water.

PubMed

Pan, Xiang; Jiang, Jingning; Li, Si; Ding, Zhenping; Pan, Chen; Gong, Xianyi

2018-04-10

A coherent-noncoherent joint processing framework is proposed for active sonar to combine diversity gain and beamforming gain for detection of a small target in shallow water environments. Sonar utilizes widely-spaced arrays to sense environments and illuminate a target of interest from multiple angles. Meanwhile, it exploits spatial diversity for time-reversal focusing to suppress reverberation, mainly strong bottom reverberation. For enhancement of robustness of time-reversal focusing, an adaptive iterative strategy is utilized in the processing framework. A probing signal is firstly transmitted and echoes of a likely target are utilized as steering vectors for the second transmission. With spatial diversity, target bearing and range are estimated using a broadband signal model. Numerical simulations show that the novel sonar outperforms the traditional phased-array sonar due to benefits of spatial diversity. The effectiveness of the proposed framework has been validated by localization of a small target in at-lake experiments.

Polarity-based fractionation in proteomics: hydrophilic interaction vs reversed-phase liquid chromatography.

PubMed

Jafari, M; Mirzaie, M; Khodabandeh, M; Rezadoost, H; Ghassempour, A; Aboul-Enein, H Y

2016-07-01

During recent decades, hydrophilic interaction liquid chromatography (HILIC) ahs been introduced to fractionate or purify especially polar solutes such as peptides and proteins while reversed-phase liquid chromatography (RPLC) is also a common strategy. RPLC is also a common dimension in multidimensional chromatography. In this study, the potential of HILIC vs RPLC chromatography was compared for proteome mapping of human peripheral blood mononuclear cell extract. In HILIC a silica-based stationary phase and for RPLC a C18 column were applied. Then separated proteins were eluted to an ion trap mass spectrometry system. Our results showed that the HILIC leads to more proteins being identified in comparison to RPLC. Among the total 181 identified proteins, 56 and 38 proteins were fractionated specifically by HILIC and RPLC, respectively. In order to demonstrate this, the physicochemical properties of identified proteins such as polarity and hydrophobicity were considered. This analysis indicated that polarity may play a major role in the HILIC separation of proteins vs RPLC. Using gene ontology enrichment analysis, it was also observed that differences in physicochemical properties conform to the cellular compartment and biological features. Finally, this study highlighted the potential of HILIC and the great orthogonality of RPLC in gel-free proteomic studies. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Blending protein separation and peptide analysis through real-time proteolytic digestion.

PubMed

Slysz, Gordon W; Schriemer, David C

2005-03-15

Typical liquid- or gel-based protein separations require enzymatic digestion as an important first step in generating protein identifications. Traditional protocols involve long-term proteolytic digestion of the separated protein, often leading to sample loss and reduced sensitivity. Previously, we presented a rapid method of proteolytic digestion that showed excellent digestion of resistant and low concentrations of protein without requiring reduction and alkylation. Here, we demonstrate on-line, real-time tryptic digestion in conjunction with reversed-phase protein separation. The studies were aimed at optimizing pH and ionic strength and the size of the digestion element, to produce maximal protein digestion with minimal effects on chromatographic integrity. Upon establishing optimal conditions, the digestion element was attached downstream from a capillary C4 reversed-phase column. A four-protein mixture was processed through the combined system, and the resulting peptides were analyzed on-line by electrospray mass spectrometry. Extracted ion chromatograms for protein chromatography based on peptide elution were generated. These were shown to emulate ion chromatograms produced in a subsequent run without the digestion element, based on protein elution. The methodology will enable rapid and sensitive analysis of liquid-based protein separations using the power of bottom-up proteomics methodologies.

Elastin-like polypeptide switches: A design strategy to detect multimeric proteins.

PubMed

Dhandhukia, Jugal P; Brill, Dab A; Kouhi, Aida; Pastuszka, Martha K; MacKay, J Andrew

2017-09-01

Elastin-Like Polypeptides (ELPs) reversibly phase separate in response to changes in temperature, pressure, concentration, pH, and ionic species. While powerful triggers, biological microenvironments present a multitude of more specific biological cues, such as antibodies, cytokines, and cell-surface receptors. To develop better biosensors and bioresponsive drug carriers, rational strategies are required to sense and respond to these target proteins. We recently reported that noncovalent association of two ELP fusion proteins to a "chemical inducer of dimerization" small molecule (1.5 kDa) induces phase separation at physiological temperatures. Having detected a small molecule, here we present the first evidence that ELP multimerization can also detect a much larger (60 kDa) protein target. To demonstrate this strategy, ELPs were biotinylated at their amino terminus and mixed with tetrameric streptavidin. At a stoichiometric ratio of [4:1], two to three biotin-ELPs associate with streptavidin into multimeric complexes with an apparent K d of 5 nM. The increased ELP density around a streptavidin core strongly promotes isothermal phase separation, which was tuned to occur at physiological temperature. This phase separation reverses upon saturation with excess streptavidin, which only favors [1:1] complexes. Together, these findings suggest that ELP association with multimeric biomolecules is a viable strategy to deliberately engineer ELPs that respond to multimeric protein substrates. © 2017 The Protein Society.

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

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

Omenn, Gilbert; States, David J.; Adamski, Marcin

2005-08-13

HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics. med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasetsmore » had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.« less

Self-Supported CoP Nanorod Arrays Grafted on Stainless Steel as an Advanced Integrated Anode for Stable and Long-Life Lithium-Ion Batteries.

PubMed

Xu, Xijun; Liu, Jun; Hu, Renzong; Liu, Jiangwen; Ouyang, Liuzhang; Zhu, Min

2017-04-19

To alleviate the capacity degradation of anode materials for Li-ion batteries, caused by serious volume expansion and particle aggregation, intensive attention has been devoted to the rational design and fabrication of novel anode architectures. Herein, self-supported CoP nanorod arrays have been facilely synthesized using hydrothemally deposited Co(CO 3 ) 0.5 (OH)⋅0.11 H 2 O nanorod arrays as the precursor, through a gas-phase phosphidation method. As the anode for Li-ion batteries, such 3D interconnected CoP nanorod arrays show an initial discharge capacity of 1067 mAh g -1 and a high reversible charge capacity of 737 mAh g -1 at 0.4 Ag -1 . After 400 cycles, their specific capacity can reach 510 mAh g -1 ; even after 900 cycles, they can still deliver a specific capacity of 390 mAh g -1 . CoP//LiCoO 2 full-cells also exhibit a high reversible capacity of 400 mAh g -1 after 50 cycles. These unique 3D interconnected CoP nanorod arrays also show ultrastable cycling performance over 500 cycles when used as the anode in a Na-ion battery. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Composition and Molecular Weight Distribution of Carob Germ Proteins Fractions

USDA-ARS?s Scientific Manuscript database

Biochemical properties of carob germ proteins were analyzed using a combination of selective extraction, reversed-phase high performance liquid chromatography (RP-HPLC), size exclusion chromatography coupled with multi-angle laser light scattering (SEC-MALS) and electrophoretic analysis. Using a mo...

Magnetic interactions and reversal mechanisms in Co nanowire and nanotube arrays

NASA Astrophysics Data System (ADS)

Proenca, M. P.; Sousa, C. T.; Escrig, J.; Ventura, J.; Vazquez, M.; Araujo, J. P.

2013-03-01

Ordered hexagonal arrays of Co nanowires (NWs) and nanotubes (NTs), with diameters between 40 and 65 nm, were prepared by potentiostatic electrodeposition into suitably modified nanoporous alumina templates. The geometrical parameters of the NW/NT arrays were tuned by the pore etching process and deposition conditions. The magnetic interactions between NWs/NTs with different diameters were studied using first-order reversal curves (FORCs). From a quantitative analysis of the FORC measurements, we are able to obtain the profiles of the magnetic interactions and the coercive field distributions. In both NW and NT arrays, the magnetic interactions were found to increase with the diameter of the NWs/NTs, exhibiting higher values for NW arrays. A comparative study of the magnetization reversal processes was also performed by analyzing the angular dependence of the coercivity and correlating the experimental data with theoretical calculations based on a simple analytical model. The magnetization in the NW arrays is found to reverse by the nucleation and propagation of a transverse-like domain wall; on the other hand, for the NT arrays a non-monotonic behavior occurs above a diameter of ˜50 nm, revealing a transition between the vortex and transverse reversal modes.

Dynamic, electronically switchable surfaces for membrane protein microarrays.

PubMed

Tang, C S; Dusseiller, M; Makohliso, S; Heuschkel, M; Sharma, S; Keller, B; Vörös, J

2006-02-01

Microarray technology is a powerful tool that provides a high throughput of bioanalytical information within a single experiment. These miniaturized and parallelized binding assays are highly sensitive and have found widespread popularity especially during the genomic era. However, as drug diagnostics studies are often targeted at membrane proteins, the current arraying technologies are ill-equipped to handle the fragile nature of the protein molecules. In addition, to understand the complex structure and functions of proteins, different strategies to immobilize the probe molecules selectively onto a platform for protein microarray are required. We propose a novel approach to create a (membrane) protein microarray by using an indium tin oxide (ITO) microelectrode array with an electronic multiplexing capability. A polycationic, protein- and vesicle-resistant copolymer, poly(l-lysine)-grafted-poly(ethylene glycol) (PLL-g-PEG), is exposed to and adsorbed uniformly onto the microelectrode array, as a passivating adlayer. An electronic stimulation is then applied onto the individual ITO microelectrodes resulting in the localized release of the polymer thus revealing a bare ITO surface. Different polymer and biological moieties are specifically immobilized onto the activated ITO microelectrodes while the other regions remain protein-resistant as they are unaffected by the induced electrical potential. The desorption process of the PLL-g-PEG is observed to be highly selective, rapid, and reversible without compromising on the integrity and performance of the conductive ITO microelectrodes. As such, we have successfully created a stable and heterogeneous microarray of biomolecules by using selective electronic addressing on ITO microelectrodes. Both pharmaceutical diagnostics and biomedical technology are expected to benefit directly from this unique method.

Radiation induced chemical changes of phenolic compounds in strawberries

NASA Astrophysics Data System (ADS)

Breitfellner, F.; Solar, S.; Sontag, G.

2003-06-01

In unirradiated strawberries four phenolic acids (gallic acid, p-coumaric acid, caffeic acid and 4-hydroxybenzoic acid), the flavonoids (+)-catechin, (-)-epicatechin and glycosides from kaempferol and quercetin were determined by reversed phase chromatography with diode array detection. Characteristic linear dose/concentration relationships were found for 4-hydroxybenzoic acid and two unidentified compounds. One of them may be usable as marker to prove an irradiation treatment.

Reverse Phase-ultra Flow Liquid Chromatography-diode Array Detector Quantification of Anticancerous and Antidiabetic Drug Mangiferin from 11 Species of Swertia from India.

PubMed

Kshirsagar, Parthraj R; Gaikwad, Nikhil B; Panda, Subhasis; Hegde, Harsha V; Pai, Sandeep R

2016-01-01

Genus Swertia is valued for its great medicinal potential, mainly Swertia chirayita (Roxb. ex Fleming) H. Karst. is used in traditional medicine for a wide range of diseases. Mangiferin one of xanthoids is referred with enormous pharmacological potentials. The aim of the study was to quantify and compare the anticancerous and antidiabetic drug mangiferin from 11 Swertia species from India. The study also evaluates hierarchical relationships between the species based on mangiferin content using multivariate analysis. The reverse phase-ultra flow liquid chromatography-diode array detector analyses was performed and chromatographic separation was achieved on a Lichrospher 100, C18e (5 μm) column (250-4.6 mm). Mobile phase consisting of 0.2% triethylamine (pH-4 with O-phosphoric acid) and acetonitrile (85:15) was used for separation with injection volume 20 μL and detection wave length at 257 nm. Results indicated that concentration of mangiferin has been found to vary largely between Swertia species collected from different regions. Content of mangiferin was found to be highest in Swertia minor compared to other Swertia species studied herein from the Western Ghats and Himalayan region also. The same was also evident in the multivariate analysis, wherein S. chirayita, S. minor and Swertia paniculata made a separate clade. Conclusively, the work herein provides insights of mangiferin content from 11 Swertia species of India and also presents their hierarchical relationships. To best of the knowledge this is the first report of higher content of mangiferin from any Swertia species. The present study quantifies and compares mangiferin in 11 species of Swertia from India. The study also evaluates hierarchical relationships between the species based on mangiferin content using multivariate analysis. The mangiferin content was highest in S. minor compared to the studied Swertia species. To the best of our knowledge this is the first report of higher content of mangiferin from Swertia species. Abbreviations used: LOD: Limit of detection, LOQ: Limit of quantification, RP-UFLC-DAD: Reverse phase-ultra flow liquid chromatography-diode array detector, RSD: Relative standard deviation, SAN: Swertia angustifolia, SAP: Swertia angustifolia var. pulchella, SBI: S. bimaculata, SCH: S. chirayita, SCO: S. corymbosa, SDE: S. densifolia, SDI: S. dialatata, SLA: S. lawii, SMI: S. minor; SNE: S. nervosa, and SPA: S. paniculata.

Developing high coercivity in large diameter cobalt nanowire arrays

NASA Astrophysics Data System (ADS)

Montazer, A. H.; Ramazani, A.; Almasi Kashi, M.; Zavašnik, J.

2016-11-01

Regardless of the synthetic method, developing high magnetic coercivity in ferromagnetic nanowires (NWs) with large diameters has been a challenge over the past two decades. Here, we report on the synthesis of highly coercive cobalt NW arrays with diameters of 65 and 80 nm, which are embedded in porous anodic alumina templates with high-aspect-ratio pores. Using a modified electrochemical deposition method enabled us to reach room temperature coercivity and remanent ratio up to 3000 Oe and 0.70, respectively, for highly crystalline as-synthesized hcp cobalt NW arrays with a length of 8 μm. The first-order reversal curve (FORC) analysis showed the presence of both soft and hard magnetic phases along the length of the resulting NWs. To develop higher coercive fields, the length of the NWs was then gradually reduced in order from bottom to top, thereby reaching NW sections governed by the hard phase. Consequently, this resulted in record high coercivities of 4200 and 3850 Oe at NW diameters of 65 and 80 nm, respectively. In this case, the FORC diagrams confirmed a significant reduction in interactions between the magnetic phases of the remaining sections of NWs. At this stage, x-ray diffraction (XRD) and dark-field transmission electron microscopy analyses indicated the formation of highly crystalline bamboo-like sections along the [0 0 2] direction during a progressive pulse-controlled electrochemical growth of NW arrays under optimized parameters. Our results both provide new insights into the growth process, crystalline characteristics and magnetic phases along the length of large diameter NW arrays and, furthermore, develop the performance of pure 3d transition magnetic NWs.

Antibody Protein Array Analysis of the Tear Film Cytokines

PubMed Central

Li, Shimin; Sack, Robert; Vijmasi, Trinka; Sathe, Sonal; Beaton, Ann; Quigley, David; Gallup, Marianne; McNamara, Nancy A.

2013-01-01

Purpose Many bioactive proteins including cytokines are reported to increase in dry eye disease although the specific profile and concentration of inflammatory mediators varies considerably from study to study. In part this variability results from inherent difficulties in quantifying low abundance proteins in a limited sample volume using relatively low sensitivity dot ELISA methods. Additional complexity comes with the use of pooled samples collected using a variety of techniques and intrinsic variation in the diurnal pattern of individual tear proteins. The current study describes a recent advance in the area of proteomics that has allowed the identification of dozens of low abundance proteins in human tear samples. Methods Commercially available stationary phase antibody protein arrays were adapted to improve suitability for use in small volume biological fluid analysis with particular emphasis on tear film proteomics. Arrays were adapted to allow simultaneous screening for a panel of inflammatory cytokines in low volume tear samples collected from individual eyes. Results A preliminary study comparing tear array results in a small population of Sjögren’s syndrome patients was conducted. The multiplex microplate array assays of cytokines in tear fluid present an unanticipated challenge due to the unique nature of tear fluid. The presence of factors that exhibit an affinity for plastic, capture antibodies and IgG and create a complex series of matrix effects profoundly impacting the reliability of dot ELISA, including with elevated levels of background reactivity and reduction in capacity to bind targeted protein. Conclusions Preliminary results using tears collected from patients with Sjögren’s syndrome reveal methodological advantages of protein array technology and support the concept that autoimmune-mediated dry eye disease has an inflammatory component. They also emphasize the inherent difficulties one can face when interpreting the results of micro-well arrays that result from blooming effects, matrix effects, image saturation and cross-talk between capture and probe antibodies that can greatly reduce signal-to-noise and limit the ability to obtain meaningful results. PMID:18677223

Synthesis and Self-Assembly of fcc Phase FePt Nanorods

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

Chen, Min; Pica, Timothy; Jiang, Ying-Bing

2007-05-01

In this paper, we report a synthesis of FePt nanorods by confining decomposition of Fe(CO) 5 and reduction of Pt(caca) 2 in surfactant reverse cylindrical micelles. The controlled nucleation and growth kinetics in confined environment allows easy control over Fe/Pt composition, nanorod uniformity, and nanorod aspect ratio. The FePt nanorods tend to self-assemble into ordered arrays along three-dimensions. Directed assembly under external magnetic field leads to two-dimensional ordered arrays, parallel to the substrate magnetic field. We expect that with optimized external magnetic fields, we should be able to assemble these nanorods into orientated one or two-dimensional arrays, providing a uniformmore » anisotropic magnetic platform for varied applications in enhanced data storage, magneto-electron transport, etc.« less

A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers.

PubMed

Şenbabaoğlu, Yasin; Sümer, Selçuk Onur; Sánchez-Vega, Francisco; Bemis, Debra; Ciriello, Giovanni; Schultz, Nikolaus; Sander, Chris

2016-02-01

Protein expression and post-translational modification levels are tightly regulated in neoplastic cells to maintain cellular processes known as 'cancer hallmarks'. The first Pan-Cancer initiative of The Cancer Genome Atlas (TCGA) Research Network has aggregated protein expression profiles for 3,467 patient samples from 11 tumor types using the antibody based reverse phase protein array (RPPA) technology. The resultant proteomic data can be utilized to computationally infer protein-protein interaction (PPI) networks and to study the commonalities and differences across tumor types. In this study, we compare the performance of 13 established network inference methods in their capacity to retrieve the curated Pathway Commons interactions from RPPA data. We observe that no single method has the best performance in all tumor types, but a group of six methods, including diverse techniques such as correlation, mutual information, and regression, consistently rank highly among the tested methods. We utilize the high performing methods to obtain a consensus network; and identify four robust and densely connected modules that reveal biological processes as well as suggest antibody-related technical biases. Mapping the consensus network interactions to Reactome gene lists confirms the pan-cancer importance of signal transduction pathways, innate and adaptive immune signaling, cell cycle, metabolism, and DNA repair; and also suggests several biological processes that may be specific to a subset of tumor types. Our results illustrate the utility of the RPPA platform as a tool to study proteomic networks in cancer.

Proteomic Screening and Lasso Regression Reveal Differential Signaling in Insulin and Insulin-like Growth Factor I (IGF1) Pathways.

PubMed

Erdem, Cemal; Nagle, Alison M; Casa, Angelo J; Litzenburger, Beate C; Wang, Yu-Fen; Taylor, D Lansing; Lee, Adrian V; Lezon, Timothy R

2016-09-01

Insulin and insulin-like growth factor I (IGF1) influence cancer risk and progression through poorly understood mechanisms. To better understand the roles of insulin and IGF1 signaling in breast cancer, we combined proteomic screening with computational network inference to uncover differences in IGF1 and insulin induced signaling. Using reverse phase protein array, we measured the levels of 134 proteins in 21 breast cancer cell lines stimulated with IGF1 or insulin for up to 48 h. We then constructed directed protein expression networks using three separate methods: (i) lasso regression, (ii) conventional matrix inversion, and (iii) entropy maximization. These networks, named here as the time translation models, were analyzed and the inferred interactions were ranked by differential magnitude to identify pathway differences. The two top candidates, chosen for experimental validation, were shown to regulate IGF1/insulin induced phosphorylation events. First, acetyl-CoA carboxylase (ACC) knock-down was shown to increase the level of mitogen-activated protein kinase (MAPK) phosphorylation. Second, stable knock-down of E-Cadherin increased the phospho-Akt protein levels. Both of the knock-down perturbations incurred phosphorylation responses stronger in IGF1 stimulated cells compared with insulin. Overall, the time-translation modeling coupled to wet-lab experiments has proven to be powerful in inferring differential interactions downstream of IGF1 and insulin signaling, in vitro. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

ON-COLUMN ENRICHMENT OF HYDROPHOBIC CYP450 PROTEINS IN HPLC FRACTIONATION OF MOUSE MICROSOMES PRIOR TO PROTEIN DIGESTION AND NANOSPRAY-LC/MSMS ANALYSIS

EPA Science Inventory

Introduction

Membrane proteins play crucial role in many cellular processes and are promising candidates for biomarker discovery but are under-represented in the field of proteomics due to their hydrophobic nature. Although standard reversed-phase LC methods often exhibit ...

Neuronal plasticity in hibernation and the proposed role of the microtubule-associated protein tau as a "master switch" regulating synaptic gain in neuronal networks.

PubMed

Arendt, Thomas; Bullmann, Torsten

2013-09-01

The present paper provides an overview of adaptive changes in brain structure and learning abilities during hibernation as a behavioral strategy used by several mammalian species to minimize energy expenditure under current or anticipated inhospitable environmental conditions. One cellular mechanism that contributes to the regulated suppression of metabolism and thermogenesis during hibernation is reversible phosphorylation of enzymes and proteins, which limits rates of flux through metabolic pathways. Reversible phosphorylation during hibernation also affects synaptic membrane proteins, a process known to be involved in synaptic plasticity. This mechanism of reversible protein phosphorylation also affects the microtubule-associated protein tau, thereby generating a condition that in the adult human brain is associated with aggregation of tau protein to paired helical filaments (PHFs), as observed in Alzheimer's disease. Here, we put forward the concept that phosphorylation of tau is a neuroprotective mechanism to escape NMDA-mediated hyperexcitability of neurons that would otherwise occur during slow gradual cooling of the brain. Phosphorylation of tau and its subsequent targeting to subsynaptic sites might, thus, work as a kind of "master switch," regulating NMDA receptor-mediated synaptic gain in a wide array of neuronal networks, thereby enabling entry into torpor. If this condition lasts too long, however, it may eventually turn into a pathological trigger, driving a cascade of events leading to neurodegeneration, as in Alzheimer's disease or other "tauopathies".

Quantitative proteomic characterization of redox-dependent post-translational modifications on protein cysteines

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

Duan, Jicheng; Gaffrey, Matthew J.; Qian, Wei-Jun

Protein cysteine thiols play a crucial role in redox signaling, regulation of enzymatic activity and protein function, and maintaining redox homeostasis in living systems. The unique chemical reactivity of thiol groups makes cysteine susceptible to oxidative modifications by reactive oxygen and nitrogen species to form a broad array of reversible and irreversible protein post-translational modifications (PTMs). The reversible modifications in particular are one of the major components of redox signaling and are involved in regulation of various cellular processes under physiological and pathological conditions. The biological significance of these redox PTMs in health and diseases has been increasingly recognized. Herein,more » we review the recent advances of quantitative proteomic approaches for investigating redox PTMs in complex biological systems, including the general considerations of sample processing, various chemical or affinity enrichment strategies, and quantitative approaches. We also highlight a number of redox proteomic approaches that enable effective profiling of redox PTMs for addressing specific biological questions. Although some technological limitations remain, redox proteomics is paving the way towards a better understanding of redox signaling and regulation in human health and diseases.« less

A reverse-phase protein microarray-based screen identifies host signaling dynamics upon Burkholderia spp. infection

PubMed Central

Chiang, Chih-Yuan; Uzoma, Ijeoma; Lane, Douglas J.; Memišević, Vesna; Alem, Farhang; Yao, Kuan; Kota, Krishna P.; Bavari, Sina; Wallqvist, Anders; Hakami, Ramin M.; Panchal, Rekha G.

2015-01-01

Burkholderia is a diverse genus of gram-negative bacteria that causes high mortality rate in humans, equines and cattle. The lack of effective therapeutic treatments poses serious public health threats. Developing insights toward host-Burkholderia spp. interaction is critical for understanding the pathogenesis of infection as well as identifying therapeutic targets for drug development. Reverse-phase protein microarray technology was previously proven to identify and characterize novel biomarkers and molecular signatures associated with infectious disease and cancer. In the present study, this technology was utilized to interrogate changes in host protein expression and phosphorylation events in macrophages infected with a collection of geographically diverse strains of Burkholderia spp. The expression or phosphorylation state of 25 proteins was altered during Burkholderia spp. infections of which eight proteins were selected for further characterization by immunoblotting. Increased phosphorylation of AMPK-α1, Src, and GSK3β suggested the importance of their roles in regulating Burkholderia spp. mediated innate immune response. Modulating the inflammatory response by perturbing their activities may provide therapeutic routes for future treatments. PMID:26284031

Folding-unfolding transitions of Rv3221c on the pressure-temperature plane

NASA Astrophysics Data System (ADS)

Somkuti, Judit; Jain, Sriyans; Ramachandran, Srinivasan; ászló Smeller, L.

2013-06-01

Rv3221c is a biotin-binding protein found in Mycobacterium tuberculosis. It has been reported that an elevated temperature is needed for it to adopt a folded conformation. We determined the complete pressure-temperature phase diagram, and determined the thermodynamical parameters of the denaturation. The phase diagram follows well the Hawley theory. The secondary structure of the protein was found to contain predominantly beta sheet. The pressure unfolding was partially reversible, resulting in pressure-sensitive aggregates, besides the correctly refolded and biotin-bound fraction of proteins.

Calibration Test Set for a Phase-Comparison Digital Tracker

NASA Technical Reports Server (NTRS)

Boas, Amy; Li, Samuel; McMaster, Robert

2007-01-01

An apparatus that generates four signals at a frequency of 7.1 GHz having precisely controlled relative phases and equal amplitudes has been designed and built. This apparatus is intended mainly for use in computer-controlled automated calibration and testing of a phase-comparison digital tracker (PCDT) that measures the relative phases of replicas of the same X-band signal received by four antenna elements in an array. (The relative direction of incidence of the signal on the array is then computed from the relative phases.) The present apparatus can also be used to generate precisely phased signals for steering a beam transmitted from a phased antenna array. The apparatus (see figure) includes a 7.1-GHz signal generator, the output of which is fed to a four-way splitter. Each of the four splitter outputs is attenuated by 10 dB and fed as input to a vector modulator, wherein DC bias voltages are used to control the in-phase (I) and quadrature (Q) signal components. The bias voltages are generated by digital-to-analog- converter circuits on a control board that receives its digital control input from a computer running a LabVIEW program. The outputs of the vector modulators are further attenuated by 10 dB, then presented at high-grade radio-frequency connectors. The attenuation reduces the effects of changing mismatch and reflections. The apparatus was calibrated in a process in which the bias voltages were first stepped through all possible IQ settings. Then in a reverse interpolation performed by use of MATLAB software, a lookup table containing 3,600 IQ settings, representing equal amplitude and phase increments of 0.1 , was created for each vector modulator. During operation of the apparatus, these lookup tables are used in calibrating the PCDT.

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer.

PubMed

Hoadley, Katherine A; Yau, Christina; Hinoue, Toshinori; Wolf, Denise M; Lazar, Alexander J; Drill, Esther; Shen, Ronglai; Taylor, Alison M; Cherniack, Andrew D; Thorsson, Vésteinn; Akbani, Rehan; Bowlby, Reanne; Wong, Christopher K; Wiznerowicz, Maciej; Sanchez-Vega, Francisco; Robertson, A Gordon; Schneider, Barbara G; Lawrence, Michael S; Noushmehr, Houtan; Malta, Tathiane M; Stuart, Joshua M; Benz, Christopher C; Laird, Peter W

2018-04-05

We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed molecular clustering using data on chromosome-arm-level aneuploidy, DNA hypermethylation, mRNA, and miRNA expression levels and reverse-phase protein arrays, of which all, except for aneuploidy, revealed clustering primarily organized by histology, tissue type, or anatomic origin. The influence of cell type was evident in DNA-methylation-based clustering, even after excluding sites with known preexisting tissue-type-specific methylation. Integrative clustering further emphasized the dominant role of cell-of-origin patterns. Molecular similarities among histologically or anatomically related cancer types provide a basis for focused pan-cancer analyses, such as pan-gastrointestinal, pan-gynecological, pan-kidney, and pan-squamous cancers, and those related by stemness features, which in turn may inform strategies for future therapeutic development. Copyright © 2018 Elsevier Inc. All rights reserved.

Coherent and Noncoherent Joint Processing of Sonar for Detection of Small Targets in Shallow Water

PubMed Central

Jiang, Jingning; Li, Si; Ding, Zhenping; Pan, Chen; Gong, Xianyi

2018-01-01

A coherent-noncoherent joint processing framework is proposed for active sonar to combine diversity gain and beamforming gain for detection of a small target in shallow water environments. Sonar utilizes widely-spaced arrays to sense environments and illuminate a target of interest from multiple angles. Meanwhile, it exploits spatial diversity for time-reversal focusing to suppress reverberation, mainly strong bottom reverberation. For enhancement of robustness of time-reversal focusing, an adaptive iterative strategy is utilized in the processing framework. A probing signal is firstly transmitted and echoes of a likely target are utilized as steering vectors for the second transmission. With spatial diversity, target bearing and range are estimated using a broadband signal model. Numerical simulations show that the novel sonar outperforms the traditional phased-array sonar due to benefits of spatial diversity. The effectiveness of the proposed framework has been validated by localization of a small target in at-lake experiments. PMID:29642637

Alterations in the sarcoplasmic protein fraction of beef muscle with postmortem aging and hydrodynamic pressure processing

USDA-ARS?s Scientific Manuscript database

Capillary electrophoresis (CE) and reversed-phase high performance liquid chromatography (RP-HPLC) analysis were utilized to detect differences in the sarcoplasmic protein profiles of beef strip loins subjected to aging and hydrodynamic pressure processing (HDP) treatments. At 48 h postmortem, stri...

Identification of the active protein in rice bran protein having an inhibitory activity of cholesterol micellar solubility.

PubMed

Wang, Jilite; Shimada, Masaya; Nagaoka, Satoshi

2017-06-01

In our previous study, rice bran protein (RBP) inhibited cholesterol micellar solubility in vitro and decreased serum cholesterol level in rats. In the present study, RBP was separated and purified by size-exclusion chromatography and reversed-phase chromatography. The active protein of RBP related to cholesterol micellar solubility was identified as lectin and non-specific lipid-transfer protein 1 using MALDI-TOF mass spectrometry analysis.

Telomerase Mechanism of Telomere Synthesis

PubMed Central

Wu, R. Alex; Upton, Heather E.; Vogan, Jacob M.; Collins, Kathleen

2017-01-01

Telomerase is the essential reverse transcriptase required for linear chromosome maintenance in most eukaryotes. Telomerase supplements the tandem array of simple-sequence repeats at chromosome ends to compensate for the DNA erosion inherent in genome replication. The template for telomerase reverse transcriptase is within the RNA subunit of the ribonucleoprotein complex, which in cells contains additional telomerase holoenzyme proteins that assemble the active ribonucleoprotein and promote its function at telomeres. Telomerase is distinct among polymerases in its reiterative reuse of an internal template. The template is precisely defined, processively copied, and regenerated by release of single-stranded product DNA. New specificities of nucleic acid handling that underlie the catalytic cycle of repeat synthesis derive from both active site specialization and new motif elaborations in protein and RNA subunits. Studies of telomerase provide unique insights into cellular requirements for genome stability, tissue renewal, and tumorigenesis as well as new perspectives on dynamic ribonucleoprotein machines. PMID:28141967

Cluster analysis of historical and modern hard red spring wheat cultivars based on parentage and HPLC analysis of gluten forming proteins

USDA-ARS?s Scientific Manuscript database

In this study, 30 hard red spring (HRS) wheat cultivars released between 1910 and 2013 were analyzed to determine how they cluster in terms of parentage and protein data, analyzed by reverse-phase HPLC (RP-HPLC) of gliadins, and size-exclusion HPLC (SE-HPLC) of unreduced proteins. Dwarfing genes in...

Novel BET protein proteolysis-targeting chimera exerts superior lethal activity than bromodomain inhibitor (BETi) against post-myeloproliferative neoplasm secondary (s) AML cells.

PubMed

Saenz, D T; Fiskus, W; Qian, Y; Manshouri, T; Rajapakshe, K; Raina, K; Coleman, K G; Crew, A P; Shen, A; Mill, C P; Sun, B; Qiu, P; Kadia, T M; Pemmaraju, N; DiNardo, C; Kim, M-S; Nowak, A J; Coarfa, C; Crews, C M; Verstovsek, S; Bhalla, K N

2017-09-01

The PROTAC (proteolysis-targeting chimera) ARV-825 recruits bromodomain and extraterminal (BET) proteins to the E3 ubiquitin ligase cereblon, leading to degradation of BET proteins, including BRD4. Although the BET-protein inhibitor (BETi) OTX015 caused accumulation of BRD4, treatment with equimolar concentrations of ARV-825 caused sustained and profound depletion (>90%) of BRD4 and induced significantly more apoptosis in cultured and patient-derived (PD) CD34+ post-MPN sAML cells, while relatively sparing the CD34+ normal hematopoietic progenitor cells. RNA-Seq, Reverse Phase Protein Array and mass cytometry 'CyTOF' analyses demonstrated that ARV-825 caused greater perturbations in messenger RNA (mRNA) and protein expressions than OTX015 in sAML cells. Specifically, compared with OTX015, ARV-825 treatment caused more robust and sustained depletion of c-Myc, CDK4/6, JAK2, p-STAT3/5, PIM1 and Bcl-xL, while increasing the levels of p21 and p27. Compared with OTX015, PROTAC ARV-771 treatment caused greater reduction in leukemia burden and further improved survival of NSG mice engrafted with luciferase-expressing HEL92.1.7 cells. Co-treatment with ARV-825 and JAK inhibitor ruxolitinib was synergistically lethal against established and PD CD34+ sAML cells. Notably, ARV-825 induced high levels of apoptosis in the in vitro generated ruxolitinib-persister or ruxolitinib-resistant sAML cells. These findings strongly support the in vivo testing of the BRD4-PROTAC based combinations against post-MPN sAML.

Ultrasound-assisted analyte extraction for the determination of sulfate and elemental sulfur in zinc sulfide by different liquid chromatography techniques.

PubMed

Dash, K; Thangavel, S; Krishnamurthy, N V; Rao, S V; Karunasagar, D; Arunachalam, J

2005-04-01

The speciation and determination of sulfate (SO4(2-)) and elemental sulfur (S degree) in zinc sulfide (ZnS) using ion-chromatography (IC) and reversed-phase liquid chromatography (RPLC) respectively is described. Three sample pretreatment approaches were employed with the aim of determining sulfate: (i) conventional water extraction of the analyte; (ii) solid-liquid aqueous extraction with an ultrasonic probe; and (iii) elimination of the zinc sulfide matrix via ion-exchange dissolution (IED). The separation of sulfate was carried out by an anion-exchange column (IonPac AS17), followed by suppressed conductivity detection. Elemental sulfur was extracted ultrasonically from the acid treated sample solution into chloroform and separated on a reversed phase HPLC column equipped with a diode array detector (DAD) at 264 nm. The achievable solid detection limits for sulfate and sulfur were 35 and 10 microg g(-1) respectively.

Expression of Iron-Related Proteins Differentiate Non-Cancerous and Cancerous Breast Tumors

PubMed Central

Pizzamiglio, Sara; De Bortoli, Maida; Taverna, Elena; Signore, Michele; Veneroni, Silvia; Chi-shing Cho, William; Orlandi, Rosaria; Verderio, Paolo; Bongarzone, Italia

2017-01-01

We have previously reported hepcidin and ferritin increases in the plasma of breast cancer patients, but not in patients with benign breast disease. We hypothesized that these differences in systemic iron homeostasis may reflect alterations in different iron-related proteins also play a key biochemical and regulatory role in breast cancer. Thus, here we explored the expression of a bundle of molecules involved in both iron homeostasis and tumorigenesis in tissue samples. Enzyme-linked immunosorbent assay (ELISA) or reverse-phase protein array (RPPA), were used to measure the expression of 20 proteins linked to iron processes in 24 non-cancerous, and 56 cancerous, breast tumors. We found that cancerous tissues had higher level of hepcidin than benign lesions (p = 0.012). The univariate analysis of RPPA data highlighted the following seven proteins differentially expressed between non-cancerous and cancerous breast tissue: signal transducer and transcriptional activator 5 (STAT5), signal transducer and activator of transcription 3 (STAT3), bone morphogenetic protein 6 (BMP6), cluster of differentiation 74 (CD74), transferrin receptor (TFRC), inhibin alpha (INHA), and STAT5_pY694. These findings were confirmed for STAT5, STAT3, BMP6, CD74 and INHA when adjusting for age. The multivariate statistical analysis indicated an iron-related 10-protein panel effective in separating non-cancerous from cancerous lesions including STAT5, STAT5_pY694, myeloid differentiation factor 88 (MYD88), CD74, iron exporter ferroportin (FPN), high mobility group box 1 (HMGB1), STAT3_pS727, TFRC, ferritin heavy chain (FTH), and ferritin light chain (FTL). Our results showed an association between some iron-related proteins and the type of tumor tissue, which may provide insight in strategies for using iron chelators to treat breast cancer. PMID:28216608

Note: Development of a multichannel magnetic probe array for magnetohydrodynamic activity studies in Sino-United Spherical Tokamak

NASA Astrophysics Data System (ADS)

Zhong, H.; Tan, Y.; Gao, Z.

2018-02-01

A 30-channel movable magnetic probe radial array measuring the poloidal magnetic field's time derivative B˙ θ has been developed and installed on the Sino-United Spherical Tokamak to investigate the magnetohydrodynamic (MHD) activities in ohmic discharges. The probe array consists of thirty identical commercial chip inductors mounted on a slim printed circuit board and shielded by a customized quartz tube of 14 mm in outer diameter. With the application of instrumentation amplifiers, the system exhibits a good signal to noise ratio and the measured vertical field spatial distribution agrees well with the simulation result. The measured spatial and temporal distribution of B˙ θ during the MHD activities exhibits a clear phase reversal layer, which is a direct proof of tearing mode and provides a reliable indication of the magnetic island chain position.

d-Limonene-induced male rat-specific nephrotoxicity: Evaluation of the association between d-limonene and alpha 2u-globulin

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

Lehman-McKeeman, L.D.; Rodriguez, P.A.; Takigiku, R.

1989-06-15

d-Limonene is a naturally occurring monoterpene, which when dosed orally, causes a male rat-specific nephrotoxicity manifested acutely as the exacerbation of protein droplets in proximal tubule cells. Experiments were conducted to examine the retention of (/sup 14/C)d-limonene in male and female rat kidney, to determine whether d-limonene or one or more of its metabolites associates with the male rat-specific protein, alpha 2u-globulin, and if so, to identify the bound material. The results indicated that, 24 hr after oral administration of 3 mmol d-limonene/kg, the renal concentration of d-limonene equivalents was approximately 2.5 times higher in male rats than in femalemore » rats. Equilibrium dialysis in the presence or absence of sodium dodecyl sulfate indicated that approximately 40% of the d-limonene equivalents in male rat kidney associated with proteins in a reversible manner, whereas no significant association was observed between d-limonene equivalents and female rat kidney proteins. Association between d-limonene and male rat kidney proteins was characterized by high-performance gel filtration and reverse-phase chromatography. Gel filtration HPLC indicated that d-limonene in male rat kidney is associated with a protein fraction having a molecular weight of approximately 20,000. Separation of alpha 2u-globulin from other kidney proteins by reverse-phase HPLC indicated that d-limonene associated with a protein present only in male rat kidney which was definitively identified as alpha 2u-globulin by amino acid sequencing. The major metabolite associated with alpha 2u-globulin was d-limonene-1,2-oxide. Parent d-limonene was also identified as a minor component in the alpha 2u-globulin fraction.« less

High-performance liquid chromatography separation and intact mass analysis of detergent-solubilized integral membrane proteins

PubMed Central

Berridge, Georgina; Chalk, Rod; D’Avanzo, Nazzareno; Dong, Liang; Doyle, Declan; Kim, Jung-In; Xia, Xiaobing; Burgess-Brown, Nicola; deRiso, Antonio; Carpenter, Elisabeth Paula; Gileadi, Opher

2011-01-01

We have developed a method for intact mass analysis of detergent-solubilized and purified integral membrane proteins using liquid chromatography–mass spectrometry (LC–MS) with methanol as the organic mobile phase. Membrane proteins and detergents are separated chromatographically during the isocratic stage of the gradient profile from a 150-mm C3 reversed-phase column. The mass accuracy is comparable to standard methods employed for soluble proteins; the sensitivity is 10-fold lower, requiring 0.2–5 μg of protein. The method is also compatible with our standard LC–MS method used for intact mass analysis of soluble proteins and may therefore be applied on a multiuser instrument or in a high-throughput environment. PMID:21093405

Cdc2-like kinase 2 is a key regulator of the cell cycle via FOXO3a/p27 in glioblastoma.

PubMed

Park, Soon Young; Piao, Yuji; Thomas, Craig; Fuller, Gregory N; de Groot, John F

2016-05-03

Cdc2-like kinase 2 (CLK2) is known as a regulator of RNA splicing that ultimately controls multiple physiological processes. However, the function of CLK2 in glioblastoma progression has not been described. Reverse-phase protein array (RPPA) was performed to identify proteins differentially expressed in CLK2 knockdown cells compared to controls. The RPPA results indicated that CLK2 knockdown influenced the expression of survival-, proliferation-, and cell cycle-related proteins in GSCs. Thus, knockdown of CLK2 expression arrested the cell cycle at the G1 and S checkpoints in multiple GSC lines. Depletion of CLK2 regulated the dephosphorylation of AKT and decreased phosphorylation of Forkhead box O3a (FOXO3a), which not only translocated to the nucleus but also increased p27 expression. In two glioblastoma xenograft models, the survival duration of mice with CLK2-knockdown GSCs was significantly longer than mice with control tumors. Additionally, tumor volumes were significantly smaller in CLK2-knockdown mice than in controls. Knockdown of CLK2 expression reduced the phosphorylation of FOXO3a and decreased Ki-67 in vivo. Finally, high expression of CLK2 protien was significantly associated with worse patient survival. These findings suggest that CLK2 plays a critical role in controlling the cell cycle and survival of glioblastoma via FOXO3a/p27.

Cdc2-like kinase 2 is a key regulator of the cell cycle via FOXO3a/p27 in glioblastoma

PubMed Central

Thomas, Craig; Fuller, Gregory N.; de Groot, John F.

2016-01-01

Cdc2-like kinase 2 (CLK2) is known as a regulator of RNA splicing that ultimately controls multiple physiological processes. However, the function of CLK2 in glioblastoma progression has not been described. Reverse-phase protein array (RPPA) was performed to identify proteins differentially expressed in CLK2 knockdown cells compared to controls. The RPPA results indicated that CLK2 knockdown influenced the expression of survival-, proliferation-, and cell cycle-related proteins in GSCs. Thus, knockdown of CLK2 expression arrested the cell cycle at the G1 and S checkpoints in multiple GSC lines. Depletion of CLK2 regulated the dephosphorylation of AKT and decreased phosphorylation of Forkhead box O3a (FOXO3a), which not only translocated to the nucleus but also increased p27 expression. In two glioblastoma xenograft models, the survival duration of mice with CLK2-knockdown GSCs was significantly longer than mice with control tumors. Additionally, tumor volumes were significantly smaller in CLK2-knockdown mice than in controls. Knockdown of CLK2 expression reduced the phosphorylation of FOXO3a and decreased Ki-67 in vivo. Finally, high expression of CLK2 protien was significantly associated with worse patient survival. These findings suggest that CLK2 plays a critical role in controlling the cell cycle and survival of glioblastoma via FOXO3a/p27. PMID:27050366

Porous polymer monolithic columns with gold nanoparticles as an intermediate ligand for the separation of proteins in reverse phase-ion exchange mixed mode

DOE PAGES

Terborg, Lydia; Masini, Jorge C.; Lin, Michelle; ...

2014-11-04

A new approach has been developed for the preparation of mixed-mode stationary phases to separate proteins. The pore surface of monolithic poly(glycidyl methacrylate- co-ethylene dimethacrylate) capillary columns was functionalized with thiols and coated with gold nanoparticles. The final mixed mode surface chemistry was formed by attaching, in a single step, alkanethiols, mercaptoalkanoic acids, and their mixtures on the free surface of attached gold nanoparticles. Use of these mixtures allowed fine tuning of the hydrophobic/hydrophilic balance. The amount of attached gold nanoparticles according to thermal gravimetric analysis was 44.8 wt.%. This value together with results of frontal elution enabled calculation ofmore » surface coverage with the alkanethiol and mercaptoalkanoic acid ligands. Interestingly, alkanethiols coverage in a range of 4.46–4.51 molecules/nm 2 significantly exceeded that of mercaptoalkanoic acids with 2.39–2.45 molecules/nm 2. The mixed mode character of these monolithic stationary phases was for the first time demonstrated in the separations of proteins that could be achieved in the same column using gradient elution conditions typical of reverse phase (using gradient of acetonitrile in water) and ion exchange chromatographic modes (applying gradient of salt in water), respectively.« less

Hydrophilic interaction liquid chromatography-solid phase extraction directly combined with protein precipitation for the determination of triptorelin in plasma.

PubMed

Wang, Jixia; Kong, Song; Yan, Jingyu; Jin, Gaowa; Guo, Zhimou; Shen, Aijin; Xu, Junyan; Zhang, Xiuli; Zou, Lijuan; Liang, Xinmiao

2014-06-01

Peptide drugs play a critical role in therapeutic treatment. However, as the complexity of plasma, determination of peptide drugs using liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a daunting task. To solve this problem, hydrophilic interaction liquid chromatography-solid phase extraction (HILIC-SPE) directly combined with protein precipitation (PPT) was developed for the selective extraction of triptorelin from plasma. The extracts were analyzed by reversed-phase liquid chromatography (RPLC). Proteins, phospholipids and highly polar interferences could be removed from plasma by the efficient combination of PPT, HILIC-SPE and RPLC-MS/MS. This method was evaluated by matrix effect, recovery and process efficiency at different concentration levels (50, 500 and 5,000 ng/mL) of triptorelin. Furthermore, the performance of HILIC-SPE was compared with that of reversed-phase C18 SPE and hydrophilic lipophilic balance (Oasis HLB) SPE. Among them, HILIC-SPE provided the minimum matrix effect (ranging from 96.02% to 103.41%), the maximum recovery (ranging from 80.68% to 90.54%) and the satisfactory process efficiency (ranging from 82.83% to 92.95%). The validated method was successfully applied to determine triptorelin in rat plasma. Copyright © 2014 Elsevier B.V. All rights reserved.

Transcript and protein profiling identifies signaling, growth arrest, apoptosis, and NF-κB survival signatures following GNRH receptor activation

PubMed Central

Meyer, Colette; Sims, Andrew H; Morgan, Kevin; Harrison, Beth; Muir, Morwenna; Bai, Jianing; Faratian, Dana; Millar, Robert P; Langdon, Simon P

2013-01-01

GNRH significantly inhibits proliferation of a proportion of cancer cell lines by activating GNRH receptor (GNRHR)-G protein signaling. Therefore, manipulation of GNRHR signaling may have an under-utilized role in treating certain breast and ovarian cancers. However, the precise signaling pathways necessary for the effect and the features of cellular responses remain poorly defined. We used transcriptomic and proteomic profiling approaches to characterize the effects of GNRHR activation in sensitive cells (HEK293-GNRHR, SCL60) in vitro and in vivo, compared to unresponsive HEK293. Analyses of gene expression demonstrated a dynamic response to the GNRH superagonist Triptorelin. Early and mid-phase changes (0.5–1.0 h) comprised mainly transcription factors. Later changes (8–24 h) included a GNRH target gene, CGA, and up- or downregulation of transcripts encoding signaling and cell division machinery. Pathway analysis identified altered MAPK and cell cycle pathways, consistent with occurrence of G2/M arrest and apoptosis. Nuclear factor kappa B (NF-κB) pathway gene transcripts were differentially expressed between control and Triptorelin-treated SCL60 cultures. Reverse-phase protein and phospho-proteomic array analyses profiled responses in cultured cells and SCL60 xenografts in vivo during Triptorelin anti-proliferation. Increased phosphorylated NF-κB (p65) occurred in SCL60 in vitro, and p-NF-κB and IκBϵ were higher in treated xenografts than controls after 4 days Triptorelin. NF-κB inhibition enhanced the anti-proliferative effect of Triptorelin in SCL60 cultures. This study reveals details of pathways interacting with intense GNRHR signaling, identifies potential anti-proliferative target genes, and implicates the NF-κB survival pathway as a node for enhancing GNRH agonist-induced anti-proliferation. PMID:23202794

Purification of α-glucosidase from mouse intestine by countercurrent chromatography coupled with a reverse micelle solvent system.

PubMed

He, Kai; Zou, Zongyao; Hu, Yinran; Yang, Yong; Xiao, Yubo; Gao, Pincao; Li, Xuegang; Ye, Xiaoli

2016-02-01

Countercurrent chromatography coupled with a reverse micelle solvent was applied to separate α-glucosidase, which is stable at pH 6.0-8.8, 15-50°C. The separation conditions are as follows: stationary phase: pH 4.0 Tris-HCl buffer phase containing 50 mM Tris-HCl and 50 mM KCl; mobile phase A: isooctane containing 50 mM anionic surfactant sodium di(2-ethylhexyl)sulfosuccinate; mobile phase B: 50 mM Tris-HCl buffer containing 500 mM KCl (pH 8.0); In total, 25 mL (23.9 mg) crude enzyme was injected through the injection valve, the enzymatic reaction and sodium dodecylsulfate polyacrylamide gel electrophoresis results imply that the activity of purified α-glucosidase is 6.63-fold higher than that of the crude enzyme. Therefore, countercurrent chromatography coupled with a reverse micelle solvent is capable for protein separation and enrichment. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

ALS/FTD Mutation-Induced Phase Transition of FUS Liquid Droplets and Reversible Hydrogels into Irreversible Hydrogels Impairs RNP Granule Function

PubMed Central

Murakami, Tetsuro; Qamar, Seema; Lin, Julie Qiaojin; Schierle, Gabriele S. Kaminski; Rees, Eric; Miyashita, Akinori; Costa, Ana R.; Dodd, Roger B.; Chan, Fiona T.S.; Michel, Claire H.; Kronenberg-Versteeg, Deborah; Li, Yi; Yang, Seung-Pil; Wakutani, Yosuke; Meadows, William; Ferry, Rodylyn Rose; Dong, Liang; Tartaglia, Gian Gaetano; Favrin, Giorgio; Lin, Wen-Lang; Dickson, Dennis W.; Zhen, Mei; Ron, David; Schmitt-Ulms, Gerold; Fraser, Paul E.; Shneider, Neil A.; Holt, Christine; Vendruscolo, Michele; Kaminski, Clemens F.; St George-Hyslop, Peter

2015-01-01

Summary The mechanisms by which mutations in FUS and other RNA binding proteins cause ALS and FTD remain controversial. We propose a model in which low-complexity (LC) domains of FUS drive its physiologically reversible assembly into membrane-free, liquid droplet and hydrogel-like structures. ALS/FTD mutations in LC or non-LC domains induce further phase transition into poorly soluble fibrillar hydrogels distinct from conventional amyloids. These assemblies are necessary and sufficient for neurotoxicity in a C. elegans model of FUS-dependent neurodegeneration. They trap other ribonucleoprotein (RNP) granule components and disrupt RNP granule function. One consequence is impairment of new protein synthesis by cytoplasmic RNP granules in axon terminals, where RNP granules regulate local RNA metabolism and translation. Nuclear FUS granules may be similarly affected. Inhibiting formation of these fibrillar hydrogel assemblies mitigates neurotoxicity and suggests a potential therapeutic strategy that may also be applicable to ALS/FTD associated with mutations in other RNA binding proteins. PMID:26526393

Cyclic interconversion of methionine containing peptide between oxidized and reduced phases monitored by reversed-phase HPLC and ESI-MS/MS.

PubMed

Jin, Yulong; Huang, Yanyan; Xie, Yunfeng; Hu, Wenbing; Wang, Fuyi; Liu, Guoquan; Zhao, Rui

2012-01-30

The cyclic oxidation and reduction of methionine (Met) containing peptides and proteins play important roles in biological system. This work was contributed to analysis the cyclic oxidation and reduction processes of a methionine containing peptide which is very likely to relate in the cell signal transduction pathways. To mimic the biological oxidation condition, hydrogen peroxide was used as the reactive oxygen species to oxidize the peptide. Reversed-phase high-performance liquid chromatography and mass spectrometry were employed to monitor the reactions and characterize the structural changes of the products. A rapid reduction procedure was developed by simply using KI as the reductant, which is green and highly efficient. By investigation of the cyclic oxidation and reduction process, our work provides a new perspective to study the function and mechanism of Met containing peptides and proteins during cell signaling processes as well as diseases. Copyright © 2011 Elsevier B.V. All rights reserved.

Simultaneous determination of 11 antibiotics and their main metabolites from four different groups by reversed-phase high-performance liquid chromatography-diode array-fluorescence (HPLC-DAD-FLD) in human urine samples.

PubMed

Fernandez-Torres, R; Consentino, M Olías; Lopez, M A Bello; Mochon, M Callejon

2010-05-15

A new, accurate and sensitive reversed-phase high-performance liquid chromatography (RP-HPLC) as analytical method for the quantitative determination of 11 antibiotics (drugs) and the main metabolites of five of them present in human urine has been worked out, optimized and validated. The analytes belong to four different groups of antibiotics (sulfonamides, tetracyclines, penicillins and anphenicols). The analyzed compounds were sulfadiazine (SDI) and its N(4)-acetylsulfadiazine (NDI) metabolite, sulfamethazine (SMZ) and its N(4)-acetylsulfamethazine (NMZ), sulfamerazine (SMR) and its N(4)-acetylsulfamerazine (NMR), sulfamethoxazole (SMX), trimetroprim (TMP), amoxicillin (AMX) and its main metabolite amoxicilloic acid (AMA), ampicillin (AMP) and its main metabolite ampicilloic acid (APA), chloramphenicol (CLF), thiamphenicol (TIF), oxytetracycline (OXT) and chlortetracycline (CLT). For HPLC analysis, diode array (DAD) and fluorescence (FLD) detectors were used. The separation of the analyzed compounds was conducted by means of a Phenomenex Gemini C(18) (150mm x 4.6mm I.D., particle size 5microm) analytical column with LiChroCART LiChrospher C(18) (4mm x 4mm, particle size 5microm) guard column. Analyzed drugs were determined within 34min using formic acid 0.1% in water and acetonitrile in gradient elution mode as mobile phase. A linear response was observed for all compounds in the range of concentration studied. Two procedures were optimized for sample preparation: a direct treatment with methanol and acetonitrile and a solid phase extraction procedure using Bond Elut Plexa columns. The method was applied to the determination of the analytes in human urine from volunteers under treatment with different pharmaceutical formulations. This method can be successfully applied to routine determination of all these drugs in human urine samples.

Antibody profiling using a recombinant protein-based multiplex ELISA array accelerates recombinant vaccine development: Case study on red sea bream iridovirus as a reverse vaccinology model.

PubMed

Matsuyama, Tomomasa; Sano, Natsumi; Takano, Tomokazu; Sakai, Takamitsu; Yasuike, Motoshige; Fujiwara, Atushi; Kawato, Yasuhiko; Kurita, Jun; Yoshida, Kazunori; Shimada, Yukinori; Nakayasu, Chihaya

2018-05-03

Predicting antigens that would be protective is crucial for the development of recombinant vaccine using genome based vaccine development, also known as reverse vaccinology. High-throughput antigen screening is effective for identifying vaccine target genes, particularly for pathogens for which minimal antigenicity data exist. Using red sea bream iridovirus (RSIV) as a research model, we developed enzyme-linked immune sorbent assay (ELISA) based RSIV-derived 72 recombinant antigen array to profile antiviral antibody responses in convalescent Japanese amberjack (Seriola quinqueradiata). Two and three genes for which the products were unrecognized and recognized, respectively, by antibodies in convalescent serum were selected for recombinant vaccine preparation, and the protective effect was examined in infection tests using Japanese amberjack and greater amberjack (S. dumerili). No protection was provided by vaccines prepared from gene products unrecognized by convalescent serum antibodies. By contrast, two vaccines prepared from gene products recognized by serum antibodies induced protective immunity in both fish species. These results indicate that ELISA array screening is effective for identifying antigens that induce protective immune responses. As this method does not require culturing of pathogens, it is also suitable for identifying protective antigens to un-culturable etiologic agents. Copyright © 2018 Elsevier Ltd. All rights reserved.

Evaluation of a method based on liquid chromatography-diode array detector-tandem mass spectrometry for a rapid and comprehensive characterization of the fat-soluble vitamin and carotenoid profile of selected plant foods.

PubMed

Gentili, Alessandra; Caretti, Fulvia

2011-02-04

The feasibility of using reversed-phase liquid chromatography/diode array/tandem mass spectrometry (LC-DAD-MS/MS) for a rapid and comprehensive profiling of fat soluble vitamins and pigments in some foods of plant origin (maize flour, green and golden kiwi) was evaluated. The instrumental approach was planned for obtaining two main outcomes within the same chromatographic run: (i) the quantitative analysis of ten target analytes, whose standards are commercially available; (ii) the screening of pigments occurring in the selected matrices. The quantitative analysis was performed simultaneously for four carotenoids (lutein, zeaxanthin, β-cryptoxanthin, and β-carotene) and six compounds with fat-soluble activity (α-tocopherol, δ-tocopherol, γ-tocopherol, ergocalciferol, phylloquinone and menaquinone-4), separated on a C30 reversed-phase column and detected by atmospheric pressure chemical ionization (APCI) tandem mass spectrometry, operating in Selected Reaction Monitoring (SRM) mode. Extraction procedure was based on matrix solid-phase dispersion with recoveries of all compounds under study exceeding 78 and 60% from maize flour and kiwi, respectively. The method intra-day precision ranged between 3 and 7%, while the inter-day one was below 12%. The mild isolation conditions precluded artefacts creation, such as cis-isomerization phenomena for carotenoids. During the quantitative LC-SRM determination of the ten target analytes, the identification power of the diode array detector joined to that of the triple quadrupole (QqQ) allowed the tentatively identification of several pigments (chlorophylls and carotenoids), without the aid of standards, on the basis of: (i) the UV-vis spectra recorded in the range of 200-700nm; (ii) the expected retention time; (iii) the two SRM transitions, chosen for the target carotenoids but also common to many of isomeric carotenoids occurring in the selected foods. Copyright © 2010 Elsevier B.V. All rights reserved.

Non-invasive transcranial ultrasound therapy based on a 3D CT scan: protocol validation and in vitro results

NASA Astrophysics Data System (ADS)

Marquet, F.; Pernot, M.; Aubry, J.-F.; Montaldo, G.; Marsac, L.; Tanter, M.; Fink, M.

2009-05-01

A non-invasive protocol for transcranial brain tissue ablation with ultrasound is studied and validated in vitro. The skull induces strong aberrations both in phase and in amplitude, resulting in a severe degradation of the beam shape. Adaptive corrections of the distortions induced by the skull bone are performed using a previous 3D computational tomography scan acquisition (CT) of the skull bone structure. These CT scan data are used as entry parameters in a FDTD (finite differences time domain) simulation of the full wave propagation equation. A numerical computation is used to deduce the impulse response relating the targeted location and the ultrasound therapeutic array, thus providing a virtual time-reversal mirror. This impulse response is then time-reversed and transmitted experimentally by a therapeutic array positioned exactly in the same referential frame as the one used during CT scan acquisitions. In vitro experiments are conducted on monkey and human skull specimens using an array of 300 transmit elements working at a central frequency of 1 MHz. These experiments show a precise refocusing of the ultrasonic beam at the targeted location with a positioning error lower than 0.7 mm. The complete validation of this transcranial adaptive focusing procedure paves the way to in vivo animal and human transcranial HIFU investigations.

Reverse bias protected solar array with integrated bypass battery

NASA Technical Reports Server (NTRS)

Landis, Geoffrey A (Inventor)

2012-01-01

A method for protecting the photovoltaic cells in a photovoltaic (PV) array from reverse bias damage by utilizing a rechargeable battery for bypassing current from a shaded photovoltaic cell or group of cells, avoiding the need for a bypass diode. Further, the method mitigates the voltage degradation of a PV array caused by shaded cells.

High intra-tumoral stromal content defines Reactive breast cancer as a low-risk breast cancer subtype

PubMed Central

Dennison, Jennifer B.; Shahmoradgoli, Maria; Liu, Wenbin; Ju, Zhenlin; Meric-Bernstam, Funda; Perou, Charles M.; Sahin, Aysegul A.; Welm, Alana; Oesterreich, Steffi; Sikora, Matthew J.; Brown, Robert E.; Mills, Gordon B.

2016-01-01

Purpose The current study evaluated associative effects of breast cancer cells with the tumor microenvironment and its influence on tumor behavior. Experimental design Formalin-fixed paraffin embedded tissue and matched protein lysates were evaluated from two independent breast cancer patient data sets (TCGA and MD Anderson). Reverse-phase protein arrays (RPPA) were utilized to create a proteomics signature to define breast tumor subtypes. Expression patterns of cell lines and normal breast tissues were utilized to determine markers that were differentially expressed in stroma and cancer cells. Protein localization and stromal contents were evaluated for matched cases by imaging. Results A subtype of breast cancers designated “Reactive,” previously identified by RPPA that was not predicted by mRNA profiling, was extensively characterized. These tumors were primarily estrogen receptor (ER)-positive/human epidermal growth factor receptor (HER)2-negative, low-risk cancers as determined by enrichment of low-grade nuclei, lobular or tubular histopathology, and the luminal A subtype by PAM50. Reactive breast cancers contained high numbers of stromal cells and the highest extracellular matrix content typically without infiltration of immune cells. For ER-positive/HER2-negative cancers, the Reactive classification predicted favorable clinical outcomes in the TCGA cohort (HR = 0.36, P < 0.05). Conclusions A protein stromal signature in breast cancers is associated with a highly differentiated phenotype. The stromal compartment content and proteins are an extended phenotype not predicted by mRNA expression that could be utilized to sub-classify ER-positive/HER2-negative breast cancers. PMID:27172895

Proteomic analysis of early phase of conidia germination in Aspergillus nidulans.

PubMed

Oh, Young Taek; Ahn, Chun-Seob; Kim, Jeong Geun; Ro, Hyeon-Su; Lee, Chang-Won; Kim, Jae Won

2010-03-01

In order to investigate proteins involved in early phase of conidia germination, proteomic analysis was performed using two-dimensional gel electrophoresis (2D-GE) in conjunction with MALDI-TOF mass spectrometry (MS). The expression levels of 241 proteins varied quantitatively with statistical significance (P<0.05) at the early phase of the germination stage. Out of these 57 were identified by MALDI-TOF MS. Through classification of physiological functions from Conserved Domain Database analysis, among the identified proteins, 21, 13, and 6 proteins were associated with energy metabolism, protein synthesis, and protein folding process, respectively. Interestingly, eight proteins, which are involved in detoxification of reactive oxygen species (ROS) including catalase A, thioredoxin reductase, and mitochondrial peroxiredoxin, were also identified. The expression levels of the genes were further confirmed using Northern blot and reverse transcriptase (RT)-PCR analyses. This study represents the first proteomic analysis of early phase of conidia germination and will contribute to a better understanding of the molecular events involved in conidia germination process. Copyright (c) 2009 Elsevier Inc. All rights reserved.

Calcium-binding protein from mouse Ehrlich ascites-tumour cells is homologous to human calcyclin.

PubMed Central

Kuźnicki, J; Filipek, A; Hunziker, P E; Huber, S; Heizmann, C W

1989-01-01

A Ca2+-binding protein was purified from mouse Ehrlich ascites-tumour cells. The protein forms monomers and disulphide-linked dimers, which can be separated by reverse-phase h.p.l.c. A partial amino acid sequence analysis demonstrated that the protein has an EF-hand structure. A striking homology was found to rat and human calcyclin (a member of the S-100 protein family), which is possibly involved in cell-cycle regulation. Images Fig. 1. Fig. 2. PMID:2597136

Optimization of multiple turbine arrays in a channel with tidally reversing flow by numerical modelling with adaptive mesh.

PubMed

Divett, T; Vennell, R; Stevens, C

2013-02-28

At tidal energy sites, large arrays of hundreds of turbines will be required to generate economically significant amounts of energy. Owing to wake effects within the array, the placement of turbines within will be vital to capturing the maximum energy from the resource. This study presents preliminary results using Gerris, an adaptive mesh flow solver, to investigate the flow through four different arrays of 15 turbines each. The goal is to optimize the position of turbines within an array in an idealized channel. The turbines are represented as areas of increased bottom friction in an adaptive mesh model so that the flow and power capture in tidally reversing flow through large arrays can be studied. The effect of oscillating tides is studied, with interesting dynamics generated as the tidal current reverses direction, forcing turbulent flow through the array. The energy removed from the flow by each of the four arrays is compared over a tidal cycle. A staggered array is found to extract 54 per cent more energy than a non-staggered array. Furthermore, an array positioned to one side of the channel is found to remove a similar amount of energy compared with an array in the centre of the channel.

Enhancing Sensitivity of Liquid Chromatography-Mass Spectrometry of Peptides and Proteins Using Supercharging Agents.

PubMed

Nshanian, Michael; Lakshmanan, Rajeswari; Chen, Hao; Ogorzalek Loo, Rachel R; Loo, Joseph A

2018-04-01

Trifluoroacetic acid (TFA) is often used as a mobile phase modifier to enhance reversed phase chromatographic performance. TFA adjusts solution pH and is an ion-pairing agent, but it is not typically suitable for electrospray ionization-mass spectrometry (ESI-MS) and liquid chromatography/MS (LC/MS) because of its significant signal suppression. Supercharging agents elevate peptide and protein charge states in ESI, increasing tandem MS (MS/MS) efficiency. Here, LC/MS protein supercharging was effected by adding agents to LC mobile phase solvents. Significantly, the ionization suppression generally observed with TFA was, for the most part, rescued by supercharging agents, with improved separation efficiency (higher number of theoretical plates) and lowered detection limits.

Protobiological informatoin, bidirectional recognition and reverse translation

NASA Technical Reports Server (NTRS)

Fox, S. W.; Nakashima, T.; Przybylski, A.; Vaughan, G.

1986-01-01

Emergence of protobiological information has been suggested by experiments in which heated mixtures of alpha-amino acids order themselves into a self limited array of thermal proteins. The polymers display selective catalytic, hormonal, and other activities. Interactions of varied cationic thermal proteins with polynucleotides indicate selective recognition in both directions. Reverse translation is partly a missing link in the molecular evolution flowsheet. The self ordering of amino acids serves conceptually as a deterministic evolutionary precursor of the modern coding mechanism. The possibility for the evolution of information at an early nontemplated protein stage is supported by findings of electrical signals from proteinoid microspheres prepared with no DNA/RNA in their history. The deposition of thermal copolyamino acids on lipid membranes in the Mueller-Rudin apparatus has here been found to produce electrical behavior like that evoked by bacterial EIM polypeptide. A new procedure is to make a film of membrane on the electrode; the results provide maximal repeatability. The principle of nonrandom biomacromolecular specificity identified by these studies in molecular evolution have been extrapolated to principles of evolution of advanced organisms.

[Simultaneous determination of canthaxanthin and astaxanthin in feedstuffs using solid phase extraction-reversed-phase high performance liquid chromatography].

PubMed

Zhang, Hua; Yang, Xin; Ma, Ying; Dong, Aijun; Zhang, Yingchun

2008-05-01

A method was developed for the simultaneous determination of canthaxanthin and astaxanthin in feedstuffs using reversed-phase high performance liquid chromatography (RP-HPLC). The sample was extracted by acetonitrile, and cleaned up by an LC-NH2 column. An Agilent ZORBAX Eclipse XDB-C18 analytical column (150 mm x 4.6 mm, 5 microm) was used and kept at 25 degrees C. Acetonitrile-methanol (95 : 5, v/v) was used as the mobile phase at a flow rate of 1.0 mL/min. The detection was performed by a diode array detector at 474 nm. The quantitive analysis of external standard calibration curves was used. The linear ranges of the method for canthaxanthin and astaxanthin were 1.0 - 30.0 mg/L (r = 0.999 0) and 1.0 - 20.0 mg/L (r = 0.999 1), respectively. The average recoveries were 90% - 101% with the relative standard deviations of 0.62% - 3.68%. The detection limits were 0.84 and 0.60 mg/L for canthaxanthin and astaxanthin, respectively. The method is simple, precise, sensitive and reproductive. It can be used to determine the contents of canthaxanthin and astaxanthin in feedstuffs.

Light-Inducible Gene Regulation with Engineered Zinc Finger Proteins

PubMed Central

Polstein, Lauren R.; Gersbach, Charles A.

2014-01-01

The coupling of light-inducible protein-protein interactions with gene regulation systems has enabled the control of gene expression with light. In particular, heterodimer protein pairs from plants can be used to engineer a gene regulation system in mammalian cells that is reversible, repeatable, tunable, controllable in a spatiotemporal manner, and targetable to any DNA sequence. This system, Light-Inducible Transcription using Engineered Zinc finger proteins (LITEZ), is based on the blue light-induced interaction of GIGANTEA and the LOV domain of FKF1 that drives the localization of a transcriptional activator to the DNA-binding site of a highly customizable engineered zinc finger protein. This chapter provides methods for modifying LITEZ to target new DNA sequences, engineering a programmable LED array to illuminate cell cultures, and using the modified LITEZ system to achieve spatiotemporal control of transgene expression in mammalian cells. PMID:24718797

A reversed-phase high-performance liquid chromatography method for bovine serum albumin assay in pharmaceutical dosage forms and protein/antigen delivery systems.

PubMed

Hamidi, Mehrdad; Zarei, Najmeh

2009-05-01

Bovine serum albumin (BSA) is among the most widely used proteins in protein formulations as well as in the development of novel delivery systems as a typical model for therapeutic/diagnostic proteins and the new versions of vaccines. The development of reliable and easily available assay methods for quantitation of this protein would therefore play a crucial role in these types of studies. A simple gradient reversed-phase high-performance liquid chromatography with ultra-violet detection (HPLC-UV) method has been developed for quantitation of BSA in dosage forms and protein delivery systems. The method produced linear responses throughout the wide BSA concentration range of 1 to 100 micro g/mL. The average within-run and between-run variations of the method within the linear concentration range of BSA were 2.46% and 2.20%, respectively, with accuracies of 104.49% and 104.58% for within-run and between-run samples, respectively. The limits of detection (LOD) and quantitation (LOQ) of the method were 0.5 and 1 microg/mL, respectively. The method showed acceptable system suitability indices, which enabled us to use it successfully during our particulate vaccine delivery research project. Copyright 2009 John Wiley & Sons, Ltd.

Resolution and identification of the protein components of the photosystem II antenna system of higher plants by reversed-phase liquid chromatography with electrospray-mass spectrometric detection.

PubMed

Corradini, D; Huber, C G; Timperio, A M; Zolla, L

2000-07-21

Reversed-phase liquid chromatography (RPLC) was interfaced to mass spectrometry (MS) with an electrospray ion (ESI) source for the separation and accurate molecular mass determination of the individual intrinsic membrane proteins that comprise the photosystem II (PS II) major light-harvesting complex (LHC II) and minor (CP24, CP26 and CP29) antenna system, whose molecular masses range between 22,000 and 29,000. PS II is a supramolecular complex intrinsic of the thylacoid membrane, which plays the important role in photosynthesis of capturing solar energy, and transferring it to photochemical reaction centers where energy conversion occurs. The protein components of the PS II major and minor antenna systems were extracted from spinach thylacoid membranes and separated using a butyl-silica column eluted by an acetonitrile gradient in 0.05% (v/v) aqueous trifluoroacetic acid. On-line electrospray MS allowed accurate molecular mass determination and identification of the protein components of PS II major and minor antenna system. The proposed RPLC-ESI-MS method holds several advantages over sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the conventional technique for studying membrane proteins, including a better protein separation, mass accuracy, speed and efficiency.

Two-dimensional chromatographic analysis using three second-dimension columns for continuous comprehensive analysis of intact proteins.

PubMed

Zhu, Zaifang; Chen, Huang; Ren, Jiangtao; Lu, Juan J; Gu, Congying; Lynch, Kyle B; Wu, Si; Wang, Zhe; Cao, Chengxi; Liu, Shaorong

2018-03-01

We develop a new two-dimensional (2D) high performance liquid chromatography (HPLC) approach for intact protein analysis. Development of 2D HPLC has a bottleneck problem - limited second-dimension (second-D) separation speed. We solve this problem by incorporating multiple second-D columns to allow several second-D separations to be proceeded in parallel. To demonstrate the feasibility of using this approach for comprehensive protein analysis, we select ion-exchange chromatography as the first-dimension and reverse-phase chromatography as the second-D. We incorporate three second-D columns in an innovative way so that three reverse-phase separations can be performed simultaneously. We test this system for separating both standard proteins and E. coli lysates and achieve baseline resolutions for eleven standard proteins and obtain more than 500 peaks for E. coli lysates. This is an indication that the sample complexities are greatly reduced. We see less than 10 bands when each fraction of the second-D effluents are analyzed by sodium dodecyl sulfate - polyacrylamide gel electrophoresis (SDS-PAGE), compared to hundreds of SDS-PAGE bands as the original sample is analyzed. This approach could potentially be an excellent and general tool for protein analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Study of reversible magnetization in FeCoNi alloy nanowires with different diameters by first order reversal curve (FORC) diagrams

NASA Astrophysics Data System (ADS)

Samanifar, S.; Kashi, M. Almasi; Ramazani, A.

2018-05-01

Magnetic nanowires electrodeposited into solid templates are of high interest due to their tunable properties which are required for magnetic recording media and spintronic devices. Here, highly ordered arrays of FeCoNi NWs with varied diameters (between 60 and 150 nm) were fabricated into nanopores of hard-anodized aluminum oxide templates using pulsed ac electrodeposition technique. X-ray diffraction patterns indicated the formation of FeCoNi NWs with fcc FeNi and bcc FeCo alloy phases, being highly textured along the bcc [110] direction. Magnetic properties were studied by hysteresis loop measurements at room temperature and they showed reductions in coercivity and squareness values by increasing diameter. First-order reversal curve measurements revealed that, with increasing diameter from 60 to 150 nm, besides a transition from a single domain (SD) state to a pseudo SD state, an increase in the reversible magnetization component of the NWs from 11% to 24% occurred.

Comparison of different extraction procedures for the comprehensive characterization of bioactive phenolic compounds in Rosmarinus officinalis by reversed-phase high-performance liquid chromatography with diode array detection coupled to electrospray time-of-flight mass spectrometry.

PubMed

Borrás Linares, I; Arráez-Román, D; Herrero, M; Ibáñez, E; Segura-Carretero, A; Fernández-Gutiérrez, A

2011-10-21

In the present work, a comparative study between two environmentally friendly and selective extraction techniques, such as supercritical fluid extraction (SFE) and pressurized liquid extraction (PLE) have been carried out focusing in the bioactive phenolic compounds present in Rosmarinus officinalis. For the analysis of the SFE and PLE extracts, a new methodology for qualitative characterization has been developed, based on the use of reversed-phase high-performance liquid chromatography (RP-HPLC), equipped with two different detection systems coupled in series: diode array detector (DAD) and time of flight mass spectrometry (TOF-MS) detector connected via an electrospray ionization interface (ESI). The use of a small particle size C(18) column (1.8 μm) provided a great resolution and made possible the separation of several isomers. Moreover, UV-visible spectrophotometry is a valuable tool for identifying the class of phenolic compounds, whereas MS data enabled to structurally characterize the compounds present in the extracts. The applied methodology was useful for the determination of many well-known phenolic compounds present in R. officinalis, such as carnosol, carnosic acid, rosmadial, rosmanol, genkwanin, homoplantaginin, scutellarein, cirsimaritin and rosmarinic acid, as well as other phenolic compounds present in other species belonging to Lamiaceae family. Copyright © 2011 Elsevier B.V. All rights reserved.

Analysis of Cysteine Redox Post-Translational Modifications in Cell Biology and Drug Pharmacology.

PubMed

Wani, Revati; Murray, Brion W

2017-01-01

Reversible cysteine oxidation is an emerging class of protein post-translational modification (PTM) that regulates catalytic activity, modulates conformation, impacts protein-protein interactions, and affects subcellular trafficking of numerous proteins. Redox PTMs encompass a broad array of cysteine oxidation reactions with different half-lives, topographies, and reactivities such as S-glutathionylation and sulfoxidation. Recent studies from our group underscore the lesser known effect of redox protein modifications on drug binding. To date, biological studies to understand mechanistic and functional aspects of redox regulation are technically challenging. A prominent issue is the lack of tools for labeling proteins oxidized to select chemotype/oxidant species in cells. Predictive computational tools and curated databases of oxidized proteins are facilitating structural and functional insights into regulation of the network of oxidized proteins or redox proteome. In this chapter, we discuss analytical platforms for studying protein oxidation, suggest computational tools currently available in the field to determine redox sensitive proteins, and begin to illuminate roles of cysteine redox PTMs in drug pharmacology.

Unbiased RNAi screen for hepcidin regulators links hepcidin suppression to proliferative Ras/RAF and nutrient-dependent mTOR signaling

PubMed Central

Mleczko-Sanecka, Katarzyna; Roche, Franziska; Rita da Silva, Ana; Call, Debora; D’Alessio, Flavia; Ragab, Anan; Lapinski, Philip E.; Ummanni, Ramesh; Korf, Ulrike; Oakes, Christopher; Damm, Georg; D’Alessandro, Lorenza A.; Klingmüller, Ursula; King, Philip D.; Boutros, Michael; Hentze, Matthias W.

2014-01-01

The hepatic hormone hepcidin is a key regulator of systemic iron metabolism. Its expression is largely regulated by 2 signaling pathways: the “iron-regulated” bone morphogenetic protein (BMP) and the inflammatory JAK-STAT pathways. To obtain broader insights into cellular processes that modulate hepcidin transcription and to provide a resource to identify novel genetic modifiers of systemic iron homeostasis, we designed an RNA interference (RNAi) screen that monitors hepcidin promoter activity after the knockdown of 19 599 genes in hepatocarcinoma cells. Interestingly, many of the putative hepcidin activators play roles in signal transduction, inflammation, or transcription, and affect hepcidin transcription through BMP-responsive elements. Furthermore, our work sheds light on new components of the transcriptional machinery that maintain steady-state levels of hepcidin expression and its responses to the BMP- and interleukin-6–triggered signals. Notably, we discover hepcidin suppression mediated via components of Ras/RAF MAPK and mTOR signaling, linking hepcidin transcriptional control to the pathways that respond to mitogen stimulation and nutrient status. Thus using a combination of RNAi screening, reverse phase protein arrays, and small molecules testing, we identify links between the control of systemic iron homeostasis and critical liver processes such as regeneration, response to injury, carcinogenesis, and nutrient metabolism. PMID:24385536

Electrochemical ion transfer across liquid/liquid interfaces confined within solid-state micropore arrays--simulations and experiments.

PubMed

Strutwolf, Jörg; Scanlon, Micheál D; Arrigan, Damien W M

2009-01-01

Miniaturised liquid/liquid interfaces provide benefits for bioanalytical detection with electrochemical methods. In this work, microporous silicon membranes which can be used for interface miniaturisation were characterized by simulations and experiments. The microporous membranes possessed hexagonal arrays of pores with radii between 10 and 25 microm, a pore depth of 100 microm and pore centre-to-centre separations between 99 and 986 microm. Cyclic voltammetry was used to monitor ion transfer across arrays of micro-interfaces between two immiscible electrolyte solutions (microITIES) formed at these membranes, with the organic phase present as an organogel. The results were compared to computational simulations taking into account mass transport by diffusion and encompassing diffusion to recessed interfaces and overlapped diffusion zones. The simulation and experimental data were both consistent with the situation where the location of the liquid/liquid (l/l) interface was on the aqueous side of the silicon membrane and the pores were filled with the organic phase. While the current for the forward potential scan (transfer of the ion from the aqueous phase to the organic phase) was strongly dependent on the location of the l/l interface, the current peak during the reverse scan (transfer of the ion from the organic phase to the aqueous phase) was influenced by the ratio of the transferring ion's diffusion coefficients in both phases. The diffusion coefficient of the transferring ion in the gelified organic phase was ca. nine times smaller than in the aqueous phase. Asymmetric cyclic voltammogram shapes were caused by the combined effect of non-symmetrical diffusion (spherical and linear) and by the inequality of the diffusion coefficient in both phases. Overlapping diffusion zones were responsible for the observation of current peaks instead of steady-state currents during the forward scan. The characterisation of the diffusion behaviour is an important requirement for application of these silicon membranes in electroanalytical chemistry.

Quantification of astaxanthin in shrimp waste hydrolysate by HPLC.

PubMed

López-Cervantes, J; Sánchez-Machado, D I; Gutiérrez-Coronado, M A; Ríos-Vázquez, N J

2006-10-01

In the present study, a simple and rapid reversed-phase HPLC method for the determination of astaxanthin in shrimp waste hydrolysate has been developed and validated. The analytical procedure involves the direct extraction of astaxanthin from the lipid fraction with methanol. The analytical column, SS Exil ODS, was operated at 25C. The mobile phase consisted of a mixture of water:methanol:dichloromethane:acetonitrile (4.5:28:22:45.5 v/v/v/v) at a flow rate of 1.0 mL/min. Detection and identification were performed using a photodiode array detector (lambda(detection) = 476 nm). The proposed HPLC method showed adequate linearity, repeatability and accuracy.

Self-assembly of Nano-rods in Photosensitive Phase Separation

NASA Astrophysics Data System (ADS)

Liu, Ya; Kuksenok, Olga; Maresov, Egor; Balazs, Anna

2012-02-01

Computer simulations reveal how photo-induced chemical reactions in polymeric mixtures can be exploited to create long-range order in materials whose features range from the sub-micron to the nanoscale. The process is initiated by shining a spatially uniform light on a photosensitive AB binary blend, which thereby undergoes both a reversible chemical reaction and phase separation. When a well-collimated, higher intensity light is rastered over the sample, the system forms defect-free, spatially periodic structures. We now build on this approach by introducing nanorods that have a preferential affinity for one the phases in a binary mixture. By rastering over the sample with the higher intensity light, we can create ordered arrays of rods within periodically ordered materials in essentially one processing step.

Assembly of Oriented Virus Arrays by Chemo-Selective Ligation Methods and Nanolithography Techniques

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

Camarero, J A; Cheung, C L; Lin, T

2002-12-02

The present work describes our ongoing efforts towards the creation of nano-scaled ordered arrays of protein/virus covalently attached to site-specific chemical linkers patterned by different nanolithograpy techniques. We will present a new and efficient solid-phase approach for the synthesis of chemically modified long alkyl-thiols. These compounds can be used to introduce chemoselective reacting groups onto gold and silicon-based surfaces. Furthermore, these modified thiols have been used to create nanometric patterns by using different nanolithography techniques. We will show that these patterns can react chemoselectively with proteins and/or virus which have been chemically or recombinantly modified to contain complementary chemical groupsmore » at specific positions thus resulting in the oriented attachment of the protein or virus to the surface.« less

Affinity-reversed-phase liquid chromatography assay to quantitate recombinant antibodies and antibody fragments in fermentation broth.

PubMed

Battersby, J E; Snedecor, B; Chen, C; Champion, K M; Riddle, L; Vanderlaan, M

2001-08-24

An automated dual-column liquid chromatography assay comprised of affinity and reversed-phase separations that quantifies the majority of antibody-related protein species found in crude cell extracts of recombinant origin is described. Although potentially applicable to any antibody preparation, we here use samples of anti-CD18 (Fab'2LZ) and a full-length antibody, anti-tissue factor (anti-TF), from various stages throughout a biopharmaceutical production process to describe the assay details. The targeted proteins were captured on an affinity column containing an anti-light-chain (kappa) Fab antibody (AME5) immobilized on controlled pore glass. The affinity column was placed in-line with a reversed-phase column and the captured components were transferred by elution with dilute acid and subsequently resolved by eluting the reversed-phase column with a shallow acetonitrile gradient. Characterization of the resolved components showed that most antibody fragment preparations contained a light-chain fragment, free light chain, light-chain dimer and multiple forms of Fab'. Analysis of full-length antibody preparations also resolved these fragments as well as a completely assembled form. Co-eluting with the full-length antibody were high-molecular-mass variants that were missing one or both light chains. Resolved components were quantified by comparison with peak areas of similarly treated standards. By comparing the two-dimensional polyacrylamide gel electrophoresis patterns of an Escherichia coli blank run, a production run and the material affinity captured (AME5) from a production run, it was determined that the AME5 antibody captured isoforms of light chain, light chain covalently attached to heavy chain, and truncated light chain isoforms. These forms comprise the bulk of the soluble product-related fragments found in E. coli cell extracts of recombinantly produced antibody fragments.

Three dimensional liquid chromatography coupling ion exchange chromatography/hydrophobic interaction chromatography/reverse phase chromatography for effective protein separation in top-down proteomics.

PubMed

Valeja, Santosh G; Xiu, Lichen; Gregorich, Zachery R; Guner, Huseyin; Jin, Song; Ge, Ying

2015-01-01

To address the complexity of the proteome in mass spectrometry (MS)-based top-down proteomics, multidimensional liquid chromatography (MDLC) strategies that can effectively separate proteins with high resolution and automation are highly desirable. Although various MDLC methods that can effectively separate peptides from protein digests exist, very few MDLC strategies, primarily consisting of 2DLC, are available for intact protein separation, which is insufficient to address the complexity of the proteome. We recently demonstrated that hydrophobic interaction chromatography (HIC) utilizing a MS-compatible salt can provide high resolution separation of intact proteins for top-down proteomics. Herein, we have developed a novel 3DLC strategy by coupling HIC with ion exchange chromatography (IEC) and reverse phase chromatography (RPC) for intact protein separation. We demonstrated that a 3D (IEC-HIC-RPC) approach greatly outperformed the conventional 2D IEC-RPC approach. For the same IEC fraction (out of 35 fractions) from a crude HEK 293 cell lysate, a total of 640 proteins were identified in the 3D approach (corresponding to 201 nonredundant proteins) as compared to 47 in the 2D approach, whereas simply prolonging the gradients in RPC in the 2D approach only led to minimal improvement in protein separation and identifications. Therefore, this novel 3DLC method has great potential for effective separation of intact proteins to achieve deep proteome coverage in top-down proteomics.

Quantitative analysis of ginger components in commercial products using liquid chromatography with electrochemical array detection

PubMed Central

Shao, Xi; Lv, Lishuang; Parks, Tiffany; Wu, Hou; Ho, Chi-Tang; Sang, Shengmin

2010-01-01

For the first time, a sensitive reversed-phase HPLC electrochemical array method has been developed for the quantitative analysis of eight major ginger components ([6]-, [8]-, and [10]-gingerol, [6]-, [8]-, and [10]-shogaol, [6]-paradol, and [1]-dehydrogingerdione) in eleven ginger-containing commercial products. This method was valid with unrivaled sensitivity as low as 7.3 – 20.2 pg of limit of detection and a range of 14.5 to 40.4 pg of limit of quantification. Using this method, we quantified the levels of eight ginger components in eleven different commercial products. Our results found that both levels and ratios among the eight compounds vary greatly in commercial products. PMID:21090746

An analysis of dissolved organic matter from freshwater Karelian Lakes using reversed-phase high-performance liquid chromatography with online absorbance and fluorescence analysis

NASA Astrophysics Data System (ADS)

Khundzhua, D. A.; Patsaeva, S. V.; Trubetskoj, O. A.; Trubetskaya, O. E.

2017-01-01

The spectral and optical properties of the fractionated components of dissolved organic matter (DOM) of three freshwater lakes in Karelia were studied using reversed-phase high-performance liquid chromatography (RP-HPLC) with online detection of fluorescence and absorption spectra. It is shown that the DOM fractions are qualitatively similar, but differ quantitatively in the ratio of components and consist of at least three types of fluorophores: (1) hydrophilic "humic-like" fluorophore(s) with the emission maximum in the region of 420 nm and an absorption band at 260-270 nm; (2) hydrophobic "humic-like" fluorophore(s) with the emission maximum at approximately 450 nm that has no characteristic absorption maxima in the region from 220 to 400 nm; and (3) a "protein-like" fluorophore with the emission maximum in the region of 340-350 nm, which is typical of proteins and peptides containing tryptophan.

Magnetization reversal in magnetic dot arrays: Nearest-neighbor interactions and global configurational anisotropy

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

Van de Wiele, Ben; Fin, Samuele; Pancaldi, Matteo

2016-05-28

Various proposals for future magnetic memories, data processing devices, and sensors rely on a precise control of the magnetization ground state and magnetization reversal process in periodically patterned media. In finite dot arrays, such control is hampered by the magnetostatic interactions between the nanomagnets, leading to the non-uniform magnetization state distributions throughout the sample while reversing. In this paper, we evidence how during reversal typical geometric arrangements of dots in an identical magnetization state appear that originate in the dominance of either Global Configurational Anisotropy or Nearest-Neighbor Magnetostatic interactions, which depends on the fields at which the magnetization reversal setsmore » in. Based on our findings, we propose design rules to obtain the uniform magnetization state distributions throughout the array, and also suggest future research directions to achieve non-uniform state distributions of interest, e.g., when aiming at guiding spin wave edge-modes through dot arrays. Our insights are based on the Magneto-Optical Kerr Effect and Magnetic Force Microscopy measurements as well as the extensive micromagnetic simulations.« less

Reverse Micelle Mediated synthesis of Calcium Phosphate Nanocarriers for Controlled Release of Bovine Serum Albumin (BSA)

PubMed Central

Dasgupta, Sudip; Bandyopadhyay, Amit; Bose, Susmita

2010-01-01

Calcium phosphate (CaP) nanoparticle with calcium to phosphorus (Ca:P) molar ratio of 1.5:1 were synthesized using reverse micro emulsion. Ca(NO3)2.4H2O and H3PO4 were used as aqueous phase, cyclohexane as organic phase, and poly(oxyethylene)12 nonylphenol ether (NP-12) as surfactant. Depending on calcination temperature between 600 and 800 °C, CaP nanoparticle showed different phases calcium deficient hydroxyapatite (CDHA) and β-tricalcium phosphate (β-TCP), particle size between 48 and 69 nm, the BET specific average surface area between 73 m2/g and 57 m2/g. Bovine serum albumin (BSA) was used as a model protein to study loading and release behavior. Adsorptive property of BSA was investigated with the change in BET surface area of these nanoparticle and the pH of the suspension. At pH 7.5, maximum amount of BSA was adsorbed onto CaP nanoparticle. The release kinetics of BSA showed a gradual time dependent increase at pH 4.0 and 6.0 buffer solutions. However, the amount of released protein was significantly smaller at pH 7.2. BSA release rate also varied depending on the presence of different phases of CaPs in the system, β-TCP or CDHA. These results suggest that BSA protein release rate can be controlled by changing particle size, surface area and phase composition of CaP nanocarriers. PMID:19435617

Expansions for infinite or finite plane circular time-reversal mirrors and acoustic curtains for wave-field-synthesis.

PubMed

Mellow, Tim; Kärkkäinen, Leo

2014-03-01

An acoustic curtain is an array of microphones used for recording sound which is subsequently reproduced through an array of loudspeakers in which each loudspeaker reproduces the signal from its corresponding microphone. Here the sound originates from a point source on the axis of symmetry of the circular array. The Kirchhoff-Helmholtz integral for a plane circular curtain is solved analytically as fast-converging expansions, assuming an ideal continuous array, to speed up computations and provide insight. By reversing the time sequence of the recording (or reversing the direction of propagation of the incident wave so that the point source becomes an "ideal" point sink), the curtain becomes a time reversal mirror and the analytical solution for this is given simultaneously. In the case of an infinite planar array, it is demonstrated that either a monopole or dipole curtain will reproduce the diverging sound field of the point source on the far side. However, although the real part of the sound field of the infinite time-reversal mirror is reproduced, the imaginary part is an approximation due to the missing singularity. It is shown that the approximation may be improved by using the appropriate combination of monopole and dipole sources in the mirror.

The Effect of Solution Thermal History on Chicken Egg White Lysozyme Nucleation

NASA Technical Reports Server (NTRS)

Burke, Michael W.; Judge, Russell A.; Pusey, Marc L.

2001-01-01

Proteins are highly flexible molecules and often exhibit defined conformational changes in response to changes in the ambient temperature. Chicken egg white lysozyme has been previously shown to undergo an apparent structural change when warmed above the tetragonal/orthorhombic phase transition temperature. This is reflected by a change in the habit of the tetragonal and orthorhombic crystals so formed. In this study, we show that possible conformational changes induced by heating are stable and apparently non-reversible by simple cooling. Exposure of protein solutions to temperatures above the phase change transition temperature, before combining with precipitant solution to begin crystallization, reduces final crystal numbers. Protein that is briefly warmed to 37 C, then cooled shows no sign of reversal to the unheated nucleation behavior even after storage for four weeks at 4 C. The change in nucleation behavior of tetragonal lysozyme crystals, attributed to a structural shift, occurs faster the greater the exposure to temperature above the equi-solubility point for the two phases. Heating for 2 hours at 48 C reduces crystal numbers by 20 fold in comparison to the same solution heated for the same time at 30 C. Thermal treatment of solutions is therefore a possible tool to reduce crystal numbers and increase crystal size. The effects of a protein's previous thermal history are now shown to be a potentially critical factor in subsequent macromolecule crystal nucleation and growth studies.

The Effect of Solution Thermal History on Chicken Egg White Lysozyme Nucleation

NASA Technical Reports Server (NTRS)

Burke, Michael W.; Judge, Russell A.; Pusey, Marc L.; Rose, M. Franklin (Technical Monitor)

2000-01-01

Proteins are highly flexible molecules and often exhibit defined conformational changes in response to changes in the ambient temperature. Chicken egg white lysozyme has been previously shown to undergo an apparent structural change when warmed above the tetragonal/orthorhombic phase transition temperature. This is reflected by a change in the habit of the tetragonal and orthorhombic crystals so formed. In this study we show that possible conformational changes induced by heating are stable and apparently non- reversible by simple cooling. Exposure of protein solutions to temperatures above the phase change transition temperature, before combining with precipitant solution to begin crystallization, reduces final crystal numbers. Protein that is briefly warmed to 37 C, then cooled shows no sign of reversal to the unheated nucleation behavior even after storage for 4 weeks at 4 C. The change in nucleation behavior of tetragonal lysozyme crystals, attributed to a structural shift, occurs faster the greater the exposure to temperature above the equi-solubility point for the two phases. Heating for 2 h at 48 C reduces crystal numbers by 20 fold in comparison to the same solution heated for the same time at 30 C. Thermal treatment of solutions is therefore a possible tool to reduce crystal numbers and increase crystal size. The effects of a protein's previous thermal history are now shown to be a potentially critical factor in subsequent macromolecule crystal nucleation and growth studies.

Determination of phenolic xenoestrogens in water by liquid chromatography with coulometric-array detection.

PubMed

Inoue, Koichi; Yoshie, Yuriko; Kondo, Sachiko; Yoshimura, Yoshihiro; Nakazawa, Hiroyuki

2002-02-08

A sensitive method for the simultaneous determination of phenolic xenoestrogens such as bisphenol A, 2,4-dichlorophenol, 4-tert,-butylphenol, 4-n2-pentylphenol, 4-n-hexylphenol, 4-n-heptylphenol, 4-octylphenol, 4-nonylphenol was developed using reversed-phase LC and coulometric-array detection. Stepwise gradient elution with phosphoric acid in water-acetonitrile was used. The calibration curves were linear in the range of 5.0 (or 10.0)-1000 ng ml(-1) with correlation coefficients of 0.9978-0.9999, the limits of detection were 0.01-0.02 ng ml(-1). Sample clean-up was performed by solid-phase extraction (SPE) using 3M Empore extraction disks. Three commercial sorbents, C18, SDB-XD (styrene-divinylbenzene polymer) and SDB-RPS (sulfonated styrene-divinylbenzene polymer) were compared. The highest recoveries were obtained with SDB-RPS. They were above 70% with a relative standard deviation of less than 15%. The proposed method was applied to the determination of phenolic xenoestrogens in various water samples.

Offline solid-phase extraction for preconcentration of pharmaceuticals and personal care products in environmental water and their simultaneous determination using the reversed phase high-performance liquid chromatography method.

PubMed

G Archana; Dhodapkar, Rita; Kumar, Anupama

2016-09-01

The present study reports a precise and simple offline solid-phase extraction (SPE) coupled with reversed-phase high-performance liquid chromatography (RP-HPLC) method for the simultaneous determination of five representative and commonly present pharmaceuticals and personal care products (PPCPs), a new class of emerging pollutants in the aquatic environment. The target list of analytes including ciprofloxacin, acetaminophen, caffeine benzophenone and irgasan were separated by a simple HPLC method. The column used was a reversed-phase C18 column, and the mobile phase was 1 % acetic acid and methanol (20:80 v/v) under isocratic conditions, at a flow rate of 1 mL min(-1). The analytes were separated and detected within 15 min using the photodiode array detector (PDA). The linearity of the calibration curves were obtained with correlation coefficients 0.98-0.99.The limit of detection (LOD), limit of quantification (LOQ), precision, accuracy and ruggedness demonstrated the reproducibility, specificity and sensitivity of the developed method. Prior to the analysis, the SPE was performed using a C18 cartridge to preconcentrate the targeted analytes from the environmental water samples. The developed method was applied to evaluate and fingerprint PPCPs in sewage collected from a residential engineering college campus, polluted water bodies such as Nag river and Pili river and the influent and effluent samples from a sewage treatment plant (STP) situated at Nagpur city, in the peak summer season. This method is useful for estimation of pollutants present in microquantities in the surface water bodies and treated sewage as compared to nanolevel pollutants detected by mass spectrometry (MS) detectors.

Separation and characterization of chemical constituents in Ginkgo biloba extract by off-line hydrophilic interaction×reversed-phase two-dimensional liquid chromatography coupled with quadrupole-time of flight mass spectrometry.

PubMed

Ji, Shuai; He, Dan-Dan; Wang, Tian-Yun; Han, Jie; Li, Zheng; Du, Yan; Zou, Jia-Hui; Guo, Meng-Zhe; Tang, Dao-Quan

2017-11-30

Ginkgo biloba extract (GBE), derived from the leaves of Ginkgo biloba L., is one of the most widely used traditional Chinese medicines worldwide. Due to high structural diversity and low abundance of chemical constituents in GBE, conventional reversed-phase liquid chromatography has limited power to meet the needs of its quality control. In this study, an off-line hydrophilic interaction×reversed-phase two-dimensional liquid chromatography (HILIC×RP 2D-LC) system coupled with diode array detection (DAD) and quadrupole time-of-flight mass spectrometry (qTOF-MS) was established to comprehensively analyze the chemical constituents of GBE. After optimizing the chromatographic columns and mobile phase of 2D-LC, a Waters XBridge Amide column using acetonitrile/water/formic acid as the mobile phase was selected as the first dimension to fractionate GBE, and the obtained fractions were further separated on an Agilent Zorbax XDB-C18 column with methanol/water/formic acid as the mobile phase. As a result, a total of 125 compounds were detected in GBE. The orthogonality of the 2D-LC system was 69.5%, and the practical peak capacity was 3864 and 2994, respectively, calculated by two different methods. The structures of 104 compounds were tentatively characterized by qTOF-MS analysis, and 21 of them were further confirmed by comparing with reference standards. This established HILIC×RP 2D-LC-qTOF/MS system can greatly improve the separation and characterization of natural products in GBE or other complicated herbal extracts. Copyright © 2017 Elsevier B.V. All rights reserved.

High-speed, large-area, p-i-n InGaAs photodiode linear array at 2-micron wavelength

NASA Astrophysics Data System (ADS)

Joshi, Abhay; Datta, Shubhashish

2012-06-01

We present 16-element and 32-element lattice-mismatched InGaAs photodiode arrays having a cut-off wavelength of ~2.2 um. Each 100 um × 200 um large pixel of the 32-element array has a capacitance of 2.5 pF at 5 V reverse bias, thereby allowing a RC-limited bandwidth of ~1.3 GHz. At room temperature, each pixel demonstrates a dark current of 25 uA at 5 V reverse bias. Corresponding results for the 16-element array having 200 um × 200 um pixels are also reported. Cooling the photodiode array to 150K is expected to reduce its dark current to < 50 nA per pixel at 5 V reverse bias. Additionally, measurement results of 2-micron single photodiodes having 16 GHz bandwidth and corresponding PIN-TIA photoreceiver having 6 GHz bandwidth are also reported.

Miniature acoustic wave lysis system and uses thereof

DOEpatents

Branch, Darren W.; Vreeland, Erika Cooley; Smith, Gennifer Tanabe

2016-12-06

The present invention relates to an acoustic lysis system including a disposable cartridge that can be reversibly coupled to a platform having a small, high-frequency piezoelectric transducer array. In particular, the system releases viable DNA, RNA, and proteins from human or bacterial cells, without chemicals or additional processing, to enable high-speed sample preparation for clinical point-of-care medical diagnostics and use with nano/microfluidic cartridges. Also described herein are methods of making and using the system of the invention.

Multiple, simultaneous, independent gradients for a versatile multidimensional liquid chromatography. Part II: Application 1 - Large increases in isoform resolution of human transferrin by use of dual simultaneous independent gradients of pH & acetonitrile on a mixed bed (anion exchange plus reversed phase) stationary phase.

PubMed

Tsonev, Latchezar I; Hirsh, Allen G

2016-10-14

We have previously described a liquid chromatographic (LC) method for uncoupling controlled, wide range pH gradients and simultaneous controlled gradients of a non-buffering solute on ion exchange resins (Hirsh and Tsonev, 2012) [1]. Here we report the application of this two dimensional LC technique to the problem of resolving Human Transferrin (HT) isoforms. This important iron transporting protein should theoretically occur in several thousand glycoforms, but only about a dozen have been reported. Using dual simultaneous independent gradients (DSIGs) of acetonitrile (ACN) and pH on a mixed bed stationary phase (SP) consisting of a mixture of an anion exchange resin and a reversed phase (RP) resin we partially resolve about 60 isoforms. These are likely to be partially refolded glycoforms generated by interaction of HT with the highly hydrophobic RP SP, as well as distinct folded glycoforms. Thus this study should have interesting implications for both glycoform separation and the study of protein folding. Copyright © 2016 Elsevier B.V. All rights reserved.

Development and Validation of a Simultaneous RP-HPLCUV/DAD Method for Determination of Polyphenols in Gels Containing S. terebinthifolius Raddi (Anacardiaceae)

PubMed Central

Carvalho, Melina G.; Aragão, Cícero F. S; Raffin, Fernanda N.; de L. Moura, Túlio F. A.

2017-01-01

Topical gels containing extracts of Schinus terebinthifolius have been used to treat bacterial vaginosis. It has been reported that this species has antimicrobial, anti-inflammatory and anti-ulcerogenic properties, which can be attributed to the presence of phenolic compounds. In this work, a sensitive and selective reversed-phase HPLC-UV/DAD method for the simultaneous assay of six polyphenols that could be present in S. terebinthifolius was developed. The method was shown to be accurate and precise. Peak purity and similarity index both exceeded 0.99. Calibration curves were linear over the concentration range studied, with correlation coefficients between 0.9931 and 0.9974. This method was used to determine the polyphenol content of a hydroalcoholic extract and pharmacy-compounded vaginal gel. Although the method is useful to assess the 6 phenolic compounds, some compounds could not be detected in the products. SUMMARY A sensitive, selective, accurate and precise reversed-phase HPLC-UV/DAD method for the simultaneous assay of six polyphenols in S. terebinthifolius Raddi Abbreviations used: RP-HPLC-UV/DAD: Reverse Phase High Performance Liquid Chromatograph with Ultraviolet and Diode Array Detector, HPLC: High Performance Liquid Chromatograph, HPLC-UV: High Performance Liquid Chromatograph with Ultraviolet Detector, ANVISA: Brazilian National Health Surveillance Agency, LOD: Limit of detection, LOQ: Limit of quantitation PMID:28539726

The carotenoid pigments of a marine Bacillus firmus strain.

PubMed

Pane, L; Radin, L; Franconi, G; Carli, A

1996-01-01

As carotenoids have important biological functions, it is important to discover new natural sources of these pigments. The bacterial strains isolated from a sea water rock pool were cultivated on marine agar containing yeast extract and identified by conventional methods. The bacterial pigments were extracted with methanol and analyzed by reversed-phase HPLC with diode array detection. The major pigment of a Bacillus firmus strain was identified as astaxanthin; the results obtained suggest potential use of this bacterium in aquaculture and in pharmaceutical field.

High-performance liquid chromatography analysis of plant saponins: An update 2005-2010

PubMed Central

Negi, Jagmohan S.; Singh, Pramod; Pant, Geeta Joshi Nee; Rawat, M. S. M.

2011-01-01

Saponins are widely distributed in plant kingdom. In view of their wide range of biological activities and occurrence as complex mixtures, saponins have been purified and separated by high-performance liquid chromatography using reverse-phase columns at lower wavelength. Mostly, saponins are not detected by ultraviolet detector due to lack of chromophores. Electrospray ionization mass spectrometry, diode array detector , evaporative light scattering detection, and charged aerosols have been used for overcoming the detection problem of saponins. PMID:22303089

Layer-by-layer cell membrane assembly

NASA Astrophysics Data System (ADS)

Matosevic, Sandro; Paegel, Brian M.

2013-11-01

Eukaryotic subcellular membrane systems, such as the nuclear envelope or endoplasmic reticulum, present a rich array of architecturally and compositionally complex supramolecular targets that are as yet inaccessible. Here we describe layer-by-layer phospholipid membrane assembly on microfluidic droplets, a route to structures with defined compositional asymmetry and lamellarity. Starting with phospholipid-stabilized water-in-oil droplets trapped in a static droplet array, lipid monolayer deposition proceeds as oil/water-phase boundaries pass over the droplets. Unilamellar vesicles assembled layer-by-layer support functional insertion both of purified and of in situ expressed membrane proteins. Synthesis and chemical probing of asymmetric unilamellar and double-bilayer vesicles demonstrate the programmability of both membrane lamellarity and lipid-leaflet composition during assembly. The immobilized vesicle arrays are a pragmatic experimental platform for biophysical studies of membranes and their associated proteins, particularly complexes that assemble and function in multilamellar contexts in vivo.

Micro-RNA profile and proteins in peritoneal fluid from women with endometriosis: their relationship with sterility.

PubMed

Marí-Alexandre, Josep; Barceló-Molina, Moisés; Belmonte-López, Elisa; García-Oms, Javier; Estellés, Amparo; Braza-Boïls, Aitana; Gilabert-Estellés, Juan

2018-04-01

To define the microRNA (miRNA) profile and its relationship with cytokines content in peritoneal fluid (PF) from endometriosis patients. Case-control study. University hospital, research institute. One hundred twenty-six women with endometriosis (EPF) and 45 control women (CPF). MiRNA arrays were prepared from six EPF and six CPF. Quantitative reverse transcription-polymerase chain reaction validation of nine selected miRNAs (miR-29c-3p, -106b-3p, -130a-3p, -150-5p, -185-5p, -195-5p, -451a, -486-5p, and -1343-5p) was performed. Vascular endothelial growth factor-A (VEGF-A), thrombospondin-1 (TSP-1), urokinase plasminogen activator (uPA), plasminogen activator inhibitor-1 (PAI-1), matrix metalloproteinase-3 (MMP3), tissue inhibitor of metalloproteinases type 1 (TIMP-1), interleukin (IL)-6, IL-8, IL-17A, macrophage inflammatory protein 1β (MIP1beta), platelet-derived growth factor α-polypeptide A, and regulated on activation, normal T cell expressed and secreted (RANTES) were quantified by ELISA and MILLIPLEX. MiRNA arrays showed 126 miRNAs differentially expressed (fold change ±1.2) (78 down-regulated, 48 up-regulated) in EPF. Validation showed higher levels of miR-106b-3p, -451a, -486-5p, IL-6, IL-8, uPA, and TIMP-1 in EPF. In menstrual phase, EPF presented up-regulation of miR-106b-3p, -130a-3p, -150-5p, -185-5p, -451a, -486-5p, VEGF-A, IL-8, MIF 1β, uPA, and PAI-1 compared with other phases; however, CPF did not. MiRNA-486-5p was up-regulated in sterile EPF compared with sterile controls, and VEGF-A, IL-8, and TIMP-1 were increased in sterile and fertile EPF compared with fertile CPF. MiRNAs seem to be involved in the peritoneal alterations in endometriosis, suggesting new mechanisms by which ectopic lesions could implant in endometriosis patients; and to serve as biomarkers for fertility outcome prediction. Copyright © 2017 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Direct phase projection and transcranial focusing of ultrasound for brain therapy.

PubMed

Pinton, Gianmarco F; Aubry, Jean-Francois; Tanter, Mickaël

2012-06-01

Ultrasound can be used to noninvasively treat the human brain with hyperthermia by focusing through the skull. To obtain an accurate focus, especially at high frequencies (>500 kHz), the phase of the transmitted wave must be modified to correct the aberrations introduced by the patient's individual skull morphology. Currently, three-dimensional finite-difference time-domain simulations are used to model a point source at the target. The outward-propagating wave crosses the measured representation of the human skull and is recorded at the therapy array transducer locations. The signal is then time reversed and experimentally transmitted back to its origin. These simulations are resource intensive and add a significant delay to treatment planning. Ray propagation is computationally efficient because it neglects diffraction and only describes two propagation parameters: the wave's direction and the phase. We propose a minimal method that is based only on the phase. The phase information is projected from the external skull surface to the array locations. This replaces computationally expensive finite-difference computations with an almost instantaneous direct phase projection calculation. For the five human skull samples considered, the phase distribution outside of the skull is shown to vary by less than λ/20 as it propagates over a 5 cm distance and the validity of phase projection is established over these propagation distances. The phase aberration introduced by the skull is characterized and is shown to have a good correspondence with skull morphology. The shape of this aberration is shown to have little variation with propagation distance. The focusing quality with the proposed phase-projection algorithm is shown to be indistinguishable from the gold-standard full finite-difference simulation. In conclusion, a spherical wave that is aberrated by the skull has a phase propagation that can be accurately described as radial, even after it has been distorted. By combining finite-difference simulations with a phase-projection algorithm, the time required for treatment planning is significantly reduced. The correlation length of the phase is used to validate the algorithm and it can also be used to provide guiding parameters for clinical array transducer design in terms of transducer spacing and phase error.

Mitigation of reversible self-association and viscosity in a human IgG1 monoclonal antibody by rational, structure-guided Fv engineering

PubMed Central

Geoghegan, James C.; Fleming, Ryan; Damschroder, Melissa; Bishop, Steven M.; Sathish, Hasige A.; Esfandiary, Reza

2016-01-01

ABSTRACT Undesired solution behaviors such as reversible self-association (RSA), high viscosity, and liquid-liquid phase separation can introduce substantial challenges during development of monoclonal antibody formulations. Although a global mechanistic understanding of RSA (i.e., native and reversible protein-protein interactions) is sufficient to develop robust formulation controls, its mitigation via protein engineering requires knowledge of the sites of protein-protein interactions. In the study reported here, we coupled our previous hydrogen-deuterium exchange mass spectrometry findings with structural modeling and in vitro screening to identify the residues responsible for RSA of a model IgG1 monoclonal antibody (mAb-C), and rationally engineered variants with improved solution properties (i.e., reduced RSA and viscosity). Our data show that mutation of either solvent-exposed aromatic residues within the heavy and light chain variable regions or buried residues within the heavy chain/light chain interface can significantly mitigate RSA and viscosity by reducing the IgG's surface hydrophobicity. The engineering strategy described here highlights the utility of integrating complementary experimental and in silico methods to identify mutations that can improve developability, in particular, high concentration solution properties, of candidate therapeutic antibodies. PMID:27050875

Context Dependence of Protein Misfolding and Structural Strains in Neurodegenerative Diseases

PubMed Central

Mehta, Anil K.; Rosen, Rebecca F.; Childers, W. Seth; Gehman, John D.; Walker, Lary C.; Lynn, David G.

2014-01-01

Vast arrays of structural forms are accessible to simple amyloid peptides and environmental conditions can direct assembly into single phases. These insights are now being applied to the aggregation of the Aβ peptide of Alzheimer’s disease (AD) and the identification of causative phases. We extend use of the imaging agent Pittsburgh compound B (PiB) to discriminate among Aβ phases and begin to define conditions of relevance to the disease state. And we specifically highlight the development of methods for defining the structures of these more complex phases. PMID:23893572

Progeny Clustering: A Method to Identify Biological Phenotypes

PubMed Central

Hu, Chenyue W.; Kornblau, Steven M.; Slater, John H.; Qutub, Amina A.

2015-01-01

Estimating the optimal number of clusters is a major challenge in applying cluster analysis to any type of dataset, especially to biomedical datasets, which are high-dimensional and complex. Here, we introduce an improved method, Progeny Clustering, which is stability-based and exceptionally efficient in computing, to find the ideal number of clusters. The algorithm employs a novel Progeny Sampling method to reconstruct cluster identity, a co-occurrence probability matrix to assess the clustering stability, and a set of reference datasets to overcome inherent biases in the algorithm and data space. Our method was shown successful and robust when applied to two synthetic datasets (datasets of two-dimensions and ten-dimensions containing eight dimensions of pure noise), two standard biological datasets (the Iris dataset and Rat CNS dataset) and two biological datasets (a cell phenotype dataset and an acute myeloid leukemia (AML) reverse phase protein array (RPPA) dataset). Progeny Clustering outperformed some popular clustering evaluation methods in the ten-dimensional synthetic dataset as well as in the cell phenotype dataset, and it was the only method that successfully discovered clinically meaningful patient groupings in the AML RPPA dataset. PMID:26267476

Rac1/Pak1/p38/MMP-2 axis regulates angiogenesis in ovarian cancer

PubMed Central

Gonzalez-Villasana, Vianey; Fuentes-Mattei, Enrique; Ivan, Cristina; Dalton, Heather J.; Rodriguez-Aguayo, Cristian; Fernandez-de Thomas, Ricardo J.; Aslan, Burcu; Monroig, Paloma del C.; Velazquez-Torres, Guermarie; Previs, Rebecca A.; Pradeep, Sunila; Kahraman, Nermin; Wang, Huamin; Kanlikilicer, Pinar; Ozpolat, Bulent; Calin, George; Sood, Anil K.; Lopez-Berestein, Gabriel

2015-01-01

Purpose Zoledronic acid (ZA) is being increasingly recognized for its anti-tumor properties, but the underlying functions are not well understood. In this study, we hypothesized that ZA inhibits ovarian cancer (OC) angiogenesis preventing Rac1 activation. Experimental Design The biological effects of ZA were examined using a series of in vitro (cell invasion, cytokine production, Rac1 activation, reverse-phase protein array and in vivo (orthotopic mouse models) experiments. Results There was significant inhibition of OC (HeyA8-MDR and OVCAR-5) cell invasion as well as reduced production of pro-angiogenic cytokines in response to ZA treatment. Furthermore, ZA inactivated Rac1 and decreased the levels of Pak1/p-38/matrix metalloproteinase-2 in OC cells. In vivo, ZA reduced tumor growth, angiogenesis and cell proliferation and inactivated Rac1 in both HeyA8-MDR and OVCAR-5 models. These in vivo antitumor effects were enhanced in both models when ZA was combined with nab-paclitaxel. Conclusion ZA has robust anti-tumor and anti-angiogenic activity and merits further clinical development as OC treatment. PMID:25595279

Efficient Exploitation of Separation Space in Two-Dimensional Liquid Chromatography System for Comprehensive and Efficient Proteomic Analyses.

PubMed

Lee, Hangyeore; Mun, Dong-Gi; So, Jeong Eun; Bae, Jingi; Kim, Hokeun; Masselon, Christophe; Lee, Sang-Won

2016-12-06

Proteomics aims to achieve complete profiling of the protein content and protein modifications in cells, tissues, and biofluids and to quantitatively determine changes in their abundances. This information serves to elucidate cellular processes and signaling pathways and to identify candidate protein biomarkers and/or therapeutic targets. Analyses must therefore be both comprehensive and efficient. Here, we present a novel online two-dimensional reverse-phase/reverse-phase liquid chromatography separation platform, which is based on a newly developed online noncontiguous fractionating and concatenating device (NCFC fractionator). In bottom-up proteomics analyses of a complex proteome, this system provided significantly improved exploitation of the separation space of the two RPs, considerably increasing the numbers of peptides identified compared to a contiguous 2D-RP/RPLC method. The fully automated online 2D-NCFC-RP/RPLC system bypassed a number of labor-intensive manual processes required with the previously described offline 2D-NCFC RP/RPLC method, and thus, it offers minimal sample loss in a context of highly reproducible 2D-RP/RPLC experiments.

Multilocus analysis of extracellular putative virulence proteins made by group A Streptococcus: population genetics, human serologic response, and gene transcription.

PubMed

Reid, S D; Green, N M; Buss, J K; Lei, B; Musser, J M

2001-06-19

Species of pathogenic microbes are composed of an array of evolutionarily distinct chromosomal genotypes characterized by diversity in gene content and sequence (allelic variation). The occurrence of substantial genetic diversity has hindered progress in developing a comprehensive understanding of the molecular basis of virulence and new therapeutics such as vaccines. To provide new information that bears on these issues, 11 genes encoding extracellular proteins in the human bacterial pathogen group A Streptococcus identified by analysis of four genomes were studied. Eight of the 11 genes encode proteins with a LPXTG(L) motif that covalently links Gram-positive virulence factors to the bacterial cell surface. Sequence analysis of the 11 genes in 37 geographically and phylogenetically diverse group A Streptococcus strains cultured from patients with different infection types found that recent horizontal gene transfer has contributed substantially to chromosomal diversity. Regions of the inferred proteins likely to interact with the host were identified by molecular population genetic analysis, and Western immunoblot analysis with sera from infected patients confirmed that they were antigenic. Real-time reverse transcriptase-PCR (TaqMan) assays found that transcription of six of the 11 genes was substantially up-regulated in the stationary phase. In addition, transcription of many genes was influenced by the covR and mga trans-acting gene regulatory loci. Multilocus investigation of putative virulence genes by the integrated approach described herein provides an important strategy to aid microbial pathogenesis research and rapidly identify new targets for therapeutics research.

Analysis of Sir2E in the cellular slime mold Dictyostelium discoideum: cellular localization, spatial expression and overexpression.

PubMed

Katayama, Takahiro; Yasukawa, Hiro

2008-10-01

It has been reported that Dictyostelium discoideum encodes four silent information regulator 2 (Sir2) proteins (Sir2A-D) showing sequence similarity to human homologues of Sir2 (SIRT1-3). Further screening in a database revealed that D. discoideum encodes an additional Sir2 homologue (Sir2E). The amino acid sequence of Sir2E is not similar to those of SIRTs but is similar to those of proteins encoded by Giardia lamblia, Cryptosporidium hominis and Cryptosporidium parvum. Fluorescence of Sir2E-green fluorescent protein fusion protein was detected in the D. discoideum nucleus, indicating that Sir2E is a nuclear localizing protein. Reverse transcription-polymerase chain reaction and whole-mount in situ hybridization analyses showed that D. discoideum expressed sir2E in amoebae in the growth phase and in prestalk cells in the developmental phase. D. discoideum overexpressing sir2E grew faster than the wild type. These results indicate that Sir2E plays important roles both in the growth phase and developmental phase of D. discoideum.

High-throughput profiling of signaling networks identifies mechanism-based combination therapy to eliminate microenvironmental resistance in acute myeloid leukemia.

PubMed

Zeng, Zhihong; Liu, Wenbin; Tsao, Twee; Qiu, YiHua; Zhao, Yang; Samudio, Ismael; Sarbassov, Dos D; Kornblau, Steven M; Baggerly, Keith A; Kantarjian, Hagop M; Konopleva, Marina; Andreeff, Michael

2017-09-01

The bone marrow microenvironment is known to provide a survival advantage to residual acute myeloid leukemia cells, possibly contributing to disease recurrence. The mechanisms by which stroma in the microenvironment regulates leukemia survival remain largely unknown. Using reverse-phase protein array technology, we profiled 53 key protein molecules in 11 signaling pathways in 20 primary acute myeloid leukemia samples and two cell lines, aiming to understand stroma-mediated signaling modulation in response to the targeted agents temsirolimus (MTOR), ABT737 (BCL2/BCL-XL), and Nutlin-3a (MDM2), and to identify the effective combination therapy targeting acute myeloid leukemia in the context of the leukemia microenvironment. Stroma reprogrammed signaling networks and modified the sensitivity of acute myeloid leukemia samples to all three targeted inhibitors. Stroma activated AKT at Ser473 in the majority of samples treated with single-agent ABT737 or Nutlin-3a. This survival mechanism was partially abrogated by concomitant treatment with temsirolimus plus ABT737 or Nutlin-3a. Mapping the signaling networks revealed that combinations of two inhibitors increased the number of affected proteins in the targeted pathways and in multiple parallel signaling, translating into facilitated cell death. These results demonstrated that a mechanism-based selection of combined inhibitors can be used to guide clinical drug selection and tailor treatment regimens to eliminate microenvironment-mediated resistance in acute myeloid leukemia. Copyright© 2017 Ferrata Storti Foundation.

Phosphopeptide Enrichment by Covalent Chromatography after Derivatization of Protein Digests Immobilized on Reversed-Phase Supports

PubMed Central

Nika, Heinz; Nieves, Edward; Hawke, David H.; Angeletti, Ruth Hogue

2013-01-01

A rugged sample-preparation method for comprehensive affinity enrichment of phosphopeptides from protein digests has been developed. The method uses a series of chemical reactions to incorporate efficiently and specifically a thiol-functionalized affinity tag into the analyte by barium hydroxide catalyzed β-elimination with Michael addition using 2-aminoethanethiol as nucleophile and subsequent thiolation of the resulting amino group with sulfosuccinimidyl-2-(biotinamido) ethyl-1,3-dithiopropionate. Gentle oxidation of cysteine residues, followed by acetylation of α- and ε-amino groups before these reactions, ensured selectivity of reversible capture of the modified phosphopeptides by covalent chromatography on activated thiol sepharose. The use of C18 reversed-phase supports as a miniaturized reaction bed facilitated optimization of the individual modification steps for throughput and completeness of derivatization. Reagents were exchanged directly on the supports, eliminating sample transfer between the reaction steps and thus, allowing the immobilized analyte to be carried through the multistep reaction scheme with minimal sample loss. The use of this sample-preparation method for phosphopeptide enrichment was demonstrated with low-level amounts of in-gel-digested protein. As applied to tryptic digests of α-S1- and β-casein, the method enabled the enrichment and detection of the phosphorylated peptides contained in the mixture, including the tetraphosphorylated species of β-casein, which has escaped chemical procedures reported previously. The isolates proved highly suitable for mapping the sites of phosphorylation by collisionally induced dissociation. β-Elimination, with consecutive Michael addition, expanded the use of the solid-phase-based enrichment strategy to phosphothreonyl peptides and to phosphoseryl/phosphothreonyl peptides derived from proline-directed kinase substrates and to their O-sulfono- and O-linked β-N-acetylglucosamine (O-GlcNAc)-modified counterparts. Solid-phase enzymatic dephosphorylation proved to be a viable tool to condition O-GlcNAcylated peptide in mixtures with phosphopeptides for selective affinity purification. Acetylation, as an integral step of the sample-preparation method, precluded reduction in recovery of the thiolation substrate caused by intrapeptide lysine-dehydroalanine cross-link formation. The solid-phase analytical platform provides robustness and simplicity of operation using equipment readily available in most biological laboratories and is expected to accommodate additional chemistries to expand the scope of solid-phase serial derivatization for protein structural characterization. PMID:23997662

Cell viability and protein turnover in nongrowing Bacillus megaterium at sporulation suppressing temperature.

PubMed

Kucerová, H; Strnadová, M; Ludvík, J; Chaloupka, J

1999-01-01

In Bacillus megaterium, a temperature that suppresses sporulation (43 degrees C) only slightly exceeds both the optimum growth temperature and the temperature still permitting sporulation (40-41 degrees C). Here we show that, when cells grown at 35 degrees C and transferred to a sporulation medium, were subjected to shifts between 35 degrees C and the sporulation suppressing temperature (SST, 43 degrees C), their development and proteolytic activities were deeply affected. During the reversible sporulation phase that took place at 35 degrees C for 2-3 h (T2-T3), the cells developed forespores and their protein turnover was characterized by degradation of short-lived proteins and proteins made accessible to the proteolytic attack because of starvation. During the following irreversible sporulation phase refractile heat-resistant spores appeared at T4-T5. Protein turnover rate increased again after T2 and up to T8 60-70% prelabelled proteins were degraded. The SST suppressed sporulation at its beginning; at T3 no asymmetric septa were observed and the amount of heat-resistant spores at T8 was by 4-5 orders lower than at 35 degrees C. However, the cells remained viable and were able to sporulate when transferred to a lower temperature. Protein degradation was increased up to T3 but then its velocity sharply dropped and the amount of degraded protein at T8 corresponded to slightly more than one-half of that found at 35 degrees C. The cytoplasmic proteolytic activity was enhanced but the activity in the membrane fraction was decreased. When a temperature shift to SST was applied at the beginning of the irreversible sporulation phase (T2.5), the sporulation process was impaired. A portion of forespores lyzed, the others were able to complete their development but most spores were not heat-resistant and their coats showed defects. Protein degradation increased again because an effective proteolytic system was developed during the reversible sporulation phase but the amount of degraded protein was slightly lower than at 35 degrees C. A later (T4) shift to SST had no effect on the sporulation process.

Task switching in rhesus macaques (Macaca mulatta) and tufted capuchin monkeys (Cebus apella) during computerized categorization tasks.

PubMed

Smith, Travis R; Beran, Michael J

2018-05-31

The present experiments extended to monkeys a previously used abstract categorization procedure (Castro & Wasserman, 2016) where pigeons had categorized arrays of clipart icons based upon two task rules: the number of clipart objects in the array or the variability of objects in the array. Experiment 1 replicated Castro and Wasserman by using capuchin monkeys and rhesus monkeys and reported that monkeys' performances were similar to pigeons' in terms of acquisition, pattern of errors, and the absence of switch costs. Furthermore, monkeys' insensitivity to the added irrelevant information suggested that an associative (rather than rule-based) categorization mechanism was dominant. Experiment 2 was conducted to include categorization cue reversals to determine (a) whether the monkeys would quickly adapt to the reversals and inhibit interference from a prereversal task rule (consistent with a rule-based mechanism) and (b) whether the latency to make a response prior to a correct or incorrect outcome was informative about the presence of a cognitive mechanism. The cue reassignment produced profound and long-lasting performance deficits, and a long reacquisition phase suggested the involvement of associative learning processes; however, monkeys also displayed longer latencies to choose prior to correct responses on challenging trials, suggesting the involvement of nonassociative processes. Together these performances suggest a mix of associative and cognitive-control processes governing monkey categorization judgments. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

The CRISPR-Associated Gene cas2 of Legionella pneumophila Is Required for Intracellular Infection of Amoebae

PubMed Central

Gunderson, Felizza F.; Cianciotto, Nicholas P.

2013-01-01

ABSTRACT Recent studies have shown that the clustered regularly interspaced palindromic repeats (CRISPR) array and its associated (cas) genes can play a key role in bacterial immunity against phage and plasmids. Upon analysis of the Legionella pneumophila strain 130b chromosome, we detected a subtype II-B CRISPR-Cas locus that contains cas9, cas1, cas2, cas4, and an array with 60 repeats and 58 unique spacers. Reverse transcription (RT)-PCR analysis demonstrated that the entire CRISPR-Cas locus is expressed during 130b extracellular growth in both rich and minimal media as well as during intracellular infection of macrophages and aquatic amoebae. Quantitative reverse transcription-PCR (RT-PCR) further showed that the levels of cas transcripts, especially those of cas1 and cas2, are elevated during intracellular growth relative to exponential-phase growth in broth. Mutants lacking components of the CRISPR-Cas locus were made and found to grow normally in broth and on agar media. cas9, cas1, cas4, and CRISPR array mutants also grew normally in macrophages and amoebae. However, cas2 mutants, although they grew typically in macrophages, were significantly impaired for infection of both Hartmannella and Acanthamoeba species. A complemented cas2 mutant infected the amoebae at wild-type levels, confirming that cas2 is required for intracellular infection of these host cells. PMID:23481601

High power transcranial beam steering for ultrasonic brain therapy

PubMed Central

Pernot, Mathieu; Aubry, Jean-François; Tanter, Mickaël; Thomas, Jean-Louis; Fink, Mathias

2003-01-01

A sparse phased array is specially designed for non-invasive ultrasound transskull brain therapy. The array is made of 200 single-elements corresponding to a new generation of high power transducers developed in collaboration with Imasonic (Besançon, France). Each element has a surface of 0.5cm2 and works at 0.9 MHz central frequency with a maximum 20W.cm−2 intensity on the transducer surface. In order to optimize the steering capabilities of the array, several transducers distributions on a spherical surface are simulated: hexagonal, annular, and quasi-random distributions. Using a quasi-random distribution significantly reduces the grating lobes. Furthermore, the simulations show the capability of the quasi-random array to electronically move the focal spot in the vicinity of the geometrical focus (up to +/− 15 mm). Based on the simulation study, the array is constructed and tested. The skull aberrations are corrected by using a time reversal mirror with amplitude correction achieved thanks to an implantable hydrophone, and a sharp focus is obtained through a human skull. Several lesions are induced in fresh liver and brain samples through human skulls, demonstrating the accuracy and the steering capabilities of the system. PMID:12974575

High power transcranial beam steering for ultrasonic brain therapy

NASA Astrophysics Data System (ADS)

Pernot, M.; Aubry, J.-F.; Tanter, M.; Thomas, J.-L.; Fink, M.

2003-08-01

A sparse phased array is specially designed for non-invasive ultrasound transskull brain therapy. The array is made of 200 single elements corresponding to a new generation of high power transducers developed in collaboration with Imasonic (Besançon, France). Each element has a surface of 0.5 cm2 and works at 0.9 MHz central frequency with a maximum 20 W cm-2 intensity on the transducer surface. In order to optimize the steering capabilities of the array, several transducer distributions on a spherical surface are simulated: hexagonal, annular and quasi-random distributions. Using a quasi-random distribution significantly reduces the grating lobes. Furthermore, the simulations show the capability of the quasi-random array to electronically move the focal spot in the vicinity of the geometrical focus (up to +/-15 mm). Based on the simulation study, the array is constructed and tested. The skull aberrations are corrected by using a time reversal mirror with amplitude correction achieved thanks to an implantable hydrophone, and a sharp focus is obtained through a human skull. Several lesions are induced in fresh liver and brain samples through human skulls, demonstrating the accuracy and the steering capabilities of the system.

miR-137 Targets p160 Steroid Receptor Coactivators SRC1, SRC2, and SRC3 and Inhibits Cell Proliferation

PubMed Central

Eedunuri, Vijay Kumar; Rajapakshe, Kimal; Fiskus, Warren; Geng, Chuandong; Chew, Sue Anne; Foley, Christopher; Shah, Shrijal S.; Shou, John; Mohamed, Junaith S.; O'Malley, Bert W.

2015-01-01

The p160 family of steroid receptor coactivators (SRCs) are pleiotropic transcription factor coactivators and “master regulators” of gene expression that promote cancer cell proliferation, survival, metabolism, migration, invasion, and metastasis. Cancers with high p160 SRC expression exhibit poor clinical outcomes and resistance to therapy, highlighting the SRCs as critical oncogenic drivers and, thus, therapeutic targets. microRNAs are important epigenetic regulators of protein expression. To examine the regulation of p160 SRCs by microRNAs, we used and combined 4 prediction algorithms to identify microRNAs that could target SRC1, SRC2, and SRC3 expression. For validation of these predictions, we assessed p160 SRC protein expression and cell viability after transfection of corresponding microRNA mimetics in breast cancer, uveal melanoma, and prostate cancer (PC) cell lines. Transfection of selected microRNA mimetics into breast cancer, uveal melanoma, and PC cells depleted SRC protein expression levels and exerted potent antiproliferative activity in these cell types. In particular, microRNA-137 (miR-137) depleted expression of SRC1, SRC2, and very potently, SRC3. The latter effect can be attributed to the presence of 3 miR-137 recognition sequences within the SRC3 3′-untranslated region. Using reverse phase protein array analysis, we identified a network of proteins, in addition to SRC3, that were modulated by miR-137 in PC cells. We also found that miR-137 and its host gene are epigenetically silenced in human cancer specimens and cell lines. These results support the development and testing of microRNA-based therapies (in particular based on restoring miR-137 levels) for targeting the oncogenic family of p160 SRCs in cancer. PMID:26066330

An antiviral protein from Bougainvillea spectabilis roots; purification and characterisation.

PubMed

Balasaraswathi, R; Sadasivam, S; Ward, M; Walker, J M

1998-04-01

An antiviral protein active against mechanical transmission of tomato spotted wilt virus was identified in the root tissues of Bougainvillea spectabilis Willd. Bougainvillea Antiviral Protein I (BAP I) was purified to apparent homogeneity from the roots of Bougainvillea by ammonium sulphate precipitation, CM- and DEAE-Sepharose chromatography and reverse phase HPLC. BAP I is a highly basic protein (pI value > 8.6) with an Mr of 28,000. The N-terminal sequence of BAP I showed homology with other plant antiviral proteins. Preliminary tests suggest that purified BAP I is capable of interfering with in vitro protein synthesis.

Course 12: Proteins: Structural, Thermodynamic and Kinetic Aspects

NASA Astrophysics Data System (ADS)

Finkelstein, A. V.

1 Introduction 2 Overview of protein architectures and discussion of physical background of their natural selection 2.1 Protein structures 2.2 Physical selection of protein structures 3 Thermodynamic aspects of protein folding 3.1 Reversible denaturation of protein structures 3.2 What do denatured proteins look like? 3.3 Why denaturation of a globular protein is the first-order phase transition 3.4 "Gap" in energy spectrum: The main characteristic that distinguishes protein chains from random polymers 4 Kinetic aspects of protein folding 4.1 Protein folding in vivo 4.2 Protein folding in vitro (in the test-tube) 4.3 Theory of protein folding rates and solution of the Levinthal paradox

Size-Sorting Combined with Improved Nanocapillary-LC-MS for Identification of Intact Proteins up to 80 kDa

PubMed Central

Vellaichamy, Adaikkalam; Tran, John C.; Catherman, Adam D.; Lee, Ji Eun; Kellie, John F.; Sweet, Steve M.M.; Zamdborg, Leonid; Thomas, Paul M.; Ahlf, Dorothy R.; Durbin, Kenneth R.; Valaskovic, Gary A.; Kelleher, Neil L.

2010-01-01

Despite the availability of ultra-high resolution mass spectrometers, methods for separation and detection of intact proteins for proteome-scale analyses are still in a developmental phase. Here we report robust protocols for on-line LC-MS to drive high-throughput top-down proteomics in a fashion similar to bottom-up. Comparative work on protein standards showed that a polymeric stationary phase led to superior sensitivity over a silica-based medium in reversed-phase nanocapillary-LC, with detection of proteins >50 kDa routinely accomplished in the linear ion trap of a hybrid Fourier-Transform mass spectrometer. Protein identification was enabled by nozzle-skimmer dissociation (NSD) and detection of fragment ions with <5 ppm mass accuracy for highly-specific database searching using custom software. This overall approach led to identification of proteins up to 80 kDa, with 10-60 proteins identified in single LC-MS runs of samples from yeast and human cell lines pre-fractionated by their molecular weight using a gel-based sieving system. PMID:20073486

From Vision to Reality: 50 Years of Phased Array Development

DTIC Science & Technology

2016-09-30

This paper cites the most prominent U.S.-deployed phased array radars as viewed by one phased-array radar advocate. Key words: radar, antenna array...phased array, phased array radar, radar antennas , array I. INTRODUCTION I welcome the opportunity to talk with today’s phased array engineers and...their test site in Fullerton, CA in the mid-1960s and was impressed by the size of the antennas . Eight apertures were deployed on each ship to

Separation and quantification of 15 carotenoids by reversed phase high performance liquid chromatography coupled to diode array detection with isosbestic wavelength approach.

PubMed

Mitrowska, Kamila; Vincent, Ursula; von Holst, Christoph

2012-04-13

The manuscript presents the development of a new reverse phase high performance liquid chromatography (RP-HPLC) photo diode array detection method allowing the separation and quantification of 15 carotenoids (adonirubin, adonixanthin, astaxanthin, astaxanthin dimethyl disuccinate, asteroidenone, beta-apo-8'-carotenal, beta-apo-8'-carotenoic acid ethyl ester, beta-carotene, canthaxanthin, capsanthin, citranaxanthin, echinenone, lutein, lycopene, and zeaxanthin), 10 of which are feed additives authorised within the European Union. The developed method allows for the reliable determination of the total carotenoid content in one run using the corresponding E-isomer as calibration standard while taking into account the E/Z-isomers composition. This is a key criterion for the application of the method, since for most of the analytes included in this study analytical standards are only available for the E-isomers. This goal was achieved by applying the isosbestic concept, in order to identify specific wavelengths, at which the absorption coefficients are identical for all stereoisomers concerned. The second target referred to the optimisation of the LC conditions. By means of an experimental design, an optimised RP-HPLC method was developed allowing for a sufficient chromatographic separation of all carotenoids. The selected method uses a Suplex pKb-100 HPLC column and applying a gradient with a mixture of acetonitrile, tert-butyl-methyl ether and water as mobile phases. The limits of detection and limits of quantification ranged from 0.06 mg L(-1) to 0.14 mg L(-1) and from 0.20 mg L(-1) to 0.48 mg L(-1), respectively. Copyright © 2012 Elsevier B.V. All rights reserved.

Hydrophobic Interaction Chromatography for Bottom-Up Proteomics Analysis of Single Proteins and Protein Complexes.

PubMed

Rackiewicz, Michal; Große-Hovest, Ludger; Alpert, Andrew J; Zarei, Mostafa; Dengjel, Jörn

2017-06-02

Hydrophobic interaction chromatography (HIC) is a robust standard analytical method to purify proteins while preserving their biological activity. It is widely used to study post-translational modifications of proteins and drug-protein interactions. In the current manuscript we employed HIC to separate proteins, followed by bottom-up LC-MS/MS experiments. We used this approach to fractionate antibody species followed by comprehensive peptide mapping as well as to study protein complexes in human cells. HIC-reversed-phase chromatography (RPC)-mass spectrometry (MS) is a powerful alternative to fractionate proteins for bottom-up proteomics experiments making use of their distinct hydrophobic properties.

Effect of pressure on secondary structure of proteins under ultra high pressure liquid chromatographic conditions.

PubMed

Makarov, Alexey; LoBrutto, Rosario; Karpinski, Paul

2013-11-29

There are several spectroscopic techniques such as IR and CD, that allow for analyzing protein secondary structure in solution. However, a majority of these techniques require using purified protein, concentrated enough in the solution, to produce a relevant spectrum. Fundamental principles for the usage of reversed-phase ultra high pressure liquid chromatography (UHPLC) as an alternative technique to study protein secondary structures in solution were investigated. Several "model" proteins, as well as several small ionizable and neutral molecules, were used for these studies. The studies were conducted with UHPLC in isocratic mode, using premixed mobile phases at constant flow rate and temperature. The pressure was modified by a backpressure regulator from about 6000psi to about 12,000psi. It was found that when using a mobile phase composition at which proteins were fully denatured (loss of alpha-helix secondary structure), the retention factors of the proteins increased upon pressure increase in the same manner as non-proteins. When using a mobile phase composition in which proteins were not fully denatured, it was observed that the retention factors of the proteins displayed a much steeper (by one order of magnitude) increase in retention upon pressure increase. It was concluded that in a mobile phase in which the protein is not initially fully denatured, the increase of pressure may facilitate the folding back of the protein to its native state (alpha-helix secondary structure). The impact of different mobile phase compositions on the denaturation of the proteins was studied using CD (Circular Dichroism). Moreover, the effect of flow rate on retention of proteins and small molecules was studied at constant pressure on the different pore size silicas and the impact of internal frictional heating was evaluated. Copyright © 2013 Elsevier B.V. All rights reserved.

Evaluation of new superficially porous particles with carbon core and nanodiamond-polymer shell for proteins characterization.

PubMed

Bobály, Balázs; Guillarme, Davy; Fekete, Szabolcs

2015-02-01

A new superficially porous material possessing a carbon core and nanodiamond-polymer shell and pore size of 180Å was evaluated for the analysis of large proteins. Because the stationary phase on this new support contains a certain amount of protonated amino groups within the shell structure, the resulting retention mechanism is most probably a mix between reversed phase and anion exchange. However, under the applied conditions (0.1-0.5% TFA in the mobile phase), it seemed that the main retention mechanism for proteins was hydrophobic interaction with the C18 alkylchains on this carbon based material. In this study, we demonstrated that there was no need to increase mobile phase temperature, as the peak capacity was not modified considerably between 30 and 80°C for model proteins. Thus, the risk of thermal on-column degradation or denaturation of large proteins is not relevant. Another important difference compared to silica-based materials is that this carbon-based column requires larger amount of TFA, comprised between 0.2 and 0.5%. Finally, it is important to mention that selectivity between closely related proteins (oxidized, native and reduced forms of Interferon α-2A variants) could be changed mostly through mobile phase temperature. Copyright © 2014 Elsevier B.V. All rights reserved.

Reverse micelle-mediated synthesis of calcium phosphate nanocarriers for controlled release of bovine serum albumin.

PubMed

Dasgupta, Sudip; Bandyopadhyay, Amit; Bose, Susmita

2009-10-01

Calcium phosphate (CaP) nanoparticles with a calcium to phosphorus (Ca:P) molar ratio of 1.5:1 were synthesized using reverse microemulsion. Ca(NO(3))(2).4H(2)O and H(3)PO(4) were used as the aqueous phase, cyclohexane as the organic phase and poly(oxyethylene)(12) nonylphenol ether (NP-12) as the surfactant. Depending on the calcination temperature between 600 and 800 degrees C, CaP nanoparticle showed different phases of calcium-deficient hydroxyapatite (CDHA) and beta-tricalcium phosphate (beta-TCP), particle size between 48 and 69 nm, and a BET specific average surface area between 73 and 57 m(2)g(-1). Bovine serum albumin (BSA) was used as a model protein to study loading and release behavior. The adsorptive property of BSA was investigated by the change in BET surface area of these nanoparticles and the pH of the suspension. At pH 7.5, the maximum amount of BSA was adsorbed onto CaP nanoparticle. The release kinetics of BSA showed a gradual time-dependent increase in pH 4.0 and 6.0 buffer solutions. However, the amount of protein released was significantly smaller at pH 7.2. The BSA release rate also varied depending on the presence of different phases of CaPs in the system, beta-TCP or CDHA. These results suggest that the BSA protein release rate can be controlled by changing the particle size, surface area and phase composition of the CaP nanocarriers.

In situ synthesis of protein arrays.

PubMed

He, Mingyue; Stoevesandt, Oda; Taussig, Michael J

2008-02-01

In situ or on-chip protein array methods use cell free expression systems to produce proteins directly onto an immobilising surface from co-distributed or pre-arrayed DNA or RNA, enabling protein arrays to be created on demand. These methods address three issues in protein array technology: (i) efficient protein expression and availability, (ii) functional protein immobilisation and purification in a single step and (iii) protein on-chip stability over time. By simultaneously expressing and immobilising many proteins in parallel on the chip surface, the laborious and often costly processes of DNA cloning, expression and separate protein purification are avoided. Recently employed methods reviewed are PISA (protein in situ array) and NAPPA (nucleic acid programmable protein array) from DNA and puromycin-mediated immobilisation from mRNA.

Analytical and semi-preparative enantioresolution of (RS)-ketorolac from pharmaceutical formulation and in human plasma by HPLC.

PubMed

Lal, Manohar; Bhushan, Ravi

2016-10-01

An efficient, simple, validated, analytical and semi-preparative HPLC method has been developed for direct enantioresolution of (RS)-Ketorolac (Ket) using monochloro-methylated derivatives of cellulose and amylose, i.e. cellulose (tris-3-chloro-4-methylphenylcarbamate) and amylose (tris-5-chloro-2-methylphenylcarbamate) as chiral stationary phases (CSPs) with photo diode array detection at 320 nm. Enantioresolution was carried out in samples of human plasma spiked with (RS)-Ket under normal and reversed-phase elution modes with suitable mobile phase compositions. The effect of nature of alcohols (MeOH, EtOH, PrOH and n-BuOH) and other solvents (MeCN and MeOH) as organic modifiers in the mobile phase was investigated on the separation performance of two CSPs in terms of retention and separation of enantiomers. The best resolution was observed on cellulose-based CSP using EtOH, while using 2-PrOH (15%) and amylose-based CSP obtained the highest retention. Under reversed-phase elution mode the best enantioseparation was observed using 30% MeCN with ammonium formate buffer. The elution order of enantiomers was ascertained by determining specific rotations. The limit of detection and quantitation values were 5 and 15.5 ng/mL for each enantiomer of (RS)-Ket, respectively. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Microfluidic free-flow electrophoresis for the discovery and characterisation of calmodulin binding partners

NASA Astrophysics Data System (ADS)

Herling, Therese; Linse, Sara; Knowles, Tuomas

2015-03-01

Non-covalent and transient protein-ligand interactions are integral to cellular function and malfunction. Key steps in signalling and regulatory pathways rely on reversible non-covalent protein-protein binding or ion chelation. Here we present a microfluidic free-flow electrophoresis method for detecting and characterising protein-ligand interactions in solution. We apply this method to probe the binding equilibria of calmodulin, a central protein to calcium signalling pathways. In this study we characterise the specific binding of calmodulin to phosphorylase kinase, a known target, and creatine kinase, which we identify as a putative binding partner through a protein array screen and surface plasmon resonance experiments. We verify the interaction between calmodulin and creatine kinase in solution using free-flow electrophoresis and investigate the effect of calcium and sodium chloride on the calmodulin-ligand binding affinity in free solution without the presence of a potentially interfering surface. Our results demonstrate the general applicability of quantitative microfluidic electrophoresis to characterise binding equilibria between biomolecules in solution.

Interaction between the Stress Phase Angle (SPA) and the Oscillatory Shear Index (OSI) Affects Endothelial Cell Gene Expression.

PubMed

Amaya, Ronny; Cancel, Limary M; Tarbell, John M

2016-01-01

Hemodynamic forces play an important role in the non-uniform distribution of atherosclerotic lesions. Endothelial cells are exposed simultaneously to fluid wall shear stress (WSS) and solid circumferential stress (CS). Due to variations in impedance (global factors) and geometric complexities (local factors) in the arterial circulation a time lag arises between these two forces that can be characterized by the temporal phase angle between CS and WSS (stress phase angle-SPA). Asynchronous flows (SPA close to -180°) that are most prominent in coronary arteries have been associated with localization of atherosclerosis. Reversing oscillatory flows characterized by an oscillatory shear index (OSI) that is great than zero are also associated with atherosclerosis localization. In this study we examined the relationship between asynchronous flows and reversing flows in altering the expression of 37 genes relevant to atherosclerosis development. In the case of reversing oscillatory flow, we observed that the asynchronous condition upregulated 8 genes compared to synchronous hemodynamics, most of them proatherogenic. Upregulation of the pro-inflammatory transcription factor NFκB p65 was confirmed by western blot, and nuclear translocation of NFκB p65 was confirmed by immunofluorescence staining. A comparative study between non-reversing flow and reversing flow found that in the case of synchronous hemodynamics, reversing flow altered the expression of 11 genes, while in the case of asynchronous hemodynamics, reversing flow altered the expression of 17 genes. Reversing flow significantly upregulated protein expression of NFκB p65 for both synchronous and asynchronous conditions. Nuclear translocation of NFκB p65 was confirmed for synchronous and asynchronous conditions in the presence of flow reversal. These data suggest that asynchronous hemodynamics and reversing flow can elicit proatherogenic responses in endothelial cells compared to synchronous hemodynamics without shear stress reversal, indicating that SPA as well as reversal flow (OSI) are important parameters characterizing arterial susceptibility to disease.

Interaction between the Stress Phase Angle (SPA) and the Oscillatory Shear Index (OSI) Affects Endothelial Cell Gene Expression

PubMed Central

Amaya, Ronny; Cancel, Limary M.; Tarbell, John M.

2016-01-01

Hemodynamic forces play an important role in the non-uniform distribution of atherosclerotic lesions. Endothelial cells are exposed simultaneously to fluid wall shear stress (WSS) and solid circumferential stress (CS). Due to variations in impedance (global factors) and geometric complexities (local factors) in the arterial circulation a time lag arises between these two forces that can be characterized by the temporal phase angle between CS and WSS (stress phase angle–SPA). Asynchronous flows (SPA close to -180°) that are most prominent in coronary arteries have been associated with localization of atherosclerosis. Reversing oscillatory flows characterized by an oscillatory shear index (OSI) that is great than zero are also associated with atherosclerosis localization. In this study we examined the relationship between asynchronous flows and reversing flows in altering the expression of 37 genes relevant to atherosclerosis development. In the case of reversing oscillatory flow, we observed that the asynchronous condition upregulated 8 genes compared to synchronous hemodynamics, most of them proatherogenic. Upregulation of the pro-inflammatory transcription factor NFκB p65 was confirmed by western blot, and nuclear translocation of NFκB p65 was confirmed by immunofluorescence staining. A comparative study between non-reversing flow and reversing flow found that in the case of synchronous hemodynamics, reversing flow altered the expression of 11 genes, while in the case of asynchronous hemodynamics, reversing flow altered the expression of 17 genes. Reversing flow significantly upregulated protein expression of NFκB p65 for both synchronous and asynchronous conditions. Nuclear translocation of NFκB p65 was confirmed for synchronous and asynchronous conditions in the presence of flow reversal. These data suggest that asynchronous hemodynamics and reversing flow can elicit proatherogenic responses in endothelial cells compared to synchronous hemodynamics without shear stress reversal, indicating that SPA as well as reversal flow (OSI) are important parameters characterizing arterial susceptibility to disease. PMID:27846267

Enhanced Peptide Detection Toward Single-Neuron Proteomics by Reversed-Phase Fractionation Capillary Electrophoresis Mass Spectrometry

NASA Astrophysics Data System (ADS)

Choi, Sam B.; Lombard-Banek, Camille; Muñoz-LLancao, Pablo; Manzini, M. Chiara; Nemes, Peter

2018-05-01

The ability to detect peptides and proteins in single cells is vital for understanding cell heterogeneity in the nervous system. Capillary electrophoresis (CE) nanoelectrospray ionization (nanoESI) provides high-resolution mass spectrometry (HRMS) with trace-level sensitivity, but compressed separation during CE challenges protein identification by tandem HRMS with limited MS/MS duty cycle. Here, we supplemented ultrasensitive CE-nanoESI-HRMS with reversed-phase (RP) fractionation to enhance identifications from protein digest amounts that approximate to a few mammalian neurons. An 1 to 20 μg neuronal protein digest was fractionated on a RP column (ZipTip), and 1 ng to 500 pg of peptides were analyzed by a custom-built CE-HRMS system. Compared with the control (no fractionation), RP fractionation improved CE separation (theoretical plates 274,000 versus 412,000 maximum, resp.), which enhanced detection sensitivity (2.5-fold higher signal-to-noise ratio), minimized co-isolation spectral interferences during MS/MS, and increased the temporal rate of peptide identification by up to 57%. From 1 ng of protein digest (<5 neurons), CE with RP fractionation identified 737 protein groups (1,753 peptides), or 480 protein groups ( 1,650 peptides) on average per analysis. The approach was scalable to 500 pg of protein digest ( a single neuron), identifying 225 protein groups (623 peptides) in technical triplicates, or 141 protein groups on average per analysis. Among identified proteins, 101 proteins were products of genes that are known to be transcriptionally active in single neurons during early development of the brain, including those involved in synaptic transmission and plasticity and cytoskeletal organization. [Figure not available: see fulltext.

Enhanced Peptide Detection Toward Single-Neuron Proteomics by Reversed-Phase Fractionation Capillary Electrophoresis Mass Spectrometry

NASA Astrophysics Data System (ADS)

Choi, Sam B.; Lombard-Banek, Camille; Muñoz-LLancao, Pablo; Manzini, M. Chiara; Nemes, Peter

2017-11-01

The ability to detect peptides and proteins in single cells is vital for understanding cell heterogeneity in the nervous system. Capillary electrophoresis (CE) nanoelectrospray ionization (nanoESI) provides high-resolution mass spectrometry (HRMS) with trace-level sensitivity, but compressed separation during CE challenges protein identification by tandem HRMS with limited MS/MS duty cycle. Here, we supplemented ultrasensitive CE-nanoESI-HRMS with reversed-phase (RP) fractionation to enhance identifications from protein digest amounts that approximate to a few mammalian neurons. An 1 to 20 μg neuronal protein digest was fractionated on a RP column (ZipTip), and 1 ng to 500 pg of peptides were analyzed by a custom-built CE-HRMS system. Compared with the control (no fractionation), RP fractionation improved CE separation (theoretical plates 274,000 versus 412,000 maximum, resp.), which enhanced detection sensitivity (2.5-fold higher signal-to-noise ratio), minimized co-isolation spectral interferences during MS/MS, and increased the temporal rate of peptide identification by up to 57%. From 1 ng of protein digest (<5 neurons), CE with RP fractionation identified 737 protein groups (1,753 peptides), or 480 protein groups ( 1,650 peptides) on average per analysis. The approach was scalable to 500 pg of protein digest ( a single neuron), identifying 225 protein groups (623 peptides) in technical triplicates, or 141 protein groups on average per analysis. Among identified proteins, 101 proteins were products of genes that are known to be transcriptionally active in single neurons during early development of the brain, including those involved in synaptic transmission and plasticity and cytoskeletal organization. [Figure not available: see fulltext.

Highly sensitive reversed-phase high-performance liquid chromatography assay for the detection of Tamm-Horsfall protein in human urine.

PubMed

Akimoto, Masaru; Hokazono, Eisaku; Ota, Eri; Tateishi, Takiko; Kayamori, Yuzo

2016-01-01

Tamm-Horsfall protein (also known as uromodulin) is the most abundant urinary protein in healthy individuals. Since initially characterized by Tamm and Horsfall, the amount of urinary excretion and structural mutations of Tamm-Horsfall protein is associated with kidney diseases. However, currently available assays for Tamm-Horsfall protein, which are mainly enzyme-linked immunosorbent assay-based, suffer from poor reproducibility and might give false negative results. We developed a novel, quantitative assay for Tamm-Horsfall protein using reversed-phase high-performance liquid chromatography. A precipitation pretreatment avoided urine matrix interference and excessive sample dilution. High-performance liquid chromatography optimization based on polarity allowed excellent separation of Tamm-Horsfall protein from other major urine components. Our method exhibited high precision (based on the relative standard deviations of intraday [≤2.77%] and interday [≤5.35%] repetitions). The Tamm-Horsfall protein recovery rate was 100.0-104.2%. The mean Tamm-Horsfall protein concentration in 25 healthy individuals was 31.6 ± 18.8 mg/g creatinine. There was a strong correlation between data obtained by high-performance liquid chromatography and enzyme-linked immunosorbent assay (r = 0.906), but enzyme-linked immunosorbent assay values tended to be lower than high-performance liquid chromatography values at low Tamm-Horsfall protein concentrations. The high sensitivity and reproducibility of our Tamm-Horsfall protein assay will reduce the number of false negative results of the sample compared with enzyme-linked immunosorbent assay. Moreover, our method is superior to other high-performance liquid chromatography methods, and a simple protocol will facilitate further research on the physiological role of Tamm-Horsfall protein. © The Author(s) 2015.

Metabolism studies of benzbromarone in rats by high performance liquid chromatography-quadrupole time of flight mass spectrometry.

PubMed

Wu, Haiqing; Peng, Ying; Wang, Shaojie; Wang, Kai; Zhao, Xunchen; Jiang, Fan

2012-12-12

A high performance liquid chromatography-quadrupole time of flight mass spectrometry (HPLC-QTOF-MS) method was employed in investigation of benzbromarone metabolites in rat plasma, urine, feces and bile samples. Meanwhile, the metabolic pathways of benzbromarone in rats were discussed. The identification was achieved on a reversed-phase C(18) column with mobile phase gradient method. The QTOF-MS was operated under full scan of MS or MS/MS in negative mode. The fragments were acquired by raising collision induced dissociation (CID) energy for speculating the structures of parent ions. According to the information from the chromatograms and mass spectra, 17 metabolites were obtained. Among them, the deoxidized phase I metabolites and an array of phase II metabolites-sulfate conjugates detected in the biological samples made the work more significant. Copyright © 2012 Elsevier B.V. All rights reserved.

Effects of tethering a multistate folding protein to a surface

NASA Astrophysics Data System (ADS)

Wei, Shuai; Knotts, Thomas A.

2011-05-01

Protein/surface interactions are important in a variety of fields and devices, yet fundamental understanding of the relevant phenomena remains fragmented due to resolution limitations of experimental techniques. Molecular simulation has provided useful answers, but such studies have focused on proteins that fold through a two-state process. This study uses simulation to show how surfaces can affect proteins which fold through a multistate process by investigating the folding mechanism of lysozyme (PDB ID: 7LZM). The results demonstrate that in the bulk 7LZM folds through a process with four stable states: the folded state, the unfolded state, and two stable intermediates. The folding mechanism remains the same when the protein is tethered to a surface at most residues; however, in one case the folding mechanism changes in such a way as to eliminate one of the intermediates. An analysis of the molecular configurations shows that tethering at this site is advantageous for protein arrays because the active site is both presented to the bulk phase and stabilized. Taken as a whole, the results offer hope that rational design of protein arrays is possible once the behavior of the protein on the surface is ascertained.

Familial 46,XY sex reversal without campomelic dysplasia caused by a deletion upstream of the SOX9 gene

PubMed Central

Layman, Lawrence C.; Ullmann, Reinhard; Shen, Yiping; Ha, Kyungsoo; Rehman, Khurram; Looney, Stephen; McDonough, Paul G.; Kim, Hyung-Goo; Carr, Bruce R.

2014-01-01

Background 46,XY sex reversal is a rare disorder and familial cases are even more rare. The purpose of the present study was to determine the molecular basis for a family with three affected siblings who had 46,XY sex reversal. Methods DNA was extracted from three females with 46,XY sex reversal, two normal sisters, and both unaffected parents. All protein coding exons of the SRY and NR5A1 genes were subjected to PCR-based DNA sequencing. In addition, array comparative genomic hybridization was performed on DNA from all seven family members. A deletion was confirmed using quantitative polymerase chain reaction. Expression of SOX9 gene was quantified using reverse transcriptase polymerase chain reaction. Results A 349kb heterozygous deletion located 353kb upstream of the SOX9 gene on the long arm of chromosome 17 was discovered in the father and three affected siblings, but not in the mother. The expression of SOX9 was significantly decreased in the affected siblings. Two of three affected sisters had gonadoblastomas. Conclusion This is the first report of 46,XY sex reversal in three siblings who have a paternally inherited deletion upstream of SOX9 associated with reduced SOX9 mRNA expression. PMID:24907458

Dramatically stabilizing multiprotein complex structure in the absence of bulk water using tuned Hofmeister salts.

PubMed

Han, Linjie; Hyung, Suk-Joon; Ruotolo, Brandon T

2013-01-01

The role that water plays in the salt-based stabilization of proteins is central to our understanding of protein biophysics. Ion hydration and the ability of ions to alter water surface tension are typically invoked, along with direct ion-protein binding, to describe Hofmeister stabilization phenomena observed for proteins experimentally, but the relative influence of these forces has been extraordinarily difficult to measure directly. Recently, we have used gas-phase measurements of proteins and large multiprotein complexes, using a combination of innovative ion mobility (IM) and mass spectrometry (MS) techniques, to assess the ability of bound cations and anions to stabilize protein ions in the absence of the solvation forces described above. Our previous work has studied a broad set of 12 anions bound to a range of proteins and protein complexes, and while primarily motivated by the analytical challenges surrounding the gas-phase measurement of solution-phase relevant protein structures, our work has also lead to a detailed physical mechanism of anion-protein complex stabilization in the absence of bulk solvent. Our more-recent work has screened a similarly-broad set of cations for their ability to stabilize gas-phase protein structure, and we have discovered surprising differences between the operative mechanisms for cations and anions in gas-phase protein stabilization. In both cases, cations and anions affect protein stabilization in the absence of solvent in a manner that is generally reversed relative to their ability to stabilize the same proteins in solution. In addition, our evidence suggests that the relative solution-phase binding affinity of the anions and cations studied here is preserved in our gas-phase measurements, allowing us to study the influence of such interactions in detail. In this report, we collect and summarize such gas-phase measurements to distill a generalized picture of salt-based protein stabilization in the absence of bulk water. Further, we communicate our most recent efforts to study the combined effects of stabilizing cations and anions on gas-phase proteins, and identify those salts that bear anion/cation pairs having the strongest stabilizing influence on protein structures

Multiplexed chemiluminescent assays in ArrayPlates for high-throughput measurement of gene expression

NASA Astrophysics Data System (ADS)

Martel, Ralph R.; Rounseville, Matthew P.; Botros, Ihab W.; Seligmann, Bruce E.

2002-06-01

Multiplexed Molecular Profiling (MMP) assays for drug discovery are performed in ArrayPlates. ArrayPlates are 96- well microtiter plates that contain a 16-element array at the bottom of each well. Each element within an array measures one analyte in a sample. A CCD imager records the quantitative chemiluminescent readout of all 1,536 elements in a 96-well plate simultaneously. Since array elements are reagent modifiable by the end-user, ArrayPlates can be adapted to a broad range of nucleic acid- and protein-based assays. Such multiplexed assays are rapidly established, flexible, robust, automation-friendly and cost-effective. Nucleic acid assays in ArrayPlates can detect DNA and RNA, including SNPs and ESTs. A multiplexed mRNA assay to measure the expression of 16 genes is described. The assay combines a homogeneous nuclease protection assay with subsequent probe immobilization to the array by means of a sandwich hybridization followed with chemiluminescent detection. This assay was used to examine cells grown and treated in microplates and avoided cloning, transfection, RNA insolation, reverse transcription, amplification and fluorochrome labeling. Standard deviations for the measurement of 16 genes ranged from 3 percent to 13 percent in samples of 30,000 cells. Such ArrayPlates transcription assays are useful in drug discovery and development for target validation, screening, lead optimization, metabolism and toxicity profiling. Chemiluminescent detection provides ArrayPlates assays with high signal-to-noise readout and simplifies imager requirements. Imaging a 2D surface that contains arrays simplifies lens requirements relative to imaging columns of liquid in microtiter plate wells. The Omix imager for ArrayPlates is described.

Rapid micro-scale proteolysis of proteins for MALDI-MS peptide mapping using immobilized trypsin

NASA Astrophysics Data System (ADS)

Gobom, Johan; Nordhoff, Eckhard; Ekman, Rolf; Roepstorff, Peter

1997-12-01

In this study we present a rapid method for tryptic digestion of proteins using micro-columns with enzyme immobilized on perfusion chromatography media. The performance of the method is exemplified with acyl-CoA-binding protein and reduced carbamidomethylated bovine serum albumin. The method proved to be significantly faster and yielded a better sequence coverage and an improved signal-to-noise ratio for the MALDI-MS peptide maps, compared to in-solution- and on-target digestion. Only a single sample transfer step is required, and therefore sample loss due to adsorption to surfaces is reduced, which is a critical issue when handling low picomole to femtomole amounts of proteins. An example is shown with on-column proteolytic digestion and subsequent elution of the digest into a reversed-phase micro-column. This is useful if the sample contains large amounts of salt or is too diluted for MALDI-MS analysis. Furthermore, by step-wise elution from the reversedphase column, a complex digest can be fractionated, which reduces signal suppression and facilitates data interpretation in the subsequent MS-analysis. The method also proved useful for consecutive digestions with enzymes of different cleavage specificity. This is exemplified with on-column tryptic digestion, followed by reversed-phase step-wise elution, and subsequent on-target V8 protease digestion.

Small scale affinity purification and high sensitivity reversed phase nanoLC-MS N-glycan characterization of mAbs and fusion proteins.

PubMed

Higel, Fabian; Seidl, Andreas; Demelbauer, Uwe; Sörgel, Fritz; Frieß, Wolfgang

2014-01-01

N-glycosylation is a complex post-translational modification with potential effects on the efficacy and safety of therapeutic proteins and known influence on the effector function of biopharmaceutical monoclonal antibodies (mAbs). Comprehensive characterization of N-glycosylation is therefore important in biopharmaceutical development. In early development, e.g. during pool or clone selection, however, only minute protein amounts of multiple samples are available for analytics. High sensitivity and high throughput methods are thus needed. An approach based on 96-well plate sample preparation and nanoLC-MS of 2- anthranilic acid or 2-aminobenzoic acid (AA) labeled N-glycans for the characterization of biopharmaceuticals in early development is reported here. With this approach, 192 samples can be processed simultaneously from complex matrices (e.g., cell culture supernatant) to purified 2-AA glycans, which are then analyzed by reversed phase nanoLC-MS. Attomolar sensitivity has been achieved by use of nanoelectrospray ionization, resulting in detailed glycan maps of mAbs and fusion proteins that are exemplarily shown in this work. Reproducibility, robustness and linearity of the approach are demonstrated, making use in a routine manner during pool or clone selection possible. Other potential fields of application, such as glycan biomarker discovery from serum samples, are also presented.

Small scale affinity purification and high sensitivity reversed phase nanoLC-MS N-glycan characterization of mAbs and fusion proteins

PubMed Central

Higel, Fabian; Seidl, Andreas; Demelbauer, Uwe; Sörgel, Fritz; Frieß, Wolfgang

2014-01-01

N-glycosylation is a complex post-translational modification with potential effects on the efficacy and safety of therapeutic proteins and known influence on the effector function of biopharmaceutical monoclonal antibodies (mAbs). Comprehensive characterization of N-glycosylation is therefore important in biopharmaceutical development. In early development, e.g. during pool or clone selection, however, only minute protein amounts of multiple samples are available for analytics. High sensitivity and high throughput methods are thus needed. An approach based on 96-well plate sample preparation and nanoLC-MS of 2- anthranilic acid or 2-aminobenzoic acid (AA) labeled N-glycans for the characterization of biopharmaceuticals in early development is reported here. With this approach, 192 samples can be processed simultaneously from complex matrices (e.g., cell culture supernatant) to purified 2-AA glycans, which are then analyzed by reversed phase nanoLC-MS. Attomolar sensitivity has been achieved by use of nanoelectrospray ionization, resulting in detailed glycan maps of mAbs and fusion proteins that are exemplarily shown in this work. Reproducibility, robustness and linearity of the approach are demonstrated, making use in a routine manner during pool or clone selection possible. Other potential fields of application, such as glycan biomarker discovery from serum samples, are also presented. PMID:24848368

Reversible ratchet effects for vortices in conformal pinning arrays

DOE PAGES

Reichhardt, Charles; Ray, Dipanjan; Reichhardt, Cynthia Jane Olson

2015-05-04

A conformal transformation of a uniform triangular pinning array produces a structure called a conformal crystal which preserves the sixfold ordering of the original lattice but contains a gradient in the pinning density. Here we use numerical simulations to show that vortices in type-II superconductors driven with an ac drive over gradient pinning arrays produce the most pronounced ratchet effect over a wide range of parameters for a conformal array, while square gradient or random gradient arrays with equivalent pinning densities give reduced ratchet effects. In the conformal array, the larger spacing of the pinning sites in the direction transversemore » to the ac drive permits easy funneling of interstitial vortices for one driving direction, producing the enhanced ratchet effect. In the square array, the transverse spacing between pinning sites is uniform, giving no asymmetry in the funneling of the vortices as the driving direction switches, while in the random array, there are numerous easy-flow channels present for either direction of drive. We find multiple ratchet reversals in the conformal arrays as a function of vortex density and ac amplitude, and correlate the features with a reversal in the vortex ordering, which is greater for motion in the ratchet direction. In conclusion, the enhanced conformal pinning ratchet effect can also be realized for colloidal particles moving over a conformal array, indicating the general usefulness of conformal structures for controlling the motion of particles.« less

Pathway Profiling and Rational Trial Design for Studies in Advanced Stage Cervical Carcinoma: A Review and a Perspective

PubMed Central

Scholl, Susy M. E.; Kenter, Gemma; Kurzeder, Christian; Beuzeboc, Philippe

2011-01-01

Multiple genetic abnormalities will have occurred in advanced cervical cancer and multiple targeting is likely to be needed to control tumor growth. To date, dominant therapeutic targets under scrutiny for cervical cancer treatment have been EGFR pathway and angiogenesis inhibition as well as anti-HPV vaccines. The potentially most effective targets to be blocked may be downstream from the membrane receptor or at the level of the nucleus. Alterations of the pathways involved in DNA repair and in checkpoint activations, as well as the specific site of HPV genome integration, appear worth assessing. For genetic mutational analysis, complete exon sequencing may become the norm in the future but at this stage frequent mutations (that matter) can be verified by PCR analysis. A precise documentation of relevant alterations of a large spectrum of protein biomarkers can be carried out by reverse phase protein array (RPPA) or by multiplex analysis. Clinical decision-making on the drug(s) of choice as a function of the biological alteration will need input from bio-informatics platforms as well as novel statistical designs. Endpoints are yet to be defined such as the loss (or reappearance) of a predictive biomarker. Single or dual targeting needs to be explored first in relevant preclinical animal and in xenograft models prior to clinical deployment. PMID:22091418

Method for distinguishing multiple targets using time-reversal acoustics

DOEpatents

Berryman, James G.

2004-06-29

A method for distinguishing multiple targets using time-reversal acoustics. Time-reversal acoustics uses an iterative process to determine the optimum signal for locating a strongly reflecting target in a cluttered environment. An acoustic array sends a signal into a medium, and then receives the returned/reflected signal. This returned/reflected signal is then time-reversed and sent back into the medium again, and again, until the signal being sent and received is no longer changing. At that point, the array has isolated the largest eigenvalue/eigenvector combination and has effectively determined the location of a single target in the medium (the one that is most strongly reflecting). After the largest eigenvalue/eigenvector combination has been determined, to determine the location of other targets, instead of sending back the same signals, the method sends back these time reversed signals, but half of them will also be reversed in sign. There are various possibilities for choosing which half to do sign reversal. The most obvious choice is to reverse every other one in a linear array, or as in a checkerboard pattern in 2D. Then, a new send/receive, send-time reversed/receive iteration can proceed. Often, the first iteration in this sequence will be close to the desired signal from a second target. In some cases, orthogonalization procedures must be implemented to assure the returned signals are in fact orthogonal to the first eigenvector found.

Targeting Src and tubulin in mucinous ovarian carcinoma

PubMed Central

Liu, Tao; Hu, Wei; Dalton, Heather J.; Choi, Hyun Jin; Huang, Jie; Kang, Yu; Pradeep, Sunila; Miyake, Takahito; Song, Jian H.; Wen, Yunfei; Lu, Chunhua; Pecot, Chad V.; Bottsford-Miller, Justin; Zand, Behrouz; Jennings, Nicholas B; Ivan, Cristina; Gallick, Gary E.; Baggerly, Keith A; Hangauer, David G.; Coleman, Robert L.; Frumovitz, Michael; Sood, Anil K.

2013-01-01

Purpose To investigate the antitumor effects of targeting Src and tubulin in mucinous ovarian carcinoma. Experimental design The in vitro and in vivo effects and molecular mechanisms of KX-01, which inhibits Src pathway and tubulin polymerization, were examined in mucinous ovarian cancer models. Results In vitro studies using RMUG-S and RMUG-L cell lines showed that KX-01 inhibited cell proliferation, induced apoptosis, arrested the cell cycle at the G2/M phase, and enhanced the cytotoxicity of oxaliplatin in the KX-01-sensitive cell line, RMUG-S. In vivo studies showed that KX-01 significantly decreased tumor burden in RMUG-S and RMUG-L mouse models relative to untreated controls, and the effects were greater when KX-01 was combined with oxaliplatin. KX-01 alone and in combination with oxaliplatin significantly inhibited tumor growth by reducing cell proliferation and inducing apoptosis in vivo. PTEN knock-in experiments in RMUG-L cells showed improved response to KX-01. Reverse phase protein array analysis showed that in addition to blocking downstream molecules of Src family kinases, KX-01 also activated acute stress-inducing molecules. Conclusion Our results showed that targeting both the Src pathway and tubulin with KX-01 significantly inhibited tumor growth in preclinical mucinous ovarian cancer models, suggesting that this may be a promising therapeutic approach for patients with mucinous ovarian carcinoma. PMID:24100628

S-phase-specific activation of Cds1 kinase defines a subpathway of the checkpoint response in Schizosaccharomyces pombe

PubMed Central

Lindsay, Howard D.; Griffiths, Dominic J.F.; Edwards, Rhian J.; Christensen, Per U.; Murray, Johanne M.; Osman, Fekret; Walworth, Nancy; Carr, Antony M.

1998-01-01

Checkpoints that respond to DNA structure changes were originally defined by the inability of yeast mutants to prevent mitosis following DNA damage or S-phase arrest. Genetic analysis has subsequently identified subpathways of the DNA structure checkpoints, including the reversible arrest of DNA synthesis. Here, we show that the Cds1 kinase is required to slow S phase in the presence of DNA-damaging agents. Cds1 is phosphorylated and activated by S-phase arrest and activated by DNA damage during S phase, but not during G1 or G2. Activation of Cds1 during S phase is dependent on all six checkpoint Rad proteins, and Cds1 interacts both genetically and physically with Rad26. Unlike its Saccharomyces cerevisiae counterpart Rad53, Cds1 is not required for the mitotic arrest checkpoints and, thus, defines an S-phase specific subpathway of the checkpoint response. We propose a model for the DNA structure checkpoints that offers a new perspective on the function of the DNA structure checkpoint proteins. This model suggests that an intrinsic mechanism linking S phase and mitosis may function independently of the known checkpoint proteins. PMID:9450932

Implication of the VirD4 coupling protein of the Lvh type 4 secretion system in virulence phenotypes of Legionella pneumophila.

PubMed

Bandyopadhyay, Purnima; Lang, Elza A S; Rasaputra, Komal S; Steinman, Howard M

2013-08-01

The genome of the Philadelphia-1 strain of Legionella pneumophila, the causative organism of Legionnaires' disease, encodes two virulence-associated type 4 secretion systems (T4SSs), the Dot/Icm type 4B (T4BSS) and the Lvh type 4A (T4ASS). Broth stationary-phase cultures of most dot/icm mutants are defective in entry and evasion of phagosome acidification. However, those virulence defects can be reversed by incubating broth cultures of dot/icm mutants in water, termed water stress (WS). WS reversal requires the lvh T4ASS locus, suggesting an interaction between the two T4SSs in producing Legionella virulence phenotypes. In the current work, the loss of WS reversal in a dotA Δlvh mutant of strain JR32 was shown to be attributable to loss of the lvh virD4 gene, encoding the putative coupling protein of the T4ASS. Transformation of a dotA Δlvh mutant with virD4 also reversed entry and phagosome acidification defects in broth cultures. In addition, broth cultures of Δlvh and ΔvirD4 mutants, which were dot/icm(+), showed 5-fold and >6-fold increases in translocation of the Dot/Icm translocation substrates, proteins RalF and SidD, respectively. These data demonstrate that the Lvh T4ASS functions in both broth stationary-phase cultures conventionally used for infection and cultures exposed to WS treatment. Our studies in a dotA Δlvh mutant and in a dot/icm(+) background establish that VirD4 and the Lvh T4ASS contribute to virulence phenotypes and are consistent with independent functioning of Dot/Icm and Lvh T4SSs or functional substitution of the Lvh VirD4 protein for a component(s) of the Dot/Icm T4BSS.

Implication of the VirD4 Coupling Protein of the Lvh Type 4 Secretion System in Virulence Phenotypes of Legionella pneumophila

PubMed Central

Bandyopadhyay, Purnima; Lang, Elza A. S.; Rasaputra, Komal S.

2013-01-01

The genome of the Philadelphia-1 strain of Legionella pneumophila, the causative organism of Legionnaires' disease, encodes two virulence-associated type 4 secretion systems (T4SSs), the Dot/Icm type 4B (T4BSS) and the Lvh type 4A (T4ASS). Broth stationary-phase cultures of most dot/icm mutants are defective in entry and evasion of phagosome acidification. However, those virulence defects can be reversed by incubating broth cultures of dot/icm mutants in water, termed water stress (WS). WS reversal requires the lvh T4ASS locus, suggesting an interaction between the two T4SSs in producing Legionella virulence phenotypes. In the current work, the loss of WS reversal in a dotA Δlvh mutant of strain JR32 was shown to be attributable to loss of the lvh virD4 gene, encoding the putative coupling protein of the T4ASS. Transformation of a dotA Δlvh mutant with virD4 also reversed entry and phagosome acidification defects in broth cultures. In addition, broth cultures of Δlvh and ΔvirD4 mutants, which were dot/icm+, showed 5-fold and >6-fold increases in translocation of the Dot/Icm translocation substrates, proteins RalF and SidD, respectively. These data demonstrate that the Lvh T4ASS functions in both broth stationary-phase cultures conventionally used for infection and cultures exposed to WS treatment. Our studies in a dotA Δlvh mutant and in a dot/icm+ background establish that VirD4 and the Lvh T4ASS contribute to virulence phenotypes and are consistent with independent functioning of Dot/Icm and Lvh T4SSs or functional substitution of the Lvh VirD4 protein for a component(s) of the Dot/Icm T4BSS. PMID:23729650

Reverse bias voltage testing of 8 cm x 8cm silicon solar cells

NASA Technical Reports Server (NTRS)

Woike, T.; Stotlar, S.; Lungu, C.

1991-01-01

A study is described of the reverse I-V characteristics of the largest space qualified silicon solar cells currently available (8 x 8 cm) and of reverse bias voltage (RBV) testing performed on these cells. This study includes production grade cells, both with and without cover glass. These cells span the typical output range seen in production. Initial characteristics of these cells are measured at both 28 and 60 C. These measurements show weak correlation between cell output and reverse characteristics. Analysis is presented to determine the proper conditions for RBV stress to simulate shadowing effects on a particular array design. After performing the RBV stress the characteristics of the stressed cells are remeasured. The degradation in cell performance is highly variable which exacerbates cell mismatching over time. The effect of this degradation on array lifetime is also discussed. Generalization of these results to other array configurations is also presented.

HPLC-DAD-ESI/MS identification of light harvesting and light screening pigments in the lake sediments at Edmonson Point.

PubMed

Giovannetti, Rita; Alibabaei, Leila; Zannotti, Marco; Ferraro, Stefano; Petetta, Laura

2013-01-01

The composition of sedimentary pigments in the Antarctic lake at Edmonson Point has been investigated and compared with the aim to provide a useful analytical method for pigments separation and identification, providing reference data for future assessment of possible changes in environmental conditions. Reversed phase high performance liquid chromatography (HPLC) with electrospray-mass spectrometry (ESI-MS) detection and diode array detection (DAD) has been used to identify light screening and light harvesting pigments. The results are discussed in terms of local environmental conditions.

Identification of phenolic compounds from the leaf part of Teucrium pseudo-Scorodonia Desf. collected from Algeria.

PubMed

Belarbi, Karima; Atik-Bekkara, Fawzia; El Haci, Imad Abdelhamid; Bensaid, Ilhem; Bekhechi, Chahrazed

2018-02-01

In the present paper,we reported for the first time, the identification of the phenolic compounds in butanolic fraction obtained from the leaf part of Teucrium pseudo-Scorodonia Desf. collected from Algeria using RP-HPLC-PDA (Reversed Phase High Performance Liquid Chromatography/Photo Diode Array) technique. Several standards were used for this purpose. The analysis led to the identification of six phenolic acids (ferulic, sinapic, rosmarinic, syringique, caffeic, p-coumaric acids) and one flavonoid (rutin), the last one, has interesting pharmacological properties.

HPLC-DAD-MS identification of bioactive secondary metabolites from Ferula communis roots.

PubMed

Arnoldi, Lolita; Ballero, Mauro; Fuzzati, Nicola; Maxia, Andrea; Mercalli, Enrico; Pagni, Luca

2004-06-01

A simple HPLC method was developed to distinguish between 'poisonous' and 'non-poisonous' chemotypes of Ferula communis. The method was performed on a C8 reverse phase analytical column using a binary eluent (aqueous TFA 0.01%-TFA 0.01% in acetonitrile) under gradient condition. The two chemotypes showed different fingerprints. The identification of five coumarins and eleven daucane derivatives by HPLC-diode array detection (HPLC-DAD) and HPLC-MS is described. A coumarin, not yet described, was detected. Copyright 2004 Elsevier B.V.

Polar Aprotic Modifiers for Chromatographic Separation and Back-Exchange Reduction for Protein Hydrogen/Deuterium Exchange Monitored by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

NASA Astrophysics Data System (ADS)

Valeja, Santosh G.; Emmett, Mark R.; Marshall, Alan G.

2012-04-01

Hydrogen/deuterium exchange monitored by mass spectrometry is an important non-perturbing tool to study protein structure and protein-protein interactions. However, water in the reversed-phase liquid chromatography mobile phase leads to back-exchange of D for H during chromatographic separation of proteolytic peptides following H/D exchange, resulting in incorrect identification of fast-exchanging hydrogens as unexchanged hydrogens. Previously, fast high-performance liquid chromatography (HPLC) and supercritical fluid chromatography have been shown to decrease back-exchange. Here, we show that replacement of up to 40% of the water in the LC mobile phase by the modifiers, dimethylformamide (DMF) and N-methylpyrrolidone (NMP) (i.e., polar organic modifiers that lack rapid exchanging hydrogens), significantly reduces back-exchange. On-line LC micro-ESI FT-ICR MS resolves overlapped proteolytic peptide isotopic distributions, allowing for quantitative determination of the extent of back-exchange. The DMF modified solvent composition also improves chromatographic separation while reducing back-exchange relative to conventional solvent.

Capillary trap column with strong cation-exchange monolith for automated shotgun proteome analysis.

PubMed

Wang, Fangjun; Dong, Jing; Jiang, Xiaogang; Ye, Mingliang; Zou, Hanfa

2007-09-01

A 150 microm internal diameter capillary monolithic column with a strong cation-exchange stationary phase was prepared by direct in situ polymerization of ethylene glycol methacrylate phosphate and bisacrylamide in a trinary porogenic solvent consisting dimethylsulfoxide, dodecanol, and N,N'-dimethylformamide. This phosphate monolithic column exhibits higher dynamic binding capacity, faster kinetic adsorption of peptides, and more than 10 times higher permeability than the column packed with commercially available strong cation-exchange particles. It was applied as a trap column in a nanoflow liquid chromatography-tandem mass spectrometry system for automated sample injection and online multidimensional separation. It was observed that the sample could be loaded at a flow rate as high as 40 microL/min with a back pressure of approximately 1300 psi and without compromising the separation efficiency. Because of its good orthogonality to the reversed phase separation mechanism, the phosphate monolithic trap column was coupled with a reversed-phase column for online multidimensional separation of 19 microg of the tryptic digest of yeast proteins. A total of 1522 distinct proteins were identified from 5608 unique peptides (total of 54,780 peptides) at the false positive rate only 0.46%.

In-phased second harmonic wave array generation with intra-Talbot-cavity frequency-doubling.

PubMed

Hirosawa, Kenichi; Shohda, Fumio; Yanagisawa, Takayuki; Kannari, Fumihiko

2015-03-23

The Talbot cavity is one promising method to synchronize the phase of a laser array. However, it does not achieve the lowest array mode with the same phase but the highest array mode with the anti-phase between every two adjacent lasers, which is called out-phase locking. Consequently, their far-field images exhibit 2-peak profiles. We propose intra-Talbot-cavity frequency-doubling. By placing a nonlinear crystal in a Talbot cavity, the Talbot cavity generates an out-phased fundamental wave array, which is converted into an in-phase-locked second harmonic wave array at the nonlinear crystal. We demonstrate numerical calculations and experiments on intra-Talbot-cavity frequency-doubling and obtain an in-phase-locked second harmonic wave array for a Nd:YVO₄ array laser.

Serum cytokine/chemokine profiles in patients with dengue fever (DF) and dengue hemorrhagic fever (FHD) by using protein array.

PubMed

Oliveira, Renato Antonio Dos Santos; Cordeiro, Marli Tenório; Moura, Patrícia Muniz Mendes Freire de; Baptista Filho, Paulo Neves Bapti; Braga-Neto, Ulisses de Mendonça; Marques, Ernesto Torres de Azevedo; Gil, Laura Helena Vega Gonzales

2017-04-01

DENV infection can induce different clinical manifestations varying from mild forms to dengue fever (DF) or the severe hemorrhagic fever (DHF). Several factors are involved in the progression from DF to DHF. No marker is available to predict this progression. Such biomarker could allow a suitable medical care at the beginning of the infection, improving patient prognosis. The aim of this study was to compare the serum expression levels of acute phase proteins in a well-established cohort of dengue fever (DF) and dengue hemorrhagic fever (DHF) patients, in order to individuate a prognostic marker of diseases severity. The serum levels of 36 cytokines, chemokines and acute phase proteins were determined in DF and DHF patients and compared to healthy volunteers using a multiplex protein array and near-infrared (NIR) fluorescence detection. Serum levels of IL-1ra, IL-23, MIF, sCD40 ligand, IP-10 and GRO-α were also determined by ELISA. At the early stages of infection, GRO-α and IP-10 expression levels were different in DF compared to DHF patients. Besides, GRO-α was positively correlated with platelet counts and IP-10 was negatively correlated with total protein levels. These findings suggest that high levels of GRO-α during acute DENV infection may be associated with a good prognosis, while high levels of IP-10 may be a warning sign of infection severity. Copyright © 2017 Elsevier B.V. All rights reserved.

A Novel Derivative of the Natural Agent Deguelin for Cancer Chemoprevention and Therapy

PubMed Central

Kim, Woo-Young; Chang, Dong Jo; Hennessy, Bryan; Kang, Hae-Jin; Yoo, Jakyung; Han, Seung-Ho; Kim, Yoo-Shin; Park, Hyun-Ju; Geo, Seung-Yong; Mills, Gordon; Kim, Kyu-Won; Hong, Waun Ki; Suh, Young-Ger; Lee, Ho-Young

2009-01-01

The natural compound deguelin has promising preventive and therapeutic activity against diverse cancers by directly binding to heat-shock protein 90 (Hsp90) and thus suppressing its function. Potential side effects of deguelin over a certain dose, however, could be a substantial obstacle to its clinical use. To develop a derivative(s) of deguelin with reduced potential side effects, we synthesized five deguelin analogues (SH-02, SH-03, SH-09, SH-14 and SH-15) and compared them with the parent compound and each other for structural and biochemical features, solubility, and antiproliferative effects on normal, premalignant and malignant human bronchial epithelial (HBE) and non-small-cell lung cancer (NSCLC) cell lines. Four derivatives destabilized hypoxia-inducible factor-1α as potently as did deguelin. Reverse-phase protein array (RPPA) analysis in H460 NSCLC cells revealed that deguelin and the derivatives suppressed expression of a number of proteins including Hsp90 clients and proteins involved in the phosphoinositide 3 kinase (PI3K)/Akt pathway. One derivative, SH-14, showed several features of potential superiority for clinical use: the highest apoptotic activity; no detectable influence on Src/signal transducer and activator of transcription (STAT) signaling, which can promote cancer progression and is closely related to pathogenesis of Parkinson’s disease (deguelin, SH-02 and SH-03 strongly activated this signaling); better aqueous solubility; and less cytotoxicity to immortalized HBE cells (versus deguelin) at a dose (1 μM) that induced apoptotic activity in most premalignant and malignant HBE and NSCLC cell lines. These collective results suggest that the novel derivative SH-14 has strong potential for cancer chemoprevention and therapy, with equivalent efficacy and lesser toxicity (versus deguelin). PMID:19139008

Palbociclib (PD0332991)-a Selective and Potent Cyclin-Dependent Kinase Inhibitor: A Review of Pharmacodynamics and Clinical Development.

PubMed

Clark, Amy S; Karasic, Thomas B; DeMichele, Angela; Vaughn, David J; O'Hara, Mark; Perini, Rodolfo; Zhang, Paul; Lal, Priti; Feldman, Michael; Gallagher, Maryann; O'Dwyer, Peter J

2016-02-01

Palbociclib (PD0332991) is a newly developed drug that received breakthrough designation and recent US Food and Drug Administration approval in combination with endocrine therapy in the treatment of hormone receptor positive, ERBB2-negative (formerly HER2 or HER2/neu) breast cancer in the first-line metastatic setting. Herein we describe the preclinical and translational data and early- and late-phase clinical trials in which palbociclib has been investigated in a broad array of tumor types. We discuss the pharmacodynamics, pharmacokinetics, toxic effects, and clinical response rates. On March 1, 2015, we conducted a review of the literature describing the development of palbociclib. We used the PubMed search terms "PD0332991," "palbociclib," and "CDK4/6 inhibitor" to find all published articles of interest, without limitation as to publication date. Palbociclib is a potent and specific oral cyclin-dependent kinase (CDK) 4/6 inhibitor that has strong preclinical data to support its activity in retinoblastoma protein-expressing tumors. Phase 1 trials have demonstrated safety, and phase 2 trials have shown single-agent activity in mantle-cell lymphoma, breast cancer, liposarcoma, and teratoma with reversible neutropenia as the main toxic effect. Addition of palbociclib to endocrine therapy improves progression-free survival in endocrine therapy-naïve and endocrine therapy-resistant metastatic settings. Palbociclib is well tolerated and has therapeutic potential for multiple cancers, including breast cancer, where its efficacy has been demonstrated alone and in combination with endocrine therapy. Additional combinations of palbociclib with endocrine therapy, chemotherapy, and targeted therapy have potential in various tumors, and phase 3 trials are under way.

Interactions and reversal-field memory in complex magnetic nanowire arrays

NASA Astrophysics Data System (ADS)

Rotaru, Aurelian; Lim, Jin-Hee; Lenormand, Denny; Diaconu, Andrei; Wiley, John. B.; Postolache, Petronel; Stancu, Alexandru; Spinu, Leonard

2011-10-01

Interactions and magnetization reversal of Ni nanowire arrays have been investigated by the first-order reversal curve (FORC) method. Several series of samples with controlled spatial distribution were considered including simple wires of different lengths and diameters (70 and 110 nm) and complex wires with a single modulated diameter along their length. Subtle features of magnetic interactions are revealed through a quantitative analysis of the local interaction field profile distributions obtained from the FORC method. In addition, the FORC analysis indicates that the nanowire systems with a mean diameter of 70 nm appear to be organized in symmetric clusters indicative of a reversal-field memory effect.

Optimised 'on demand' protein arraying from DNA by cell free expression with the 'DNA to Protein Array' (DAPA) technology.

PubMed

Schmidt, Ronny; Cook, Elizabeth A; Kastelic, Damjana; Taussig, Michael J; Stoevesandt, Oda

2013-08-02

We have previously described a protein arraying process based on cell free expression from DNA template arrays (DNA Array to Protein Array, DAPA). Here, we have investigated the influence of different array support coatings (Ni-NTA, Epoxy, 3D-Epoxy and Polyethylene glycol methacrylate (PEGMA)). Their optimal combination yields an increased amount of detected protein and an optimised spot morphology on the resulting protein array compared to the previously published protocol. The specificity of protein capture was improved using a tag-specific capture antibody on a protein repellent surface coating. The conditions for protein expression were optimised to yield the maximum amount of protein or the best detection results using specific monoclonal antibodies or a scaffold binder against the expressed targets. The optimised DAPA system was able to increase by threefold the expression of a representative model protein while conserving recognition by a specific antibody. The amount of expressed protein in DAPA was comparable to those of classically spotted protein arrays. Reaction conditions can be tailored to suit the application of interest. DAPA represents a cost effective, easy and convenient way of producing protein arrays on demand. The reported work is expected to facilitate the application of DAPA for personalized medicine and screening purposes. Copyright © 2013 Elsevier B.V. All rights reserved.

Arraying proteins by cell-free synthesis.

PubMed

He, Mingyue; Wang, Ming-Wei

2007-10-01

Recent advances in life science have led to great motivation for the development of protein arrays to study functions of genome-encoded proteins. While traditional cell-based methods have been commonly used for generating protein arrays, they are usually a time-consuming process with a number of technical challenges. Cell-free protein synthesis offers an attractive system for making protein arrays, not only does it rapidly converts the genetic information into functional proteins without the need for DNA cloning, but also presents a flexible environment amenable to production of folded proteins or proteins with defined modifications. Recent advancements have made it possible to rapidly generate protein arrays from PCR DNA templates through parallel on-chip protein synthesis. This article reviews current cell-free protein array technologies and their proteomic applications.

Development of a Bio-inspired Microflap Array for Passive Control of Flow Separation

NASA Astrophysics Data System (ADS)

Devey, Sean; Morris, Jackson; Hubner, Paul; Lang, Amy

2017-11-01

The shortfin mako shark benefits from its flexible microscopic scales, or denticles; which can passively limit flow separation in water. These denticles can be passively actuated by incipient reversing flow in the lower 5% of the boundary layer, thereby impeding further flow reversal and promoting increased momentum exchange. In air, an array of flow actuated microflaps has the potential to provide similar benefits to man-made systems. Multiple iterations of microflap arrays have been developed and tested in the University of Alabama's Boundary Layer Tunnel. A variety of 3D-printed flaps derived from mako denticle geometries were arranged in rows with freedom to rotate, like mako denticles, to angles up to 50 degrees. Placing the microflap array in separated flow regions allowed for direct observation of the microflap response. Like mako denticles, microflaps with lengths of about 4 mm have been shown to actuate in response to reversing surface flows. This presentation will focus on the development and implementation of passive microflap arrays. This research was supported by Boeing, the US Army, and the National Science Foundation REU program.

A multipoint study of a substorm occurring on 7 December, 1992, and its theoretical implications

NASA Astrophysics Data System (ADS)

Fox, N. J.; Cowley, S. W. H.; Davda, V. N.; Enno, G.; Friis-Christensen, E.; Greenwald, R. A.; Hairston, M. R.; Lester, M.; Lockwood, M.; Lühr, H.; Milling, D. K.; Murphree, J. S.; Pinnock, M.; Reeves, G. D.

1999-11-01

On 7 December 1992, a moderate substorm was observed by a variety of satellites and ground-based instruments. Ionospheric flows were monitored near dusk by the Goose Bay HF radar and near midnight by the EISCAT radar. The observed flows are compared here with magnetometer observations by the IMAGE array in Scandinavia and the two Greenland chains, the auroral distribution observed by Freja and the substorm cycle observations by the SABRE radar, the SAMNET magnetometer array and LANL geosynchronous satellites. Data from Galileo Earth-encounter II are used to estimate the IMF Bz component. The data presented show that the substorm onset electrojet at midnight was confined to closed field lines equatorward of the pre-existing convection reversal boundaries observed in the dusk and midnight regions. No evidence of substantial closure of open flux was detected following this substorm onset. Indeed the convection reversal boundary on the duskside continued to expand equatorward after onset due to the continued presence of strong southward IMF, such that growth and expansion phase features were simultaneously present. Clear indications of closure of open flux were not observed until a subsequent substorm intensification 25 min after the initial onset. After this time, the substorm auroral bulge in the nightside hours propagated well poleward of the pre-existing convection reversal boundary, and strong flow perturbations were observed by the Goose Bay radar, indicative of flows driven by reconnection in the tail.

Effect of diet textural characteristics on the temporal rhythms of feeding in rats.

PubMed

Mok, E; Thibault, L

To examine whether the diurnal rhythms of protein-rich and carbohydrate-rich diet ingestion can be altered by presenting the diets in different textural forms, adult male Wistar rats were assigned to two dietary groups. One group received a two-way choice between high-protein powder and high-carbohydrate granular (HPP-HCG) diets. In the other group the textures were reversed [high-protein granular and high-carbohydrate powder (HPG-HCP) diets]. Rats fed HPP-HCG diets selected significantly less protein (kcal) vs. rats fed HPG-HCP diets, during the 24-h and 12-h dark phase and during the 4-h early and late dark phases. Carbohydrate intakes of the two dietary groups were not significantly different. Total caloric intake for the HPG-HCP dietary group was significantly higher than that of the HPP-HCG dietary group during the 24-h and 12-h dark phase. Body weight was significantly lower in rats fed HPP-HCG diets. In conclusion, macronutrient-rich diets presented in different textural forms alter protein-rich diet ingestion and total energy intake.

A Study of Phased Array Antennas for NASA's Deep Space Network

NASA Technical Reports Server (NTRS)

Jamnejad, Vahraz; Huang, John; Cesarone, Robert J.

2001-01-01

In this paper we briefly discuss various options but focus on the feasibility of the phased arrays as a viable option for this application. Of particular concern and consideration will be the cost, reliability, and performance compared to the present 70-meter antenna system, particularly the gain/noise temperature levels in the receive mode. Many alternative phased arrays including planar horizontal arrays, hybrid mechanically/electronically steered arrays, phased array of mechanically steered reflectors, multi-faceted planar arrays, phased array-fed lens antennas, and planar reflect-arrays are compared and their viability is assessed. Although they have many advantages including higher reliability, near-instantaneous beam switching or steering capability, the cost of such arrays is presently prohibitive and it is concluded that the only viable array options at the present are the arrays of a few or many small reflectors. The active planar phased arrays, however, may become feasible options in the next decade and can be considered for deployment in smaller configurations as supplementary options.

CHPA, a Cysteine- and Histidine-Rich-Domain-Containing Protein, Contributes to Maintenance of the Diploid State in Aspergillus nidulans

PubMed Central

Sadanandom, Ari; Findlay, Kim; Doonan, John H.; Schulze-Lefert, Paul; Shirasu, Ken

2004-01-01

The alternation of eukaryotic life cycles between haploid and diploid phases is crucial for maintaining genetic diversity. In some organisms, the growth and development of haploid and diploid phases are nearly identical, and one might suppose that all genes required for one phase are likely to be critical for the other phase. Here, we show that targeted disruption of the chpA (cysteine- and histidine-rich-domain- [CHORD]-containing protein A) gene in haploid Aspergillus nidulans strains gives rise to chpA knockout haploids and heterozygous diploids but no chpA knockout diploids. A. nidulans chpA heterozygous diploids showed impaired conidiophore development and reduced conidiation. Deletion of chpA from diploid A. nidulans resulted in genome instability and reversion to a haploid state. Thus, our data suggest a vital role for chpA in maintenance of the diploid phase in A. nidulans. Furthermore, the human chpA homolog, Chp-1, was able to complement haploinsufficiency in A. nidulans chpA heterozygotes, suggesting that the function of CHORD-containing proteins is highly conserved in eukaryotes. PMID:15302831

Andexanet alfa to reverse the anticoagulant activity of factor Xa inhibitors: a review of design, development and potential place in therapy.

PubMed

Sartori, Michelangelo; Cosmi, Benilde

2018-04-01

Direct oral anticoagulants are associated with rates of major bleeding which are not negligible, albeit lower than those associated with vitamin K antagonists. No specific reversal agent for factor Xa (FXa) direct inhibitors is currently available for clinical use. A modified activated human FXa decoy protein, andexanet alfa, is being developed that binds FXa direct inhibitors in their active site, thus reversing their anticoagulant effect. The purpose of this article is to review the design, development and clinical trials of andexanet alfa. Andexanet alfa was shown to reverse FXa inhibitors anticoagulant activity both in thrombosis animal models, healthy volunteers and patients with acute major bleeding. Andexanet alfa has been studied in double-blind, placebo-controlled phase II and III studies. A preliminary report of the phase III study showed that an effective hemostasis was obtained after andexanet alfa infusion in the majority of the patients with acute major bleeding associated with FXa inhibitors. Additional studies are ongoing and andexanet alfa is expected to be launched in the market in the near future.

Monolithic Integration of Two-Dimensional Liquid Chromatography-Capillary Electrophoresis and Electrospray Ionization on a Microfluidic Device

PubMed Central

Chambers, Andrew G.; Mellors, J. Scott; Henley, W. Hampton; Ramsey, J. Michael

2011-01-01

A microfluidic device capable of two-dimensional reversed-phase liquid chromatography-capillary electrophoresis with integrated electrospray ionization (LC-CE-ESI) for mass spectrometry (MS)-based proteomic applications is described. Traditional instrumentation was used for the LC sample injection and delivery of the LC mobile phase. The glass microfabricated device incorporated a sample-trapping region and an LC channel packed with reversed-phase particles. Rapid electrokinetic injections of the LC effluent into the CE dimension were performed at a cross channel intersection. The CE separation channel terminated at a corner of the square device, which functioned as an integrated electrospray tip. In addition to LC-CE-ESI, this device was used for LC-ESI without any instrumental modifications. To evaluate the system, LC-MS and LC-CE-MS analysis of protein digests were performed and compared. PMID:21214194

Characterization of the pigment fraction in sweet bell peppers (Capsicum annuum L.) harvested at green and overripe yellow and red stages by offline multidimensional convergence chromatography/liquid chromatography-mass spectrometry.

PubMed

Bonaccorsi, Ivana; Cacciola, Francesco; Utczas, Margita; Inferrera, Veronica; Giuffrida, Daniele; Donato, Paola; Dugo, Paola; Mondello, Luigi

2016-09-01

Offline multidimensional supercritical fluid chromatography combined with reversed-phase liquid chromatography was employed for the carotenoid and chlorophyll characterization in different sweet bell peppers (Capsicum annuum L.) for the first time. The first dimension consisted of an Acquity HSS C18 SB (100 × 3 mm id, 1.8 μm particles) column operated with a supercritical mobile phase in an ultra-performance convergence chromatography system, whereas the second dimension was performed in reversed-phase mode with a C30 (250 × 4.6 mm id, 3.0 μm particles) stationary phase combined with photodiode array and mass spectrometry detection. This approach allowed the determination of 115 different compounds belonging to chlorophylls, free xanthophylls, free carotenes, xanthophyll monoesters, and xanthophyll diesters, and proved to be a significant improvement in the pigments determination compared to the conventional one-dimensional liquid chromatography approach so far applied to the carotenoid analysis in the studied species. Moreover, the present study also aimed to investigate and to compare the carotenoid stability and composition in overripe yellow and red bell peppers collected directly from the plant, thus also evaluating whether biochemical changes are linked to carotenoid degradation in the nonclimacteric investigated fruits, for the first time. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Integration of magnetic solid phase fishing and off-line two-dimensional high-performance liquid chromatography-diode array detector-mass spectrometry for screening and identification of human serum albumin binders from Radix Astragali.

PubMed

Zhang, Yuping; Nie, Mingkun; Shi, Shuyun; You, Qingping; Guo, Junfang; Liu, Liangliang

2014-03-01

Radix Astragali is one of the most popular traditional medicinal herb and healthy dietary supplement. Isoflavonoids and astragalosides are the main bioactive ingredients. However, the systematic bioactive component analysis is inadequate so far. Then a facile method based on Fe3O4@SiO2-human serum albumin (Fe3O4@SiO2-HSA) magnetic solid phase fishing integrated with two-dimensional high-performance liquid chromatography-diode array detector-mass spectrometry (2D HPLC-DAD-MS(n)) was developed to fish out and identify HSA binders from Radix Astragali. The immobilized HSA displayed a high stability with 96.2% retained after ten consecutive cycles. 2D HPLC system (size exclusion chromatography×reversed phase chromatography, SEC×RP) were developed and optimised. Forty-seven bioactive compounds including thirty-four isoflavonoids and thirteen astragalosides were screened and identified or tentatively deduced based on their retention time, ultraviolet (UV), accurate molecular weight and diagnostic fragment ions. The results indicated that the integrated method could be widely applied for systematical fishing and identification of bioactive compounds, especially for low-abundance and overlapped compounds, from complex mixtures. Copyright © 2013 Elsevier Ltd. All rights reserved.

Implication of Proteins Containing Tetratricopeptide Repeats in Conditional Virulence Phenotypes of Legionella pneumophila

PubMed Central

Bandyopadhyay, Purnima; Sumer, Eren U.; Jayakumar, Deepak; Liu, Shuqing; Xiao, Huifang

2012-01-01

Legionella pneumophila, the causative agent of Legionnaires' disease, is a ubiquitous freshwater bacterium whose virulence phenotypes require a type IV secretion system (T4SS). L. pneumophila strain JR32 contains two virulence-associated T4SSs, the Dot/Icm and Lvh T4SSs. Defective entry and phagosome acidification phenotypes of dot/icm mutants are conditional and reversed by incubating broth-grown stationary-phase cultures in water (WS treatment) prior to infection, as a mimic of the aquatic environment of Legionella. Reversal of dot/icm virulence defects requires the Lvh T4SS and is associated with a >10-fold induction of LpnE, a tetratricopeptide repeat (TPR)-containing protein. In the current study, we demonstrated that defective entry and phagosome acidification phenotypes of mutants with changes in LpnE and EnhC, another TPR-containing protein, were similarly reversed by WS treatment. In contrast to dot/icm mutants for which the Lvh T4SS was required, reversal for the ΔlpnE or the ΔenhC mutant required that the other TPR-containing protein be present. The single and double ΔlpnE and ΔenhC mutants showed a hypersensitivity to sodium ion, a phenotype associated with dysfunction of the Dot/Icm T4SS. The ΔlpnE single and the ΔlpnE ΔenhC double mutant showed 3- to 9-fold increases in translocation of Dot/Icm T4SS substrates, LegS2/SplY and LepB. Taken together, these data identify TPR-containing proteins in a second mechanism by which the WS mimic of a Legionella environmental niche can reverse virulence defects of broth-grown cultures and implicate LpnE and EnhC directly or indirectly in translocation of Dot/Icm T4SS protein substrates. PMID:22563053

Formation of highly structured cubic micellar lipid nanoparticles of soy phosphatidylcholine and glycerol dioleate and their degradation by triacylglycerol lipase.

PubMed

Wadsäter, Maria; Barauskas, Justas; Nylander, Tommy; Tiberg, Fredrik

2014-05-28

Lipid nanoparticles of reversed internal phase structures, such as cubic micellar (I2) structure show good drug loading ability of peptides and proteins as well as some small molecules. Due to their controllable small size and inner morphology, such nanoparticles are suitable for drug delivery using several different administration routes, including intravenous, intramuscular, and subcutaneous injection. A very interesting system in this regard, is the two component soy phosphatidylcholine (SPC)/glycerol dioleate (GDO) system, which depending on the ratio of the lipid components form a range of reversed liquid crystalline phases. For a 50/50 (w/w) ratio in excess water, these lipids have been shown to form a reversed cubic micellar (I2) phase of the Fd3m structure. Here, we demonstrate that this SPC/GDO phase, in the presence of small quantities (5-10 wt %) of Polysorbate 80 (P80), can be dispersed into nanoparticles, still with well-defined Fd3m structure. The resulting nanoparticle dispersion has a narrow size distribution and exhibit good long-term stability. In pharmaceutical applications, biodegradation pathways of the drug delivery vehicles and their components are important considerations. In the second part of the study we show how the structure of the particles evolves during exposure to a triacylglycerol lipase (TGL) under physiological-like temperature and pH. TGL catalyzes the lipolytic degradation of acylglycerides, such as GDO, to monoglycerides, glycerol, and free fatty acids. During the degradation, the interior phase of the particles is shown to undergo continuous phase transitions from the reversed I2 structure to structures of less negative curvature (2D hexagonal, bicontinuous cubic, and sponge), ultimately resulting in the formation of multilamellar vesicles.

The allosteric HIV-1 integrase inhibitor BI-D affects virion maturation but does not influence packaging of a functional RNA genome.

PubMed

van Bel, Nikki; van der Velden, Yme; Bonnard, Damien; Le Rouzic, Erwann; Das, Atze T; Benarous, Richard; Berkhout, Ben

2014-01-01

The viral integrase (IN) is an essential protein for HIV-1 replication. IN inserts the viral dsDNA into the host chromosome, thereby aided by the cellular co-factor LEDGF/p75. Recently a new class of integrase inhibitors was described: allosteric IN inhibitors (ALLINIs). Although designed to interfere with the IN-LEDGF/p75 interaction to block HIV DNA integration during the early phase of HIV-1 replication, the major impact was surprisingly found on the process of virus maturation during the late phase, causing a reverse transcription defect upon infection of target cells. Virus particles produced in the presence of an ALLINI are misformed with the ribonucleoprotein located outside the virus core. Virus assembly and maturation are highly orchestrated and regulated processes in which several viral proteins and RNA molecules closely interact. It is therefore of interest to study whether ALLINIs have unpredicted pleiotropic effects on these RNA-related processes. We confirm that the ALLINI BI-D inhibits virus replication and that the produced virus is non-infectious. Furthermore, we show that the wild-type level of HIV-1 genomic RNA is packaged in virions and these genomes are in a dimeric state. The tRNAlys3 primer for reverse transcription was properly placed on this genomic RNA and could be extended ex vivo. In addition, the packaged reverse transcriptase enzyme was fully active when extracted from virions. As the RNA and enzyme components for reverse transcription are properly present in virions produced in the presence of BI-D, the inhibition of reverse transcription is likely to reflect the mislocalization of the components in the aberrant virus particle.

FUSION-Guided Hypothesis Development Leads to the Identification of N6,N6-Dimethyladenosine, a Marine-Derived AKT Pathway Inhibitor

PubMed Central

Vaden, Rachel M.; Oswald, Nathaniel W.; Potts, Malia B.; MacMillan, John B.; White, Michael A.

2017-01-01

Chemicals found in nature have evolved over geological time scales to productively interact with biological molecules, and thus represent an effective resource for pharmaceutical development. Marine-derived bacteria are rich sources of chemically diverse, bioactive secondary metabolites, but harnessing this diversity for biomedical benefit is limited by challenges associated with natural product purification and determination of biochemical mechanism. Using Functional Signature Ontology (FUSION), we report the parallel isolation and characterization of a marine-derived natural product, N6,N6-dimethyladenosine, that robustly inhibits AKT signaling in a variety of non-small cell lung cancer cell lines. Upon validation of the elucidated structure by comparison with a commercially available sample, experiments were initiated to understand the small molecule’s breadth of effect in a biological setting. One such experiment, a reverse phase protein array (RPPA) analysis of >50 kinases, indicated a specific cellular response to treatment. In all, leveraging the FUSION platform allowed for the rapid generation and validation of a biological mechanism of action hypothesis for an unknown natural product and permitted accelerated purification of the bioactive component from a chemically complex fraction. PMID:28294973

Metal-directed design of supramolecular protein assemblies

PubMed Central

Bailey, Jake B.; Subramanian, Rohit H.; Churchfield, Lewis A.

2016-01-01

Owing to their central roles in cellular signaling, construction, and biochemistry, protein-protein interactions (PPIs) and protein self-assembly have become a major focus of molecular design and synthetic biology. In order to circumvent the complexity of constructing extensive non-covalent interfaces, which are typically involved in natural PPIs and protein self-assembly, we have developed two design strategies, Metal-Directed Protein Self-Assembly (MDPSA) and Metal-Templated Interface Redesign (MeTIR). These strategies, inspired by both the proposed evolutionary roles of metals and their prevalence in natural PPIs, take advantage of the favorable properties of metal coordination (bonding strength, directionality, and reversibility) to guide protein self-assembly with minimal design and engineering. Using a small, monomeric protein (cytochrome cb562) as a model building block, we employed MDPSA and MeTIR to create a diverse array of functional supramolecular architectures which range from structurally tunable oligomers to metalloprotein complexes that can properly self-assemble in living cells into novel metalloenzymes. The design principles and strategies outlined herein should be readily applicable to other protein systems with the goal of creating new PPIs and protein assemblies with structures and functions not yet produced by natural evolution. PMID:27586336

Ultrasound extracted flavonoids from four varieties of Portuguese red grape skins determined by reverse-phase high-performance liquid chromatography with electrochemical detection.

PubMed

Novak, Ivana; Janeiro, Patricia; Seruga, Marijan; Oliveira-Brett, Ana Maria

2008-12-23

Several flavonoids present in red grape skins from four varieties of Portuguese grapes were determined by reverse-phase high-performance liquid chromatography (RP-HPLC) with electrochemical detection (ECD). Extraction of flavonoids from red grape skins was performed by ultrasonication, and hydrochloric acid in methanol was used as extraction solvent. The developed RP-HPLC method used combined isocratic and gradient elution with amperometric detection with a glassy carbon-working electrode. Good peak resolution was obtained following direct injection of a sample of red grape extract in a pH 2.20 mobile phase. Eleven different flavonoids: cyanidin-3-O-glucoside (kuromanin), delphinidin-3-O-glucoside (myrtillin), petunidin-3-O-glucoside, peonidin-3-O-glucoside, malvidin-3-O-glucoside (oenin), (+)-catechin, rutin, fisetin, myricetin, morin and quercetin, can be separated in a single run by direct injection of sample solution. The limit of detection obtained for these compounds by ECD was 20-90 pg/L, 1000 times lower when compared with photodiode array (PDA) limit of detection of 12-55 ng/L. RP-HPLC-ECD was characterized by an excellent sensitivity and selectivity, and appropriate for the simultaneous determination of these electroactive phenolic compounds present in red grape skins.

Liquid chromatographic determination of sennosides in Cassia angustifolia leaves.

PubMed

Srivastava, Alpuna; Pandey, Richa; Verma, Ram K; Gupta, Madan M

2006-01-01

A simple liquid chromatographic method was developed for the determination of sennosides B and A in leaves of Cassia angustifolia. These compounds were extracted from leaves with a mixture of methanol-water (70 + 30, v/v) after defatting with hexane. Analyte separation and quantitation were achieved by gradient reversed-phase liquid chromatography and UV absorbance at 270 nm using a photodiode array detector. The method involves the use of an RP-18 Lichrocart reversed-phase column (5 microm, 125 x 4.0 mm id) and a binary gradient mobile-phase profile. The various other aspects of analysis, namely, peak purity, similarity, recovery, repeatability, and robustness, were validated. Average recoveries of 98.5 and 98.6%, with a coefficient of variation of 0.8 and 0.3%, were obtained by spiking sample solution with 3 different concentration solutions of standards (60, 100, and 200 microg/mL). Detection limits were 10 microg/mL for sennoside B and 35 microg/mL for sennoside A, present in the sample solution. The quantitation limits were 28 and 100 microg/mL. The analytical method was applied to a large number of senna leaf samples. The new method provides a reliable tool for rapid screening of C. angustifolia samples in large numbers, which is needed in breeding/genetic engineering and genetic mapping experiments.

Rapid and Sensitive Reverse-phase High-performance Liquid Chromatography Method for Estimation of Ketorolac in Pharmaceuticals Using Weighted Regression

PubMed Central

Dubey, S. K.; Duddelly, S.; Jangala, H.; Saha, R. N.

2013-01-01

A reliable, rapid and sensitive isocratic reverse phase high-performance liquid chromatography method has been developed and validated for assay of ketorolac tromethamine in tablets and ophthalmic dosage forms using diclofenac sodium as an internal standard. An isocratic separation of ketorolac tromethamine was achieved on Oyster BDS (150×4.6 mm i.d., 5 μm particle size) column using mobile phase of methanol:acetonitrile:sodium dihydrogen phosphate (20 mM; pH 5.5) (50:10:40, %v/v) at a flow rate of 1.0 ml/min. The eluents were monitored at 322 nm for ketorolac and at 282 nm for diclofenac sodium with a photodiode array detector. The retention times of ketorolac and diclofenac sodium were found to be 1.9 min and 4.6 min, respectively. Response was a linear function of drug concentration in the range of 0.01-15 μg/ml (R2=0.994; linear regression model using weighing factor 1/x2) with a limit of detection and quantification of 0.002 μg/ml and 0.007 μg/ml, respectively. The % recovery and % relative standard deviation values indicated the method was accurate and precise. PMID:23901166

Holographic arrays for multi-path imaging artifact reduction

DOEpatents

McMakin, Douglas L.; Sheen, David M.; Hall, Thomas E.

2007-11-13

A method and apparatus to remove human features utilizing at least one transmitter transmitting a signal between 200 MHz and 1 THz, the signal having at least one characteristic of elliptical polarization, and at least one receiver receiving the reflection of the signal from the transmitter. A plurality of such receivers and transmitters are arranged together in an array which is in turn mounted to a scanner, allowing the array to be passed adjacent to the surface of the item being imaged while the transmitter is transmitting electromagnetic radiation. The array is passed adjacent to the surface of the item, such as a human being, that is being imaged. The portions of the received signals wherein the polarity of the characteristic has been reversed and those portions of the received signal wherein the polarity of the characteristic has not been reversed are identified. An image of the item from those portions of the received signal wherein the polarity of the characteristic was reversed is then created.

Proteomics of light-harvesting proteins in different plant species. Analysis and comparison by liquid chromatography-electrospray ionization mass spectrometry. Photosystem I.

PubMed

Zolla, Lello; Rinalducci, Sara; Timperio, Anna Maria; Huber, Christian G

2002-12-01

The light-harvesting proteins (Lhca) of photosystem I (PSI) from four monocot and five dicot species were extracted from plant material, separated by reversed-phase high-performance liquid chromatography (HPLC) and subsequently identified on the basis of their intact molecular masses upon on-line hyphenation with electrospray ionization mass spectrometry. Although their migration behavior in gel electrophoresis was very similar, the elution times among the four antenna types in reversed-phase-HPLC differed significantly, even more than those observed for the light-harvesting proteins of photosystem II. Identification of proteins is based on the good agreement between the measured intact molecular masses and the values calculated on the basis of their nucleotide-derived amino acid sequences, which makes the intact molecular masses applicable as intact mass tags. These values match excellently for Arabidopsis, most probably because of the availability of high-quality DNA sequence data. In all species examined, the four antennae eluted in the same order, namely Lhca1 > Lhca3 > Lhca4 > Lhca2. These characteristic patterns enabled an unequivocal assignment of the proteins in preparations from different species. Interestingly, in all species examined, Lhca1 and Lhca2 were present in two or three isoforms. A fifth antenna protein, corresponding to the Lhca6 gene, was found in tomato (Lycopersicon esculentum). However PSI showed a lower heterogeneity than photosystem II. In most plant species, Lhca2 and Lhca4 proteins are the most abundant PSI antenna proteins. The HPLC method used in this study was found to be highly reproducible, and the chromatograms may serve as a highly confident fingerprint for comparison within a single and among different species for future studies of the PSI antenna.

Unique protein expression signatures of survival time in kidney renal clear cell carcinoma through a pan-cancer screening.

PubMed

Han, Guangchun; Zhao, Wei; Song, Xiaofeng; Kwok-Shing Ng, Patrick; Karam, Jose A; Jonasch, Eric; Mills, Gordon B; Zhao, Zhongming; Ding, Zhiyong; Jia, Peilin

2017-10-03

In 2016, it is estimated that there will be 62,700 new cases of kidney cancer in the United States, and 14,240 patients will die from the disease. Because the incidence of kidney renal clear cell carcinoma (KIRC), the most common type of kidney cancer, is expected to continue to increase in the US, there is an urgent need to find effective diagnostic biomarkers for KIRC that could help earlier detection of and customized treatment strategies for the disease. Accordingly, in this study we systematically investigated KIRC's prognostic biomarkers for survival using the reverse phase protein array (RPPA) data and the high throughput sequencing data from The Cancer Genome Atlas (TCGA). With comprehensive data available in TCGA, we systematically screened protein expression based survival biomarkers in 10 major cancer types, among which KIRC presented many protein prognostic biomarkers of survival time. This is in agreement with a previous report that expression level changes (mRNAs, microRNA and protein) may have a better performance for prognosis of KIRC. In this study, we also identified 52 prognostic genes for KIRC, many of which are involved in cell-cycle and cancer signaling, as well as 15 tumor-stage-specific prognostic biomarkers. Notably, we found fewer prognostic biomarkers for early-stage than for late-stage KIRC. Four biomarkers (the RPPA protein IDs: FASN, ACC1, Cyclin_B1 and Rad51) were found to be prognostic for survival based on both protein and mRNA expression data. Through pan-cancer screening, we found that many protein biomarkers were prognostic for patients' survival in KIRC. Stage-specific survival biomarkers in KIRC were also identified. Our study indicated that these protein biomarkers might have potential clinical value in terms of predicting survival in KIRC patients and developing individualized treatment strategies. Importantly, we found many biomarkers in KIRC at both the mRNA expression level and the protein expression level. These biomarkers shared a significant overlap, indicating that they were technically replicable.

Separating DDTs in edible animal fats using matrix solid-phase dispersion extraction with activated carbon filter, Toyobo-KF.

PubMed

Furusawa, Naoto

2006-09-01

A technique is presented for the economical, routine, and quantitative analysis of contamination by dichloro-diphenyl-trichloroethanes (DDTs) [pp'-DDT, pp'-dichlorodiphenyl dichloroethylene, and pp'-dichlorodiphenyl dichloreothane in beef tallow and chicken fat samples, based on their separation using matrix solid-phase dispersion (MSPD) extraction with Toyobo-KF, an activated carbon fiber. Toyobo-KF is a newly applied MSPD sorbent, and it is followed by reversed-phase high-performance liquid chromatography (HPLC) with a photodiode array detector. The resulting analytical performance parameters [recoveries of spiked DDTs (0.1, 0.2, and 0.4 microg/g) > or = 81%, with relative standard deviations of < or = 8% (n = 5), and quantitation limits < or = 0.03 microg/g], with minimal handling and cost-efficiency, indicate that the present MSPD-HPLC method may be a useful tool for routine monitoring of DDT contamination in meat.

Elastin-like polypeptides: Therapeutic applications for an emerging class of nanomedicines.

PubMed

Despanie, Jordan; Dhandhukia, Jugal P; Hamm-Alvarez, Sarah F; MacKay, J Andrew

2016-10-28

Elastin-like polypeptides (ELPs) constitute a genetically engineered class of 'protein polymers' derived from human tropoelastin. They exhibit a reversible phase separation whereby samples remain soluble below a transition temperature (T t ) but form amorphous coacervates above T t . Their phase behavior has many possible applications in purification, sensing, activation, and nanoassembly. As humanized polypeptides, they are non-immunogenic, substrates for proteolytic biodegradation, and can be decorated with pharmacologically active peptides, proteins, and small molecules. Recombinant synthesis additionally allows precise control over ELP architecture and molecular weight, resulting in protein polymers with uniform physicochemical properties suited to the design of multifunctional biologics. As such, ELPs have been employed for various uses including as anti-cancer agents, ocular drug delivery vehicles, and protein trafficking modulators. This review aims to offer the reader a catalogue of ELPs, their various applications, and potential for commercialization across a broad spectrum of fields. Copyright © 2015. Published by Elsevier B.V.

Smart polymer brush nanostructures guide the self-assembly of pore-spanning lipid bilayers with integrated membrane proteins

NASA Astrophysics Data System (ADS)

Wilhelmina de Groot, G.; Demarche, Sophie; Santonicola, M. Gabriella; Tiefenauer, Louis; Vancso, G. Julius

2014-01-01

Nanopores in arrays on silicon chips are functionalized with pH-responsive poly(methacrylic acid) (PMAA) brushes and used as supports for pore-spanning lipid bilayers with integrated membrane proteins. Robust platforms are created by the covalent grafting of polymer brushes using surface-initiated atom transfer radical polymerization (ATRP), resulting in sensor chips that can be successfully reused over several assays. His-tagged proteins are selectively and reversibly bound to the nitrilotriacetic acid (NTA) functionalization of the PMAA brush, and consequently lipid bilayer membranes are formed. The enhanced membrane resistance as determined by electrochemical impedance spectroscopy and free diffusion of dyed lipids observed as fluorescence recovery after photobleaching confirmed the presence of lipid bilayers. Immobilization of the His-tagged membrane proteins on the NTA-modified PMAA brush near the pore edges is characterized by fluorescence microscopy. This system allows us to adjust the protein density in free-standing bilayers, which are stabilized by the polymer brush underneath. The potential application of the integrated platform for ion channel protein assays is demonstrated.

Development of High-Fill-Factor Large-Aperture Micromirrors for Agile Optical Phased Arrays

DTIC Science & Technology

2010-02-28

Final Project Report Contract/Grant Title: Development of High-Fill-Factor Large-Aperture Micromirrors for Agile Optical Phased Arrays...factor (HFF) micromirror array (MMA) has been proposed, fabricated and tested. Optical-phased-array (OPA) beam steering based on the HFF MMA has also...electrically tuned to multiple 2. 1. Background High-fill-factor (HFF) micromirror arrays (MMAs) can form optical phased arrays (OPAs) for laser beam

Characterization of nonlinear ultrasound fields of 2D therapeutic arrays

PubMed Central

Yuldashev, Petr V.; Kreider, Wayne; Sapozhnikov, Oleg A.; Farr, Navid; Partanen, Ari; Bailey, Michael R.; Khokhlova, Vera

2015-01-01

A current trend in high intensity focused ultrasound (HIFU) technologies is to use 2D focused phased arrays that enable electronic steering of the focus, beamforming to avoid overheating of obstacles (such as ribs), and better focusing through inhomogeneities of soft tissue using time reversal methods. In many HIFU applications, the acoustic intensity in situ can reach thousands of W/cm2 leading to nonlinear propagation effects. At high power outputs, shock fronts develop in the focal region and significantly alter the bioeffects induced. Clinical applications of HIFU are relatively new and challenges remain for ensuring their safety and efficacy. A key component of these challenges is the lack of standard procedures for characterizing nonlinear HIFU fields under operating conditions. Methods that combine low-amplitude pressure measurements and nonlinear modeling of the pressure field have been proposed for axially symmetric single element transducers but have not yet been validated for the much more complex 3D fields generated by therapeutic arrays. Here, the method was tested for a clinical HIFU source comprising a 256-element transducer array. A numerical algorithm based on the Westervelt equation was used to enable 3D full-diffraction nonlinear modeling. With the acoustic holography method, the magnitude and phase of the acoustic field were measured at a low power output and used to determine the pattern of vibrations at the surface of the array. This pattern was then scaled to simulate a range of intensity levels near the elements up to 10 W/cm2. The accuracy of modeling was validated by comparison with direct measurements of the focal waveforms using a fiber-optic hydrophone. Simulation results and measurements show that shock fronts with amplitudes up to 100 MPa were present in focal waveforms at clinically relevant outputs, indicating the importance of strong nonlinear effects in ultrasound fields generated by HIFU arrays. PMID:26203345

The action of a dietary retinoid on gene expression and cancer induction in electron-irradiated rat skin

NASA Technical Reports Server (NTRS)

Burns, Fredric J.; Chen, Shuaili; Xu, Guijuan; Wu, Feng; Tang, Moon-Shong

2002-01-01

Current models of radiation carcinogenesis generally assume that the DNA is damaged in a variety of ways by the radiation and that subsequent cell divisions contribute to the conversion of the damage to heritable mutations. Cancer may seem complex and intractable, but its complexity provides multiple opportunities for preventive interventions. Mitotic inhibitors are among the strongest cancer preventive agents, not only slowing the growth rate of preneoplasias but also increasing the fidelity of DNA repair processes. Ionizing radiation, including electrons, is a strong inducer of cancer in rat skin, and dietary retinoids have shown potent cancer preventive activity in the same system. A non-toxic dietary dose of retinyl acetate altered gene expression levels 24 hours after electron irradiation of rat skin. Of the 8740 genes on an Affymetrix rat expression array, the radiation significantly (5 fold or higher) altered 188, while the retinoid altered 231, including 16 radiation-altered genes that were reversely altered. While radiation strongly affected the expression of stress response, immune/inflammation and nucleic acid metabolism genes, the retinoid most strongly affected proliferation-related genes, including some significant reversals, such as, keratin 14, retinol binding protein, and calcium binding proteins. These results point to reversal of proliferation-relevant genes as a likely basis for the anti-radiogenic effects of dietary retinyl acetate.

Two-dimensional turbulent flow chromatography coupled on-line to liquid chromatography-mass spectrometry for solution-based ligand screening against multiple proteins.

PubMed

Zhou, Jian-Liang; An, Jing-Jing; Li, Ping; Li, Hui-Jun; Jiang, Yan; Cheng, Jie-Fei

2009-03-20

We present herein a novel bioseparation/chemical analysis strategy for protein-ligand screening and affinity ranking in compound mixtures, designed to increase screening rates and improve sensitivity and ruggedness in performance. The strategy is carried out by combining on-line two-dimensional turbulent flow chromatography (2D-TFC) with liquid chromatography-mass spectrometry (LC-MS), and accomplished through the following steps: (1) a reversed-phase TFC stage to separate the protein/ligand complex from the unbound free molecules, (2) an on-line dissociation process to release the bound ligands from the complexes, and (3) a second mixed-mode cation-exchange/reversed-phase TFC stage to trap the bound ligands and to remove the proteins and salts, followed by LC-MS analysis for identification and determination of the binding affinities. The technique can implement an ultra-fast isolation of protein/ligand complex with the retention time of a complex peak in about 5s, and on-line prepare the "clean" sample to be directly compatible with the LC-MS analysis. The improvement in performance of this 2D-TFC/LC-MS approach over the conventional approach has been demonstrated by determining affinity-selected ligands of the target proteins acetylcholinesterase and butyrylcholinesterase from a small library with known binding affinities and a steroidal alkaloid library composed of structurally similar compounds. Our results show that 2D-TFC/LC-MS is a generic and efficient tool for high-throughput screening of ligands with low-to-high binding affinities, and structure-activity relationship evaluation.

3D printed titanium micro-bore columns containing polymer monoliths for reversed-phase liquid chromatography.

PubMed

Gupta, Vipul; Talebi, Mohammad; Deverell, Jeremy; Sandron, Sara; Nesterenko, Pavel N; Heery, Brendan; Thompson, Fletcher; Beirne, Stephen; Wallace, Gordon G; Paull, Brett

2016-03-03

The potential of 3D selective laser melting (SLM) technology to produce compact, temperature and pressure stable titanium alloy chromatographic columns is explored. A micro bore channel (0.9 mm I.D. × 600 mm long) was produced within a 5 × 30 × 30 mm titanium alloy (Ti-6Al-4V) cuboid, in form of a double handed spiral. A poly(butyl methacrylate-co-ethyleneglycoldimethacrylate) (BuMA-co-EDMA) monolithic stationary phase was thermally polymerised within the channel for application in reversed-phase high-performance liquid chromatography. The prepared monolithic column was applied to the liquid chromatographic separation of intact proteins and peptides. Peak capacities of 69-76 (for 6-8 proteins respectively) were observed during isothermal separation of proteins at 44 °C which were further increased to 73-77 using a thermal step gradient with programmed temperature from 60 °C to 35 °C using an in-house built direct-contact heater/cooler platform based upon matching sized Peltier thermoelectric modules. Rapid temperature gradients were possible due to direct-contact between the planar metal column and the Peltier module, and the high thermal conductivity of the titanium column as compared to a similar stainless steel printed column. The separation of peptides released from a digestion of E.coli was also achieved in less than 35 min with ca. 40 distinguishable peaks at 210 nm. Copyright © 2016 Elsevier B.V. All rights reserved.

Optimizing Satellite Communications With Adaptive and Phased Array Antennas

NASA Technical Reports Server (NTRS)

Ingram, Mary Ann; Romanofsky, Robert; Lee, Richard Q.; Miranda, Felix; Popovic, Zoya; Langley, John; Barott, William C.; Ahmed, M. Usman; Mandl, Dan

2004-01-01

A new adaptive antenna array architecture for low-earth-orbiting satellite ground stations is being investigated. These ground stations are intended to have no moving parts and could potentially be operated in populated areas, where terrestrial interference is likely. The architecture includes multiple, moderately directive phased arrays. The phased arrays, each steered in the approximate direction of the satellite, are adaptively combined to enhance the Signal-to-Noise and Interference-Ratio (SNIR) of the desired satellite. The size of each phased array is to be traded-off with the number of phased arrays, to optimize cost, while meeting a bit-error-rate threshold. Also, two phased array architectures are being prototyped: a spacefed lens array and a reflect-array. If two co-channel satellites are in the field of view of the phased arrays, then multi-user detection techniques may enable simultaneous demodulation of the satellite signals, also known as Space Division Multiple Access (SDMA). We report on Phase I of the project, in which fixed directional elements are adaptively combined in a prototype to demodulate the S-band downlink of the EO-1 satellite, which is part of the New Millennium Program at NASA.

Magnetic Diagnostics on the Magnetized Shock Experiment (MSX)

NASA Astrophysics Data System (ADS)

Hutchinson, T. M.; Weber, T. E.; Boguski, J. C.; Intrator, T. P.; Smith, R. J.; Dunn, J. P.

2013-10-01

The Magnetized Shock Experiment (MSX) at Los Alamos National Laboratory was built to investigate the physics of high-Alfvénic, supercritical, magnetized shocks through the acceleration and subsequent stagnation of a Field Reversed Configuration (FRC) plasmoid against a magnetic mirror and/or plasma target. An array of high-bandwidth, multi-axis, robust, internal magnetic probes has been constructed to characterize flux compression ratios, instability formation, and turbulent macro-scale features of the post-shock plasma. The mirror magnet is mounted on a linear translation stage, providing a capability to axially move the shock layer through the probe field of view. An independent, external probe array also provides conventional information on the FRC shape, velocity, and total pressure during the formation and acceleration phases. Probe design, characterization, configuration, and initial results are presented. This work is supported by the DOE OFES and NNSA under LANS contract DE-AC52-06NA25369. LA-UR-13-25189.

PROTEOMIC ANALYSIS OPTIMIZATION: SELECTIVE PROTEIN SAMPLE ON-COLUMN RETENTION IN REVERSE-PHASE LIQUID CHROMATOGRAPHY

EPA Science Inventory

Why work was done?

To be able to identify, on a proteomic level, cytochromes P450 (CYP) and UDP-glucuronosyltransferases (UGT) in mouse liver microsomes for the conazole exposure study IRP # NHEERL-ECD-SCN-CZ-2002-01-R1_Addendum 1. The new enrichment method was necessary beca...

Influence of Whey Peptides on the Surface Activity of k-casein and ß-lactoglobulin

USDA-ARS?s Scientific Manuscript database

Whey protein hydrolysate (WPH) was fractionated by reverse-phase chromatography to obtain fractions of varying surface-hydrophobicities. A model oil–water interface (MI) was pre-coated with the WPH or fractions thereof. Contact angle (') of sessile drops of '-casein ('-CN) or ß-lactoglobulin A (ß-LG...

Roles of water molecules in bacteria and viruses

NASA Astrophysics Data System (ADS)

Cox, C. S.

1993-02-01

In addition to water, microbes mainly comprise lipids, carbohydrates, proteins and nucleic acids. Their structure and function singularly and conjointly is affected by water activity. Desiccation leads to dramatic lipid phase changes whereas carbohydrates, proteins and nucleic acids initially suffer spontaneous, reversible low activation energy Maillard reactions forming products that more slowly re-arrange, cross-link etc. to give non-native states. While initial products spontaneously may reverse to native states by raising water activity, later products only do so through energy consumption and enzymatic activity eg. repair. Yet, native states of lipid membranes and associated enzymes are required to generate energy. Consequently, good reserves of high energy compounds (e.g. ATP) and of membrane stabilisers (e.g. trehalose) may be expected to enhance survival following drying and rehydration (e.g. anhydrobiotic organisms).

Towards a Model of Cold Denaturation of Proteins

NASA Astrophysics Data System (ADS)

Sanchez, Isaac

2010-10-01

Proteins/enzymes can undergo cold denaturation or cold deactivation. In the active or natured state, a protein exists in a unique folded/ordered state. In the deactivated (denatured) state, a protein unfolds and exists in a disordered expanded state. This protein folding/unfolding or order/disorder transition can be triggered by a temperature change. What seems paradoxical is that the active (ordered) state can be induced by heating, or equivalently, the disordered inactive state can be induced by cooling. This is equivalent to an Ising spin model passing from a disordered array of spins to an ordered array by increasing temperature! Hydrogels and their corresponding polyelectrolyte chains behave similarly, i.e., the swollen disordered state can be induced by cooling while the more ordered collapsed or globular state is induced by heating (an entropically driven phase transition). In a living cell at the physiological temperature of 37 C, activation and deactivation of proteins is triggered by local environmental changes in pH, salinity, etc. The important physics is that the denaturation temperature can be moved up or down relative to 37 C by these stimuli. Moving the transition temperature up can destabilize the active protein while moving it down leads to stabilization. An analytical polymer model will be described that exhibits cold denaturation behavior.

BDNF is essential to promote persistence of long-term memory storage

PubMed Central

Bekinschtein, Pedro; Cammarota, Martín; Katche, Cynthia; Slipczuk, Leandro; Rossato, Janine I.; Goldin, Andrea; Izquierdo, Ivan; Medina, Jorge H.

2008-01-01

Persistence is a characteristic attribute of long-term memories (LTMs). However, little is known about the molecular mechanisms that mediate this process. We recently showed that persistence of LTM requires a late protein synthesis- and BDNF-dependent phase in the hippocampus. Here, we show that intrahippocampal delivery of BDNF reverses the deficit in memory persistence caused by inhibition of hippocampal protein synthesis. Importantly, we demonstrate that BDNF induces memory persistence by itself, transforming a nonlasting LTM trace into a persistent one in an ERK-dependent manner. Thus, BDNF is not only necessary, but sufficient to induce a late postacquisition phase in the hippocampus essential for persistence of LTM storage. PMID:18263738

Novel iron oxide nanotube arrays as high-performance anodes for lithium ion batteries

NASA Astrophysics Data System (ADS)

Zhong, Yuan; Fan, Huiqing; Chang, Ling; Shao, Haibo; Wang, Jianming; Zhang, Jianqing; Cao, Chu-nan

2015-11-01

Nanostructured iron oxides can be promising anode materials for lithium ion batteries (LIBs). However, improvement on the rate capability and/or electrochemical cycling stability of iron oxide anode materials remains a key challenge because of their poor electrical conductivities and large volume expansion during cycling. Herein, the vertically aligned arrays of one-dimensional (1D) iron oxide nanotubes with 5.8 wt% carbon have been fabricated by a novel surfactant-free self-corrosion process and subsequent thermal treatment. The as-fabricated nanotube array electrode delivers a reversible capacity of 932 mAh g-1 after 50 charge-discharge cycles at a current of 0.6 A g-1. The electrode still shows a reversible capacity of 610 mAh g-1 even at a very high rate (8.0 A g-1), demonstrating its prominent rate capability. Furthermore, the nanotube array electrode also exhibits the excellent electrochemical cycling stability with a reversible capacity of 880 mAh g-1 after 500 cycles at a current of 4 A g-1. The nanotube array electrode with superior lithium storage performance reveals the promising potential as a high-performance anode for LIBs.

Topologically protected excitons in porphyrin thin films

NASA Astrophysics Data System (ADS)

Yuen-Zhou, Joel; Saikin, Semion K.; Yao, Norman Y.; Aspuru-Guzik, Alán

2014-11-01

The control of exciton transport in organic materials is of fundamental importance for the development of efficient light-harvesting systems. This transport is easily deteriorated by traps in the disordered energy landscape. Here, we propose and analyse a system that supports topological Frenkel exciton edge states. Backscattering of these chiral Frenkel excitons is prohibited by symmetry, ensuring that the transport properties of such a system are robust against disorder. To implement our idea, we propose a two-dimensional periodic array of tilted porphyrins interacting with a homogeneous magnetic field. This field serves to break time-reversal symmetry and results in lattice fluxes that mimic the Aharonov-Bohm phase acquired by electrons. Our proposal is the first blueprint for realizing topological phases of matter in molecular aggregates and suggests a paradigm for engineering novel excitonic materials.

Topologically protected excitons in porphyrin thin films.

PubMed

Yuen-Zhou, Joel; Saikin, Semion K; Yao, Norman Y; Aspuru-Guzik, Alán

2014-11-01

The control of exciton transport in organic materials is of fundamental importance for the development of efficient light-harvesting systems. This transport is easily deteriorated by traps in the disordered energy landscape. Here, we propose and analyse a system that supports topological Frenkel exciton edge states. Backscattering of these chiral Frenkel excitons is prohibited by symmetry, ensuring that the transport properties of such a system are robust against disorder. To implement our idea, we propose a two-dimensional periodic array of tilted porphyrins interacting with a homogeneous magnetic field. This field serves to break time-reversal symmetry and results in lattice fluxes that mimic the Aharonov-Bohm phase acquired by electrons. Our proposal is the first blueprint for realizing topological phases of matter in molecular aggregates and suggests a paradigm for engineering novel excitonic materials.

Determination of the molecular weight of poly(ethylene glycol) in biological samples by reversed-phase LC-MS with in-source fragmentation.

PubMed

Warrack, Bethanne M; Redding, Brian P; Chen, Guodong; Bolgar, Mark S

2013-05-01

PEGylation has been widely used to improve the biopharmaceutical properties of therapeutic proteins and peptides. Previous studies have used multiple analytical techniques to determine the fate of both the therapeutic molecule and unconjugated poly(ethylene glycol) (PEG) after drug administration. A straightforward strategy utilizing liquid chromatography-mass spectrometry (LC-MS) to characterize high-molecular weight PEG in biologic matrices without a need for complex sample preparation is presented. The method is capable of determining whether high-MW PEG is cleaved in vivo to lower-molecular weight PEG species. Reversed-phase chromatographic separation is used to take advantage of the retention principles of polymeric materials whereby elution order correlates with PEG molecular weight. In-source collision-induced dissociation (CID) combined with selected reaction monitoring (SRM) or selected ion monitoring (SIM) mass spectrometry (MS) is then used to monitor characteristic PEG fragment ions in biological samples. MS provides high sensitivity and specificity for PEG and the observed retention times in reversed-phase LC enable estimation of molecular weight. This method was successfully used to characterize PEG molecular weight in mouse serum samples. No change in molecular weight was observed for 48 h after dosing.

Phased Antenna Array for Global Navigation Satellite System Signals

NASA Technical Reports Server (NTRS)

Turbiner, Dmitry (Inventor)

2015-01-01

Systems and methods for phased array antennas are described. Supports for phased array antennas can be constructed by 3D printing. The array elements and combiner network can be constructed by conducting wire. Different parameters of the antenna, like the gain and directivity, can be controlled by selection of the appropriate design, and by electrical steering. Phased array antennas may be used for radio occultation measurements.

Magnetization mechanisms in ordered arrays of polycrystalline Fe100-xCox nanowires

NASA Astrophysics Data System (ADS)

Viqueira, M. S.; Bajales, N.; Urreta, S. E.; Bercoff, P. G.

2015-05-01

Magnetization reversal processes and coercivity mechanisms in polycrystalline Fe100-xCox nanowire arrays, resulting from an AC electrodeposition process, are investigated. The array coercivity is described on the basis of polarization reversal mechanisms operating in individual wires, under the effect of inter-wire dipolar interactions described by a mean field approximation. For individual wires, a reversal mechanism involving the nucleation and further expansion of domain-wall like spin configuration is considered. The wires have a mean grain size larger than both the nanowire diameter and the exchange length, so localized and non-cooperative nucleation modes are considered. As the Co content increases, the alloy saturation polarization gradually decreases, but the coercive field and the relative remanence of the arrays increase, indicating that they are not controlled by the shape anisotropy in all the composition range. The coercive field dependence on the angle between the applied field and the wire long axis is not well described by reversal mechanisms involving nucleation and further displacement of neither vortex nor transverse ideal domain walls. On the contrary, the angular dependence of the coercive field observed at room temperature is well predicted by a model considering nucleation of inverse domains by localized curling, in regions smaller than the grain size, exhibiting quite small aspect ratios as compared to those of the entire nanowire. In arrays with higher Co contents, a transition from an initial (small angle) localized curling nucleation mechanism to another one, involving localized coherent rotation is observed at about π/4.

Probing topological protection using a designer surface plasmon structure

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

Gao, Fei; Gao, Zhen; Shi, Xihang

Topological photonic states, inspired by robust chiral edge states in topological insulators, have recently been demonstrated in a few photonic systems, including an array of coupled on-chip ring resonators at communication wavelengths. However, the intrinsic difference between electrons and photons determines that the 'topological protection' in time-reversal-invariant photonic systems does not share the same robustness as its counterpart in electronic topological insulators. Here in a designer surface plasmon platform consisting of tunable metallic sub-wavelength structures, we construct photonic topological edge states and probe their robustness against a variety of defect classes, including some common time-reversal-invariant photonic defects that can breakmore » the topological protection, but do not exist in electronic topological insulators. Furthermore, this is also an experimental realization of anomalous Floquet topological edge states, whose topological phase cannot be predicted by the usual Chern number topological invariants.« less

Probing topological protection using a designer surface plasmon structure

DOE PAGES

Gao, Fei; Gao, Zhen; Shi, Xihang; ...

2016-05-20

Topological photonic states, inspired by robust chiral edge states in topological insulators, have recently been demonstrated in a few photonic systems, including an array of coupled on-chip ring resonators at communication wavelengths. However, the intrinsic difference between electrons and photons determines that the 'topological protection' in time-reversal-invariant photonic systems does not share the same robustness as its counterpart in electronic topological insulators. Here in a designer surface plasmon platform consisting of tunable metallic sub-wavelength structures, we construct photonic topological edge states and probe their robustness against a variety of defect classes, including some common time-reversal-invariant photonic defects that can breakmore » the topological protection, but do not exist in electronic topological insulators. Furthermore, this is also an experimental realization of anomalous Floquet topological edge states, whose topological phase cannot be predicted by the usual Chern number topological invariants.« less

Chemical heterogeneity as a result of hydroxylamine cleavage of a fusion protein of human insulin-like growth factor I.

PubMed Central

Canova-Davis, E; Eng, M; Mukku, V; Reifsnyder, D H; Olson, C V; Ling, V T

1992-01-01

Recombinant DNA techniques were used to biosynthesize human insulin-like growth factor I (hIGF-I) as a fusion protein wherein the fusion polypeptide is an IgG-binding moiety derived from staphylococcal protein A. This fusion protein is produced in Escherichia coli and secreted into the fermentation broth. In order to release mature recombinant-derived hIGF-I (rhIGF-I), the fusion protein is treated with hydroxylamine, which cleaves a susceptible Asn-Gly bond that has been engineered into the fusion protein gene. Reversed-phase h.p.l.c. was used to estimate the purity of the rhIGF-I preparations, especially for the quantification of the methionine sulphoxide-containing variant. It was determined that hydroxylamine cleavage of the fusion protein produced, as a side reaction, hydroxamates of the asparagine and glutamine residues in rhIGF-I. Although isoelectric focusing was effective in detecting, and reversed-phase h.p.l.c. for producing enriched fractions of the hydroxamate variants, ion-exchange chromatography was a more definitive procedure, as it allowed quantification and facile removal of these variants. The identity of the variants as hydroxamates was established by Staphylococcus aureus V8 proteinase digestion, followed by m.s., as the modification was transparent to amino acid and N-terminal sequence analyses. The biological activity of rhIGF-I was established by its ability to incorporate [3H]thymidine into the DNA of BALB/c373 cells and by a radioreceptor assay utilizing human placental membranes. Both assays demonstrate that the native, recombinant and methionine sulphoxide and hydroxamate IGF-I variants are essentially equipotent. Images Fig. 2. PMID:1637301

Phased Arrays of Ground and Airborne Mobile Terminals for Satellite Communications

NASA Technical Reports Server (NTRS)

Huang, John

1996-01-01

Phased array antenna is beginning to play an important in the arena of mobile/satellite communications. Two examples of mobile terminal phased arrays will be shown. Their technical background, challenges, and cost drivers will be discussed. A possible solution to combat some of the deficiencies of the conventional phased array by exploiting the phased reflectarray technology will be briefly presented.

Sample displacement chromatography as a method for purification of proteins and peptides from complex mixtures

PubMed Central

Gajdosik, Martina Srajer; Clifton, James; Josic, Djuro

2012-01-01

Sample displacement chromatography (SDC) in reversed-phase and ion-exchange modes was introduced approximately twenty years ago. This method takes advantage of relative binding affinities of components in a sample mixture. During loading, there is a competition among different sample components for the sorption on the surface of the stationary phase. SDC was first used for the preparative purification of proteins. Later, it was demonstrated that this kind of chromatography can also be performed in ion-exchange, affinity and hydrophobic-interaction mode. It has also been shown that SDC can be performed on monoliths and membrane-based supports in both analytical and preparative scale. Recently, SDC in ion-exchange and hydrophobic interaction mode was also employed successfully for the removal of trace proteins from monoclonal antibody preparations and for the enrichment of low abundance proteins from human plasma. In this review, the principals of SDC are introduced, and the potential for separation of proteins and peptides in micro-analytical, analytical and preparative scale is discussed. PMID:22520159

Regulation of HIF-1α signaling and chemoresistance in acute lymphocytic leukemia under hypoxic conditions of the bone marrow microenvironment

PubMed Central

Frolova, Olga; Samudio, Ismael; Benito, Juliana Maria; Jacamo, Rodrigo; Kornblau, Steven M.; Markovic, Ana; Schober, Wendy; Lu, Hongbo; Qiu, Yi Hua; Buglio, Daniela; McQueen, Teresa; Pierce, Sherry; Shpall, Elizabeth; Konoplev, Sergej; Thomas, Deborah; Kantarjian, Hagop; Lock, Richard; Andreeff, Michael; Konopleva, Marina

2012-01-01

Overcoming resistance to chemotherapy is the main therapeutic challenge in the treatment of acute lymphocytic leukemia (ALL). Interactions between leukemia cells and the microenvironment promote leukemia cell survival and confer resistance to chemotherapy. Hypoxia is an integral component of bone marrow (BM) microenvironment. Hypoxia-inducible factor-1α (HIF-1), a key regulator of the cellular response to hypoxia, regulates cell growth and metabolic adaptation to hypoxia. HIF-1α expression, analyzed by Reverse Phase Protein Arrays in 92 specimens from newly diagnosed patients with pre-B-ALL, had a negative prognostic impact on survival (p = 0.0025). Inhibition of HIF-1α expression by locked mRNA antagonist (LNA) promoted chemosensitivity under hypoxic conditions, while pharmacological or genetic stabilization of HIF-1α under normoxia inhibited cell growth and reduced apoptosis induction by chemotherapeutic agents. Co-culture of pre-B ALL or REH cells with BM-derived mesenchymal stem cells (MSC) under hypoxia resulted in further induction of HIF-1α protein and acquisition of the glycolytic phenotype, in part via stroma-induced AKT/mTOR signaling. mTOR blockade with everolimus reduced HIF-1α expression, diminished glucose uptake and glycolytic rate and partially restored the chemosensitivity of ALL cells under hypoxia/stroma co-cultures. Hence, mTOR inhibition or blockade of HIF-1α-mediated signaling may play an important role in chemosensitization of ALL cells under hypoxic conditions of the BM microenvironment. PMID:22785211

Methods for processing microarray data.

PubMed

Ares, Manuel

2014-02-01

Quality control must be maintained at every step of a microarray experiment, from RNA isolation through statistical evaluation. Here we provide suggestions for analyzing microarray data. Because the utility of the results depends directly on the design of the experiment, the first critical step is to ensure that the experiment can be properly analyzed and interpreted. What is the biological question? What is the best way to perform the experiment? How many replicates will be required to obtain the desired statistical resolution? Next, the samples must be prepared, pass quality controls for integrity and representation, and be hybridized and scanned. Also, slides with defects, missing data, high background, or weak signal must be rejected. Data from individual slides must be normalized and combined so that the data are as free of systematic bias as possible. The third phase is to apply statistical filters and tests to the data to determine genes (1) expressed above background, (2) whose expression level changes in different samples, and (3) whose RNA-processing patterns or protein associations change. Next, a subset of the data should be validated by an alternative method, such as reverse transcription-polymerase chain reaction (RT-PCR). Provided that this endorses the general conclusions of the array analysis, gene sets whose expression, splicing, polyadenylation, protein binding, etc. change in different samples can be classified with respect to function, sequence motif properties, as well as other categories to extract hypotheses for their biological roles and regulatory logic.

Biotin Attachment Domain-Containing Proteins Irreversibly Inhibit Acetyl CoA Carboxylase

DOE PAGES

Keereetaweep, Jantana; Liu, Hui; Zhai, Zhiyang; ...

2018-04-06

The first committed step in fatty acid synthesis is mediated by Acetyl-CoA carboxylase (ACCase), a biotin-dependent enzyme that carboxylates acetyl-CoA to produce malonyl-CoA. ACCase can be feedback-regulated by short-term (reversible) and longer-term (irreversible) inhibition upon oversupply of fatty acids (FA) provided by Tween80 (predominantly containing oleic acid; 18:1). Biotin-Attachment-Domain-Containing (BADC) proteins are inactive analogs of biotin carboxyl transfer protein (BCCP) that lack biotin and their incorporation into ACCase downregulates it by displacing active (biotin-containing) BCCP subunits. Individual T-DNA insertion lines of BADC1, BADC2, and BADC3 were used to generate badc1badc2 and badc1badc3. The badc1badc3 mutant and wild-type exhibited normal growthmore » and development, however ACCase activity was 26% higher in badc1badc3 relative to wild-type and its seeds contained 30.1 %DW more FA and 32.6 %DW more TAG than wild-type. Cell suspension cultures were generated from leaves of badc1badc3 and wild-type plants to test whether BADC contributes to the irreversible phase of ACCase inhibition resulting from culture in medium containing 10mM Tween80. While the reversible phase of ACCase inhibition after two days of Tween80 feeding was equivalent for badc1badc3 and wild-type, the irreversible phase of inhibition following four days of Tween80 feeding was reduced by 50% in badc1badc3 relative to wild-type. In this work we present evidence for two important homeostatic roles for BADC proteins in downregulating ACCase activity: during normal growth and development, and by contributing to its long-term irreversible feedback inhibition resulting from oversupply of fatty acids.« less

Biotin Attachment Domain-Containing Proteins Irreversibly Inhibit Acetyl CoA Carboxylase

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

Keereetaweep, Jantana; Liu, Hui; Zhai, Zhiyang

The first committed step in fatty acid synthesis is mediated by Acetyl-CoA carboxylase (ACCase), a biotin-dependent enzyme that carboxylates acetyl-CoA to produce malonyl-CoA. ACCase can be feedback-regulated by short-term (reversible) and longer-term (irreversible) inhibition upon oversupply of fatty acids (FA) provided by Tween80 (predominantly containing oleic acid; 18:1). Biotin-Attachment-Domain-Containing (BADC) proteins are inactive analogs of biotin carboxyl transfer protein (BCCP) that lack biotin and their incorporation into ACCase downregulates it by displacing active (biotin-containing) BCCP subunits. Individual T-DNA insertion lines of BADC1, BADC2, and BADC3 were used to generate badc1badc2 and badc1badc3. The badc1badc3 mutant and wild-type exhibited normal growthmore » and development, however ACCase activity was 26% higher in badc1badc3 relative to wild-type and its seeds contained 30.1 %DW more FA and 32.6 %DW more TAG than wild-type. Cell suspension cultures were generated from leaves of badc1badc3 and wild-type plants to test whether BADC contributes to the irreversible phase of ACCase inhibition resulting from culture in medium containing 10mM Tween80. While the reversible phase of ACCase inhibition after two days of Tween80 feeding was equivalent for badc1badc3 and wild-type, the irreversible phase of inhibition following four days of Tween80 feeding was reduced by 50% in badc1badc3 relative to wild-type. In this work we present evidence for two important homeostatic roles for BADC proteins in downregulating ACCase activity: during normal growth and development, and by contributing to its long-term irreversible feedback inhibition resulting from oversupply of fatty acids.« less

Phased Array Beamforming and Imaging in Composite Laminates Using Guided Waves

NASA Technical Reports Server (NTRS)

Tian, Zhenhua; Leckey, Cara A. C.; Yu, Lingyu

2016-01-01

This paper presents the phased array beamforming and imaging using guided waves in anisotropic composite laminates. A generic phased array beamforming formula is presented, based on the classic delay-and-sum principle. The generic formula considers direction-dependent guided wave properties induced by the anisotropic material properties of composites. Moreover, the array beamforming and imaging are performed in frequency domain where the guided wave dispersion effect has been considered. The presented phased array method is implemented with a non-contact scanning laser Doppler vibrometer (SLDV) to detect multiple defects at different locations in an anisotropic composite plate. The array is constructed of scan points in a small area rapidly scanned by the SLDV. Using the phased array method, multiple defects at different locations are successfully detected. Our study shows that the guided wave phased array method is a potential effective method for rapid inspection of large composite structures.

Delamination Detection Using Guided Wave Phased Arrays

NASA Technical Reports Server (NTRS)

Tian, Zhenhua; Yu, Lingyu; Leckey, Cara

2016-01-01

This paper presents a method for detecting multiple delaminations in composite laminates using non-contact phased arrays. The phased arrays are implemented with a non-contact scanning laser Doppler vibrometer (SLDV). The array imaging algorithm is performed in the frequency domain where both the guided wave dispersion effect and direction dependent wave properties are considered. By using the non-contact SLDV array with a frequency domain imaging algorithm, an intensity image of the composite plate can be generated for delamination detection. For the proof of concept, a laboratory test is performed using a non-contact phased array to detect two delaminations (created through quasi-static impact test) at different locations in a composite plate. Using the non-contact phased array and frequency domain imaging, the two impact-induced delaminations are successfully detected. This study shows that the non-contact phased array method is a potentially effective method for rapid delamination inspection in large composite structures.

SPECIAL ISSUE DEVOTED TO THE 80TH ANNIVERSARY OF ACADEMICIAN N G BASOV'S BIRTH: Structural rearrangements in the aqueous phase of cell suspensions and protein solutions induced by a light-oxygen effect

NASA Astrophysics Data System (ADS)

Zakharov, S. D.; Ivanov, Andrei V.; Wolf, E. B.; Danilov, V. P.; Murina, T. M.; Nguen, K. T.; Novikov, E. G.; Panasenko, N. A.; Perov, S. N.; Skopinov, S. A.; Timofeev, Yu P.

2003-02-01

Temperature-dependent transient processes initiated by a direct photogeneration of singlet oxygen in suspensions of human erythrocytes and solutions of serum albumin are studied. The processes appear as anomalous jumps in the temperature dependences of the deformability coefficient of erythrocytes and the refractive index of the extracellular medium and protein solution. In the temperature regions of anomalous jumps, cells and proteins transfer to a metastable state of a lower activity, but they can be isothermally photoreactivated. Simultaneously, a reversible rearrangement of the aqueous phase occurs near the cell and protein surfaces, accompanied by the formation of an extended corona (hydrogel). The transient processes are interpreted as phase transitions in the membrane of erythrocytes and conformation transitions in proteins. The interaction between erythrocytes and albumin via hydrogel is discovered (hydro-conformational interaction). A qualitative physical model of the early stages of the light-oxygen effect is proposed, in which collective magnetic interactions between the electron spins of oxygen molecules and the nuclear magnetic moments of protons in H2O molecules play a dominant role.

Signal detectability in diffusive media using phased arrays in conjunction with detector arrays.

PubMed

Kang, Dongyel; Kupinski, Matthew A

2011-06-20

We investigate Hotelling observer performance (i.e., signal detectability) of a phased array system for tasks of detecting small inhomogeneities and distinguishing adjacent abnormalities in uniform diffusive media. Unlike conventional phased array systems where a single detector is located on the interface between two sources, we consider a detector array, such as a CCD, on a phantom exit surface for calculating the Hotelling observer detectability. The signal detectability for adjacent small abnormalities (2 mm displacement) for the CCD-based phased array is related to the resolution of reconstructed images. Simulations show that acquiring high-dimensional data from a detector array in a phased array system dramatically improves the detectability for both tasks when compared to conventional single detector measurements, especially at low modulation frequencies. It is also observed in all studied cases that there exists the modulation frequency optimizing CCD-based phased array systems, where detectability for both tasks is consistently high. These results imply that the CCD-based phased array has the potential to achieve high resolution and signal detectability in tomographic diffusive imaging while operating at a very low modulation frequency. The effect of other configuration parameters, such as a detector pixel size, on the observer performance is also discussed.

Monolithic optical phased-array transceiver in a standard SOI CMOS process.

PubMed

Abediasl, Hooman; Hashemi, Hossein

2015-03-09

Monolithic microwave phased arrays are turning mainstream in automotive radars and high-speed wireless communications fulfilling Gordon Moores 1965 prophecy to this effect. Optical phased arrays enable imaging, lidar, display, sensing, and holography. Advancements in fabrication technology has led to monolithic nanophotonic phased arrays, albeit without independent phase and amplitude control ability, integration with electronic circuitry, or including receive and transmit functions. We report the first monolithic optical phased array transceiver with independent control of amplitude and phase for each element using electronic circuitry that is tightly integrated with the nanophotonic components on one substrate using a commercial foundry CMOS SOI process. The 8 × 8 phased array chip includes thermo-optical tunable phase shifters and attenuators, nano-photonic antennas, and dedicated control electronics realized using CMOS transistors. The complex chip includes over 300 distinct optical components and over 74,000 distinct electrical components achieving the highest level of integration for any electronic-photonic system.

Phased-array-fed antenna configuration study. Volume 1: Technology assessment

NASA Technical Reports Server (NTRS)

Sorbello, R. M.; Zaghloul, A. I.; Lee, B. S.; Siddiqi, S.; Geller, B. D.; Gerson, H. I.; Srinivas, D. N.

1983-01-01

The status of the technologies for phased-array-fed dual reflector systems is reviewed. The different aspects of these technologies, including optical performances, phased array systems, problems encountered in phased array design, beamforming networks, MMIC design and its incorporation into waveguide systems, reflector antenna structures, and reflector deployment mechanisms are addressed.

Simultaneous quantitative determination of six active components in traditional Chinese medicinal preparation Cerebralcare Granule® by RP-HPLC coupled with diode array detection for quality control.

PubMed

Wang, Xiang-yang; Ma, Xiao-hui; Li, Wei; Chu, Yang; Guo, Jia-hua; Zhou, Shui-ping; Zhu, Yong-hong

2014-09-01

A simple, accurate and reliable method for the simultaneous separation and determination of six active components (protocatechuic acid, chlorogenic acid, caffeic acid, paeoniflorin, ferulic acid and rosmarinic acid) in traditional Chinese medicinal preparation Cerebralcare Granule(®) (CG) was developed using reverse-phase high-performance liquid chromatography coupled with diode array detector detection. The chromatographic separation was performed on a Hypersil GOLD C18 column with aqueous formic acid (0.1%, v/v) and acetonitrile as mobile phase at a flow rate of 0.2 ml/min at 30 °C. Because of the different UV characteristics of these components, change detection wavelength method was used for quantitative analysis. All of the analytes showed good linearity (r > 0.9992). The established method showed good precision and relative standard deviations (%) for intra-day and inter-day variations of 0.15-1.81 and 0.11-1.98%, respectively. The validated method was successfully applied to the simultaneously determination of six active components in CG from different batches. © The Author [2013]. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Development of a precolumn derivatization HPLC method with diode-array detection for the determination of amino sugars in peat and soil humic acids.

PubMed

Beňo, Erik; Góra, Róbert; Hutta, Milan

2018-02-01

The work is focused on the development of a high-performance liquid chromatography method with diode-array detection for the separation and quantitation of the three most abundant amino sugars; d-glucosamine, d-galactosamine, and d-mannosamine. The high-performance liquid chromatography separation was carried out by reversed-phase chromatography on Chromolith Performance RP-18e monolithic column after acid hydrolysis (5 M HCl) and precolumn derivatization of samples using diethyl ethoxymethylenemalonate. Gradient elution and a mobile phase composed of ammonium formate buffer solution (10 mmol/L, pH 3.60) and methanol with flow rate of 1.0 mL/min were used. The monitoring wavelength was set at 280 nm. The limits of detection and quantitation for analytes ranged from 0.017 to 0.122 mg/L and from 0.057 to 0.407 mg/L, respectively. The proposed method was successfully applied for the determination of amino sugars in samples of humic acids isolated from different soils and peat. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Observation of small cluster formation in concentrated monoclonal antibody solutions and its implications to solution viscosity.

PubMed

Yearley, Eric J; Godfrin, Paul D; Perevozchikova, Tatiana; Zhang, Hailiang; Falus, Peter; Porcar, Lionel; Nagao, Michihiro; Curtis, Joseph E; Gawande, Pradad; Taing, Rosalynn; Zarraga, Isidro E; Wagner, Norman J; Liu, Yun

2014-04-15

Monoclonal antibodies (mAbs) are a major class of biopharmaceuticals. It is hypothesized that some concentrated mAb solutions exhibit formation of a solution phase consisting of reversibly self-associated aggregates (or reversible clusters), which is speculated to be responsible for their distinct solution properties. Here, we report direct observation of reversible clusters in concentrated solutions of mAbs using neutron spin echo. Specifically, a stable mAb solution is studied across a transition from dispersed monomers in dilute solution to clustered states at more concentrated conditions, where clusters of a preferred size are observed. Once mAb clusters have formed, their size, in contrast to that observed in typical globular protein solutions, is observed to remain nearly constant over a wide range of concentrations. Our results not only conclusively establish a clear relationship between the undesirable high viscosity of some mAb solutions and the formation of reversible clusters with extended open structures, but also directly observe self-assembled mAb protein clusters of preferred small finite size similar to that in micelle formation that dominate the properties of concentrated mAb solutions. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Identification of discriminant proteins through antibody profiling, methods and apparatus for identifying an individual

DOEpatents

Apel, William A.; Thompson, Vicki S; Lacey, Jeffrey A.; Gentillon, Cynthia A.

2016-08-09

A method for determining a plurality of proteins for discriminating and positively identifying an individual based from a biological sample. The method may include profiling a biological sample from a plurality of individuals against a protein array including a plurality of proteins. The protein array may include proteins attached to a support in a preselected pattern such that locations of the proteins are known. The biological sample may be contacted with the protein array such that a portion of antibodies in the biological sample reacts with and binds to the proteins forming immune complexes. A statistical analysis method, such as discriminant analysis, may be performed to determine discriminating proteins for distinguishing individuals. Proteins of interest may be used to form a protein array. Such a protein array may be used, for example, to compare a forensic sample from an unknown source with a sample from a known source.

Identification of discriminant proteins through antibody profiling, methods and apparatus for identifying an individual

DOEpatents

Thompson, Vicki S; Lacey, Jeffrey A; Gentillon, Cynthia A; Apel, William A

2015-03-03

A method for determining a plurality of proteins for discriminating and positively identifying an individual based from a biological sample. The method may include profiling a biological sample from a plurality of individuals against a protein array including a plurality of proteins. The protein array may include proteins attached to a support in a preselected pattern such that locations of the proteins are known. The biological sample may be contacted with the protein array such that a portion of antibodies in the biological sample reacts with and binds to the proteins forming immune complexes. A statistical analysis method, such as discriminant analysis, may be performed to determine discriminating proteins for distinguishing individuals. Proteins of interest may be used to form a protein array. Such a protein array may be used, for example, to compare a forensic sample from an unknown source with a sample from a known source.

Spectroscopic Analysis of 10MAG/LDAO Reverse Micelles to Determine Characteristic Properties and Behavioral Extrema

NASA Astrophysics Data System (ADS)

Berg, Joshua; Mawson, Cara; Norris, Zach; Nucci, Nathaniel

Reverse micelles are spontaneously organizing complexes of surfactant that encapsulate a nanoscale pool of water in a bulk non-polar solvent. Reverse micelle (RM) mixtures have a wide range of applications, including biophysical investigation of protein systems. A new RM mixture composed of decyl-1-monoglycerol (10MAG) and lauryldimethylammonium-N-oxide (LDAO) was recently described. This mixture has the potential to prove more widely applicable for use of RMs in applications that involve encapsulation of macromolecules, yet little is known about the phase behavior or size of reverse micelles created by this mixture. Data describing such behaviors for this mixture are presented here. We have used dynamic light scattering (DLS) and fluorescence spectroscopy to investigate the size and partitioning behavior of RMs in varying mixtures of 10MAG, LDAO, water, pentane, and hexanol. These data demonstrate that the 10MAG/LDAO RM mixture exhibits markedly different phase and RM size behavior than that of commonly used RM surfactant mixtures. The implications of these findings for use of the 10MAG/LDAO mix for RM applications will also be addressed. Funding provided by Rowan University.

Characterization of patient-derived tumor xenografts (PDXs) as models for estrogen receptor positive (ER+HER2- and ER+HER2+) breast cancers.

PubMed

Kanaya, Noriko; Somlo, George; Wu, Jun; Frankel, Paul; Kai, Masaya; Liu, Xueli; Wu, Shang Victoria; Nguyen, Duc; Chan, Nymph; Hsieh, Meng-Yin; Kirschenbaum, Michele; Kruper, Laura; Vito, Courtney; Badie, Behnam; Yim, John H; Yuan, Yuan; Hurria, Arti; Peiguo, Chu; Mortimer, Joanne; Chen, Shiuan

2017-06-01

The research was to appraise the utility of the patient-derived tumor xenografts (PDXs) as models of estrogen receptor positive (ER+HER2- and ER+HER2+) breast cancers. We compared protein expression profiles by Reverse Phase Protein Array (RPPA) in tumors that resulted in PDXs compared to those that did not. Our overall PDX intake rate for ER+ breast cancer was 9% (9/97). The intake rate for ER+HER2+ tumors (3/16, 19%) was higher than for ER+HER2- tumors (6/81, 7%). Heat map analyses of RPPA data showed that ER+HER2- tumors were divided into 2 groups by luminal A/B signature [protein expression of ER, AR, Bcl-2, Bim (BCL2L11), GATA3 and INPP4b], and this expression signature was also associated with the rate of PDX intake. Cell survival pathways such as the PI3K/AKT signaling and RAS/ERK pathways were more activated in the specimens that could be established as PDX in both classes. Expression of the ER protein itself may have a bearing on the potential success of an ER+ PDX model. In addition, HER2 and its downstream protein expressions were up-regulated in the ER+HER2+ patient tumors that were successfully established as PDX models. Moreover, the comparison of RPPA data between original and PDX tumors suggested that the selection/adaptation process required to grow the tumors in mice is unavoidable for generation of ER+ PDX models, and we identified differences between patient tumor samples and paired PDX tumors. A better understanding of the biological characteristics of ER+PDX would be the key to using PDX models in assessing treatment strategies in a preclinical setting. Copyright © 2016 Elsevier Ltd. All rights reserved.

Photonic Breast Tomography and Tumor Aggressiveness Assessment

DTIC Science & Technology

2010-07-01

removal of breast tumours (Specific Aim 4). While the TROT approach [7] has been introduced in other areas, such as, array processing for acoustic and...to the time-reversal matrix used in the general area of array processing for acoustic and radar time-reversal imaging [15]. The eigenvalue equation...spectrum [Eq.(1) in Ref. 8] is calculated directly for all voxels in the sample using the vector subspace method, Multiple Signal Classification ( MUSIC

Development and validation of an high-performance liquid chromatography-diode array detector method for the simultaneous determination of six phenolic compounds in abnormal savda munziq decoction

PubMed Central

Tian, Shuge; Liu, Wenxian; Liu, Feng; Zhang, Xuejia; Upur, Halmuart

2015-01-01

Aims: Given the high-effectiveness and low-toxicity of abnormal savda munziq (ASMQ), its herbal formulation has long been used in traditional Uyghur medicine to treat complex diseases, such as cancer, diabetes, and cardiovascular diseases. Settings and Design: ASMQ decoction by reversed-phase high-performance liquid chromatography coupled with a diode array detector was successfully developed for the simultaneous quality assessment of gallic acid, protocatechuic acid, caffeic acid, rutin, rosmarinic acid, and luteolin. The six phenolic compounds were separated on an Agilent TC-C18 reversed-phase analytical column (4.6 × 250 mm, 5 μm) by gradient elution using 0.3% aqueous formic acid (v/v) and 0.3% methanol formic acid (v/v) at 1.0 mL/min. Materials and Methods: The plant material was separately ground and mixed at the following ratios (10): Cordia dichotoma (10.6), Anchusa italic (10.6), Euphorbia humifusa (4.9), Adiantum capillus-veneris (4.9), Ziziphus jujube (4.9), Glycyrrhiza uralensis (7.1), Foeniculum vulgare (4.9), Lavandula angustifolia (4.9), Dracocephalum moldavica L. (4.9), and Alhagi pseudoalhagi (42.3). Statistical Analysis Used: The precisions of all six compounds were <0.60%, and the average recoveries ranged from 99.39% to 104.85%. Highly significant linear correlations were found between component concentrations and specific chromatographic peak areas (R2 > 0.999). Results: The proposed method was successfully applied to determine the levels of six active components in ASMQ. Conclusions: Given the simplicity, precision, specificity, and sensitivity of the method, it can be utilized as a quality control approach to simultaneously determining the six phenolic compounds in AMSQ. PMID:25709227

Simultaneous Determination of Procainamide and N-acetylprocainamide in Rat Plasma by Ultra-High-Pressure Liquid Chromatography Coupled with a Diode Array Detector and Its Application to a Pharmacokinetic Study in Rats.

PubMed

Balla, Anusha; Cho, Kwan Hyung; Kim, Yu Chul; Maeng, Han-Joo

2018-03-30

A simple, sensitive, and reliable reversed-phase, Ultra-High-Pressure Liquid Chromatography (UHPLC) coupled with a Diode Array Detector (DAD) method for the simultaneous determination of Procainamide (PA) and its major metabolite, N -acetylprocainamide (NAPA), in rat plasma was developed and validated. A simple deproteinization method with methanol was applied to the rat plasma samples, which were analyzed using UHPLC equipped with DAD at 280 nm, and a Synergi™ 4 µm polar, reversed-phase column using 1% acetic acid (pH 5.5) and methanol (76:24, v / v ) as eluent in isocratic mode at a flow rate 0.2 mL/min. The method showed good linearity ( r ² > 0.998) over the concentration range of 20-100,000 and 20-10,000 ng/mL for PA and NAPA, respectively. Intra- and inter-day accuracies ranged from 97.7 to 110.9%, and precision was <10.5% for PA and 99.7 to 109.2 and <10.5%, respectively, for NAPA. The lower limit of quantification was 20 ng/mL for both compounds. This is the first report of the UHPLC-DAD bioanalytical method for simultaneous measurement of PA and NAPA. The most obvious advantage of this method over previously reported HPLC methods is that it requires small sample and injection volumes, with a straightforward, one-step sample preparation. It overcomes the limitations of previous methods, which use large sample volume and complex sample preparation. The devised method was successfully applied to the quantification of PA and NAPA after an intravenous bolus administration of 10 mg/kg procainamide hydrochloride to rats.

Expanded separation technique for chlorophyll metabolites in Oriental tobacco leaf using non aqueous reversed phase chromatography.

PubMed

Ishida, Naoyuki

2011-08-26

An improved separation method for chlorophyll metabolites in Oriental tobacco leaf was developed. While Oriental leaf still gives the green color even after the curing process, little attention has been paid to the detailed composition of the remaining green pigments. This study aimed to identify the green pigments using non aqueous reversed phase chromatography (NARPC). To this end, liquid chromatograph (LC) equipped with a photo diode array detector (DAD) and an atmospheric pressure chemical ionization/mass spectrometer (APCI/MSD) was selected, because it is useful for detecting low polar non-volatile compounds giving green color such as pheophytin a. Identification was based on the wavelength spectrum, mass spectrum and retention time, comparing the analytes in Oriental leaf with the commercially available and synthesized components. Consequently, several chlorophyll metabolites such as hydroxypheophytin a, solanesyl pheophorbide a and solanesyl hydroxypheophorbide a were newly identified, in addition to typical green pigments such as chlorophyll a and pheophytin a. Chlorophyll metabolites bound to solanesol were considered the tobacco specific components. NARPC expanded the number of detectable low polar chlorophyll metabolites in Oriental tobacco leaf. Copyright © 2011 Elsevier B.V. All rights reserved.

Localization and Ordering of Lipids Around Aquaporin-0: Protein and Lipid Mobility Effects.

PubMed

Briones, Rodolfo; Aponte-Santamaría, Camilo; de Groot, Bert L

2017-01-01

Hydrophobic matching, lipid sorting, and protein oligomerization are key principles by which lipids and proteins organize in biological membranes. The Aquaporin-0 channel (AQP0), solved by electron crystallography (EC) at cryogenic temperatures, is one of the few protein-lipid complexes of which the structure is available in atomic detail. EC and room-temperature molecular dynamics (MD) of dimyristoylglycerophosphocholine (DMPC) annular lipids around AQP0 show similarities, however, crystal-packing and temperature might affect the protein surface or the lipids distribution. To understand the role of temperature, lipid phase, and protein mobility in the localization and ordering of AQP0-lipids, we used MD simulations of an AQP0-DMPC bilayer system. Simulations were performed at physiological and at DMPC gel-phase temperatures. To decouple the protein and lipid mobility effects, we induced gel-phase in the lipids or restrained the protein. We monitored the lipid ordering effects around the protein. Reducing the system temperature or inducing lipid gel-phase had a marginal effect on the annular lipid localization. However, restraining the protein mobility increased the annular lipid localization around the whole AQP0 surface, resembling EC. The distribution of the inter-phosphate and hydrophobic thicknesses showed that stretching of the DMPC annular layer around AQP0 surface is the mechanism that compensates the hydrophobic mismatch in this system. The distribution of the local area-per-lipid and the acyl-chain order parameters showed particular fluid- and gel-like areas that involved several lipid layers. These areas were in contact with the surfaces of higher and lower protein mobility, respectively. We conclude that the AQP0 surfaces induce specific fluid- and gel-phase prone areas. The presence of these areas might guide the AQP0 lipid sorting interactions with other membrane components, and is compatible with the squared array oligomerization of AQP0 tetramers separated by a layer of annular lipids.

A 2x2 W-Band Reference Time-Shifted Phase-Locked Transmitter Array in 65nm CMOS Technology

NASA Technical Reports Server (NTRS)

Tang, Adrian; Virbila, Gabriel; Hsiao, Frank; Wu, Hao; Murphy, David; Mehdi, Imran; Siegel, P. H.; Chang, M-C. Frank

2013-01-01

This paper presents a complete 2x2 phased array transmitter system operating at W-band (90-95 GHz) which employs a PLL reference time-shifting approach instead of using traditional mm-wave phase shifters. PLL reference shifting enables a phased array to be distributed over multiple chips without the need for coherent mm-wave signal distribution between chips. The proposed phased array transmitter system consumes 248 mW per array element when implemented in a 65 nm CMOS technology.

Folding and Stabilization of Native-Sequence-Reversed Proteins

PubMed Central

Zhang, Yuanzhao; Weber, Jeffrey K; Zhou, Ruhong

2016-01-01

Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we investigate how the reverse-sequences of native proteins might fold by examining a series of small proteins of increasing structural complexity (α-helix, β-hairpin, α-helix bundle, and α/β-protein). Employing a tandem protein structure prediction algorithmic and molecular dynamics simulation approach, we find that the ability of reverse sequences to adopt native-like folds is strongly influenced by protein size and the flexibility of the native hydrophobic core. For β-hairpins with reverse-sequences that fail to fold, we employ a simple mutational strategy for guiding stable hairpin formation that involves the insertion of amino acids into the β-turn region. This systematic look at reverse sequence duality sheds new light on the problem of protein sequence-structure mapping and may serve to inspire new protein design and protein structure prediction protocols. PMID:27113844

Folding and Stabilization of Native-Sequence-Reversed Proteins

NASA Astrophysics Data System (ADS)

Zhang, Yuanzhao; Weber, Jeffrey K.; Zhou, Ruhong

2016-04-01

Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we investigate how the reverse-sequences of native proteins might fold by examining a series of small proteins of increasing structural complexity (α-helix, β-hairpin, α-helix bundle, and α/β-protein). Employing a tandem protein structure prediction algorithmic and molecular dynamics simulation approach, we find that the ability of reverse sequences to adopt native-like folds is strongly influenced by protein size and the flexibility of the native hydrophobic core. For β-hairpins with reverse-sequences that fail to fold, we employ a simple mutational strategy for guiding stable hairpin formation that involves the insertion of amino acids into the β-turn region. This systematic look at reverse sequence duality sheds new light on the problem of protein sequence-structure mapping and may serve to inspire new protein design and protein structure prediction protocols.

Low-Cost Phased Array Antenna for Sounding Rockets, Missiles, and Expendable Launch Vehicles

NASA Technical Reports Server (NTRS)

Mullinix, Daniel; Hall, Kenneth; Smith, Bruce; Corbin, Brian

2012-01-01

A low-cost beamformer phased array antenna has been developed for expendable launch vehicles, rockets, and missiles. It utilizes a conformal array antenna of ring or individual radiators (design varies depending on application) that is designed to be fed by the recently developed hybrid electrical/mechanical (vendor-supplied) phased array beamformer. The combination of these new array antennas and the hybrid beamformer results in a conformal phased array antenna that has significantly higher gain than traditional omni antennas, and costs an order of magnitude or more less than traditional phased array designs. Existing omnidirectional antennas for sounding rockets, missiles, and expendable launch vehicles (ELVs) do not have sufficient gain to support the required communication data rates via the space network. Missiles and smaller ELVs are often stabilized in flight by a fast (i.e. 4 Hz) roll rate. This fast roll rate, combined with vehicle attitude changes, greatly increases the complexity of the high-gain antenna beam-tracking problem. Phased arrays for larger ELVs with roll control are prohibitively expensive. Prior techniques involved a traditional fully electronic phased array solution, combined with highly complex and very fast inertial measurement unit phased array beamformers. The functional operation of this phased array is substantially different from traditional phased arrays in that it uses a hybrid electrical/mechanical beamformer that creates the relative time delays for steering the antenna beam via a small physical movement of variable delay lines. This movement is controlled via an innovative antenna control unit that accesses an internal measurement unit for vehicle attitude information, computes a beam-pointing angle to the target, then points the beam via a stepper motor controller. The stepper motor on the beamformer controls the beamformer variable delay lines that apply the appropriate time delays to the individual array elements to properly steer the beam. The array of phased ring radiators is unique in that it provides improved gain for a small rocket or missile that uses spin stabilization for stability. The antenna pattern created is symmetric about the roll axis (like an omnidirectional wraparound), and is thus capable of providing continuous coverage that is compatible with very fast spinning rockets. For larger ELVs with roll control, a linear array of elements can be used for the 1D scanned beamformer and phased array, or a 2D scanned beamformer can be used with an NxN element array.

Off-Line Multidimensional Liquid Chromatography and Auto Sampling Result in Sample Loss in LC/LC–MS/MS

PubMed Central

2015-01-01

Large-scale proteomics often employs two orthogonal separation methods to fractionate complex peptide mixtures. Fractionation can involve ion exchange separation coupled to reversed-phase separation or, more recently, two reversed-phase separations performed at different pH values. When multidimensional separations are combined with tandem mass spectrometry for protein identification, the strategy is often referred to as multidimensional protein identification technology (MudPIT). MudPIT has been used in either an automated (online) or manual (offline) format. In this study, we evaluated the performance of different MudPIT strategies by both label-free and tandem mass tag (TMT) isobaric tagging. Our findings revealed that online MudPIT provided more peptide/protein identifications and higher sequence coverage than offline platforms. When employing an off-line fractionation method with direct loading of samples onto the column from an eppendorf tube via a high-pressure device, a 5.3% loss in protein identifications is observed. When off-line fractionated samples are loaded via an autosampler, a 44.5% loss in protein identifications is observed compared with direct loading of samples onto a triphasic capillary column. Moreover, peptide recovery was significantly lower after offline fractionation than in online fractionation. Signal-to-noise (S/N) ratio, however, was not significantly altered between experimental groups. It is likely that offline sample collection results in stochastic peptide loss due to noncovalent adsorption to solid surfaces. Therefore, the use of the offline approaches should be considered carefully when processing minute quantities of valuable samples. PMID:25040086

Determination of catechins and catechin gallates in tissues by liquid chromatography with coulometric array detection and selective solid phase extraction.

PubMed

Chu, Kai On; Wang, Chi Chiu; Chu, Ching Yan; Rogers, Michael Scott; Choy, Kwong Wai; Pang, Chi Pui

2004-10-25

Catechins levels in organ tissues, particularly liver, determined by published methods are unexpectedly low, probably due to the release of oxidative enzymes, metal ions and reactive metabolites from tissue cells during homogenization and to the pro-oxidant effects of ascorbic acid during sample processing in the presence of metal ions. We describe a new method for simultaneous analysis of eight catechins in tissue: (+)-catechin (C), (-)-epicatechin (EC), (-)-gallocatechin (GC), (-)-epigallocatechin (EGC), (-)-catechin gallate (CG), (-)-epicatechin gallate (ECG), (-)-gallocatechin gallate (GCG) and (-)-epigallocatechin gallate (EGCG) (Fig. 1). The new extraction procedure utilized a methanol/ethylacetate/dithionite (2:1:3) mixture during homogenization for simultaneous enzyme precipitation and antioxidant protection. Selective solid phase extraction was used to remove most interfering bio-matrices. Reversed phase HPLC with CoulArray detection was used to determine the eight catechins simultaneously within 25 min. Good linearity (>0.9922) was obtained in the range 20-4000 ng/g. The coefficients of variance (CV) were less than 5%. Absolute recovery ranged from 62 to 96%, accuracy 92.5 +/- 4.5 to 104.9 +/- 6%. The detection limit was 5 ng/g. This method is capable for determining catechins in rat tissues of liver, brain, spleen, and kidney. The method is robust, reproducible, with high recovery, and has been validated for both in vitro and in vivo sample analysis.

Analysis of streptokinase by validated liquid chromatography methods and correlation with an in vitro bioassay.

PubMed

Cardoso, Clóvis Dervil Appratto; Perobelli, Rafaela Ferreira; Xavier, Bruna; Maldaner, Fernanda Pavani Stamm; da Silva, Francielle Santos; Dalmora, Sérgio Luiz

2017-01-01

Reversed-phase and size-exclusion liquid chromatography methods were validated for the assessment of streptokinase. The reversed-phase method was carried out on a Jupiter C 4 column (250 mm × 4.6 mm id) maintained at 25°C. The mobile phase consisted of 50 mM sodium sulfate solution pH 7.0 and methanol (90:10, v/v), run isocratically at a flow rate of 0.8 mL/min. The size-exclusion method was carried out on a Protein KW 802.5 column (300 mm × 8.0 mm id), at 25°C. The mobile phase consisted of 40 mM sodium acetate solution pH 7.0, run isocratically at a flow rate of 1.0 mL/min. Retention times were 19.3 min, and 14.1 min, and calibration curves were linear over the concentration range of 0.25-250 μg/mL (25.75-25 750 IU/mL) (r 2 = 0.9997) and 5-80 μg/mL (515-8240 IU/mL) (r 2 = 0.9996), respectively, for reversed-phase and size exclusion, with detection at 220 and 204 nm. Chromatographic methods were employed in conjunction with the in vitro bioassay for the content/potency assessment of Streptokinase, contributing to improve the quality control and ensure the efficacy of the biotherapeutic. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development of a perfusion reversed-phase high performance liquid chromatography method for the characterisation of maize products using multivariate analysis.

PubMed

Rodriguez-Nogales, J M; Garcia, M C; Marina, M L

2006-02-03

A perfusion reversed-phase high performance liquid chromatography (RP-HPLC) method has been designed to allow rapid (3.4 min) separations of maize proteins with high resolution. Several factors, such as extraction conditions, temperature, detection wavelength and type and concentration of ion-pairing agent were optimised. A fine optimisation of the gradient elution was also performed by applying experimental design. Commercial maize products for human consumption (flours, precocked flours, fried snacks and extruded snacks) were characterised for the first time by perfusion RP-HPLC and their chromatographic profiles allowed a differentiation among products relating the different technological process used for their preparation. Furthermore, applying discriminant analysis makes it possible to group the samples according with the technological process suffered by maize products, obtaining a good prediction in 92% of the samples.

Bone morphogenetic protein 9 regulates tumor growth of osteosarcoma cells through the Wnt/β-catenin pathway.

PubMed

Lv, Zilan; Wang, Chuan; Yuan, Taixian; Liu, Yuehong; Song, Tao; Liu, Yueliang; Chen, Chu; Yang, Min; Tang, Zuchuan; Shi, Qiong; Weng, Yaguang

2014-02-01

Bone morphogenetic protein 9 (BMP9) is a member of the transforming growth factor-β (TGF-β) family, which has been shown to regulate the progression of several tumors. Recent studies indicated that BMP9 affects osteosarcoma (OS) processes, but its specific roles and molecular mechanisms have yet to be fully elucidated. The human OS cell lines 143B and MG63 were used for the present study. We found that BMP9 overexpression suppressed the growth of OS cells, whereas inhibition of BMP9 reversed this effect. Our results also showed that BMP9 overexpression induced G0/G1 phase arrest and apoptosis in OS cells. We further investigated the possible molecular mechanisms mediating the biological role of BMP9. We observed that BMP9 overexpression reduced β-catenin mRNA and protein levels, and also downregulated its downstream proteins c-Myc and osteoprotegerin (OPG) and inhibited the phosphorylation levels of GSK-3β (Ser 9) in OS cells, whereas inhibition of BMP9 reversed these effects. Moreover, the suppressive effects of BMP9 overexpression on OS cells was reversed by exogenous β-catenin expression, but augmented by β-catenin silencing. In conclusion, our results revealed that BMP9 can regulate tumor growth of OS cells through the Wnt/β-catenin pathway. Therefore, BMP9 may be a new therapeutic target in OS.

On the (Frequency) Modulation of Coupled Oscillator Arrays in Phased Array Beam Control

NASA Technical Reports Server (NTRS)

Pogorzelski, R.; Acorn, J.; Zawadzki, M.

2000-01-01

It has been shown that arrays of voltage controlled oscillators coupled to nearest neighbors can be used to produce useful aperture phase distributions for phased array antennas. However, placing information of the transmitted signal requires that the oscillations be modulated.

A systems biology approach to the pathogenesis of obesity-related nonalcoholic fatty liver disease using reverse phase protein microarrays for multiplexed cell signaling analysis.

PubMed

Calvert, Valerie S; Collantes, Rochelle; Elariny, Hazem; Afendy, Arian; Baranova, Ancha; Mendoza, Michael; Goodman, Zachary; Liotta, Lance A; Petricoin, Emanuel F; Younossi, Zobair M

2007-07-01

Nonalcoholic fatty liver disease (NAFLD) is a common cause of chronic liver disease. Omental adipose tissue, a biologically active organ secreting adipokines and cytokines, may play a role in the development of NAFLD. We tested this hypothesis with reverse-phase protein microarrays (RPA) for multiplexed cell signaling analysis of adipose tissue from patients with NAFLD. Omental adipose tissue was obtained from 99 obese patients. Liver biopsies obtained at the time of surgery were all read by the same hepatopathologist. Adipose tissue was exposed to rapid pressure cycles to extract protein lysates. RPA was used to investigate intracellular signaling. Analysis of 54 different kinase substrates and cell signaling endpoints showed that an insulin signaling pathway is deranged in different locations in NAFLD patients. Furthermore, components of insulin receptor-mediated signaling differentiate most of the conditions on the NAFLD spectrum. For example, PKA (protein kinase A) and AKT/mTOR (protein kinase B/mammalian target of rapamycin) pathway derangement accurately discriminates patients with NASH from those with the non-progressive forms of NAFLD. PKC (protein kinase C) delta, AKT, and SHC phosphorylation changes occur in patients with simple steatosis. Amounts of the FKHR (forkhead factor Foxo1)phosphorylated at S256 residue were significantly correlated with AST/ALT ratio in all morbidly obese patients. Furthermore, amounts of cleaved caspase 9 and pp90RSK S380 were positively correlated in patients with NASH. Specific insulin pathway signaling events are altered in the adipose tissue of patients with NASH compared with patients with nonprogressive forms of NAFLD. These findings provide evidence for the role of omental fat in the pathogenesis, and potentially, the progression of NAFLD.

Phased array antenna matching: Simulation and optimization of a planar phased array of circular waveguide elements

NASA Technical Reports Server (NTRS)

Dudgeon, J. E.

1972-01-01

A computerized simulation of a planar phased array of circular waveguide elements is reported using mutual coupling and wide angle impedance matching in phased arrays. Special emphasis is given to circular polarization. The aforementioned computer program has as variable inputs: frequency, polarization, grid geometry, element size, dielectric waveguide fill, dielectric plugs in the waveguide for impedance matching, and dielectric sheets covering the array surface for the purpose of wide angle impedance matching. Parameter combinations are found which produce reflection peaks interior to grating lobes, while dielectric cover sheets are successfully employed to extend the usable scan range of a phased array. The most exciting results came from the application of computer aided optimization techniques to the design of this type of array.

Manipulation of Liquids Using Phased Array Generation of Acoustic Radiation Pressure

NASA Technical Reports Server (NTRS)

Oeftering, Richard C. (Inventor)

2000-01-01

A phased array of piezoelectric transducers is used to control and manipulate contained as well as uncontained fluids in space and earth applications. The transducers in the phased array are individually activated while being commonly controlled to produce acoustic radiation pressure and acoustic streaming. The phased array is activated to produce a single pulse, a pulse burst or a continuous pulse to agitate, segregate or manipulate liquids and gases. The phased array generated acoustic radiation pressure is also useful in manipulating a drop, a bubble or other object immersed in a liquid. The transducers can be arranged in any number of layouts including linear single or multi- dimensional, space curved and annular arrays. The individual transducers in the array are activated by a controller, preferably driven by a computer.

Supercritical fluid chromatography-photodiode array detection-electrospray ionization mass spectrometry as a framework for impurity fate mapping in the development and manufacture of drug substances.

PubMed

Pirrone, Gregory F; Mathew, Rose M; Makarov, Alexey A; Bernardoni, Frank; Klapars, Artis; Hartman, Robert; Limanto, John; Regalado, Erik L

2018-03-30

Impurity fate and purge studies are critical in order to establish an effective impurity control strategy for approval of the commercial filing application of new medicines. Reversed phase liquid chromatography-diode array-mass spectrometry (RPLC-DAD-MS) has traditionally been the preferred tool for impurity fate mapping. However, separation of some reaction mixtures by LC can be very problematic requiring combination LC-UV for area % analysis and a different LC-MS method for peak identification. In addition, some synthetic intermediates might be chemically susceptible to the aqueous conditions used in RPLC separations. In this study, the use of supercritical fluid chromatography-photodiode array-electrospray ionization mass spectrometry (SFC-PDA-ESIMS) for fate and purge of two specified impurities in the 1-uridine starting material from the synthesis of a bis-piv 2'keto-uridine, an intermediate in the synthesis of uprifosbuvir, a treatment under investigation for chronic hepatitis C infection. Readily available SFC instrumentation with a Chiralpak IC column (4.6 × 150 mm, 3 μm) and ethanol: carbon dioxide based mobile phase eluent enabled the separation of closely related components from complex reaction mixtures where RLPC failed to deliver optimal chromatographic performance. These results illustrate how SFC combined with PDA and ESI-MS detection can become a powerful tool for direct impurity fate mapping across multiple reaction steps. Copyright © 2018 Elsevier B.V. All rights reserved.

Magnetization mechanisms in ordered arrays of polycrystalline Fe{sub 100−x}Co{sub x} nanowires

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

Viqueira, M. S.; Bajales, N.; Urreta, S. E.

2015-05-28

Magnetization reversal processes and coercivity mechanisms in polycrystalline Fe{sub 100−x}Co{sub x} nanowire arrays, resulting from an AC electrodeposition process, are investigated. The array coercivity is described on the basis of polarization reversal mechanisms operating in individual wires, under the effect of inter-wire dipolar interactions described by a mean field approximation. For individual wires, a reversal mechanism involving the nucleation and further expansion of domain-wall like spin configuration is considered. The wires have a mean grain size larger than both the nanowire diameter and the exchange length, so localized and non-cooperative nucleation modes are considered. As the Co content increases, themore » alloy saturation polarization gradually decreases, but the coercive field and the relative remanence of the arrays increase, indicating that they are not controlled by the shape anisotropy in all the composition range. The coercive field dependence on the angle between the applied field and the wire long axis is not well described by reversal mechanisms involving nucleation and further displacement of neither vortex nor transverse ideal domain walls. On the contrary, the angular dependence of the coercive field observed at room temperature is well predicted by a model considering nucleation of inverse domains by localized curling, in regions smaller than the grain size, exhibiting quite small aspect ratios as compared to those of the entire nanowire. In arrays with higher Co contents, a transition from an initial (small angle) localized curling nucleation mechanism to another one, involving localized coherent rotation is observed at about π/4.« less

Progress and prospects of silicon-based design for optical phased array

NASA Astrophysics Data System (ADS)

Hu, Weiwei; Peng, Chao; Chang-Hasnain, Connie

2016-03-01

The high-speed, high-efficient, compact phase modulator array is indispensable in the Optical-phased array (OPA) which has been considered as a promising technology for realizing flexible and efficient beam steering. In our research, two methods are presented to utilize high-contrast grating (HCG) as high-efficient phase modulator. One is that HCG possesses high-Q resonances that origins from the cancellation of leaky waves. As a result, sharp resonance peaks appear on the reflection spectrum thus HCGs can be utilized as efficient phase shifters. Another is that low-Q mode HCG is utilized as ultra-lightweight mirror. With MEMS technology, small HCG displacement (~50 nm) leads to large phase change (~1.7π). Effective beam steering is achieved in Connie Chang-Hasnian's group. On the other hand, we theoretically and experimentally investigate the system design for silicon-based optical phased array, including the star coupler, phased array, emission elements and far-field patterns. Further, the non-uniform optical phased array is presented.

5-ASA affects cell cycle progression in colorectal cells by reversibly activating a replication checkpoint.

PubMed

Luciani, M Gloria; Campregher, Christoph; Fortune, John M; Kunkel, Thomas A; Gasche, Christoph

2007-01-01

Individuals with inflammatory bowel disease are at risk of developing colorectal cancer (CRC). Epidemiologic, animal, and laboratory studies suggest that 5-amino-salicylic acid (5-ASA) protects from the development of CRC by altering cell cycle progression and by inducing apoptosis. Our previous results indicate that 5-ASA improves replication fidelity in colorectal cells, an effect that is active in reducing mutations. In this study, we hypothesized that 5-ASA restrains cell cycle progression by activating checkpoint pathways in colorectal cell lines, which would prevent tumor development and improve genomic stability. CRC cells with different genetic backgrounds such as HT29, HCT116, HCT116(p53-/-), HCT116+chr3, and LoVo were treated with 5-ASA for 2-96 hours. Cell cycle progression, phosphorylation, and DNA binding of cell cycle checkpoint proteins were analyzed. We found that 5-ASA at concentrations between 10 and 40 mmol/L affects cell cycle progression by inducing cells to accumulate in the S phase. This effect was independent of the hMLH1, hMSH2, and p53 status because it was observed to a similar extent in all cell lines under investigation. Moreover, wash-out experiments demonstrated reversibility within 48 hours. Although p53 did not have a causative role, p53 Ser15 was strongly phosphorylated. Proteins involved in the ATM-and-Rad3-related kinase (ATR)-dependent S-phase checkpoint response (Chk1 and Rad17) were also phosphorylated but not ataxia telengectasia mutated kinase. Our data demonstrate that 5-ASA causes cells to reversibly accumulate in S phase and activate an ATR-dependent checkpoint. The activation of replication checkpoint may slow down DNA replication and improve DNA replication fidelity, which increases the maintenance of genomic stability and counteracts carcinogenesis.

A Simple, Fast, Low Cost, HPLC/UV Validated Method for Determination of Flutamide: Application to Protein Binding Studies.

PubMed

Esmaeilzadeh, Sara; Valizadeh, Hadi; Zakeri-Milani, Parvin

2016-06-01

The main goal of this study was development of a reverse phase high performance liquid chromatography (RP-HPLC) method for flutamide quantitation which is applicable to protein binding studies. Ultrafilteration method was used for protein binding study of flutamide. For sample analysis, flutamide was extracted by a simple and low cost extraction method using diethyl ether and then was determined by HPLC/UV. Acetanilide was used as an internal standard. The chromatographic system consisted of a reversed-phase C8 column with C8 pre-column, and the mobile phase of a mixture of 29% (v/v) methanol, 38% (v/v) acetonitrile and 33% (v/v) potassium dihydrogen phosphate buffer (50 mM) with pH adjusted to 3.2. Acetanilide and flutamide were eluted at 1.8 and 2.9 min, respectively. The linearity of method was confirmed in the range of 62.5-16000 ng/ml (r(2) > 0.99). The limit of quantification was shown to be 62.5 ng/ml. Precision and accuracy ranges found to be (0.2-1.4%, 90-105%) and (0.2-5.3 %, 86.7-98.5 %) respectively. Acetanilide and flutamide capacity factor values of 1.35 and 2.87, tailing factor values of 1.24 and 1.07 and resolution values of 1.8 and 3.22 were obtained in accordance with ICH guidelines. Based on the obtained results a rapid, precise, accurate, sensitive and cost-effective analysis procedure was proposed for quantitative determination of flutamide.

A Simple, Fast, Low Cost, HPLC/UV Validated Method for Determination of Flutamide: Application to Protein Binding Studies

PubMed Central

Esmaeilzadeh, Sara; Valizadeh, Hadi; Zakeri-Milani, Parvin

2016-01-01

Purpose: The main goal of this study was development of a reverse phase high performance liquid chromatography (RP-HPLC) method for flutamide quantitation which is applicable to protein binding studies. Methods: Ultrafilteration method was used for protein binding study of flutamide. For sample analysis, flutamide was extracted by a simple and low cost extraction method using diethyl ether and then was determined by HPLC/UV. Acetanilide was used as an internal standard. The chromatographic system consisted of a reversed-phase C8 column with C8 pre-column, and the mobile phase of a mixture of 29% (v/v) methanol, 38% (v/v) acetonitrile and 33% (v/v) potassium dihydrogen phosphate buffer (50 mM) with pH adjusted to 3.2. Results: Acetanilide and flutamide were eluted at 1.8 and 2.9 min, respectively. The linearity of method was confirmed in the range of 62.5-16000 ng/ml (r2 > 0.99). The limit of quantification was shown to be 62.5 ng/ml. Precision and accuracy ranges found to be (0.2-1.4%, 90-105%) and (0.2-5.3 %, 86.7-98.5 %) respectively. Acetanilide and flutamide capacity factor values of 1.35 and 2.87, tailing factor values of 1.24 and 1.07 and resolution values of 1.8 and 3.22 were obtained in accordance with ICH guidelines. Conclusion: Based on the obtained results a rapid, precise, accurate, sensitive and cost-effective analysis procedure was proposed for quantitative determination of flutamide. PMID:27478788

Quantitative determination of reserpine, ajmaline, and ajmalicine in Rauvolfia serpentina by reversed-phase high-performance liquid chromatography.

PubMed

Srivastava, A; Tripathi, A K; Pandey, R; Verma, R K; Gupta, M M

2006-10-01

A sensitive and reproducible reversed-phase high-performance liquid chromatography (HPLC) method using photodiode array detection is established for the simultaneous quantitation of important root alkaloids of Rauvolfia serpentina, namely, reserpine, ajmaline, and ajmalicine. A Chromolith Performance RP-18e column (100 x 4.6-mm i.d.) and a binary gradient mobile phase composed of 0.01 M (pH 3.5) phosphate buffer (NaH(2)PO(4)) containing 0.5% glacial acetic acid and acetonitrile are used. Analysis is run at a flow rate of 1.0 mL/min with the detector operated at a wavelength of 254 nm. The calibration curves are linear over a concentration range of 1-20 microg/mL (r = 1.000) for all the alkaloids. The various other aspects of analysis (i.e., peak purity, similarity, recovery, and repeatability) are also validated. For the three components, the recoveries are found to be 98.27%, 97.03%, and 98.38%, respectively. The limits of detection are 6, 4, and 8 microg/mL for ajmaline, ajmalicine, and reserpine, respectively, and the limits of quantitation are 19, 12, and 23 microg/mL for ajmaline, ajmalicine, and reserpine, respectively. The developed method is simple, reproducible, and easy to operate. It is useful for the evaluation of R. serpentina.

S-band antenna phased array communications system

NASA Technical Reports Server (NTRS)

Delzer, D. R.; Chapman, J. E.; Griffin, R. A.

1975-01-01

The development of an S-band antenna phased array for spacecraft to spacecraft communication is discussed. The system requirements, antenna array subsystem design, and hardware implementation are examined. It is stated that the phased array approach offers the greatest simplicity and lowest cost. The objectives of the development contract are defined as: (1) design of a medium gain active phased array S-band communications antenna, (2) development and test of a model of a seven element planar array of radiating elements mounted in the appropriate cavity matrix, and (3) development and test of a breadboard transmit/receive microelectronics module.

Ultrasonic phased array controller for hyperthermia applications.

PubMed

Benkeser, P J; Pao, T L; Yoon, Y J

1991-01-01

Multiple and mechanically scanned ultrasound transducer systems have demonstrated the efficacy of using ultrasound to produce deep localized hyperthermia. The use of ultrasonic phased arrays has been proposed as an alternative to these systems. A phased array offers a more flexible approach to heating tumours in that the size, shape, and position of its focal region can be altered during the course of treatment in order to achieve the desired temperature distribution. This added flexibility comes at the cost of increased complexity of the hardware necessary to drive the transducer because each element requires its own amplifer with both phase and amplitude control. In order for phased arrays with large numbers of elements to be feasible for hyperthermia applications, the complexity of this circuitry must be minimized. This paper describes a circuit design which simplifies the electronics required to control a phased array transducer system for hyperthermia applications. The design is capable of controlling virtually any type of phased array transducer operating at frequencies less than 2 MHz. The system performance was verified through beam profile measurements using a 48-element tapered phased array transducer.

HDL cholesterol transport during inflammation.

PubMed

van der Westhuyzen, Deneys R; de Beer, Frederick C; Webb, Nancy R

2007-04-01

The aim of this article is to review recent advances made towards understanding how inflammation and acute phase proteins, particularly serum amyloid A and group IIa secretory phospholipase A2, may alter reverse cholesterol transport by HDL during inflammation and the acute phase response. Findings suggest that the decreased apoA-I content and markedly increased serum amyloid A content in HDL during the acute phase response result from reciprocal and coordinate transcriptional regulation of these proteins as well as HDL remodeling by group IIa secretory phospholipase A2. Serum amyloid A functions efficiently in a lipid-free or lipid-poor form to promote cholesterol efflux by ATP binding cassette protein ABCA1, evidently by functioning directly as an acceptor for cholesterol efflux as well as by increasing the availability of cellular free cholesterol. Serum amyloid A increases the ability of acute phase HDL to serve as an acceptor for SR-BI-dependent cellular cholesterol efflux. Altered remodeling of HDL by group IIa secretory phospholipase A2 in concert with cholesterol ester transfer protein may contribute to the generation of lipid-poor apoA-I and serum amyloid A acceptors for cholesterol efflux. Current data support a model for the acute phase response in which serum amyloid A and sPLA2-IIa, present at sites of inflammation and tissue damage, play a protective role by enhancing cellular cholesterol efflux, thereby promoting the removal of excess cholesterol from macrophages.

Monolithic poly[(trimethylsilyl-4-methylstyrene)-co- bis(4-vinylbenzyl)dimethylsilane] stationary phases for the fast separation of proteins and oligonucleotides.

PubMed

Jakschitz, Thomas A E; Huck, Christian W; Lubbad, Said; Bonn, Günther K

2007-04-13

In this paper the synthesis, optimisation and application of a silane based monolithic copolymer for the rapid separation of proteins and oligonucleotides is described. The monolith was prepared by thermal initiated in situ copolymerisation of trimethylsilyl-4-methylstyrene (TMSiMS) and bis(4-vinylbenzyl)dimethylsilane (BVBDMSi) in a silanised 200 microm I.D. fused silica column. Different ratios of monomer and crosslinker, as well as different ratios of micro- (toluene) and macro-porogen (2-propanol) were used for optimising the physical properties of the stationary phase regarding separation efficiency. The prepared monolithic stationary phases were characterised by measurement of permeability with different solvents, determination of pore size distribution by mercury intrusion porosimetry (MIP). Morphology was studied by scanning electron microscopy (SEM). Applying optimised conditions, a mixture comprised of five standard proteins ribunuclease A, cytochrome c, alpha-lactalbumine, myoglobine and ovalbumine was separated within 1 min by ion-pair reversed-phase liquid chromatography (IP-RPLC) obtaining half-height peak widths between 1.8 and 2.4 s. Baseline separation of oligonucleotides d(pT)(12-18) was achieved within 1.8 min obtaining half-height peak widths between 3.6 and 5.4 s. The results demonstrate the high potential of this stationary phase for fast separation of high-molecular weight biomolecules such as oligonucleotides and proteins.

Computed narrow-band azimuthal time-reversing array retrofocusing in shallow water.

PubMed

Dungan, M R; Dowling, D R

2001-10-01

The process of acoustic time reversal sends sound waves back to their point of origin in reciprocal acoustic environments even when the acoustic environment is unknown. The properties of the time-reversed field commonly depend on the frequency of the original signal, the characteristics of the acoustic environment, and the configuration of the time-reversing transducer array (TRA). In particular, vertical TRAs are predicted to produce horizontally confined foci in environments containing random volume refraction. This article validates and extends this prediction to shallow water environments via monochromatic Monte Carlo propagation simulations (based on parabolic equation computations using RAM). The computational results determine the azimuthal extent of a TRA's retrofocus in shallow-water sound channels either having random bottom roughness or containing random internal-wave-induced sound speed fluctuations. In both cases, randomness in the environment may reduce the predicted azimuthal angular width of the vertical TRA retrofocus to as little as several degrees (compared to 360 degrees for uniform environments) for source-array ranges from 5 to 20 km at frequencies from 500 Hz to 2 kHz. For both types of randomness, power law scalings are found to collapse the calculated azimuthal retrofocus widths for shallow sources over a variety of acoustic frequencies, source-array ranges, water column depths, and random fluctuation amplitudes and correlation scales. Comparisons are made between retrofocusing on shallow and deep sources, and in strongly and mildly absorbing environments.

Hot Chili Peppers: Extraction, Cleanup, and Measurement of Capsaicin

NASA Astrophysics Data System (ADS)

Huang, Jiping; Mabury, Scott A.; Sagebiel, John C.

2000-12-01

Capsaicin, the pungent ingredient of the red pepper or Capsicum annuum, is widely used in food preparation. The purpose of this experiment was to acquaint students with the active ingredients of hot chili pepper (capsaicin and dihydrocapsaicin), the extraction, cleanup, and analysis of these chemicals, as a fun and informative analytical exercise. Fresh peppers were prepared and extracted with acetonitrile, removing plant co-extractives by addition to a C-18 solid-phase extraction cartridge. Elution of the capsaicinoids was accomplished with a methanol-acetic acid solution. Analysis was completed by reverse-phase HPLC with diode-array or variable wavelength detection and calibration with external standards. Levels of capsaicin and dihydrocapsaicin were typically found to correlate with literature values for a specific hot pepper variety. Students particularly enjoyed relating concentrations of capsaicinoids to their perceived valuation of "hotness".

Integrated optical phased arrays for quasi-Bessel-beam generation.

PubMed

Notaros, Jelena; Poulton, Christopher V; Byrd, Matthew J; Raval, Manan; Watts, Michael R

2017-09-01

Integrated optical phased arrays for generating quasi-Bessel beams are proposed and experimentally demonstrated in a CMOS-compatible platform. Owing to their elongated central beams, Bessel beams have applications in a range of fields, including multiparticle trapping and laser lithography. In this Letter, continuous Bessel theory is manipulated to formulate the phase and amplitude conditions necessary for generating free-space-propagating Bessel-Gauss beams using on-chip optical phased arrays. Discussion of the effects of select phased array parameters on the generated beam's figures of merit is included. A one-dimensional splitter-tree-based phased array architecture is modified to enable arbitrary passive control of the array's element phase and amplitude distributions. This architecture is used to experimentally demonstrate on-chip quasi-Bessel-beam generation with a ∼14  mm Bessel length and ∼30  μm power full width at half maximum.

Design, Assembly, and Characterization of TALE-Based Transcriptional Activators and Repressors.

PubMed

Thakore, Pratiksha I; Gersbach, Charles A

2016-01-01

Transcription activator-like effectors (TALEs) are modular DNA-binding proteins that can be fused to a variety of effector domains to regulate the epigenome. Nucleotide recognition by TALE monomers follows a simple cipher, making this a powerful and versatile method to activate or repress gene expression. Described here are methods to design, assemble, and test TALE transcription factors (TALE-TFs) for control of endogenous gene expression. In this protocol, TALE arrays are constructed by Golden Gate cloning and tested for activity by transfection and quantitative RT-PCR. These methods for engineering TALE-TFs are useful for studies in reverse genetics and genomics, synthetic biology, and gene therapy.

Identification of IGFBP2 and IGFBP3 As Compensatory Biomarkers for CA19-9 in Early-Stage Pancreatic Cancer Using a Combination of Antibody-Based and LC-MS/MS-Based Proteomics

PubMed Central

Yoneyama, Toshihiro; Ohtsuki, Sumio; Honda, Kazufumi; Kobayashi, Makoto; Iwasaki, Motoki; Uchida, Yasuo; Okusaka, Takuji; Nakamori, Shoji; Shimahara, Masashi; Ueno, Takaaki; Tsuchida, Akihiko; Sata, Naohiro; Ioka, Tatsuya; Yasunami, Yohichi; Kosuge, Tomoo; Kaneda, Takashi; Kato, Takao; Yagihara, Kazuhiro; Fujita, Shigeyuki; Huang, Wilber; Yamada, Tesshi; Tachikawa, Masanori; Terasaki, Tetsuya

2016-01-01

Pancreatic cancer is one of the most lethal tumors, and reliable detection of early-stage pancreatic cancer and risk diseases for pancreatic cancer is essential to improve the prognosis. As 260 genes were previously reported to be upregulated in invasive ductal adenocarcinoma of pancreas (IDACP) cells, quantification of the corresponding proteins in plasma might be useful for IDACP diagnosis. Therefore, the purpose of the present study was to identify plasma biomarkers for early detection of IDACP by using two proteomics strategies: antibody-based proteomics and liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics. Among the 260 genes, we focused on 130 encoded proteins with known function for which antibodies were available. Twenty-three proteins showed values of the area under the curve (AUC) of more than 0.8 in receiver operating characteristic (ROC) analysis of reverse-phase protein array (RPPA) data of IDACP patients compared with healthy controls, and these proteins were selected as biomarker candidates. We then used our high-throughput selected reaction monitoring or multiple reaction monitoring (SRM/MRM) methodology, together with an automated sample preparation system, micro LC and auto analysis system, to quantify these candidate proteins in plasma from healthy controls and IDACP patients on a large scale. The results revealed that insulin-like growth factor-binding protein (IGFBP)2 and IGFBP3 have the ability to discriminate IDACP patients at an early stage from healthy controls, and IGFBP2 appeared to be increased in risk diseases of pancreatic malignancy, such as intraductal papillary mucinous neoplasms (IPMNs). Furthermore, diagnosis of IDACP using the combination of carbohydrate antigen 19–9 (CA19-9), IGFBP2 and IGFBP3 is significantly more effective than CA19-9 alone. This suggests that IGFBP2 and IGFBP3 may serve as compensatory biomarkers for CA19-9. Early diagnosis with this marker combination may improve the prognosis of IDACP patients. PMID:27579675

A Modified MuDPIT Separation Identified 4,488 Proteins in a System Wide Analysis of Quiescence in Yeast

PubMed Central

Webb, Kristofor J.; Xu, Tao; Park, Sung Kyu; Yates, John R.

2013-01-01

A modified multidimensional protein identification technology (MudPIT) separation was coupled to an LTQ Orbitrap Velos mass spectrometer and used to rapidly identify the near complete yeast proteome from a whole cell tryptic digest. This modified on-line two dimensional liquid chromatography separation consists of 39 strong cation exchange steps followed by a short 18.5 min reversed-phase (RP) gradient. A total of 4,269 protein identifications were made from 4,189 distinguishable protein families from yeast during log phase growth. The “Micro” MudPIT separation performed as well as a standard MudPIT separation in 40% less gradient time. The majority of the yeast proteome can now be routinely covered in less than a days’ time with high reproducibility and sensitivity. The newly devised separation method was used to detect changes in protein expression during cellular quiescence in yeast. An enrichment in the GO annotations ‘oxidation reduction’, ‘catabolic processing’ and ‘cellular response to oxidative stress’ was seen in the quiescent cellular fraction, consistent with their long lived stress resistant phenotypes. Heterogeneity was observed in the stationary phase fraction with a less dense cell population showing reductions in KEGG pathway categories of ‘Ribosome’ and ‘Proteasome’, further defining the complex nature of yeast populations present during stationary phase growth. In total 4,488 distinguishable protein families were identified in all cellular conditions tested. PMID:23540446

High-Performance Liquid Chromatography (HPLC)-Based Detection and Quantitation of Cellular c-di-GMP.

PubMed

Petrova, Olga E; Sauer, Karin

2017-01-01

The modulation of c-di-GMP levels plays a vital role in the regulation of various processes in a wide array of bacterial species. Thus, investigation of c-di-GMP regulation requires reliable methods for the assessment of c-di-GMP levels and turnover. Reversed-phase high-performance liquid chromatography (RP-HPLC) analysis has become a commonly used approach to accomplish these goals. The following describes the extraction and HPLC-based detection and quantification of c-di-GMP from Pseudomonas aeruginosa samples, a procedure that is amenable to modifications for the analysis of c-di-GMP in other bacterial species.

Amelioration of chronic fluoride toxicity by calcium and fluoride-free water in rats.

PubMed

Shankar, Priyanka; Ghosh, Sudip; Bhaskarachary, K; Venkaiah, K; Khandare, Arjun L

2013-07-14

The study was undertaken to explore the amelioration of chronic fluoride (F) toxicity (with low and normal Ca) in rats. The study was conducted in two phases. In phase I (6 months), seventy-six Wistar, weanling male rats were assigned to four treatment groups: normal-Ca (0·5 %) diet (NCD), Ca+F - ; low-Ca (0·25 %) diet (LCD), Ca - F - ; NCD +100 parts per million (ppm) F water, Ca+F+; LCD +100 ppm F water, Ca - F+. In phase II (reversal experiment, 3 months), LCD was replaced with the NCD. Treatment groups Ca+F+ and Ca - F+ were divided into two subgroups to compare the effect of continuation v. discontinuation along with Ca supplementation on reversal of chronic F toxicity. In phase I, significantly reduced food efficiency ratio (FER), body weight gain (BWG), faecal F excretion, serum Ca and increased bone F deposition were observed in the treatment group Ca - F+. Reduced serum 25-hydroxy-vitamin D3, increased 1,25-dihydroxy-vitamin D3 and up-regulation of Ca-sensing receptor, vitamin D receptor and S100 Ca-binding protein G (S100G) were observed in treatment groups Ca - F - and Ca - F+. In phase II (reversal phase), FER, BWG and serum Ca in treatment groups Ca - F+/Ca+F - and Ca - F+/Ca+F+ were still lower, as compared with other groups. However, other variables were comparable. Down-regulation of S100G was observed in F-fed groups (Ca+F+/Ca+F+ and Ca - F+/Ca+F+) in phase II. It is concluded that low Ca aggravates F toxicity, which can be ameliorated after providing adequate Ca and F-free water. However, chronic F toxicity can interfere with Ca absorption by down-regulating S100G expression irrespective of Ca nutrition.

Development of an Influenza virus protein array using Sortagging technology

PubMed Central

Sinisi, Antonia; Popp, Maximilian Wei-Lin; Antos, John M.; Pansegrau, Werner; Savino, Silvana; Nissum, Mikkel; Rappuoli, Rino; Ploegh, Hidde L.; Buti, Ludovico

2013-01-01

Protein array technology is an emerging tool that enables high throughput screening of protein-protein or protein-lipid interactions and identification of immunodominant antigens during the course of a bacterial or viral infection. In this work we developed an Influenza virus protein array using the sortase-mediated transpeptidation reaction known as “Sortagging”. LPETG-tagged Influenza virus proteins from bacterial and eukaryotic cellular extracts were immobilized at their carboxyl-termini onto a pre-activated amine-glass slide coated with a Gly3 linker. Immobilized proteins were revealed by specific antibodies and the newly generated Sortag-protein chip can be used as a device for antigen and/or antibody screening. The specificity of the Sortase A (SrtA) reaction avoids purification steps in array building and allows immobilization of proteins in an oriented fashion. Previously, this versatile technology has been successfully employed for protein labeling and protein conjugation. Here, the tool is implemented to covalently link proteins of a viral genome onto a solid support. The system could readily be scaled up to proteins of larger genomes in order to develop protein arrays for high throughput screening. PMID:22594688

Out-of-plane coercive field of Ni 80Fe 20 antidot arrays

NASA Astrophysics Data System (ADS)

Gao, Chunhong; Chen, Ke; Lü, Ling; Zhao, Jianwei; Chen, Peng

2010-11-01

The out-of-plane magnetic anisotropy and out-of-plane magnetization reversal process of nanoscale Ni 80Fe 20 antidot arrays deposited by magnetron sputtering technique on an anodic aluminum oxide (AAO) membrane are investigated. The angular dependence of out-of-plane remanent magnetization of Ni 80Fe 20 antidot arrays shows that the maximum remanence is in-plane and the squareness of the out-of-plane hysteresis loop follow a |cos θ| dependence. The angular dependence of out-of-plane coercivity of Ni 80Fe 20 antidot arrays shows that the maximum coercivity lies on the surface of a cone with its symmetric axis normal to the sample plane, which indicates a transition of magnetic reversal from curling to coherent rotation when changing the angle between the applied magnetic field and the sample plane.

Structural Features of Antiviral APOBEC3 Proteins are Linked to Their Functional Activities

PubMed Central

Kitamura, Shingo; Ode, Hirotaka; Iwatani, Yasumasa

2011-01-01

Human APOBEC3 (A3) proteins are cellular cytidine deaminases that potently restrict the replication of retroviruses by hypermutating viral cDNA and/or inhibiting reverse transcription. There are seven members of this family including A3A, B, C, DE, F, G, and H, all encoded in a tandem array on human chromosome 22. A3F and A3G are the most potent inhibitors of HIV-1, but only in the absence of the virus-encoded protein, Vif. HIV-1 utilizes Vif to abrogate A3 functions in the producer cells. More specifically, Vif, serving as a substrate receptor, facilitates ubiquitination of A3 proteins by forming a Cullin5 (Cul5)-based E3 ubiquitin ligase complex, which targets A3 proteins for rapid proteasomal degradation. The specificity of A3 degradation is determined by the ability of Vif to bind to the target. Several lines of evidence have suggested that three distinct regions of A3 proteins are involved in the interaction with Vif. Here, we review the biological functions of A3 family members with special focus on A3G and base our analysis on the available structural information. PMID:22203821

Reconfigurable Wave Velocity Transmission Lines for Phased Arrays

NASA Technical Reports Server (NTRS)

Host, Nick; Chen, Chi-Chih; Volakis, John L.; Miranda, Felix

2013-01-01

Phased array antennas showcase many advantages over mechanically steered systems. However, they are also more complex, heavy and most importantly costly. This presentation paper presents a concept which overcomes these detrimental attributes by eliminating all of the phase array backend (including phase shifters). Instead, a wave velocity reconfigurable transmission line is used in a series fed array arrangement to allow phase shifting with one small (100mil) mechanical motion. Different configurations of the reconfigurable wave velocity transmission line are discussed and simulated and experimental results are presented.

Systematical Optimization of Reverse-phase Chromatography for Shotgun Proteomics

PubMed Central

Xu, Ping; Duong, Duc M.; Peng, Junmin

2009-01-01

Summary We report the optimization of a common LC/MS/MS platform to maximize the number of proteins identified from a complex biological sample. The platform uses digested yeast lysate on a 75 μm internal diameter × 12 cm reverse-phase column that is combined with an LTQ-Orbitrap mass spectrometer. We first generated a yeast peptide mix that was quantified by multiple methods including the strategy of stable isotope labeling with amino acids in cell culture (SILAC). The peptide mix was analyzed on a highly reproducible, automated nanoLC/MS/MS system with systematic adjustment of loading amount, flow rate, elution gradient range and length. Interestingly, the column was found to be almost saturated by loading ~1 μg of the sample. Whereas the optimal flow rate (~0.2 μl/min) and elution buffer range (13–32% of acetonitrile) appeared to be independent of the loading amount, the best gradient length varied according to the amount of samples: 160 min for 1 μg of the peptide mix, but 40 min for 10 ng of the same sample. The effect of these parameters on elution peptide peak width is evaluated. After full optimization, 1,012 proteins (clustered in 806 groups) with an estimated protein false discovery rate of ~3% were identified in 1 μg of yeast lysate in a single 160-min LC/MS/MS run. PMID:19566079

Interferon-alpha 2b quantification in inclusion bodies using reversed phase-ultra performance liquid chromatography (RP-UPLC).

PubMed

Cueto-Rojas, H F; Pérez, N O; Pérez-Sánchez, G; Ocampo-Juárez, I; Medina-Rivero, E

2010-04-15

Interferon-alpha 2b (IFN-alpha 2b) is a recombinant therapeutic cytokine produced as inclusion bodies using a strain of Escherichia coli as expression system. After fermentation and recovery, it is necessary to know the amount of recombinant IFN-alpha 2b, in order to determine the yield and the load for solubilization, and chromatographic protein purification steps. The present work details the validation of a new short run-time and fast sample-preparation method to quantify IFN-alpha 2b in inclusion bodies using Reversed Phase-Ultra Performance Liquid Chromatography (RP-UPLC). The developed method demonstrated an accuracy of 100.28%; the relative standard deviations for method precision, repeatability and inter-day precision tests were found to be 0.57%, 1.54% and 1.83%, respectively. Linearity of the method was assessed in the range of concentrations from 0.05 mg/mL to 0.5 mg/mL, the curve obtained had a determination coefficient (r(2)) of 0.9989. Detection and quantification limits were found to be 0.008 mg/mL and 0.025 mg/mL, respectively. The method also demonstrated robustness for changes in column temperature, and specificity against host proteins and other recombinant protein expressed in the same E. coli strain. Copyright 2010 Elsevier B.V. All rights reserved.

Over 4,100 protein identifications from a Xenopus laevis fertilized egg digest using reversed-phase chromatographic prefractionation followed by capillary zone electrophoresis - electrospray ionization - tandem mass spectrometry analysis

PubMed Central

Yan, Xiaojing; Sun, Liangliang; Zhu, Guijie; Cox, Olivia F.; Dovichi, Norman J.

2016-01-01

A tryptic digest generated from Xenopus laevis fertilized embryos was fractionated by reversed phase liquid chromatography. One set of 30 fractions was analyzed by 100-min CZE-ESI-MS/MS separations (50 hr total instrument time), and a second set of 15 fractions was analyzed by 3-hr UPLC-ESI-MS/MS separations (45 hr total instrument time). CZE-MS/MS produced 70% as many protein IDs (4,134 vs. 5,787) and 60% as many peptide IDs (22,535 vs. 36,848) as UPLC-MS/MS with similar instrument time (50 h vs. 45 h) but with 50 times smaller total consumed sample amount (1.5 μg vs. 75 μg). Surprisingly, CZE generated peaks that were 25% more intense than UPLC for peptides that were identified by both techniques, despite the 50-fold lower loading amount; this high sensitivity reflects the efficient ionization produced by the electrokinetically-pumped nanospray interface used in CZE. This report is the first comparison of CZE-MS/MS and UPLC-MS/MS for large-scale eukaryotic proteomic analysis. The numbers of protein and peptide identifications produced by CZE-ESI-MS/MS approach those produced by UPLC-MS/MS, but with nearly two orders of magnitude lower sample amounts. PMID:27723263

ANALYSIS OF PROTEIN DIGESTS BY nano- SCX/RP/MSMS WITH pH SALT GRADIENT SCX ELUTION

EPA Science Inventory

The objective of this study was to optimize chromatographic parameters for complex peptide mixture analyses using two dimensional nano-LC/MSMS system. It used a strong cation exchange (SCX) and reversed phase chromatography (RP). The SCX solvent system was designed to promote pep...

Novel angiotensin I-converting enzyme inhibitory peptides produced in fermented milk by specific wild Lactococcus lactis strains.

PubMed

Rodríguez-Figueroa, J C; González-Córdova, A F; Torres-Llanez, M J; Garcia, H S; Vallejo-Cordoba, B

2012-10-01

The ability of specific wild Lactococcus lactis strains to hydrolyze milk proteins to release angiotensin I-converting enzyme (ACE) inhibitory peptides was evaluated. The peptide profiles were obtained from the <3 kDa water-soluble extract and subsequently fractionated by reversed-phase HPLC. The fractions with the lowest half-maximal inhibitory concentration estimated values (peptide concentration necessary to inhibit ACE activity by 50%) were Lc. lactis NRRL B-50571 fraction (F)1 (0.034 ± 0.002 μg/mL; mean ± SD) and Lc. lactis NRRL B-50572B F 0005 (0.041 ± 0.003 μg/mL; mean ± SD). All peptide fractions were analyzed by reversed-phase HPLC tandem mass spectrometry. Twenty-one novel peptide sequences associated with ACE inhibitory (ACEI) activity were identified. Several novel ACEI peptides presented peptides encrypted with proven hypotensive activity. In conclusion, specific wild Lc. lactis strains were able to hydrolyze milk proteins to generate potent ACEI peptides. However, further studies are necessary to find out the relationship between Lc. lactis strain proteolytic systems and their ability to biogenerate hypotensive peptides. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Flat-Top Sector Beams Using Only Array Element Phase Weighting: A Metaheuristic Optimization Approach

DTIC Science & Technology

2012-10-10

IrwIn D. OlIn Flat-Top Sector Beams Using Only Array Element Phase Weighting: A Metaheuristic Optimization Approach Sotera Defense Solutions, Inc...2012 Formal Report Flat-Top Sector Beams Using Only Array Element Phase Weighting: A Metaheuristic Optimization Approach Irwin D. Olin* Naval...Manuscript approved June 30, 2012. 1 FLAT-TOP SECTOR BEAMS USING ONLY ARRAY ELEMENT PHASE WEIGHTING: A METAHEURISTIC

Nitrosation of thiols and thioethers in the gas phase: a combined theoretical and experimental study.

PubMed

Gerbaux, Pascal; Wantier, Pascale; Flammang, Robert

2004-03-01

Recent studies have demonstrated the biological importance of the interaction of nitric oxide with proteins such as cytochrome-c or hemoglobin. In particular, the possibility that the nitrosonium cation, NO(+), could reversibly bind to sulfide atom type was proposed. At pH values of biological relevance, nitrosation was proposed to occur through the action of NO(+) carriers such as nitrosothiols or nitrosamines. In this context, the gas phase chemistry of protonated nitrosothiols is studied in the present work by a combination of mass spectrometry and computational methods.

Phased-array radar for airborne systems

NASA Astrophysics Data System (ADS)

Tahim, Raghbir S.; Foshee, James J.; Chang, Kai

2003-09-01

Phased array antenna systems, which support high pulse rates and high transmit power, are well suited for radar and large-scale surveillance. Sensors and communication systems can function as the eyes and ears for ballistic missile defense applications, providing early warning of attack, target detection and identification, target tracking, and countermeasure decision. In such applications, active array radar systems that contain solid-state transmitter sources and low-noise preamplifiers for transmission and reception are preferred over the conventional radar antennas, because the phased array radar offers the advantages of power management and efficiency, reliability, signal reception, beam steering target detection. The current phased array radar designs are very large, complex and expensive and less efficient because of high RF losses in the phase control circuits used for beam scan. Several thousands of phase shifters and drivers may be required for a single system thus making the system very complex and expensive. This paper describes the phased array radar system based on high power T/R modules, wide-band radiating planar antenna elements and very low loss wide-band phase control circuits (requiring reduced power levels) for beam scan. The phase shifter design is based on micro-strip feed lines perturbed by the proximity of voltage controlled piezoelectric transducer (PET). Measured results have shown an added insertion loss of less than 1 dB for a phase shift of 450 degrees from 2 to 20 GHz. The new wideband phased array radar design provides significant reduction in size cost and weight. Compared to the conventional phased array systems, the cost saving is more than 15 to 1.

First experimental demonstration of self-synchronous phase locking of an optical array

NASA Astrophysics Data System (ADS)

Shay, T. M.; Benham, Vincent; Baker, J. T.; Ward, Benjamin; Sanchez, Anthony D.; Culpepper, Mark A.; Pilkington, D.; Spring, Justin; Nelson, Douglas J.; Lu, Chunte A.

2006-12-01

A novel, highly accurate, all electronic technique for phase locking arrays of optical fibers is demonstrated. We report the first demonstration of the only electronic phase locking technique that doesn’t require a reference beam. The measured phase error is λ/20. Excellent phase locking has been demonstrated for fiber amplifier arrays.

Depth determination and source characteristics of the North Korean Nuclear Tests (2006, 2009, 2013 and 2016) using local and teleseismic arrays

NASA Astrophysics Data System (ADS)

Kim, S. G.

2016-12-01

Depth determination and source characteristics of the North Korea Nuclear tests (2006, 2009, 2013 and 2016) using seismic arrays with azimuthal optium coverage So Gu Kim1,*, Yefim Gitterman2, Václav Vavryčuk3 and Seoung-kyu Lee1 1Korea Seismological Institute, Goyang 10332, Republic of Korea 2Seismology Division, Geophysical Institute of Israel, P.O.B. 182, Lod 71100, Israel 3Institute of Geophysics, Academy of Sciences, Prague 14100, Czech Republic Abstract The source depths for the North Korean nuclear tests (2006, 2009, 2013 and 2016) were determined using depth phases (pP, sP, pPn and sPn) and Rayleigh wave spectra from local and global arrays. The emplacement depths were estimated at 2.21, 2.10, 2.10 and 2.08 km for the 2006, 2009. 2013 and 2016 nuclear tests respectively. It was also found that the mechanism of the 2006 test generated roughly a reverse faulting accompanying mostly Rayleigh waves, whereas the 2009 and 2013 tests were an oblique-reverse faulting generating SH and Love waves as well as Rayleigh waves. The generation of SH and Love waves for the 2009 and 2013 nuclear tests was attributed to not only release of tectonic stress but also other factors such as relaxation of cavity fractures, source configuration and source mechanism. We infer that the 2009, 2013 and 2016 tests must have well contained nuclear debris through long winding horizontal drifts in the light of the absence of radioisotopes to the atmosphere compared with 2006 test which may have been conducted in the vertical shift as a vertically distributed source. ______________________________________________ *Corresponding author: So Gu Kim (sogukim@hanmail.net)

High-performance liquid chromatography as a technique to determine protein adsorption onto hydrophilic/hydrophobic surfaces.

PubMed

Huang, Tongtong; Anselme, Karine; Sarrailh, Segolene; Ponche, Arnaud

2016-01-30

The purpose of this study is to evaluate the potential of simple high performance liquid chromatography (HPLC) setup for quantification of adsorbed proteins on various type of plane substrates with limited area (<3 cm(2)). Protein quantification was investigated with a liquid chromatography chain equipped with a size exclusion column or a reversed-phase column. By evaluating the validation of the method according to guidelines of the International Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH), all the results obtained by HPLC were reliable. By simple adsorption test at the contact of hydrophilic (glass) and hydrophobic (polydimethylsiloxane: PDMS) surfaces, kinetics of adsorption were determined and amounts of adsorbed bovine serum albumin, myoglobin and lysozyme were obtained: as expected for each protein, the amount adsorbed at the plateau on glass (between 0.15 μg/cm(2) and 0.4 μg/cm(2)) is lower than for hydrophobic PDMS surfaces (between 0.45 μg/cm(2) and 0.8 μg/cm(2)). These results were consistent with bicinchoninic acid protein determination. According to ICH guidelines, both Reversed Phase and Size Exclusion HPLC can be validated for quantification of adsorbed protein. However, we consider the size exclusion approach more interesting in this field because additional informations can be obtained for aggregative proteins. Indeed, monomer, dimer and oligomer of bovine serum albumin (BSA) were observed in the chromatogram. On increasing the temperature, we found a decrease of peak intensity of bovine serum albumin as well as the fraction of dimer and oligomer after contact with PDMS and glass surface. As the surface can act as a denaturation parameter, these informations can have a huge impact on the elucidation of the interfacial behavior of protein and in particular for aggregation processes in pharmaceutical applications. Copyright © 2015 Elsevier B.V. All rights reserved.

High density diffusion-free nanowell arrays.

PubMed

Takulapalli, Bharath R; Qiu, Ji; Magee, D Mitchell; Kahn, Peter; Brunner, Al; Barker, Kristi; Means, Steven; Miersch, Shane; Bian, Xiaofang; Mendoza, Alex; Festa, Fernanda; Syal, Karan; Park, Jin G; LaBaer, Joshua; Wiktor, Peter

2012-08-03

Proteomics aspires to elucidate the functions of all proteins. Protein microarrays provide an important step by enabling high-throughput studies of displayed proteins. However, many functional assays of proteins include untethered intermediates or products, which could frustrate the use of planar arrays at very high densities because of diffusion to neighboring features. The nucleic acid programmable protein array (NAPPA) is a robust in situ synthesis method for producing functional proteins just-in-time, which includes steps with diffusible intermediates. We determined that diffusion of expressed proteins led to cross-binding at neighboring spots at very high densities with reduced interspot spacing. To address this limitation, we have developed an innovative platform using photolithographically etched discrete silicon nanowells and used NAPPA as a test case. This arrested protein diffusion and cross-binding. We present confined high density protein expression and display, as well as functional protein-protein interactions, in 8000 nanowell arrays. This is the highest density of individual proteins in nanovessels demonstrated on a single slide. We further present proof of principle results on ultrahigh density protein arrays capable of up to 24000 nanowells on a single slide.

Ultrasonic brain therapy: First trans-skull in vivo experiments on sheep using adaptive focusing

NASA Astrophysics Data System (ADS)

Pernot, Mathieu; Aubry, Jean-Francois; Tanter, Michael; Fink, Mathias; Boch, Anne-Laure; Kujas, Michèle

2004-05-01

A high-power prototype dedicated to trans-skull therapy has been tested in vivo on 20 sheep. The array is made of 200 high-power transducers working at 1-MHz central and is able to reach 260 bars at focus in water. An echographic array connected to a Philips HDI 1000 system has been inserted in the therapeutic array in order to perform real-time monitoring of the treatment. A complete craniotomy has been performed on half of the treated animal models in order to get a reference model. On the other animals, a minimally invasive surgery has been performed thanks to a time-reversal experiment: a hydrophone was inserted at the target inside the brain thanks to a 1-mm2 craniotomy. A time-reversal experiment was then conducted through the skull bone with the therapeutic array to treat the targeted point. For all the animals a specified region around the target was treated thanks to electronic beam steering. Animals were finally divided into three groups and sacrificed, respectively, 0, 1, and 2 weeks after treatment. Finally, histological examination confirmed tissue damage. These in vivo experiments highlight the strong potential of high-power time-reversal technology.

Multiscale Molecular Dynamics Simulations of Beta-Amyloid Interactions with Neurons

NASA Astrophysics Data System (ADS)

Qiu, Liming; Vaughn, Mark; Cheng, Kelvin

2012-10-01

Early events of human beta-amyloid protein interactions with cholesterol-containing membranes are critical to understanding the pathogenesis of Alzheimer's disease (AD) and to exploring new therapeutic interventions of AD. Atomistic molecular dynamics (AMD) simulations have been extensively used to study the protein-lipid interaction at high atomic resolutions. However, traditional MD simulations are not efficient in sampling the phase space of complex lipid/protein systems with rugged free energy landscapes. Meanwhile, coarse-grained MD (CGD) simulations are efficient in the phase space sampling but suffered from low spatial resolutions and from the fact that the energy landscapes are not identical to those of the AMD. Here, a multiscale approach was employed to simulate the protein-lipid interactions of beta-amyloid upon its release from proteolysis residing in the neuronal membranes. We utilized a forward (AMD to CGD) and reverse (CGD-AMD) strategy to explore new transmembrane and surface protein configuration and evaluate the stabilization mechanisms by measuring the residue-specific protein-lipid or protein conformations. The detailed molecular interactions revealed in this multiscale MD approach will provide new insights into understanding the early molecular events leading to the pathogenesis of AD.

Reverse Shape Memory Effect Related to α → γ Transformation in a Fe-Mn-Al-Ni Shape Memory Alloy

NASA Astrophysics Data System (ADS)

Peng, Huabei; Huang, Pan; Zhou, Tiannan; Wang, Shanling; Wen, Yuhua

2017-05-01

In this study, we investigated the shape memory behavior and phase transformations of solution-treated Fe43.61Mn34.74Al13.38Ni8.27 alloy between room temperature and 1173 K (900 °C). This alloy exhibits the reverse shape memory effect resulting from the phase transformation of α (bcc) → γ (fcc) between 673 K and 1073 K (400 °C and 800 °C) in addition to the shape memory effect resulting from the martensitic reverse transformation of γ' (fcc) → α (bcc) below 673 K (400 °C). There is a high density of hairpin-shaped dislocations in the α phase undergoing the martensitic reverse transformation of γ' → α. The lath γ phase, which preferentially nucleates and grows in the reversed α phase, has the same crystal orientation with the reverse-transformed γ' martensite. However, the vermiculate γ phase, which is precipitated in the α phase between lath γ phase, has different crystal orientations. The lath γ phase is beneficial to attaining better reverse shape memory effect than the vermiculate γ phase.

Monolithic optical integrated control circuitry for GaAs MMIC-based phased arrays

NASA Technical Reports Server (NTRS)

Bhasin, K. B.; Ponchak, G. E.; Kascak, T. J.

1985-01-01

Gallium arsenide (GaAs) monolithic microwave integrated circuits (MMIC's) show promise in phased-array antenna applications for future space communications systems. Their efficient usage will depend on the control of amplitude and phase signals for each MMIC element in the phased array and in the low-loss radiofrequency feed. For a phased array contining several MMIC elements a complex system is required to control and feed each element. The characteristics of GaAs MMIC's for 20/30-GHz phased-array systems are discussed. The optical/MMIC interface and the desired characteristics of optical integrated circuits (OIC's) for such an interface are described. Anticipated fabrication considerations for eventual full monolithic integration of optical integrated circuits with MMIC's on a GaAs substrate are presented.

A Catalog of Proteins Expressed in the AG Secreted Fluid during the Mature Phase of the Chinese Mitten Crabs (Eriocheir sinensis)

PubMed Central

He, Lin; Li, Qing; Liu, Lihua; Wang, Yuanli; Xie, Jing; Yang, Hongdan; Wang, Qun

2015-01-01

The accessory gland (AG) is an important component of the male reproductive system of arthropods, its secretions enhance fertility, some AG proteins bind to the spermatozoa and affect its function and properties. Here we report the first comprehensive catalog of the AG secreted fluid during the mature phase of the Chinese mitten crab (Eriocheir sinensis). AG proteins were separated by one-dimensional gel electrophoresis and analyzed by reverse phase high-performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS). Altogether, the mass spectra of 1173 peptides were detected (1067 without decoy and contaminants) which allowed for the identification of 486 different proteins annotated upon the NCBI database (http://www.ncbi.nlm.nih.gov/) and our transcritptome dataset. The mass spectrometry proteomics data have been deposited at the ProteomeXchange with identifier PXD000700. An extensive description of the AG proteome will help provide the basis for a better understanding of a number of reproductive mechanisms, including potentially spermatophore breakdown, dynamic functional and morphological changes in sperm cells and sperm acrosin enzyme vitality. Thus, the comprehensive catalog of proteins presented here can serve as a valuable reference for future studies of sperm maturation and regulatory mechanisms involved in crustacean reproduction. PMID:26305468

Phased array feed design technology for Large Aperture Microwave Radiometer (LAMR) Earth observations

NASA Technical Reports Server (NTRS)

Schuman, H. K.

1992-01-01

An assessment of the potential and limitations of phased array antennas in space-based geophysical precision radiometry is described. Mathematical models exhibiting the dependence of system and scene temperatures and system sensitivity on phased array antenna parameters and components such as phase shifters and low noise amplifiers (LNA) are developed. Emphasis is given to minimum noise temperature designs wherein the LNA's are located at the array level, one per element or subarray. Two types of combiners are considered: array lenses (space feeds) and corporate networks. The result of a survey of suitable components and devices is described. The data obtained from that survey are used in conjunction with the mathematical models to yield an assessment of effective array antenna noise temperature for representative geostationary and low Earth orbit systems. Practical methods of calibrating a space-based, phased array radiometer are briefly addressed as well.

Protein mass analysis of histones.

PubMed

Galasinski, Scott C; Resing, Katheryn A; Ahn, Natalie G

2003-09-01

Posttranslational modification of chromatin-associated proteins, including histones and high-mobility-group (HMG) proteins, provides an important mechanism to control gene expression, genome integrity, and epigenetic inheritance. Protein mass analysis provides a rapid and unbiased approach to monitor multiple chemical modifications on individual molecules. This review describes methods for acid extraction of histones and HMG proteins, followed by separation by reverse-phase chromatography coupled to electrospray ionization mass spectrometry (LC/ESI-MS). Posttranslational modifications are detected by analysis of full-length protein masses. Confirmation of protein identity and modification state is obtained through enzymatic digestion and peptide sequencing by MS/MS. For differentially modified forms of each protein, the measured intensities are semiquantitative and allow determination of relative abundance and stoichiometry. The method simultaneously detects covalent modifications on multiple proteins and provides a facile assay for comparing chromatin modification states between different cell types and/or cellular responses.

A broadband phased-array system for direct phosphorus and sodium metabolic MRI on a clinical scanner.

PubMed

Lee, R F; Giaquinto, R; Constantinides, C; Souza, S; Weiss, R G; Bottomley, P A

2000-02-01

Despite their proven gains in signal-to-noise ratio and field-of-view for routine clinical MRI, phased-array detection systems are currently unavailable for nuclei other than protons (1H). A broadband phased-array system was designed and built to convert the 1H transmitter signal to the non-1H frequency for excitation and to convert non-1H phased-array MRI signals to the 1H frequency for presentation to the narrowband 1H receivers of a clinical whole-body 1.5 T MRI system. With this system, the scanner operates at the 1H frequency, whereas phased-array MRI occurs at the frequency of the other nucleus. Pulse sequences were developed for direct phased-array sodium (23Na) and phosphorus (31P) MRI of high-energy phosphates using chemical selective imaging, thereby avoiding the complex processing and reconstruction required for phased-array magnetic resonance spectroscopy data. Flexible 4-channel 31P and 23Na phased-arrays were built and the entire system tested in phantom and human studies. The array produced a signal-to-noise ratio improvement of 20% relative to the best-positioned single coil, but gains of 300-400% were realized in many voxels located outside the effective field-of-view of the single coil. Cardiac phosphorus and sodium MRI were obtained in 6-13 min with 16 and 0.5 mL resolution, respectively. Lower resolution human cardiac 23Na MRI were obtained in as little as 4 sec. The system provides a practical approach to realizing the advantages of phased-arrays for nuclei other than 1H, and imaging metabolites directly.

FUS Phase Separation Is Modulated by a Molecular Chaperone and Methylation of Arginine Cation-π Interactions.

PubMed

Qamar, Seema; Wang, GuoZhen; Randle, Suzanne J; Ruggeri, Francesco Simone; Varela, Juan A; Lin, Julie Qiaojin; Phillips, Emma C; Miyashita, Akinori; Williams, Declan; Ströhl, Florian; Meadows, William; Ferry, Rodylyn; Dardov, Victoria J; Tartaglia, Gian G; Farrer, Lindsay A; Kaminski Schierle, Gabriele S; Kaminski, Clemens F; Holt, Christine E; Fraser, Paul E; Schmitt-Ulms, Gerold; Klenerman, David; Knowles, Tuomas; Vendruscolo, Michele; St George-Hyslop, Peter

2018-04-19

Reversible phase separation underpins the role of FUS in ribonucleoprotein granules and other membrane-free organelles and is, in part, driven by the intrinsically disordered low-complexity (LC) domain of FUS. Here, we report that cooperative cation-π interactions between tyrosines in the LC domain and arginines in structured C-terminal domains also contribute to phase separation. These interactions are modulated by post-translational arginine methylation, wherein arginine hypomethylation strongly promotes phase separation and gelation. Indeed, significant hypomethylation, which occurs in FUS-associated frontotemporal lobar degeneration (FTLD), induces FUS condensation into stable intermolecular β-sheet-rich hydrogels that disrupt RNP granule function and impair new protein synthesis in neuron terminals. We show that transportin acts as a physiological molecular chaperone of FUS in neuron terminals, reducing phase separation and gelation of methylated and hypomethylated FUS and rescuing protein synthesis. These results demonstrate how FUS condensation is physiologically regulated and how perturbations in these mechanisms can lead to disease. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Isolation and purification of an early pregnancy factor-like molecule from culture supernatants obtained from lymphocytes of pregnant women: II. Identification of the molecule as a Fc-receptor-like molecule: a preliminary report.

PubMed

Aranha, C; Bordekar, A; Shahani, S

1998-11-01

Early pregnancy factor (EPF)-like activity from culture supernatants obtained from stimulated lymphocytes of pregnant women was characterized and identified. The enzyme-linked immunosorbent assay depending on the presence of "Fc" receptors on bovine spermatozoa was used to identify the EPF-like molecule purified by gel filtration and reverse-phase high-performance liquid chromatography. The results indicated that the crude lymphocyte culture supernatant, the EPF-positive G IV fraction obtained on gel filtration, and the EPF-positive reverse-phase high-performance liquid chromatography protein readily bound with the different concentrations of aggregated human gamma-globulin in a manner similar to that in which the standard control of aggregated human gamma-globulin binds to the bovine spermatozoa. EPF-like activity synthesized and secreted by lymphocytes during pregnancy may be a Fc-receptor-like molecule.

Development and validation of a reversed-phase fluorescence HPLC method for determination of bucillamine in human plasma using pre-column derivatization with monobromobimane.

PubMed

Lee, Kang Choon; Chun, Young Goo; Kim, Insoo; Shin, Beom Soo; Park, Eun-Seok; Yoo, Sun Dong; Youn, Yu Seok

2009-07-15

A simple, specific and sensitive derivatization with monobromobimane (mBrB) and the corresponding HPLC-fluorescence quantitation method for the analysis of bucillamine in human plasma was developed and validated. The analytical procedure involves a simple protein precipitation, pre-column fluorescence derivatization, and separation by reversed-phase high performance liquid chromatography (RP-HPLC). The calibration curve showed good linearity over a wide concentration range (50 ng/mL to 10 microg/mL) in human plasma (r(2)=0.9998). The lower limit of quantitation (LLOQ) was 50 ng/mL. The average precision and accuracy at LLOQ were within 6.3% and 107.6%, respectively. This method was successfully applied to a pharmacokinetic study after oral administration of a dose (300 mg) of bucillamine to 20 healthy Korean volunteers.

Plasma Membrane ATPase Activity following Reversible and Irreversible Freezing Injury 1

PubMed Central

Iswari, S.; Palta, Jiwan P.

1989-01-01

Plasma membrane ATPase has been proposed as a site of functional alteration during early stages of freezing injury. To test this, plasma membrane was purified from Solanum leaflets by a single step partitioning of microsomes in a dextran-polyethylene glycol two phase system. Addition of lysolecithin in the ATPase assay produced up to 10-fold increase in ATPase activity. ATPase activity was specific for ATP with a Km around 0.4 millimolar. Presence of the ATPase enzyme was identified by immunoblotting with oat ATPase antibodies. Using the phase partitioning method, plasma membrane was isolated from Solanum commersonii leaflets which had four different degrees of freezing damage, namely, slight (reversible), partial (partially reversible), substantial and total (irreversible). With slight (reversible) damage the plasma membrane ATPase specific activity increased 1.5- to 2-fold and its Km was decreased by about 3-fold, whereas the specific activity of cytochrome c reductase and cytochrome c oxidase in the microsomes were not different from the control. However, with substantial (lethal, irreversible) damage, there was a loss of membrane protein, decrease in plasma membrane ATPase specific activity and decrease in Km, while cytochrome c oxidase and cytochrome c reductase were unaffected. These results support the hypothesis that plasma membrane ATPase is altered by slight freeze-thaw stress. Images Figure 1 Figure 2 PMID:16666856

Four-to-one power combiner for 20 GHz phased array antenna using RADC MMIC phase shifters

NASA Technical Reports Server (NTRS)

1991-01-01

The design and microwave simulation of two-to-one microstrip power combiners is described. The power combiners were designed for use in a four element phase array receive antenna subarray at 20 GHz. Four test circuits are described which were designed to enable testing of the power combiner and the four element phased array antenna. Test Circuit 1 enables measurement of the two-to-one power combiner. Test Circuit 2 enables measurement of the four-to-one power combiner. Test Circuit 3 enables measurement of a four element antenna array without phase shifting MMIC's in order to characterize the power combiner with the antenna patch-to-microstrip coaxial feedthroughs. Test circuit 4 is the four element phased array antenna including the RADC MMIC phase shifters and appropriate interconnects to provide bias voltages and control phase bits.

Fluorescent Molecular Rotor-in-Paraffin Waxes for Thermometry and Biometric Identification.

PubMed

Jin, Young-Jae; Dogra, Rubal; Cheong, In Woo; Kwak, Giseop

2015-07-08

Novel thermoresponsive sensor systems consisting of a molecular rotor (MR) and paraffin wax (PW) were developed for various thermometric and biometric identification applications. Polydiphenylacetylenes (PDPAs) coupled with long alkyl chains were used as MRs, and PWs of hydrocarbons having 16-20 carbons were utilized as phase-change materials. The PDPAs were successfully dissolved in the molten PWs and did not act as an impurity that prevents phase transition of the PWs. These PDPA-in-PW hybrids had almost the same enthalpies and phase-transition temperatures as the corresponding pure PWs. The hybrids exhibited highly reversible fluorescence (FL) changes at the critical temperatures during phase transition of the PWs. These hybrids were impregnated into common filter paper in the molten state by absorption or were encapsulated into urea resin to enhance their mechanical integrity and cyclic stability during repeated use. The wax papers could be utilized in highly advanced applications including FL image writing/erasing, an array-type thermo-indicator, and fingerprint/palmprint identification. The present findings should facilitate the development of novel fluorescent sensor systems for biometric identification and are potentially applicable for biological and biomedical thermometry.

The NMR phased array.

PubMed

Roemer, P B; Edelstein, W A; Hayes, C E; Souza, S P; Mueller, O M

1990-11-01

We describe methods for simultaneously acquiring and subsequently combining data from a multitude of closely positioned NMR receiving coils. The approach is conceptually similar to phased array radar and ultrasound and hence we call our techniques the "NMR phased array." The NMR phased array offers the signal-to-noise ratio (SNR) and resolution of a small surface coil over fields-of-view (FOV) normally associated with body imaging with no increase in imaging time. The NMR phased array can be applied to both imaging and spectroscopy for all pulse sequences. The problematic interactions among nearby surface coils is eliminated (a) by overlapping adjacent coils to give zero mutual inductance, hence zero interaction, and (b) by attaching low input impedance preamplifiers to all coils, thus eliminating interference among next nearest and more distant neighbors. We derive an algorithm for combining the data from the phased array elements to yield an image with optimum SNR. Other techniques which are easier to implement at the cost of lower SNR are explored. Phased array imaging is demonstrated with high resolution (512 x 512, 48-cm FOV, and 32-cm FOV) spin-echo images of the thoracic and lumbar spine. Data were acquired from four-element linear spine arrays, the first made of 12-cm square coils and the second made of 8-cm square coils. When compared with images from a single 15 x 30-cm rectangular coil and identical imaging parameters, the phased array yields a 2X and 3X higher SNR at the depth of the spine (approximately 7 cm).

Wirelessly Networked Digital Phased Array: Analysis and Development of a Phase Synchronization Concept

DTIC Science & Technology

2007-09-01

NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS Approved for public release; distribution is unlimited WIRELESSLY NETWORKED...DIGITAL PHASED ARRAY: ANALYSIS AND DEVELOPMENT OF A PHASE SYNCHRONIZATION CONCEPT by Micael Grahn September 2007 Thesis Advisor...September 2007 3. REPORT TYPE AND DATES COVERED Master’s Thesis 4. TITLE AND SUBTITLE Wirelessly Networked Digital Phased Array: Analysis and

Analysis and experimental demonstration of conformal adaptive phase-locked fiber array for laser communications and beam projection applications

NASA Astrophysics Data System (ADS)

Liu, Ling

The primary goal of this research is the analysis, development, and experimental demonstration of an adaptive phase-locked fiber array system for free-space optical communications and laser beam projection applications. To our knowledge, the developed adaptive phase-locked system composed of three fiber collimators (subapertures) with tip-tilt wavefront phase control at each subaperture represents the first reported fiber array system that implements both phase-locking control and adaptive wavefront tip-tilt control capabilities. This research has also resulted in the following innovations: (a) The first experimental demonstration of a phase-locked fiber array with tip-tilt wave-front aberration compensation at each fiber collimator; (b) Development and demonstration of the fastest currently reported stochastic parallel gradient descent (SPGD) system capable of operation at 180,000 iterations per second; (c) The first experimental demonstration of a laser communication link based on a phase-locked fiber array; (d) The first successful experimental demonstration of turbulence and jitter-induced phase distortion compensation in a phase-locked fiber array optical system; (e) The first demonstration of laser beam projection onto an extended target with a randomly rough surface using a conformal adaptive fiber array system. Fiber array optical systems, the subject of this study, can overcome some of the draw-backs of conventional monolithic large-aperture transmitter/receiver optical systems that are usually heavy, bulky, and expensive. The primary experimental challenges in the development of the adaptive phased-locked fiber-array included precise (<5 microrad) alignment of the fiber collimators and development of fast (100kHz-class) phase-locking and wavefront tip-tilt control systems. The precise alignment of the fiber collimator array is achieved through a specially developed initial coarse alignment tool based on high precision piezoelectric picomotors and a dynamic fine alignment mechanism implemented with specially designed and manufactured piezoelectric fiber positioners. Phase-locking of the fiber collimators is performed by controlling the phases of the output beams (beamlets) using integrated polarization-maintaining (PM) fiber-coupled LiNbO3 phase shifters. The developed phase-locking controllers are based on either the SPGD algorithm or the multi-dithering technique. Subaperture wavefront phase tip-tilt control is realized using piezoelectric fiber positioners that are controlled using a computer-based SPGD controller. Both coherent (phase-locked) and incoherent beam combining in the fiber array system are analyzed theoretically and experimentally. Two special fiber-based beam-combining testbeds have been built to demonstrate the technical feasibility of phase-locking compensation prior to free-space operation. In addition, the reciprocity of counter-propagating beams in a phase-locked fiber array system has been investigated. Coherent beam combining in a phase-locking system with wavefront phase tip-tilt compensation at each subaperture is successfully demonstrated when laboratory-simulated turbulence and wavefront jitters are present in the propagation path of the beamlets. In addition, coherent beam combining with a non-cooperative extended target in the control loop is successfully demonstrated.

An integrated molecular analysis of lung adenocarcinomas identifies potential therapeutic targets among TTF1-negative tumors including DNA repair proteins and Nrf2

PubMed Central

Cardnell, Robert J.G.; Behrens, Carmen; Diao, Lixia; Fan, YouHong; Tang, Ximing; Tong, Pan; John D., Minna; Mills, Gordon B.; Heymach, John V.; Wistuba, Ignacio I.; Wang, Jing; Byers., Lauren A.

2015-01-01

Purpose Thyroid transcription factor-1 (TTF1) immunohistochemistry (IHC) is used clinically to differentiate primary lung adenocarcinomas (LUAD) from squamous lung cancers and metastatic adenocarcinomas from other primary sites. However, a subset of LUAD (15-20%) does not express TTF1 and TTF1-negative patients have worse clinical outcomes. As there are no established targeted agents with activity in TTF1-negative LUAD, we performed an integrated molecular analysis to identify potential therapeutic targets. Experimental Design Using two clinical LUAD cohorts (274 tumors), one from our institution (PROSPECT) and the TCGA, we interrogated proteomic profiles (by reverse-phase protein array (RPPA)), gene expression, and mutational data. Drug response data from 74 cell lines were used to validate potential therapeutic agents. Results Strong correlations were observed between TTF1 IHC and TTF1 measurements by RPPA (Rho=0.57, p<0.001) and gene expression (NKX2-1, Rho=0.61, p<0.001). Established driver mutations (e.g. BRAF and EGFR) were associated with high TTF1 expression. In contrast, TTF1-negative LUAD had a higher frequency of inactivating KEAP1 mutations (p=0.001). Proteomic profiling identified increased expression of DNA repair proteins (e.g., Chk1 and the DNA repair score) and suppressed PI3K/MAPK signaling among TTF1-negative tumors, with differences in total proteins confirmed at the mRNA level. Cell line analysis showed drugs targeting DNA repair to be more active in TTF1-low cell lines. Conclusions Combined genomic and proteomic analyses demonstrated infrequent alteration of validated lung cancer targets (including the absence of BRAF mutations in TTF1-negative LUAD), but identified novel potential targets for TTF1-negative LUAD includingKEAP1/Nrf2 and DNA repair pathways. PMID:25878335

Influence of the properties of soft collective spin wave modes on the magnetization reversal in finite arrays of dipolarly coupled magnetic dots

NASA Astrophysics Data System (ADS)

Stebliy, Maxim; Ognev, Alexey; Samardak, Alexander; Chebotkevich, Ludmila; Verba, Roman; Melkov, Gennadiy; Tiberkevich, Vasil; Slavin, Andrei

2015-06-01

Magnetization reversal in finite chains and square arrays of closely packed cylindrical magnetic dots, having vortex ground state in the absence of the external bias field, has been studied experimentally by measuring static hysteresis loops, and also analyzed theoretically. It has been shown that the field Bn of a vortex nucleation in a dot as a function of the finite number N of dots in the array's side may exhibit a monotonic or an oscillatory behavior depending on the array geometry and the direction of the external bias magnetic field. The oscillations in the dependence Bn(N) are shown to be caused by the quantization of the collective soft spin wave mode, which corresponds to the vortex nucleation in a finite array of dots. These oscillations are directly related to the form and symmetry of the dispersion law of the soft SW mode: the oscillation could appear only if the minimum of the soft mode spectrum is not located at any of the symmetric points inside the first Brillouin zone of the array's lattice. Thus, the purely static measurements of the hysteresis loops in finite arrays of coupled magnetic dots can yield important information about the properties of the collective spin wave excitations in these arrays.

A design concept for an MMIC (Monolithic Microwave Integrated Circuit) microstrip phased array

NASA Technical Reports Server (NTRS)

Lee, Richard Q.; Smetana, Jerry; Acosta, Roberto

1987-01-01

A conceptual design for a microstrip phased array with monolithic microwave integrated circuit (MMIC) amplitude and phase controls is described. The MMIC devices used are 20 GHz variable power amplifiers and variable phase shifters recently developed by NASA contractors for applications in future Ka proposed design, which concept is for a general NxN element array of rectangular lattice geometry. Subarray excitation is incorporated in the MMIC phased array design to reduce the complexity of the beam forming network and the number of MMIC components required.

The myeloperoxidase-derived oxidant HOSCN inhibits protein tyrosine phosphatases and modulates cell signalling via the mitogen-activated protein kinase (MAPK) pathway in macrophages

PubMed Central

Lane, Amanda E.; Tan, Joanne T. M.; Hawkins, Clare L.; Heather, Alison K.; Davies, Michael J.

2010-01-01

MPO (myeloperoxidase) catalyses the oxidation of chloride, bromide and thiocyanate by hydrogen peroxide to HOCl (hypochlorous acid), HOBr (hypobromous acid) and HOSCN (hypothiocyanous acid) respectively. Specificity constants indicate that SCN− is a major substrate for MPO. HOSCN is also a major oxidant generated by other peroxidases including salivary, gastric and eosinophil peroxidases. While HOCl and HOBr are powerful oxidizing agents, HOSCN is a less reactive, but more specific, oxidant which targets thiols and especially low pKa species. In the present study we show that HOSCN targets cysteine residues present in PTPs (protein tyrosine phosphatases) with this resulting in a loss of PTP activity for the isolated enzyme, in cell lysates and intact J774A.1 macrophage-like cells. Inhibition also occurs with MPO-generated HOCl and HOBr, but is more marked with MPO-generated HOSCN, particularly at longer incubation times. This inhibition is reversed by dithiothreitol, particularly at early time points, consistent with the reversible oxidation of the active site cysteine residue to give either a cysteine–SCN adduct or a sulfenic acid. Inhibition of PTP activity is associated with increased phosphorylation of p38a and ERK2 (extracellular-signal-regulated kinase 2) as detected by Western blot analysis and phosphoprotein arrays, and results in altered MAPK (mitogen-activated protein kinase) signalling. These data indicate that the highly selective targeting of some protein thiols by HOSCN can result in perturbation of cellular phosphorylation and altered cell signalling. These changes occur with (patho)physiological concentrations of SCN− ions, and implicate HOSCN as an important mediator of inflammation-induced oxidative damage, particularly in smokers who have elevated plasma levels of SCN−. PMID:20528774

Sarcoplasmic calcium-binding protein: identification as a new allergen of the black tiger shrimp Penaeus monodon.

PubMed

Shiomi, Kazuo; Sato, Yuichiro; Hamamoto, Shohei; Mita, Hajime; Shimakura, Kuniyoshi

2008-01-01

Tropomyosin and arginine kinase have been identified as crustacean allergens. During purification of arginine kinase from black tiger shrimp Penaeus monodon, we found a new allergen of 20-kDa. A 20-kDa allergen was purified from the abdominal muscle of black tiger shrimp by salting-out, anion-exchange HPLC and reverse-phase HPLC. Following digestion of the 20-kDa allergen with lysyl endopeptidase, peptide fragments were isolated by reverse-phase HPLC, and 2 of them were sequenced. The 20-kDa allergen, together with tropomyosin and arginine kinase purified from black tiger shrimp, was evaluated for IgE reactivity by ELISA. Five species of crustaceans (kuruma shrimp, American lobster, pink shrimp, king crab and snow crab) were surveyed for the 20-kDa allergen by immunoblotting. The 20-kDa allergen was purified from black tiger shrimp and identified as a sarcoplasmic calcium-binding protein (SCP) based on the determined amino acid sequences of 2 enzymatic fragments. Of 16 sera from crustacean-allergic patients, 8 and 13 reacted to SCP and tropomyosin, respectively; the reactivity to arginine kinase was weakly recognized with 10 sera. In immunoblotting, an IgE-reactive 20-kDa protein was also detected in kuruma shrimp, American lobster and pink shrimp but not in 2 species of crab. Preadsorption of the sera with black tiger shrimp SCP abolished the IgE reactivity of the 20-kDa protein, suggesting the 20-kDa protein to be an SCP. SCP is a new crustacean allergen, and distribution of IgE-reactive SCP is probably limited to shrimp and crayfish. (c) 2008 S. Karger AG, Basel.

Expression and purification of mouse peptide ESP4 in Escherichia coli.

PubMed

Hirakane, Makoto; Taniguchi, Masahiro; Yoshinaga, Sosuke; Misumi, Shogo; Terasawa, Hiroaki

2014-04-01

Pheromones are species-specific chemical signals that regulate a wide range of social and sexual behaviors in many animals. In mice, the male-specific peptide ESP1 (exocrine gland-secreting peptide 1) is secreted into tear fluids and enhances female sexual receptive behavior. ESP1 belongs to the ESP family, a multigene family with 38 genes in mice. ESP1 shares the highest homology with ESP4. ESP1 is expressed in the extraorbital lacrimal gland, whereas ESP4 is expressed in some exocrine glands. Thus, ESP4 is expected to have a function that has not been elucidated yet. Large amounts of the purified ESP4 protein are required for structural and biochemical studies. Here we present an expression and purification scheme for the recombinant ESP4 protein. The N-terminally histidine-tagged ESP4 fusion protein was expressed in Escherichia coli as inclusion bodies, which were solubilized and purified by nickel affinity chromatography. The histidine tag was cleaved with thrombin and removed by a second nickel affinity chromatography step. The ESP4 protein was isolated with high purity by reversed-phase chromatography. For NMR analyses, we prepared a stable isotope-labeled ESP4 protein. Three repeated freeze-drying steps after the reversed-phase chromatography were required, to remove a volatile contaminating compound and to obtain an NMR spectrum with a homogeneous line shape. AMS-modification and far-UV CD spectroscopic analyses suggested that ESP4 has an intramolecular disulfide bridge and a helical structure, respectively. The present study provides a powerful tool for structural and biochemical studies of ESP4, leading toward the elucidation of the roles of the ESP family members. Copyright © 2014 Elsevier Inc. All rights reserved.

Heterogeneity of Arabinogalactan-Proteins on the Plasma Membrane of Rose Cells.

PubMed Central

Serpe, M. D.; Nothnagel, E. A.

1996-01-01

Arabinogalactan-proteins (AGPs) have been purified from the plasma membrane of suspension-cultured Paul's Scarlet rose (Rosa sp.) cells. The two most abundant and homogeneous plasma membrane AGP fractions were named plasma membrane AGP1 (PM-AGP1) and plasma membrane AGP2 (PM-AGP2) and had apparent molecular masses of 140 and 217 kD, respectively. Both PM-AGP1 and PM-AGP2 had [beta]-(1-3)-, [beta]-(1,6)-, and [beta]-(1,3,6)-galactopyranosyl residues, predominantly terminal [alpha]-arabinofuranosyl residues, and (1,4)- and terminal glucuronopyranosyl residues. The protein moieties of PM-AGP1 and PM-AGP2 were both rich in hydroxyproline, alanine, and serine, but differed in the abundance of hydroxyproline, which was 1.6 times higher in PM-AGP2 than in PM-AGP1. Another difference was the overall protein content, which was 3.7% (w/w) in PM-AGP1 and 15% in PM-AGP2. As judged by their behavior on reverse-phase chromatography, PM-AGP1 and PM-AGP2 were not more hydrophobic than AGPs from the cell wall or culture medium. In contrast, a minor plasma membrane AGP fraction eluted later on reverse-phase chromatography and was more negatively charged at pH 5 than either PM-AGP1 or PM-AGP2. The more negatively charged fraction contained molecules with a glycosyl composition characteristic of AGPs and included at least two different macromolecules. The results of this investigation indicate that Rosa plasma membrane contains at least four distinct AGPs or AGP-like molecules. These molecules differed from each other in size, charge, hydrophobicity, amino-acyl composition, and/or protein content. PMID:12226444

Phased Array Antenna Testbed Development at the NASA Glenn Research Center

NASA Technical Reports Server (NTRS)

Lambert, Kevin M.; Kubat, Gregory; Johnson, Sandra K.; Anzic, Godfrey

2003-01-01

Ideal phased array antennas offer advantages for communication systems, such as wide-angle scanning and multibeam operation, which can be utilized in certain NASA applications. However, physically realizable, electronically steered, phased array antennas introduce additional system performance parameters, which must be included in the evaluation of the system. The NASA Glenn Research Center (GRC) is currently conducting research to identify these parameters and to develop the tools necessary to measure them. One of these tools is a testbed where phased array antennas may be operated in an environment that simulates their use. This paper describes the development of the testbed and its use in characterizing a particular K-Band, phased array antenna.

Dehydration induced phase transitions in a microfluidic droplet array for the separation of biomolecules

NASA Astrophysics Data System (ADS)

Nelson, Chris; Anna, Shelley

2013-11-01

Droplet-based strategies for fluid manipulation have seen significant application in microfluidics due to their ability to compartmentalize solutions and facilitate highly parallelized reactions. Functioning as micro-scale reaction vessels, droplets have been used to study protein crystallization, enzyme kinetics, and to encapsulate whole cells. Recently, the mass transport out of droplets has been used to concentrate solutions and induce phase transitions. Here, we show that droplets trapped in a microfluidic array will spontaneously dehydrate over the course of several hours. By loading these devices with an initially dilute aqueous polymer solution, we use this slow dehydration to observe phase transitions and the evolution of droplet morphology in hundreds of droplets simultaneously. As an example, we trap and dehydrate droplets of a model aqueous two-phase system consisting of polyethylene glycol and dextran. Initially the drops are homogenous, then after some time the polymer concentration reaches a critical point and two phases form. As water continues to leave the system, the drops transition from a microemulsion of DEX in PEG to a core-shell configuration. Eventually, changes in interfacial tension, driven by dehydration, cause the DEX core to completely de-wet from the PEG shell. Since aqueous two phase systems are able to selectively separate a variety of biomolecules, this core shedding behavior has the potential to provide selective, on-chip separation and concentration.

Enhanced Energy Localization in Hyperthermia Treatment Based on Hybrid Electromagnetic and Ultrasonic System: Proof of Concept with Numerical Simulations.

PubMed

Nizam-Uddin, N; Elshafiey, Ibrahim

2017-01-01

This paper proposes a hybrid hyperthermia treatment system, utilizing two noninvasive modalities for treating brain tumors. The proposed system depends on focusing electromagnetic (EM) and ultrasound (US) energies. The EM hyperthermia subsystem enhances energy localization by incorporating a multichannel wideband setting and coherent-phased-array technique. A genetic algorithm based optimization tool is developed to enhance the specific absorption rate (SAR) distribution by reducing hotspots and maximizing energy deposition at tumor regions. The treatment performance is also enhanced by augmenting an ultrasonic subsystem to allow focused energy deposition into deep tumors. The therapeutic faculty of ultrasonic energy is assessed by examining the control of mechanical alignment of transducer array elements. A time reversal (TR) approach is then investigated to address challenges in energy focus in both subsystems. Simulation results of the synergetic effect of both modalities assuming a simplified model of human head phantom demonstrate the feasibility of the proposed hybrid technique as a noninvasive tool for thermal treatment of brain tumors.

Rapid method for the determination of 14 isoflavones in food using UHPLC coupled to photo diode array detection.

PubMed

Shim, You-Shin; Yoon, Won-Jin; Hwang, Jin-Bong; Park, Hyun-Jin; Seo, Dongwon; Ha, Jaeho

2015-11-15

A rapid method for the determination of 14 types of isoflavones in food using ultra-high performance liquid chromatography (UHPLC) was validated in terms of precision, accuracy, sensitivity and linearity. The UHPLC separation was performed on a reverse-phase C18 column (particle size 2 μm, i.d. 2 mm, length 100 mm) using a photo diode array detector that was fixed to 260 nm. The limits of detection and quantification of the UHPLC analyses ranged from 0.03 to 0.33 mg kg(-1). The intra-day and inter-day precision of the individual isoflavones were less than 11.77% and calibration curves exhibited good linearity (r(2) = 0.99) within the tested ranges. These results suggest that the rapid method used in this study could be available to determine of 14 types of isoflavones in a variety of food such as soy bean, black bean, red bean and soybean paste. Copyright © 2015 Elsevier Ltd. All rights reserved.

Emergent reduced dimensionality by vertex frustration in artificial spin ice

NASA Astrophysics Data System (ADS)

Gilbert, Ian; Lao, Yuyang; Carrasquillo, Isaac; O'Brien, Liam; Watts, Justin D.; Manno, Michael; Leighton, Chris; Scholl, Andreas; Nisoli, Cristiano; Schiffer, Peter

2016-02-01

Reducing the dimensionality of a physical system can have a profound effect on its properties, as in the ordering of low-dimensional magnetic materials, phonon dispersion in mercury chain salts, sliding phases, and the electronic states of graphene. Here we explore the emergence of quasi-one-dimensional behaviour in two-dimensional artificial spin ice, a class of lithographically fabricated nanomagnet arrays used to study geometrical frustration. We extend the implementation of artificial spin ice by fabricating a new array geometry, the so-called tetris lattice. We demonstrate that the ground state of the tetris lattice consists of alternating ordered and disordered bands of nanomagnetic moments. The disordered bands can be mapped onto an emergent thermal one-dimensional Ising model. Furthermore, we show that the level of degeneracy associated with these bands dictates the susceptibility of island moments to thermally induced reversals, thus establishing that vertex frustration can reduce the relevant dimensionality of physical behaviour in a magnetic system.

Enhanced Energy Localization in Hyperthermia Treatment Based on Hybrid Electromagnetic and Ultrasonic System: Proof of Concept with Numerical Simulations

PubMed Central

Elshafiey, Ibrahim

2017-01-01

This paper proposes a hybrid hyperthermia treatment system, utilizing two noninvasive modalities for treating brain tumors. The proposed system depends on focusing electromagnetic (EM) and ultrasound (US) energies. The EM hyperthermia subsystem enhances energy localization by incorporating a multichannel wideband setting and coherent-phased-array technique. A genetic algorithm based optimization tool is developed to enhance the specific absorption rate (SAR) distribution by reducing hotspots and maximizing energy deposition at tumor regions. The treatment performance is also enhanced by augmenting an ultrasonic subsystem to allow focused energy deposition into deep tumors. The therapeutic faculty of ultrasonic energy is assessed by examining the control of mechanical alignment of transducer array elements. A time reversal (TR) approach is then investigated to address challenges in energy focus in both subsystems. Simulation results of the synergetic effect of both modalities assuming a simplified model of human head phantom demonstrate the feasibility of the proposed hybrid technique as a noninvasive tool for thermal treatment of brain tumors. PMID:28840125

Mass Spectrometric Characterization of Benzoxazinoid Glycosides from Rhizopus-Elicited Wheat (Triticum aestivum) Seedlings.

PubMed

de Bruijn, Wouter J C; Vincken, Jean-Paul; Duran, Katharina; Gruppen, Harry

2016-08-17

Benzoxazinoids function as defense compounds and have been suggested to possess health-promoting effects. In this work, the mass spectrometric behavior of benzoxazinoids from the classes benzoxazin-3-ones (with subclasses lactams, hydroxamic acids, and methyl derivatives) and benzoxazolinones was studied. Wheat seeds were germinated with simultaneous elicitation by Rhizopus. The seedling extract was screened for the presence of benzoxazinoid (glycosides) using reversed-phase ultra-high-performance liquid chromatography with photodiode array detection coupled in line to multiple-stage mass spectrometry (RP-UHPLC-PDA-MS(n)). Benzoxazin-3-ones from the different subclasses showed distinctly different ionization and fragmentation behaviors. These features were incorporated into a newly proposed decision guideline to aid the classification of benzoxazinoids. Glycosides of the methyl derivative 2-hydroxy-4-methoxy-1,4-benzoxazin-3-one were tentatively identified for the first time in wheat. We conclude that wheat seedlings germinated with simultaneous fungal elicitation contain a diverse array of benzoxazinoids, mainly constituted by benzoxazin-3-one glycosides.

Emergent reduced dimensionality by vertex frustration in artificial spin ice

DOE PAGES

Gilbert, Ian; Lao, Yuyang; Carrasquillo, Isaac; ...

2015-10-26

Reducing the dimensionality of a physical system can have a profound effect on its properties, as in the ordering of low-dimensional magnetic materials, phonon dispersion in mercury chain salts, sliding phases, and the electronic states of graphene. Here we explore the emergence of quasi-one-dimensional behaviour in two-dimensional artificial spin ice, a class of lithographically fabricated nanomagnet arrays used to study geometrical frustration. We extend the implementation of artificial spin ice by fabricating a new array geometry, the so-called tetris lattice. We demonstrate that the ground state of the tetris lattice consists of alternating ordered and disordered bands of nanomagnetic moments.more » The disordered bands can be mapped onto an emergent thermal one-dimensional Ising model. Furthermore, we show that the level of degeneracy associated with these bands dictates the susceptibility of island moments to thermally induced reversals, thus establishing that vertex frustration can reduce the relevant dimensionality of physical behaviour in a magnetic system.« less

Impact: a low cost, reconfigurable, digital beamforming common module building block for next generation phased arrays

NASA Astrophysics Data System (ADS)

Paulsen, Lee; Hoffmann, Ted; Fulton, Caleb; Yeary, Mark; Saunders, Austin; Thompson, Dan; Chen, Bill; Guo, Alex; Murmann, Boris

2015-05-01

Phased array systems offer numerous advantages to the modern warfighter in multiple application spaces, including Radar, Electronic Warfare, Signals Intelligence, and Communications. However, a lack of commonality in the underlying technology base for DoD Phased Arrays has led to static systems with long development cycles, slow technology refreshes in response to emerging threats, and expensive, application-specific sub-components. The IMPACT module (Integrated Multi-use Phased Array Common Tile) is a multi-channel, reconfigurable, cost-effective beamformer that provides a common building block for multiple, disparate array applications.

Noncanonical expression of a murine cytomegalovirus early protein CD8 T-cell epitope as an immediate early epitope based on transcription from an upstream gene.

PubMed

Fink, Annette; Büttner, Julia K; Thomas, Doris; Holtappels, Rafaela; Reddehase, Matthias J; Lemmermann, Niels A W

2014-02-14

Viral CD8 T-cell epitopes, represented by viral peptides bound to major histocompatibility complex class-I (MHC-I) glycoproteins, are often identified by "reverse immunology", a strategy not requiring biochemical and structural knowledge of the actual viral protein from which they are derived by antigen processing. Instead, bioinformatic algorithms predicting the probability of C-terminal cleavage in the proteasome, as well as binding affinity to the presenting MHC-I molecules, are applied to amino acid sequences deduced from predicted open reading frames (ORFs) based on the genomic sequence. If the protein corresponding to an antigenic ORF is known, it is usually inferred that the kinetic class of the protein also defines the phase in the viral replicative cycle during which the respective antigenic peptide is presented for recognition by CD8 T cells. We have previously identified a nonapeptide from the predicted ORFm164 of murine cytomegalovirus that is presented by the MHC-I allomorph H-2 Dd and that is immunodominant in BALB/c (H-2d haplotype) mice. Surprisingly, although the ORFm164 protein gp36.5 is expressed as an Early (E) phase protein, the m164 epitope is presented already during the Immediate Early (IE) phase, based on the expression of an upstream mRNA starting within ORFm167 and encompassing ORFm164.

Differentially expressed genes in nonsmall cell lung cancer: expression profiling of cancer-related genes in squamous cell lung cancer.

PubMed

Kettunen, Eeva; Anttila, Sisko; Seppänen, Jouni K; Karjalainen, Antti; Edgren, Henrik; Lindström, Irmeli; Salovaara, Reijo; Nissén, Anna-Maria; Salo, Jarmo; Mattson, Karin; Hollmén, Jaakko; Knuutila, Sakari; Wikman, Harriet

2004-03-01

The expression patterns of cancer-related genes in 13 cases of squamous cell lung cancer (SCC) were characterized and compared with those in normal lung tissue and 13 adenocarcinomas (AC), the other major type of nonsmall cell lung cancer (NSCLC). cDNA array was used to screen the gene expression levels and the array results were verified using a real-time reverse-transcriptase-polymerase chain reaction (RT-PCR). Thirty-nine percent of the 25 most upregulated and the 25 most downregulated genes were common to SCC and AC. Of these genes, DSP, HMGA1 (alias HMGIY), TIMP1, MIF, CCNB1, TN, MMP11, and MMP12 were upregulated and COPEB (alias CPBP), TYROBP, BENE, BMPR2, SOCS3, TIMP3, CAV1, and CAV2 were downregulated. The expression levels of several genes from distinct protein families (cytokeratins and hemidesmosomal proteins) were markedly increased in SCC compared with AC and normal lung. In addition, several genes, overexpressed in SCC, such as HMGA1, CDK4, IGFBP3, MMP9, MMP11, MMP12, and MMP14, fell into distinct chromosomal loci, which we have detected as gained regions on the basis of comparative genomic hybridization data. Our study revealed new candidate genes involved in NSCLC.

Drought stress and carbon assimilation in a warming climate: Reversible and irreversible impacts.

PubMed

Feller, Urs

2016-09-20

Global change is characterized by increased CO 2 concentration in the atmosphere, increasing average temperature and more frequent extreme events including drought periods, heat waves and flooding. Especially the impacts of drought and of elevated temperature on carbon assimilation are considered in this review. Effects of extreme events on the subcellular level as well as on the whole plant level may be reversible, partially reversible or irreversible. The photosynthetically active biomass depends on the number and the size of mature leaves and the photosynthetic activity in this biomass during stress and subsequent recovery phases. The total area of active leaves is determined by leaf expansion and senescence, while net photosynthesis per leaf area is primarily influenced by stomatal opening (stomatal conductance), mesophyll conductance, activity of the photosynthetic apparatus (light absorption and electron transport, activity of the Calvin cycle) and CO 2 release by decarboxylation reactions (photorespiration, dark respiration). Water status, stomatal opening and leaf temperature represent a "magic triangle" of three strongly interacting parameters. The response of stomata to altered environmental conditions is important for stomatal limitations. Rubisco protein is quite thermotolerant, but the enzyme becomes at elevated temperature more rapidly inactivated (decarbamylation, reversible effect) and must be reactivated by Rubisco activase (carbamylation of a lysine residue). Rubisco activase is present under two forms (encoded by separate genes or products of alternative splicing of the pre-mRNA from one gene) and is very thermosensitive. Rubisco activase was identified as a key protein for photosynthesis at elevated temperature (non-stomatal limitation). During a moderate heat stress Rubisco activase is reversibly inactivated, but during a more severe stress (higher temperature and/or longer exposure) the protein is irreversibly inactivated, insolubilized and finally degraded. On the level of the leaf, this loss of photosynthetic activity may still be reversible when new Rubisco activase is produced by protein synthesis. Rubisco activase as well as enzymes involved in the detoxification of reactive oxygen species or in osmoregulation are considered as important targets for breeding crop plants which are still productive under drought and/or at elevated leaf temperature in a changing climate. Copyright © 2016 Elsevier GmbH. All rights reserved.

A Phase Correction Technique Based on Spatial Movements of Antennas in Real-Time (S.M.A.R.T.) for Designing Self-Adapting Conformal Array Antennas

NASA Astrophysics Data System (ADS)

Roy, Sayan

This research presents a real-time adaptive phase correction technique for flexible phased array antennas on conformal surfaces of variable shapes. Previously reported pattern correctional methods for flexible phased array antennas require prior knowledge on the possible non-planar shapes in which the array may adapt for conformal applications. For the first time, this initial requirement of shape curvature knowledge is no longer needed and the instantaneous information on the relative location of array elements is used here for developing a geometrical model based on a set of Bezier curves. Specifically, by using an array of inclinometer sensors and an adaptive phase-correctional algorithm, it has been shown that the proposed geometrical model can successfully predict different conformal orientations of a 1-by-4 antenna array in real-time without the requirement of knowing the shape-changing characteristics of the surface the array is attached upon. Moreover, the phase correction technique is validated by determining the field patterns and broadside gain of the 1-by-4 antenna array on four different conformal surfaces with multiple points of curvatures. Throughout this work, measurements are shown to agree with the analytical solutions and full-wave simulations.

A Phased Array Coil for Human Cardiac Imaging

PubMed Central

Constantinides, Chris D.; Westgate, Charles R.; O'Dell, Walter G.; Zerhouni, Elias A.; McVeigh, Elliot R.

2007-01-01

A prototype cardiac phased array receiver coil was constructed that comprised a cylindrical array and a separate planar array. Both arrays had two coil loops with the same coil dimensions. Data acquisition with the cylindrical array placed on the human chest, and the planar array placed under the back, yielded an overall enhancement of the signal-to-noise ratio (SNR) over the entire heart by a factor of 1.1–2.85 over a commercially available flexible coil and a commercially available four-loop planar phased array coil. This improvement in SNR can be exploited in cardiac imaging to increase the spatial resolution and reduce the image acquisition time. PMID:7674903

Microwave scanning beam approach and landing system phased array antenna volume I

DOT National Transportation Integrated Search

1973-02-01

The use of phased arrays for the proposed landing system (MLS) is discussed. Studies relating to ground reflections, near field focusing, and phased-array errors are presented. Two experimental antennas which were fabricated and tested are described....

Microwave scanning beam approach and landing system phased array antenna : volume II

DOT National Transportation Integrated Search

1973-02-01

The use of phased arrays for the proposed landing system (MLS) is discussed. Studies relating to ground reflections, near field focusing, and phased-array errors are presented. Two experimental antennas which were fabricated and tested are described....

IGFBP2 is a candidate biomarker for Ink4a-Arf status and a therapeutic target for high-grade gliomas.

PubMed

Moore, Lynette M; Holmes, Kristen M; Smith, Sarah M; Wu, Ying; Tchougounova, Elena; Uhrbom, Lene; Sawaya, Raymond; Bruner, Janet M; Fuller, Gregory N; Zhang, Wei

2009-09-29

The levels of insulin-like growth factor-binding protein 2 (IGFBP2) are elevated during progression of many human cancers. By using a glial-specific transgenic mouse system (RCAS/Ntv-a), we reported previously that IGFBP2 is an oncogenic factor for glioma progression in combination with platelet-derived growth factor-beta (PDGFB). Because the INK4a-ARF locus is often deleted in high-grade gliomas (anaplastic oligodendroglioma and glioblastoma), we investigated the effect of the Ink4a-Arf-null background on IGFBP2-mediated progression of PDGFB-initiated oligodendroglioma. We demonstrate here that homozygous deletion of Ink4a-Arf bypasses the requirement of exogenously introduced IGFBP2 for glioma progression. Instead, absence of Ink4a-Arf resulted in elevated endogenous tumor cell IGFBP2. An inverse relationship between p16(INK4a) and IGFBP2 expression was also observed in human glioma tissue samples and in 90 different cancer cell lines by using Western blotting and reverse-phase protein lysate arrays. When endogenous IGFBP2 expression was attenuated by an RCAS vector expressing antisense IGFBP2 in our mouse model, a decreased incidence of anaplastic oligodendroglioma as well as prolonged survival was observed. Thus, p16(INK4a) is a negative regulator of the IGFBP2 oncogene. Loss of Ink4a-Arf results in increased IGFBP2, which contributes to glioma progression, thereby implicating IGFBP2 as a marker and potential therapeutic target for Ink4a-Arf-deleted gliomas.

IGFBP2 is a candidate biomarker for Ink4a-Arf status and a therapeutic target for high-grade gliomas

PubMed Central

Moore, Lynette M.; Holmes, Kristen M.; Smith, Sarah M.; Wu, Ying; Tchougounova, Elena; Uhrbom, Lene; Sawaya, Raymond; Bruner, Janet M.; Fuller, Gregory N.; Zhang, Wei

2009-01-01

The levels of insulin-like growth factor-binding protein 2 (IGFBP2) are elevated during progression of many human cancers. By using a glial-specific transgenic mouse system (RCAS/Ntv-a), we reported previously that IGFBP2 is an oncogenic factor for glioma progression in combination with platelet-derived growth factor-β (PDGFB). Because the INK4a-ARF locus is often deleted in high-grade gliomas (anaplastic oligodendroglioma and glioblastoma), we investigated the effect of the Ink4a-Arf-null background on IGFBP2-mediated progression of PDGFB-initiated oligodendroglioma. We demonstrate here that homozygous deletion of Ink4a-Arf bypasses the requirement of exogenously introduced IGFBP2 for glioma progression. Instead, absence of Ink4a-Arf resulted in elevated endogenous tumor cell IGFBP2. An inverse relationship between p16INK4a and IGFBP2 expression was also observed in human glioma tissue samples and in 90 different cancer cell lines by using Western blotting and reverse-phase protein lysate arrays. When endogenous IGFBP2 expression was attenuated by an RCAS vector expressing antisense IGFBP2 in our mouse model, a decreased incidence of anaplastic oligodendroglioma as well as prolonged survival was observed. Thus, p16INK4a is a negative regulator of the IGFBP2 oncogene. Loss of Ink4a-Arf results in increased IGFBP2, which contributes to glioma progression, thereby implicating IGFBP2 as a marker and potential therapeutic target for Ink4a-Arf-deleted gliomas. PMID:19805356

A validated high-performance liquid chromatography method with diode array detection for simultaneous determination of nine flavonoids in Senecio cannabifolius Less.

PubMed

Niu, Tian-Zeng; Zhang, Yu-Wei; Bao, Yong-Li; Wu, Yin; Yu, Chun-Lei; Sun, Lu-Guo; Yi, Jing-Wen; Huang, Yan-Xin; Li, Yu-Xin

2013-03-25

A reversed phase high performance liquid chromatography method coupled with a diode array detector (HPLC-DAD) was developed for the first time for the simultaneous determination of 9 flavonoids in Senecio cannabifolius, a traditional Chinese medicinal herb. Agilent Zorbax SB-C18 column was used at room temperature and the mobile phase was a mixture of acetonitrile and 0.5% formic acid (v/v) in water in the gradient elution mode at a flow-rate of 1.0mlmin(-1), detected at 360nm. Validation of this method was performed to verify the linearity, precision, limits of detection and quantification, intra- and inter-day variabilities, reproducibility and recovery. The calibration curves showed good linearities (R(2)>0.9995) within the test ranges. The relative standard deviation (RSD) of the method was less than 3.0% for intra- and inter-day assays. The samples were stable for at least 96h, and the average recoveries were between 90.6% and 102.5%. High sensitivity was demonstrated with detection limits of 0.028-0.085μg/ml for flavonoids. The newly established HPLC method represents a powerful technique for the quality assurance of S. cannabifolius. Copyright © 2012 Elsevier B.V. All rights reserved.

Simultaneous determination of bioactive constituents in Danggui Buxue Tang for quality control by HPLC coupled with a diode array detector, an evaporative light scattering detector and mass spectrometry.

PubMed

Yi, Ling; Qi, Lian-Wen; Li, Ping; Ma, Yi-Han; Luo, Yong-Jing; Li, Hai-Yun

2007-09-01

Danggui Buxue Tang (DBT), a classical traditional Chinese formula comprising Radix Angelicae Sinensis (RAS) and Radix Astragali (RA), has been widely used to treat menopausal irregularity in Chinese women for nearly 800 years. In this study, a comprehensive analytical method of simultaneously determining the main types of bioactive constituents, eighteen in all from the formula, involving flavonoids, saponins, organic acid and some volatile compounds, was developed. This method was based on HPLC coupled to a diode array and evaporative light scattering detectors (HPLC-DAD-ELSD) on a common reverse-phase C(18) column. Liquid chromatography coupled with on-line electrospray ionization mass spectrometry (LC-ESI-MS) was also used to further validate and analyze the constituents. It was found that 0.3% aqueous formic acid and acetonitrile was the optimum mobile phase for gradient elution. This method, which showed good precision and accuracy, was successfully used to quantify the bioactive constituents in six products. As a result, the validated HPLC method, together with the LC-ESI-MS analysis, provided a new basis for assessing the quality of traditional Chinese medicinal compound preparations (TCMCPs) consisting of many bioactive components.

Determination of target fat-soluble micronutrients in rainbow trout's muscle and liver tissues by liquid chromatography with diode array-tandem mass spectrometry detection.

PubMed

Pérez Fernández, Virginia; Ventura, Salvatore; Tomai, Pierpaolo; Curini, Roberta; Gentili, Alessandra

2017-03-01

This paper describes an analytical approach, based on LC-diode array detector-MS/MS (LC-DAD-MS/MS), for characterizing the fat-soluble micronutrient fraction in rainbow trout (Oncorhynchus mykiss). Two different procedures were applied to isolate the analytes from liver and muscle tissue: overnight cold saponification to hydrolyze bound forms and to simplify the analysis; matrix solid-phase dispersion to avoid artifacts and to maintain unaltered the naturally occurring forms. Analytes were separated on a C 30 analytical column by using a nonaqueous reversed mobile phase compatible with the atmospheric pressure chemical ionization. Compared to other works, the most relevant advantage of the here illustrated method is the large amount of information obtained with few analytical steps: nine fat-soluble vitamins (3,4-dehydroretinol, retinol, cholecalciferol, ergocalciferol, α-tocopherol, γ-tocopherol, δ-tocopherol, phylloquinone, and menaquinone-4) and eight carotenoids (all-trans-lutein, all-trans-astaxanthin, all-trans-zeaxanthin, all-trans-β-cryptoxanthin, all-trans-canthaxanthin, all-trans-ζ-carotene, all-trans-β-carotene, and all-trans-γ-carotene) were quantified after the method validation, while other untargeted carotenoids were tentatively identified by exploiting the identification power of the LC-DAD-MS/MS hyphenation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Expression and inhibition of aquaporins in germinating Arabidopsis seeds.

PubMed

Vander Willigen, Clare; Postaire, Olivier; Tournaire-Roux, Colette; Boursiac, Yann; Maurel, Christophe

2006-09-01

Extensive and kinetically well-defined water exchanges occur during germination of seeds. A putative role for aquaporins in this process was investigated in Arabidopsis. Macro-arrays carrying aquaporin gene-specific tags and antibodies raised against aquaporin subclasses revealed two distinct aquaporin expression programs between dry seeds and young seedlings. High expression levels of a restricted number of tonoplast intrinsic protein (TIP) isoforms (TIP3;1 and/or TIP3;2, and TIP5;1) together with a low expression of all 13 plasma membrane aquaporin (PIP) isoforms was observed in dry and germinating materials. In contrast, prevalent expression of aquaporins of the TIP1, TIP2 and PIP subgroups was induced during seedling establishment. Mercury (5 microM HgCl(2)), a general blocker of aquaporins in various organisms, reduced the speed of seed germination and induced a true delay in maternal seed coat (testa) rupture and radicle emergence, by 8-9 and 25-30 h, respectively. Most importantly, mercury did not alter seed lot homogeneity nor the seed germination developmental sequence, and its effects were largely reversed by addition of 2 mM dithiothreitol, suggesting that these effects were primarily due to oxidation of cell components, possibly aquaporins, without irreversible alteration of cell integrity. Measurements of water uptake in control and mercury-treated seeds suggested that aquaporin functions are not involved in early seed imbibition (phase I) but would rather be associated with a delayed initiation of phase III, i.e. water uptake accompanying expansion and growth of the embryo. A possible role for aquaporins in germinating seeds and more generally in plant tissue growth is discussed.

Spectrally resolved modal characteristics of leaky-wave-coupled quantum cascade phase-locked laser arrays

NASA Astrophysics Data System (ADS)

Sigler, Chris; Gibson, Ricky; Boyle, Colin; Kirch, Jeremy D.; Lindberg, Donald; Earles, Thomas; Botez, Dan; Mawst, Luke J.; Bedford, Robert

2018-01-01

The modal characteristics of nonresonant five-element phase-locked arrays of 4.7-μm emitting quantum cascade lasers (QCLs) have been studied using spectrally resolved near- and far-field measurements and correlated with results of device simulation. Devices are fabricated by a two-step metal-organic chemical vapor deposition process and operate predominantly in an in-phase array mode near threshold, although become multimode at higher drive levels. The wide spectral bandwidth of the QCL's core region is found to be a factor in promoting multispatial-mode operation at high drive levels above threshold. An optimized resonant-array design is identified to allow sole in-phase array-mode operation to high drive levels above threshold, and indicates that for phase-locked laser arrays full spatial coherence to high output powers does not require full temporal coherence.

Alternative preparation of inclusion bodies excludes interfering non-protein contaminants and improves the yield of recombinant proinsulin.

PubMed

Mackin, Robert B

2014-01-01

The goal of simple, high-yield expression and purification of recombinant human proinsulin has proven to be a considerable challenge. First, proinsulin forms inclusion bodies during bacterial expression. While this phenomenon can be exploited as a capture step, conventionally prepared inclusion bodies contain significant amounts of non-protein contaminants that interfere with subsequent chromatographic purification. Second, the proinsulin molecules within the inclusion bodies are incorrectly folded, and likely cross-linked to one another, making it difficult to quantify the amount of expressed proinsulin. Third, proinsulin is an intermediate between the initial product of ribosomal translation (preproinsulin) and the final product secreted by pancreatic beta cells (insulin). Therefore, to be efficiently produced in bacteria, it must be produced as an N-terminally extended fusion protein, which has to be converted to authentic proinsulin during the purification scheme. To address all three of these problems, while simultaneously streamlining the procedure and increasing the yield of recombinant proinsulin, we have made three substantive modifications to our previous method for producing proinsulin:.•Conditions for the preparation of inclusion bodies have been altered so contaminants that interfere with semi-preparative reversed-phase chromatography are excluded while the proinsulin fusion protein is retained at high yield.•Aliquots are taken following important steps in the procedure and the quantity of proinsulin-related polypeptide in the sample is compared to the amount present prior to that step.•Final purification is performed using a silica-based reversed-phase matrix in place of a polystyrene-divinylbenzene-based matrix.

Alternative preparation of inclusion bodies excludes interfering non-protein contaminants and improves the yield of recombinant proinsulin

PubMed Central

Mackin, Robert B.

2014-01-01

The goal of simple, high-yield expression and purification of recombinant human proinsulin has proven to be a considerable challenge. First, proinsulin forms inclusion bodies during bacterial expression. While this phenomenon can be exploited as a capture step, conventionally prepared inclusion bodies contain significant amounts of non-protein contaminants that interfere with subsequent chromatographic purification. Second, the proinsulin molecules within the inclusion bodies are incorrectly folded, and likely cross-linked to one another, making it difficult to quantify the amount of expressed proinsulin. Third, proinsulin is an intermediate between the initial product of ribosomal translation (preproinsulin) and the final product secreted by pancreatic beta cells (insulin). Therefore, to be efficiently produced in bacteria, it must be produced as an N-terminally extended fusion protein, which has to be converted to authentic proinsulin during the purification scheme. To address all three of these problems, while simultaneously streamlining the procedure and increasing the yield of recombinant proinsulin, we have made three substantive modifications to our previous method for producing proinsulin:.•Conditions for the preparation of inclusion bodies have been altered so contaminants that interfere with semi-preparative reversed-phase chromatography are excluded while the proinsulin fusion protein is retained at high yield.•Aliquots are taken following important steps in the procedure and the quantity of proinsulin-related polypeptide in the sample is compared to the amount present prior to that step.•Final purification is performed using a silica-based reversed-phase matrix in place of a polystyrene-divinylbenzene-based matrix. PMID:26150942

Enrichment and Detection of Molecules Secreted by Tumor Cells Using Magnetic Reversed-Phase Particles and LC-MALDI-TOF-MS

PubMed Central

Peter, Jochen F.; Otto, Angela M.; Wolf, Bernhard

2007-01-01

Tumor cells change their genetic expression pattern as they progress to states of increasing malignancy. Investigations at the DNA and RNA level alone cannot provide all the information resulting after the translation and processing of the corresponding proteins, which is one reason for a poor correlation between mRNA and the respective protein abundance. In diagnostics, differentially expressed peptides or proteins are important markers for the early detection of cancer. Unfortunately, tumor cells secrete peptides and proteins in only very low amounts, making mass spectrometric determination very difficult. In this publication, methods have been developed for the effective enrichment and cleanup of substances secreted by cultivated cancer cells. To obviate peptides from fetal calf serum used in cell culture, a serum surrogate was developed, which maintained growth of the cancer cells. After the binding of substances from cell-culture supernatants to custom-made magnetic reversed-phase particles, the substances were eluted and separated by capillary high-performance liquid chromatography. Fractions were spotted directly on a MALDI target, and MALDI-TOF mass spectrometric data acquisition was performed in automatic mode. This technology was used to detect substances secreted by two mammary carcinoma cell lines differing in their malignancy (MCF-7, MDA-MB231). Unequivocal differences in the peptide secretion patterns were observed. In conclusion, this system allows the sensitive investigation of peptides secreted by cancer cells in culture and provides a valuable tool for the investigation of cancer cells in different states of malignancy. PMID:18166672

1.9 μm superficially porous packing material with radially oriented pores and tailored pore size for ultra-fast separation of small molecules and biomolecules.

PubMed

Min, Yi; Jiang, Bo; Wu, Ci; Xia, Simin; Zhang, Xiaodan; Liang, Zhen; Zhang, Lihua; Zhang, Yukui

2014-08-22

In this work, 1.9 μm reversed-phase packing materials with superficially porous structure were prepared to achieve the rapid and high efficient separation of peptides and proteins. The silica particles were synthesized via three steps, nonporous silica particle preparation by a modified seeded growth method, mesoporous shell formation by a one pot templated dissolution and redeposition strategy, and pore size expansion via acid-refluxing. By such a method, 1.9 μm superficially porous materials with 0.18 μm shell thickness and tailored pore diameter (10 nm, 15 nm) were obtained. After pore enlargement, the formerly dense arrays of mesoporous structure changed, the radially oriented pores dominated the superficially porous structure. The chromatographic performance of such particles was investigated after C18 derivatization. For packing materials with 1.9 μm diameter and 10 nm pore size, the column efficiency could reach 211,300 plates per m for naphthalene. To achieve the high resolution separation of peptides and proteins, particles with pore diameter of 15 nm were tailored, by which the baseline separation of 5 peptides and 5 intact proteins could be respectively achieved within 1 min, demonstrating the superiority in the high efficiency and high throughput analysis of biomolecules. Furthermore, BSA digests were well separated with peak capacity of 120 in 30 min on a 15 cm-long column. Finally, we compared our columns with a 1.7 μm Kinetex C18 column under the same conditions, our particles with 10nm pore size demonstrated similar performance for separation of the large intact proteins. Moreover, the particles with 15 nm pore size showed more symmetrical peaks for the separation of large proteins (BSA, OVA and IgG) and provided rapid separation of protein extracts from Escherichia coli in 5 min. All these results indicated that the synthesized 1.9 μm superficially porous silica packing materials would be promising in the ultra-fast and high-resolution separation of biomolecules. Copyright © 2014 Elsevier B.V. All rights reserved.

Comparison of pelvic phased-array versus endorectal coil magnetic resonance imaging at 3 Tesla for local staging of prostate cancer.

PubMed

Kim, Bum Soo; Kim, Tae-Hwan; Kwon, Tae Gyun; Yoo, Eun Sang

2012-05-01

Several studies have demonstrated the superiority of endorectal coil magnetic resonance imaging (MRI) over pelvic phased-array coil MRI at 1.5 Tesla for local staging of prostate cancer. However, few have studied which evaluation is more accurate at 3 Tesla MRI. In this study, we compared the accuracy of local staging of prostate cancer using pelvic phased-array coil or endorectal coil MRI at 3 Tesla. Between January 2005 and May 2010, 151 patients underwent radical prostatectomy. All patients were evaluated with either pelvic phased-array coil or endorectal coil prostate MRI prior to surgery (63 endorectal coils and 88 pelvic phased-array coils). Tumor stage based on MRI was compared with pathologic stage. We calculated the specificity, sensitivity and accuracy of each group in the evaluation of extracapsular extension and seminal vesicle invasion. Both endorectal coil and pelvic phased-array coil MRI achieved high specificity, low sensitivity and moderate accuracy for the detection of extracapsular extension and seminal vesicle invasion. There were statistically no differences in specificity, sensitivity and accuracy between the two groups. Overall staging accuracy, sensitivity and specificity were not significantly different between endorectal coil and pelvic phased-array coil MRI.

Improved Accuracy of Low Affinity Protein-Ligand Equilibrium Dissociation Constants Directly Determined by Electrospray Ionization Mass Spectrometry

NASA Astrophysics Data System (ADS)

Jaquillard, Lucie; Saab, Fabienne; Schoentgen, Françoise; Cadene, Martine

2012-05-01

There is continued interest in the determination by ESI-MS of equilibrium dissociation constants (KD) that accurately reflect the affinity of a protein-ligand complex in solution. Issues in the measurement of KD are compounded in the case of low affinity complexes. Here we present a KD measurement method and corresponding mathematical model dealing with both gas-phase dissociation (GPD) and aggregation. To this end, a rational mathematical correction of GPD (fsat) is combined with the development of an experimental protocol to deal with gas-phase aggregation. A guide to apply the method to noncovalent protein-ligand systems according to their kinetic behavior is provided. The approach is validated by comparing the KD values determined by this method with in-solution KD literature values. The influence of the type of molecular interactions and instrumental setup on fsat is examined as a first step towards a fine dissection of factors affecting GPD. The method can be reliably applied to a wide array of low affinity systems without the need for a reference ligand or protein.

Edge resonant fluctuations and particle transport in a reversed-field pinch

NASA Astrophysics Data System (ADS)

Möller, A.

1998-12-01

Electrostatic fluctuations are measured in the Extrap T2 reversed-field pinch [J. R. Drake et al., in Plasma Physics and Controlled Nuclear Fusion Research 1996 (International Atomic Energy Agency, Vienna, 1997), Vol. 2, pp. 193-199] using a Langmuir probe array. The electrostatic fluctuation, driven particle transport ΓnΦ is derived and found to constitute a large fraction of the total particle transport. The spectral density of all measured quantities exhibits a peak in the frequency range 100-250 kHz, which originates from fluctuations that are resonant close to the edge [n=-(40-80)]. This peak contains only about 10-20% of the total fluctuation power, but is shown to dominate ΓnΦ. The main reason for this is the high toroidal mode number as compared with internally resonant magnetohydrodynamic fluctuations. The edge resonant fluctuations also features a higher coherence (γ=0.5) and close to 90° phase shift between density and potential fluctuations.

Numerical simulation of high intensity focused ultrasound temperature distribution for transcranial brain therapy

NASA Astrophysics Data System (ADS)

Zhang, Qian; Wang, Yizhe; Zhou, Wenzheng; Zhang, Ji; Jian, Xiqi

2017-03-01

To provide a reference for the HIFU clinical therapeutic planning, the temperature distribution and lesion volume are analyzed by the numerical simulation. The adopted numerical simulation is based on a transcranial ultrasound therapy model, including an 8 annular-element curved phased array transducer. The acoustic pressure and temperature elevation are calculated by using the approximation of Westervelt Formula and the Pennes Heat Transfer Equation. In addition, the Time Reversal theory and eliminating hot spot technique are combined to optimize the temperature distribution. With different input powers and exposure times, the lesion volume is evaluated based on temperature threshold theory. The lesion region could be restored at the expected location by the time reversal theory. Although the lesion volume reduces after eliminating the peak temperature in the skull and more input power and exposure time is required, the injury of normal tissue around skull could be reduced during the HIFU therapy. The prediction of thermal deposition in the skull and the lesion region could provide a reference for clinical therapeutic dose.

Enhanced model of photovoltaic cell/panel/array considering the direct and reverse modes

NASA Astrophysics Data System (ADS)

Zegaoui, Abdallah; Boutoubat, Mohamed; Sawicki, Jean-Paul; Kessaissia, Fatma Zohra; Djahbar, Abdelkader; Aillerie, Michel

2018-05-01

This paper presents an improved generalized physical model for photovoltaic, PV cells, panels and arrays taking into account the behavior of these devices when considering their biasing existing in direct and reverse modes. Existing PV physical models generally are very efficient for simulating influence of irradiation changes on the short circuit current but they could not visualize the influences of temperature changes. The Enhanced Direct and Reverse Mode model, named EDRM model, enlightens the influence on the short-circuit current of both temperature and irradiation in the reverse mode of the considered PV devices. Due to its easy implementation, the proposed model can be a useful power tool for the development of new photovoltaic systems taking into account and in a more exhaustive manner, environmental conditions. The developed model was tested on a marketed PV panel and it gives a satisfactory results compared with parameters given in the manufacturer datasheet.

Simple Reversed-Phase HPLC Method with Spectrophotometric Detection for Measuring Acetaminophen-Protein Adducts in Rat Liver Samples

PubMed Central

Acharya, Miteshkumar; Lau-Cam, Cesar A.

2012-01-01

A simple reversed-phase HPLC method for measuring hepatic levels of acetaminophen- (APAP-) protein adduct following an overdose of APAP was developed. An aliquot of liver homogenate in phosphate-buffered saline pH 7.4 (PBS) was placed on a Nanosep centrifugal device, which was centrifuged to obtain a protein residue. This residue was incubated with a solution of p-aminobenzoic acid (PABA), the internal standard, and bacterial protease in PBS, transferred to a Nanosep centrifugal device, and centrifuged. A 100 μL portion of the filtrate was analyzed on a YMC-Pack ODS-AMQ C18 column, using 100 mM potassium dihydrogen phosphate-methanol-acetic acid (100 : 0.6 : 0.1) as the mobile phase, a flow rate of 1 mL/min, and photometric detection at 254 nm. PABA and APAP-cystein-S-yl (APAP-Cys) eluted at ~14.7 min and 22.7 min, respectively. Method linearity, based on on-column concentrations of APAP-Cys, was observed over the range 0.078–40 μg. Recoveries of APAP-Cys from spiked blank liver homogenates ranged from ~83% to 91%. Limits of detection and of quantification of APAP-Cys, based on column concentrations, were 0.06 μg and 0.14 μg, respectively. RSD values for interday and intraday analyses of a blank liver homogenate spiked with APAP-Cyst at three levels were, in all cases, ≤1.0% and <1.5%, respectively. The proposed method was found appropriate for comparing the antidotal properties of N-acetylcysteine and taurine in a rat model of APAP poisoning. PMID:22619591

A Novel HPLC Method for the Concurrent Analysis and Quantitation of Seven Water-Soluble Vitamins in Biological Fluids (Plasma and Urine): A Validation Study and Application

PubMed Central

Grotzkyj Giorgi, Margherita; Howland, Kevin; Martin, Colin; Bonner, Adrian B.

2012-01-01

An HPLC method was developed and validated for the concurrent detection and quantitation of seven water-soluble vitamins (C, B1, B2, B5, B6, B9, B12) in biological matrices (plasma and urine). Separation was achieved at 30°C on a reversed-phase C18-A column using combined isocratic and linear gradient elution with a mobile phase consisting of 0.01% TFA aqueous and 100% methanol. Total run time was 35 minutes. Detection was performed with diode array set at 280 nm. Each vitamin was quantitatively determined at its maximum wavelength. Spectral comparison was used for peak identification in real samples (24 plasma and urine samples from abstinent alcohol-dependent males). Interday and intraday precision were <4% and <7%, respectively, for all vitamins. Recovery percentages ranged from 93% to 100%. PMID:22536136

A novel HPLC method for the concurrent analysis and quantitation of seven water-soluble vitamins in biological fluids (plasma and urine): a validation study and application.

PubMed

Giorgi, Margherita Grotzkyj; Howland, Kevin; Martin, Colin; Bonner, Adrian B

2012-01-01

An HPLC method was developed and validated for the concurrent detection and quantitation of seven water-soluble vitamins (C, B(1), B(2), B(5), B(6), B(9), B(12)) in biological matrices (plasma and urine). Separation was achieved at 30°C on a reversed-phase C18-A column using combined isocratic and linear gradient elution with a mobile phase consisting of 0.01% TFA aqueous and 100% methanol. Total run time was 35 minutes. Detection was performed with diode array set at 280 nm. Each vitamin was quantitatively determined at its maximum wavelength. Spectral comparison was used for peak identification in real samples (24 plasma and urine samples from abstinent alcohol-dependent males). Interday and intraday precision were <4% and <7%, respectively, for all vitamins. Recovery percentages ranged from 93% to 100%.

High Density Diffusion-Free Nanowell Arrays

PubMed Central

Takulapalli, Bharath R; Qiu, Ji; Magee, D. Mitchell; Kahn, Peter; Brunner, Al; Barker, Kristi; Means, Steven; Miersch, Shane; Bian, Xiaofang; Mendoza, Alex; Festa, Fernanda; Syal, Karan; Park, Jin; LaBaer, Joshua; Wiktor, Peter

2012-01-01

Proteomics aspires to elucidate the functions of all proteins. Protein microarrays provide an important step by enabling high-throughput studies of displayed proteins. However, many functional assays of proteins include untethered intermediates or products, which could frustrate the use of planar arrays at very high densities because of diffusion to neighboring features. The nucleic acid programmable protein array (NAPPA), is a robust, in situ synthesis method for producing functional proteins just-in-time, which includes steps with diffusible intermediates. We determined that diffusion of expressed proteins led to cross-binding at neighboring spots at very high densities with reduced inter-spot spacing. To address this limitation, we have developed an innovative platform using photolithographically-etched discrete silicon nanowells and used NAPPA as a test case. This arrested protein diffusion and cross-binding. We present confined high density protein expression and display, as well as functional protein-protein interactions, in 8,000 nanowell arrays. This is the highest density of individual proteins in nano-vessels demonstrated on a single slide. We further present proof of principle results on ultra-high density protein arrays capable of up to 24,000 nanowells on a single slide. PMID:22742968

Phase-locked laser array having a non-uniform spacing between lasing regions

NASA Technical Reports Server (NTRS)

Ackley, Donald E. (Inventor)

1986-01-01

A phase-locked semiconductor array wherein the lasing regions of the array are spaced an effective distance apart such that the modes of oscillation of the different lasing regions are phase-locked to one another. The center-to-center spacing between the lasing regions is non-uniform. This variation in spacing perturbs the preferred 180.degree. phase difference between adjacent lasing regions thereby providing an increased yield of arrays exhibiting a single-lobed, far-field radiation pattern.

Phase and Frequency Control of Laser Arrays for Pulse Synthesis

DTIC Science & Technology

2015-01-02

with the laser array to understand the phase noise of elements on a common heat sink, and the relationship between linewidth and feedback speed...spatial brightness operation of a phase-locked stripe -array diode laser,” Laser Phys. 22, 160 (2012). [2] J. R. Leger, “Lateral mode control of an AlGaAs...Jechow, D. Skoczowsky, and R. Menzel, “Multi-wavelength, high spatial brightness operation of a phase-locked stripe -array diode laser,” Laser Phys. 22

An Update on Phased Array Results Obtained on the GE Counter-Rotating Open Rotor Model

NASA Technical Reports Server (NTRS)

Podboy, Gary; Horvath, Csaba; Envia, Edmane

2013-01-01

Beamform maps have been generated from 1) simulated data generated by the LINPROP code and 2) actual experimental phased array data obtained on the GE Counter-rotating open rotor model. The beamform maps show that many of the tones in the experimental data come from their corresponding Mach radius. If the phased array points to the Mach radius associated with a tone then it is likely that the tone is a result of the loading and thickness noise on the blades. In this case, the phased array correctly points to where the noise is coming from and indicates the axial location of the loudest source in the image but not necessarily the correct vertical location. If the phased array does not point to the Mach radius associated with a tone then some mechanism other than loading and thickness noise may control the amplitude of the tone. In this case, the phased array may or may not point to the actual source. If the source is not rotating it is likely that the phased array points to the source. If the source is rotating it is likely that the phased array indicates the axial location of the loudest source but not necessarily the correct vertical location. These results indicate that you have to be careful in how you interpret phased array data obtained on an open rotor since they may show the tones coming from a location other than the source location. With a subsonic tip speed open rotor the tones can come form locations outboard of the blade tips. This has implications regarding noise shielding.

Bias-polarity-dependent UV/visible transferable electroluminescence from ZnO nanorod array LED with graphene oxide electrode supporting layer

NASA Astrophysics Data System (ADS)

Liu, Weizhen; Wang, Wei; Xu, Haiyang; Li, Xinghua; Yang, Liu; Ma, Jiangang; Liu, Yichun

2015-09-01

A simple top electrode preparation process, employing continuous graphene oxide films as electrode supporting layers, was adopted to fabricate a ZnO nanorod array/p-GaN heterojunction LED. The achieved LED demonstrated different electroluminescence behaviors under forward and reverse biases: a yellow-red emission band was observed under forward bias, whereas a blue-UV emission peak was obtained under reverse bias. Electroluminescence spectra under different currents and temperatures, as well as heterojunction energy-band alignments, reveal that the yellow-red emission under forward bias originates from recombinations related to heterointerface defects, whereas the blue-UV electroluminescence under reverse bias is ascribed to transitions from near-band-edge and Mg-acceptor levels in p-GaN.

Building biochips: a protein production pipeline

NASA Astrophysics Data System (ADS)

de Carvalho-Kavanagh, Marianne G. S.; Albala, Joanna S.

2004-06-01

Protein arrays are emerging as a practical format in which to study proteins in high-throughput using many of the same techniques as that of the DNA microarray. The key advantage to array-based methods for protein study is the potential for parallel analysis of thousands of samples in an automated, high-throughput fashion. Building protein arrays capable of this analysis capacity requires a robust expression and purification system capable of generating hundreds to thousands of purified recombinant proteins. We have developed a method to utilize LLNL-I.M.A.G.E. cDNAs to generate recombinant protein libraries using a baculovirus-insect cell expression system. We have used this strategy to produce proteins for analysis of protein/DNA and protein/protein interactions using protein microarrays in order to understand the complex interactions of proteins involved in homologous recombination and DNA repair. Using protein array techniques, a novel interaction between the DNA repair protein, Rad51B, and histones has been identified.

Coupled-mode analysis of gain and wavelength oscillation characteristics of diode laser phased arrays

NASA Technical Reports Server (NTRS)

Butler, J. K.; Ettenberg, M.; Ackley, D. E.

1985-01-01

The lasing wavelengths and gain characteristics of the modes of phase-locked arrays of channel-substrate-planar (CSP) lasers are presented. The gain values for the array modes are determined from complex coupling coefficients calculated using the fields of neighboring elements of the array. The computations show that, for index guided lasers which have nearly planar phase fronts, the highest order array mode will be preferred. The 'in-phase' or fundamental mode, which produces only one major lobe in the far-field radiation pattern, has the lowest modal gain of all array modes. The modal gain differential between the highest order and fundamental modes is less than 10/cm for weak coupling between the elements.

Progress toward Understanding Protein S-acylation: Prospective in Plants

PubMed Central

Li, Yaxiao; Qi, Baoxiu

2017-01-01

S-acylation, also known as S-palmitoylation or palmitoylation, is a reversible post-translational lipid modification in which long chain fatty acid, usually the 16-carbon palmitate, covalently attaches to a cysteine residue(s) throughout the protein via a thioester bond. It is involved in an array of important biological processes during growth and development, reproduction and stress responses in plant. S-acylation is a ubiquitous mechanism in eukaryotes catalyzed by a family of enzymes called Protein S-Acyl Transferases (PATs). Since the discovery of the first PAT in yeast in 2002 research in S-acylation has accelerated in the mammalian system and followed by in plant. However, it is still a difficult field to study due to the large number of PATs and even larger number of putative S-acylated substrate proteins they modify in each genome. This is coupled with drawbacks in the techniques used to study S-acylation, leading to the slower progress in this field compared to protein phosphorylation, for example. In this review we will summarize the discoveries made so far based on knowledge learnt from the characterization of protein S-acyltransferases and the S-acylated proteins, the interaction mechanisms between PAT and its specific substrate protein(s) in yeast and mammals. Research in protein S-acylation and PATs in plants will also be covered although this area is currently less well studied in yeast and mammalian systems. PMID:28392791

Optimising reversed-phase liquid chromatographic separation of an acidic mixture on a monolithic stationary phase with the aid of response surface methodology and experimental design.

PubMed

Wang, Y; Harrison, M; Clark, B J

2006-02-10

An optimization strategy for the separation of an acidic mixture by employing a monolithic stationary phase is presented, with the aid of experimental design and response surface methodology (RSM). An orthogonal array design (OAD) OA(16) (2(15)) was used to choose the significant parameters for the optimization. The significant factors were optimized by using a central composite design (CCD) and the quadratic models between the dependent and the independent parameters were built. The mathematical models were tested on a number of simulated data set and had a coefficient of R(2) > 0.97 (n = 16). On applying the optimization strategy, the factor effects were visualized as three-dimensional (3D) response surfaces and contour plots. The optimal condition was achieved in less than 40 min by using the monolithic packing with the mobile phase of methanol/20 mM phosphate buffer pH 2.7 (25.5/74.5, v/v). The method showed good agreement between the experimental data and predictive value throughout the studied parameter space and were suitable for optimization studies on the monolithic stationary phase for acidic compounds.

Advanced Microstrip Antenna Developments : Volume I. Technology Studies for Aircraft Phased Arrays

DOT National Transportation Integrated Search

1981-06-01

Work has continued on improvement of microstrip phased-array antenna technology since the first microstrip phased-array was flight-tested during the FAA 1974-1975 ATS-6 test program. The present development has extended this earlier work in three are...

Simulation and experiment for the inspection of stainless steel bolts in servicing using an ultrasonic phased array

NASA Astrophysics Data System (ADS)

Chen, Jinzhong; He, Renyang; Kang, Xiaowei; Yang, Xuyun

2015-10-01

The non-destructive testing of small-sized (M12-M20) stainless steel bolts in servicing is always a technical problem. This article focuses on the simulation and experimental research of stainless steel bolts with an artificial defect reflector using ultrasonic phased array inspection. Based on the observation of the sound field distribution of stainless steel bolts in ultrasonic phased array as well as simulation modelling and analysis of the phased array probes' detection effects with various defect sizes, different artificial defect reflectors of M16 stainless steel bolts are machined in reference to the simulation results. Next, those bolts are tested using a 10-wafer phased array probe with 5 MHz. The test results finally prove that ultrasonic phased array can detect 1-mm cracks in diameter with different depths of M16 stainless steel bolts and a metal loss of Φ1 mm of through-hole bolts, which provides technical support for future non-destructive testing of stainless steel bolts in servicing.

Phase-locked, high power, mid-infrared quantum cascade laser arrays

NASA Astrophysics Data System (ADS)

Zhou, W.; Slivken, S.; Razeghi, M.

2018-04-01

We demonstrate phase-locked, high power quantum cascade laser arrays, which are combined using a monolithic, tree array multimode interferometer, with emission wavelengths around 4.8 μm. A maximum output power of 15 W was achieved from an eight-element laser array, which has only a slightly higher threshold current density and a similar slope efficiency compared to a Fabry-Perot laser of the same length. Calculated multimode interferometer splitting loss is on the order of 0.27 dB for the in-phase supermode. In-phase supermode operation with nearly ideal behavior is demonstrated over the working current range of the array.

Flat dielectric metasurface lens array for three dimensional integral imaging

NASA Astrophysics Data System (ADS)

Zhang, Jianlei; Wang, Xiaorui; Yang, Yi; Yuan, Ying; Wu, Xiongxiong

2018-05-01

In conventional integral imaging, the singlet refractive lens array limits the imaging performance due to its prominent aberrations. Different from the refractive lens array relying on phase modulation via phase change accumulated along the optical paths, metasurfaces composed of nano-scatters can produce phase abrupt over the scale of wavelength. In this letter, we propose a novel lens array consisting of two neighboring flat dielectric metasurfaces for integral imaging system. The aspherical phase profiles of the metasurfaces are optimized to improve imaging performance. The simulation results show that our designed 5 × 5 metasurface-based lens array exhibits high image quality at designed wavelength 865 nm.

A non-chromatographic protein purification strategy using Src 3 homology domains as generalized capture domains.

PubMed

Kim, Heejae; Chen, Wilfred

2016-09-20

Protein purification using inverse phase transition of elastin-like polypeptide (ELP) domains is a useful alternative to chromatography. Genetic fusions of ELP domains to various proteins have the ability to reversibly transition between soluble monomers and micron-sized aggregates and this has been used to selectively purify many ELP fusions. Affinity domains can enhance this technology by using specific protein binding domains to enable ELP mediated affinity capture (EMAC) of proteins of interest (POI) that have been fused to corresponding affinity ligands. In this paper, we highlight the use of Src homology 3 (SH3) domains and corresponding peptide ligands in EMAC that have differential binding affinities towards SH3 for efficient capture and elution of proteins. Furthermore, differences between capture and elution of a monomeric and a multimeric protein were also studied. Copyright © 2016 Elsevier B.V. All rights reserved.

Target tracking and pointing for arrays of phase-locked lasers

NASA Astrophysics Data System (ADS)

Macasaet, Van P.; Hughes, Gary B.; Lubin, Philip; Madajian, Jonathan; Zhang, Qicheng; Griswold, Janelle; Kulkarni, Neeraj; Cohen, Alexander; Brashears, Travis

2016-09-01

Arrays of phase-locked lasers are envisioned for planetary defense and exploration systems. High-energy beams focused on a threatening asteroid evaporate surface material, creating a reactionary thrust that alters the asteroid's orbit. The same system could be used to probe an asteroid's composition, to search for unknown asteroids, and to propel interplanetary and interstellar spacecraft. Phased-array designs are capable of producing high beam intensity, and allow beam steering and beam profile manipulation. Modular designs allow ongoing addition of emitter elements to a growing array. This paper discusses pointing control for extensible laser arrays. Rough pointing is determined by spacecraft attitude control. Lateral movement of the laser emitter tips behind the optical elements provides intermediate pointing adjustment for individual array elements and beam steering. Precision beam steering and beam formation is accomplished by coordinated phase modulation across the array. Added cells are incorporated into the phase control scheme by precise alignment to local mechanical datums using fast, optical relative position sensors. Infrared target sensors are also positioned within the datum scheme, and provide information about the target vector relative to datum coordinates at each emitter. Multiple target sensors allow refined determination of the target normal plane, providing information to the phase controller for each emitter. As emitters and sensors are added, local position data allows accurate prediction of the relative global position of emitters across the array, providing additional constraints to the phase controllers. Mechanical design and associated phase control that is scalable for target distance and number of emitters is presented.

Analysis of quaternary ammonium and phosphonium ionic liquids by reversed-phase high-performance liquid chromatography with charged aerosol detection and unified calibration.

PubMed

Stojanovic, Anja; Lämmerhofer, Michael; Kogelnig, Daniel; Schiesel, Simone; Sturm, Martin; Galanski, Markus; Krachler, Regina; Keppler, Bernhard K; Lindner, Wolfgang

2008-10-31

Several hydrophobic ionic liquids (ILs) based on long-chain aliphatic ammonium- and phosphonium cations and selected aromatic anions were analyzed by reversed-phase high-performance liquid chromatography (RP-HPLC) employing trifluoroacetic acid as ion-pairing additive to the acetonitrile-containing mobile phase and adopting a step-gradient elution mode. The coupling of charged aerosol detection (CAD) for the non-chromophoric aliphatic cations with diode array detection (DAD) for the aromatic anions allowed their simultaneous analysis in a set of new ILs derived from either tricaprylmethylammonium chloride (Aliquat 336) and trihexyltetradecylphosphonium chloride as precursors. Aliquat 336 is a mix of ammonium cations with distinct aliphatic chain lengths. In the course of the studies it turned out that CAD generates an identical detection response for all the distinct aliphatic cations. Due to lack of single component standards of the individual Aliquat 336 cation species, a unified calibration function was established for the quantitative analysis of the quaternary ammonium cations of the ILs. The developed method was validated according to ICH guidelines, which confirmed the validity of the unified calibration. The application of the method revealed molar ratios of cation to anion close to 1 indicating a quantitative exchange of the chloride ions of the precursors by the various aromatic anions in the course of the synthesis of new ILs. Anomalies of CAD observed for the detection of some aromatic anions (thiosalicylate and benzoate) are discussed.

Magnetite-doped polydimethylsiloxane (PDMS) for phosphopeptide enrichment.

PubMed

Sandison, Mairi E; Jensen, K Tveen; Gesellchen, F; Cooper, J M; Pitt, A R

2014-10-07

Reversible phosphorylation plays a key role in numerous biological processes. Mass spectrometry-based approaches are commonly used to analyze protein phosphorylation, but such analysis is challenging, largely due to the low phosphorylation stoichiometry. Hence, a number of phosphopeptide enrichment strategies have been developed, including metal oxide affinity chromatography (MOAC). Here, we describe a new material for performing MOAC that employs a magnetite-doped polydimethylsiloxane (PDMS), that is suitable for the creation of microwell array and microfluidic systems to enable low volume, high throughput analysis. Incubation time and sample loading were explored and optimized and demonstrate that the embedded magnetite is able to enrich phosphopeptides. This substrate-based approach is rapid, straightforward and suitable for simultaneously performing multiple, low volume enrichments.

Design, Assembly, and Characterization of TALE-Based Transcriptional Activators and Repressors

PubMed Central

Thakore, Pratiksha I.; Gersbach, Charles A.

2016-01-01

Transcription activator-like effectors (TALEs) are modular DNA-binding proteins that can be fused to a variety of effector domains to regulate the epigenome. Nucleotide recognition by TALE monomers follows a simple cipher, making this a powerful and versatile method to activate or repress gene expression. Described here are methods to design, assemble, and test TALE transcription factors (TALE-TFs) for control of endogenous gene expression. In this protocol, TALE arrays are constructed by Golden Gate cloning and tested for activity by transfection and quantitative RT-PCR. These methods for engineering TALE-TFs are useful for studies in reverse genetics and genomics, synthetic biology, and gene therapy. PMID:26443215

An efficient separation and method development for the quantifying of two basic impurities of Nicergoline by reversed-phase high performance liquid chromatography using ion-pairing counter ions.

PubMed

Yalçin, Güler; Yüktaş, Nüray

2006-10-11

A quantification method was developed for the two basic impurities, one of which is also a metabolite, of Nicergoline (NIC), by using reversed-phase high performance liquid chromatography (RP-HPLC) and diode array detector (DAD). One of these compounds,10-methoxy-6-methylergoline-8beta-methanol-5-bromo-3-pyridinecarboxylate (1-DN) is the metabolite as well as the impurity whereas, the other 10-methoxy-1,6-dimethylergoline-8beta-methanol-5-chloro-3-pyridinecarboxylate (5-CN) is only an impurity. The chromatographic column was Phenomenex, Luna, 5 microm, C18 (2), 250 mm x 4.6 mm. Mobile phase was 0.1 M ammonium acetate (NH4Ac) solution containing 4 mM 1-octanesulfonicacid sodium salt (OSASS) and 6 mM tetrabutylammonium hydrogen sulphate (TBAHS) (pH: 5.9)/acetonitrile (ACN) (62:38) for 1-DN and (64:36) for 5-CN. Flow rate was 1.0 mL min-1. The diode array detector was operated at 285 nm, band width: 4 nm. Linearity was obtained in the concentration range of 0.032 x 10-5 to 3.828 x 10-5 M, y = 116.88x + 0.2773 (r2 = 0.99989); the limit of detection (LOD) and limit of quantification (LOQ) were determined as 0.012 x 10-5 and 0.041 x 10-5 M for 1-DN, respectively. Linearity was obtained in the concentration range of 0.034 x 10-5 to 4.092 x 10-5 M, y = 104.24x + 0.7486 (r2 = 0.99996); (LOD) and (LOQ) were determined as 0.014 x 10-5 and 0.046 x 10-5 M for 5-CN, respectively. The recovery was 100.65% for 1-DN and 100.32% for 5-CN. The amount of 1-DN in 30 mg NIC was found as 209.65 microg (0.70%) and the amount of 5-CN in 30 mg NIC was found as 27.62 microg (0.09%).

Using peptide array to identify binding motifs and interaction networks for modular domains.

PubMed

Li, Shawn S-C; Wu, Chenggang

2009-01-01

Specific protein-protein interactions underlie all essential biological processes and form the basis of cellular signal transduction. The recognition of a short, linear peptide sequence in one protein by a modular domain in another represents a common theme of macromolecular recognition in cells, and the importance of this mode of protein-protein interaction is highlighted by the large number of peptide-binding domains encoded by the human genome. This phenomenon also provides a unique opportunity to identify protein-protein binding events using peptide arrays and complementary biochemical assays. Accordingly, high-density peptide array has emerged as a useful tool by which to map domain-mediated protein-protein interaction networks at the proteome level. Using the Src-homology 2 (SH2) and 3 (SH3) domains as examples, we describe the application of oriented peptide array libraries in uncovering specific motifs recognized by an SH2 domain and the use of high-density peptide arrays in identifying interaction networks mediated by the SH3 domain. Methods reviewed here could also be applied to other modular domains, including catalytic domains, that recognize linear peptide sequences.

Ka-Band Multibeam Aperture Phased Array Being Developed

NASA Technical Reports Server (NTRS)

Reinhart, Richard C.; Kacpura, Thomas J.

2004-01-01

Phased-array antenna systems offer many advantages to low-Earth-orbiting satellite systems. Their large scan angles and multibeam capabilities allow for vibration-free, rapid beam scanning and graceful degradation operation for high rate downlink of data to users on the ground. Technology advancements continue to reduce the power, weight, and cost of these systems to make phased arrays a competitive alternative in comparison to the gimbled reflector system commonly used in science missions. One effort to reduce the cost of phased arrays is the development of a Ka-band multibeam aperture (MBA) phased array by Boeing Corporation under a contract jointly by the NASA Glenn Research Center and the Office of Naval Research. The objective is to develop and demonstrate a space-qualifiable dual-beam Ka-band (26.5-GHz) phased-array antenna. The goals are to advance the state of the art in Ka-band active phased-array antennas and to develop and demonstrate multibeam transmission technology compatible with spacecraft in low Earth orbit to reduce the cost of future missions by retiring certain development risks. The frequency chosen is suitable for space-to-space and space-to-ground communication links. The phased-array antenna has a radiation pattern designed by combining a set of individual radiating elements, optimized with the type of radiating elements used, their positions in space, and the amplitude and phase of the currents feeding the elements. This arrangement produces a directional radiation pattern that is proportional to the number of individual radiating elements. The arrays of interest here can scan the main beam electronically with a computerized algorithm. The antenna is constructed using electronic components with no mechanical parts, and the steering is performed electronically, without any resulting vibration. The speed of the scanning is limited primarily by the control electronics. The radiation performance degrades gracefully if a portion of the elements fail. The arrays can be constructed to conform to a mounting surface, and multibeam capability is integral to the design. However, there are challenges for mission designers using monolithic-microwave-integrated-circuit- (MMIC-) based arrays because of reduced power efficiency, higher costs, and certain system effects that result in link degradations. The multibeam aperture phased-array antenna development is attempting to address some of these issues, particularly manufacturing, costs, and system performance.

Employment of Adaptive Learning Techniques for the Discrimination of Acoustic Emissions.

DTIC Science & Technology

1983-11-01

Dereverberation Simulations ... ............ .. 96 Ŗ 4. ARRAY OPTIMIZATION ......... ...................... . 115 * 4.1 Phased Array Fundamentals... 115 4.2 Phased Array Diffraction Suboptimization ......... ... 121 , .i Page s 4.3 Diffraction Pattern Simulations of Phased Arrays...by differentiating (2.13.14) with respect to z and • -- equating equal powers of z , giving n-i c n bn + I/n kckbn-k (2.13.15)nk= This is very

Ultrabroadband Phased-Array Receivers Based on Optical Techniques

DTIC Science & Technology

2016-02-26

AFRL-AFOSR-VA-TR-2016-0121 Ultrabroadband Phased- array Receivers Based on Optical Techniques Christopher Schuetz UNIVERSITY OF DELAWARE Final Report...Jul 15 4. TITLE AND SUBTITLE Ultrabroadband Phased- Array Receivers Based on Optical Techniques 5a. CONTRACT NUMBER 5b. GRANT NUMBER FA9550-12-1...receiver that enables us to capture and convert signals across an array using photonic modulators, routing these signals to a central location using

Grain sorghum proteomics: integrated approach toward characterization of endosperm storage proteins in kafirin allelic variants.

PubMed

Cremer, Julia E; Bean, Scott R; Tilley, Michael M; Ioerger, Brian P; Ohm, Jae B; Kaufman, Rhett C; Wilson, Jeff D; Innes, David J; Gilding, Edward K; Godwin, Ian D

2014-10-08

Grain protein composition determines quality traits, such as value for food, feedstock, and biomaterials uses. The major storage proteins in sorghum are the prolamins, known as kafirins. Located primarily on the periphery of the protein bodies surrounding starch, cysteine-rich β- and γ-kafirins may limit enzymatic access to internally positioned α-kafirins and starch. An integrated approach was used to characterize sorghum with allelic variation at the kafirin loci to determine the effects of this genetic diversity on protein expression. Reversed-phase high performance liquid chromatography and lab-on-a-chip analysis showed reductions in alcohol-soluble protein in β-kafirin null lines. Gel-based separation and liquid chromatography-tandem mass spectrometry identified a range of redox active proteins affecting storage protein biochemistry. Thioredoxin, involved in the processing of proteins at germination, has reported impacts on grain digestibility and was differentially expressed across genotypes. Thus, redox states of endosperm proteins, of which kafirins are a subset, could affect quality traits in addition to the expression of proteins.

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

Sharma, Seema; Simpson, David C.; Tolic, Nikola

We investigated the combination of weak anion exchange (WAX) fractionation and on-line reversed phase liquid chromatography (RPLC) separation using a 12 T FTICR mass spectrometer for the detection of intact proteins from a Shewanella oneidensis MR-1 cell lysate. 715 intact proteins were detected and the combined results from the WAX fractions and the unfractionated cell lysate were aligned using LC-MS features to facilitate protein abundance measurements. Protein identifications and post translational modifications were assigned for ~10% of the detected proteins by comparing intact protein mass measurements to proteins identified in peptide MS/MS analysis of an aliquot of the same fraction.more » Intact proteins were also detected for S. oneidensis lysates obtained from cells grown on 13C, 15N depleted media under aerobic and sub-oxic conditions. This work aimed at optimizing intact protein detection for profiling proteins at a level that incorporates their modification complement. The strategy can be readily applied for measuring differential protein abundances, and provides a platform for high-throughput selection of biologically relevant targets for further characterization.« less

A Methodology for Phased Array Radar Threshold Modeling Using the Advanced Propagation Model (APM)

DTIC Science & Technology

2017-10-01

TECHNICAL REPORT 3079 October 2017 A Methodology for Phased Array Radar Threshold Modeling Using the Advanced Propagation Model (APM...Head 55190 Networks Division iii EXECUTIVE SUMMARY This report summarizes the methodology developed to improve the radar threshold modeling...PHASED ARRAY RADAR CONFIGURATION ..................................................................... 1 3. METHODOLOGY

A phased array bread board for future remote sensing applications

NASA Astrophysics Data System (ADS)

Zahn, R. W.; Schmidt, E.

The next generation of SAR antennas will be of the active phased-array type. The ongoing development of a phased-array breadboard for remote sensing is described. Starting from a detailed system design, a functional representative breadboard was developed. The design and the performance of the breadboard are discussed.

Development of components for an S-band phased array antenna subsystem

NASA Technical Reports Server (NTRS)

1975-01-01

The system requirements, module test data, and S-band phased array subsystem test data are discussed. Of the two approaches to achieving antenna gain (mechanically steered reflector or electronically steered phased array), the phased array approach offers the greatest simplicity and lowest cost (size, weight, power, and dollars) for this medium gain. A competitive system design is described as well as hardware evaluation which will lead to timely availability of this technology for implementing such a system. The objectives of the study were: to fabricate and test six engineering model transmit/receive microelectronics modules; to design, fabricate, and test one dc and logic multilayer manifold; and to integrate and test an S-band phased array antenna subsystem composed of antenna elements, seven T/R modules, RF manifolds and dc manifold.

Isolation of an inhibitory insulin-like growth factor (IGF) binding protein from bone cell-conditioned medium: A potential local regulator of IGF action

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

Mohan, S.; Bautista, C.M.; Wergedal, J.

1989-11-01

Inhibitory insulin-like growth factor binding protein (In-IGF-BP) has been purified to homogeneity from medium conditioned by TE89 human osteosarcoma cells by two different methods using Sephadex G-100 gel filtration, FPLC Mono Q ion-exchange, HPLC C{sub 4} reverse-phase, HPLC CN reverse-phase and affinity chromatographies. In-IGF-BP thus purified appeared to be homogeneous and unique by the following criteria. (i) N-terminal sequence analysis yielded a unique sequence (Asp-Glu-Ala-Ile-His-Cys-Pro-Pro-Glu-Ser-Glu-Ala-Lys-Leu-Ala). (ii) Amino acid composition of In-IGF-BP revealed marked differences with the amino acid compositions of other known PBs. (iii) In-IGF-BP exhibited a single band with molecular mass of 25 kDa under reducing conditions on sodiummore » dodecyl sulfate/polyacrylamide gels. IGF-I and IGF-II but not insulin displaced the binding of {sup 125}I-labeled IGF-I or {sup 125}I-labeled IGF-II binding to In-IGF-BP. In-IGF-BP inhibited basal, IGF-stimulated bone cell proliferation and serum-stimulated bone cell proliferation. Forskolin increases synthesis of In-IGF-BP in TE85 human osteosarcoma cells in a dose-dependent manner. Based on these findings, the authors conclude that In-IGF-BP is a protein that has a unique sequence and significant biological actions on bone cells.« less

Comparison of Pelvic Phased-Array versus Endorectal Coil Magnetic Resonance Imaging at 3 Tesla for Local Staging of Prostate Cancer

PubMed Central

Kim, Bum Soo; Kim, Tae-Hwan; Kwon, Tae Gyun

2012-01-01

Purpose Several studies have demonstrated the superiority of endorectal coil magnetic resonance imaging (MRI) over pelvic phased-array coil MRI at 1.5 Tesla for local staging of prostate cancer. However, few have studied which evaluation is more accurate at 3 Tesla MRI. In this study, we compared the accuracy of local staging of prostate cancer using pelvic phased-array coil or endorectal coil MRI at 3 Tesla. Materials and Methods Between January 2005 and May 2010, 151 patients underwent radical prostatectomy. All patients were evaluated with either pelvic phased-array coil or endorectal coil prostate MRI prior to surgery (63 endorectal coils and 88 pelvic phased-array coils). Tumor stage based on MRI was compared with pathologic stage. We calculated the specificity, sensitivity and accuracy of each group in the evaluation of extracapsular extension and seminal vesicle invasion. Results Both endorectal coil and pelvic phased-array coil MRI achieved high specificity, low sensitivity and moderate accuracy for the detection of extracapsular extension and seminal vesicle invasion. There were statistically no differences in specificity, sensitivity and accuracy between the two groups. Conclusion Overall staging accuracy, sensitivity and specificity were not significantly different between endorectal coil and pelvic phased-array coil MRI. PMID:22476999

Two-Dimensional Array Beam Scanning Via Externally and Mutually Injection Locked Coupled Oscillators

NASA Technical Reports Server (NTRS)

Pogorzelski, Ronald J.

2000-01-01

Some years ago, Stephan proposed an approach to one dimensional (linear) phased array beam steering which requires only a single phase shifter. This involves the use of a linear array of voltage-controlled electronic oscillators coupled to nearest neighbors. The oscillators are mutually injection locked by controlling their coupling and tuning appropriately. Stephan's approach consists of deriving two signals from a master oscillator, one signal phase shifted with respect to the other by means of a single phase shifter. These two signals are injected into the end oscillators of the array. The result is a linear phase progression across the oscillator array. Thus, if radiating elements are connected to each oscillator and spaced uniformly along a line, they will radiate a beam at an angle to that line determined by the phase gradient which is, in turn, determined by the phase difference between the injection signals.The beam direction is therefore controlled by adjusting this phase difference. Recently, Pogorzelski and York presented a formulation which facilitates theoretical analysis of the above beam steering technique. This was subsequently applied by Pogorzelski in analysis of two dimensional beam steering using perimeter detuning of a coupled oscillator array. The formulation is based on a continuum model in which the oscillator phases are represented by a continuous function satisfying a partial differential equation of diffusion type. This equation can be solved via the Laplace transform and the resulting solution exhibits the dynamic behavior of the array as the beam is steered. Stephan's beam steering technique can be similarly generalized to two-dimensional arrays in which the beam control signals are applied to the oscillators on the perimeter of the array. In this paper the continuum model for this two-dimensional case is developed and the dynamic solution for the corresponding aperture phase function is obtained. The corresponding behavior of the resulting far-zone radiation pattern is displayed as well.

Phased-array sources based on nonlinear metamaterial nanocavities

PubMed Central

Wolf, Omri; Campione, Salvatore; Benz, Alexander; Ravikumar, Arvind P.; Liu, Sheng; Luk, Ting S.; Kadlec, Emil A.; Shaner, Eric A.; Klem, John F.; Sinclair, Michael B.; Brener, Igal

2015-01-01

Coherent superposition of light from subwavelength sources is an attractive prospect for the manipulation of the direction, shape and polarization of optical beams. This phenomenon constitutes the basis of phased arrays, commonly used at microwave and radio frequencies. Here we propose a new concept for phased-array sources at infrared frequencies based on metamaterial nanocavities coupled to a highly nonlinear semiconductor heterostructure. Optical pumping of the nanocavity induces a localized, phase-locked, nonlinear resonant polarization that acts as a source feed for a higher-order resonance of the nanocavity. Varying the nanocavity design enables the production of beams with arbitrary shape and polarization. As an example, we demonstrate two second harmonic phased-array sources that perform two optical functions at the second harmonic wavelength (∼5 μm): a beam splitter and a polarizing beam splitter. Proper design of the nanocavity and nonlinear heterostructure will enable such phased arrays to span most of the infrared spectrum. PMID:26126879

First light from a kilometer-baseline Scintillation Auroral GPS Array.

PubMed

Datta-Barua, S; Su, Y; Deshpande, K; Miladinovich, D; Bust, G S; Hampton, D; Crowley, G

2015-05-28

We introduce and analyze the first data from an array of closely spaced Global Positioning System (GPS) scintillation receivers established in the auroral zone in late 2013 to measure spatial and temporal variations in L band signals at 100-1000 m and subsecond scales. The seven receivers of the Scintillation Auroral GPS Array (SAGA) are sited at Poker Flat Research Range, Alaska. The receivers produce 100 s scintillation indices and 100 Hz carrier phase and raw in-phase and quadrature-phase samples. SAGA is the largest existing array with baseline lengths of the ionospheric diffractive Fresnel scale at L band. With an initial array of five receivers, we identify a period of simultaneous amplitude and phase scintillation. We compare SAGA power and phase data with collocated 630.0 nm all-sky images of an auroral arc and incoherent scatter radar electron precipitation measurements, to illustrate how SAGA can be used in multi-instrument observations for subkilometer-scale studies. A seven-receiver Scintillation Auroral GPS Array (SAGA) is now at Poker Flat, Alaska SAGA is the largest subkilometer array to enable phase/irregularities studies Simultaneous scintillation, auroral arc, and electron precipitation are observed.

First light from a kilometer-baseline Scintillation Auroral GPS Array

PubMed Central

Datta-Barua, S; Su, Y; Deshpande, K; Miladinovich, D; Bust, G S; Hampton, D; Crowley, G

2015-01-01

We introduce and analyze the first data from an array of closely spaced Global Positioning System (GPS) scintillation receivers established in the auroral zone in late 2013 to measure spatial and temporal variations in L band signals at 100–1000 m and subsecond scales. The seven receivers of the Scintillation Auroral GPS Array (SAGA) are sited at Poker Flat Research Range, Alaska. The receivers produce 100 s scintillation indices and 100 Hz carrier phase and raw in-phase and quadrature-phase samples. SAGA is the largest existing array with baseline lengths of the ionospheric diffractive Fresnel scale at L band. With an initial array of five receivers, we identify a period of simultaneous amplitude and phase scintillation. We compare SAGA power and phase data with collocated 630.0 nm all-sky images of an auroral arc and incoherent scatter radar electron precipitation measurements, to illustrate how SAGA can be used in multi-instrument observations for subkilometer-scale studies. Key Points A seven-receiver Scintillation Auroral GPS Array (SAGA) is now at Poker Flat, Alaska SAGA is the largest subkilometer array to enable phase/irregularities studies Simultaneous scintillation, auroral arc, and electron precipitation are observed PMID:26709318

Actinidin enhances protein digestion in the small intestine as assessed using an in vitro digestion model.

PubMed

Kaur, Lovedeep; Rutherfurd, Shane M; Moughan, Paul J; Drummond, Lynley; Boland, Mike J

2010-04-28

This paper describes an in vitro study that tests the proposition that actinidin from green kiwifruit influences the digestion of proteins in the small intestine. Different food proteins, from sources including soy, meat, milk, and cereals, were incubated in the presence or absence of green kiwifruit extract (containing actinidin) using a two-stage in vitro digestion system consisting of an incubation with pepsin at stomach pH (simulating gastric digestion) and then with added pancreatin at small intestinal pH, simulating upper tract digestion in humans. The digests from the small intestinal stage (following the gastric digestion phase) were subjected to gel electrophoresis (SDS-PAGE) to assess loss of intact protein and development of large peptides during the in vitro simulated digestion. Kiwifruit extract influenced the digestion patterns of all of the proteins to various extents. For some proteins, actinidin had little impact on digestion. However, for other proteins, the presence of kiwifruit extract resulted in a substantially greater loss of intact protein and different peptide patterns from those seen after digestion with pepsin and pancreatin alone. In particular, enhanced digestion of whey protein isolate, zein, gluten, and gliadin was observed. In addition, reverse-phase HPLC (RP-HPLC) analysis showed that a 2.5 h incubation of sodium caseinate with kiwifruit extract alone resulted in approximately 45% loss of intact protein.

HuR interacts with human immunodeficiency virus type 1 reverse transcriptase, and modulates reverse transcription in infected cells

PubMed Central

Lemay, Julie; Maidou-Peindara, Priscilla; Bader, Thomas; Ennifar, Eric; Rain, Jean-Christophe; Benarous, Richard; Liu, Lang Xia

2008-01-01

Reverse transcription of the genetic material of human immunodeficiency virus type 1 (HIV-1) is a critical step in the replication cycle of this virus. This process, catalyzed by reverse transcriptase (RT), is well characterized at the biochemical level. However, in infected cells, reverse transcription occurs in a multiprotein complex – the reverse transcription complex (RTC) – consisting of viral genomic RNA associated with viral proteins (including RT) and, presumably, as yet uncharacterized cellular proteins. Very little is known about the cellular proteins interacting with the RTC, and with reverse transcriptase in particular. We report here that HIV-1 reverse transcription is affected by the levels of a nucleocytoplasmic shuttling protein – the RNA-binding protein HuR. A direct protein-protein interaction between RT and HuR was observed in a yeast two-hybrid screen and confirmed in vitro by homogenous time-resolved fluorescence (HTRF). We mapped the domain interacting with HuR to the RNAse H domain of RT, and the binding domain for RT to the C-terminus of HuR, partially overlapping the third RRM RNA-binding domain of HuR. HuR silencing with specific siRNAs greatly impaired early and late steps of reverse transcription, significantly inhibiting HIV-1 infection. Moreover, by mutagenesis and immunoprecipitation studies, we could not detect the binding of HuR to the viral RNA. These results suggest that HuR may be involved in and may modulate the reverse transcription reaction of HIV-1, by an as yet unknown mechanism involving a protein-protein interaction with HIV-1 RT. PMID:18544151

Incorporation of a Bio-Active Reverse-Turn Heterocycle into a Peptide Template Using Solid-Phase Synthesis to Probe Melanocortin Receptor Selectivity and Ligand Conformations by 2D 1H NMR

PubMed Central

Singh, Anamika; Wilczynski, Andrzej; Holder, Jerry R.; Witek, Rachel M.; Dirain, Marvin L.; Xiang, Zhimin; Edison, Arthur S.; Haskell-Luevano, Carrie

2011-01-01

Using a solid-phase synthetic approach, a bioactive reverse turn heterocyclic was incorporated into a cyclic peptide template to probe melanocortin receptor potency and ligand structural conformations. The five melanocortin receptor isoforms (MC1R-MC5R) are G-protein coupled receptors (GPCRs) that are regulated by endogenous agonists and antagonists. This pathway is involved in pigmentation, weight, and energy homeostasis. Herein, we report novel analogues of the chimeric AGRP-melanocortin peptide template integrated with a small molecule moiety to probe the structural and functional consequences of the core His-Phe-Arg-Trp peptide domain using a reverse-turn heterocycle. A series of six compounds are reported that result in inactive to full agonists with nM potency. Biophysical structural analysis [2D 1H NMR and computer-assisted molecular modeling (CAMM)] were performed on selected analogues, resulting in the identification that these peptide-small molecule hybrids possessed increased flexibility and fewer discrete conformational families as compared to the reference peptide and result in a novel template for further structure-function studies. PMID:21306168

Periodic protein adsorption at the gold/biotin aqueous solution interface: evidence of kinetics with time delay

NASA Astrophysics Data System (ADS)

Neff, H.; Laborde, H. M.; Lima, A. M. N.

2016-11-01

An oscillatory molecular adsorption pattern of the protein neutravidin from aqueous solution onto gold, in presence of a pre-deposited self assembled mono-molecular biotin film, is reported. Real time surface Plasmon resonance sensing was utilized for evaluation of the adsorption kinetics. Two different fractions were identified: in the initial phase, protein molecules attach irreversibly onto the Biotin ligands beneath towards the jamming limit, forming a neutravidin-biotin fraction. Afterwards, the growth rate exhibits distinct, albeit damped adsorption-desorption oscillations over an extended time span, assigned to a quasi reversibly bound fraction. These findings agree with, and firstly confirm a previously published model, proposing macro-molecular adsorption with time delay. The non-linear dynamic model is applicable to and also resembles non-damped oscillatory binding features of the hetero-catalytic oxidation of carbon monoxide molecules on platinum in the gas phase. An associated surface residence time can be linked to the dynamics and time scale required for self-organization.

Photoabsorption of green and red fluorescent protein chromophore anions in vacuo.

PubMed

Wan, Songbo; Liu, Shasha; Zhao, Guangjiu; Chen, Maodu; Han, Keli; Sun, Mengtao

2007-09-01

Photoabsorption properties of green and red fluorescent protein chromophore anions in vacuo were investigated theoretically, based on the experimental results in gas phase [Phys. Rev. Lett. 2001, 87, 228102; Phys. Rev. Lett. 2003, 90, 118103]. Their calculated transition energies in absorption with TD-DFT and ZINDO methods are directly compared to the experimental reports in gas phase, and the calculations with ZINDO method can correctly reproduce the absorption spectra. The orientation and strength of their transition dipole moments were revealed with transition density. We also showed the orientation and result of their intramolecular charge transfer with transition difference density. The calculated results show that with the increase of the extended conjugated system, the orientation of transition dipole moments and the orientation of charge transfer can be reversed. They are the linear responds with the external electric fields. These theoretical results reveal the insight understanding of the photoinduced dynamics of green and red fluorescent protein chromophore anions and cations in vacuo.

TRMM Solar Array Panels

NASA Technical Reports Server (NTRS)

1998-01-01

This final report presents conclusions/recommendations concerning the TRMM Solar Array; deliverable list and schedule summary; waivers and deviations; as-shipped performance data, including flight panel verification matrix, panel output detail, shadow test summary, humidity test summary, reverse bias test panel; and finally, quality assurance summary.

Concept of an interlaced phased array for beam switching

NASA Astrophysics Data System (ADS)

Reddy, C. A.; Janardhanan, K. V.; Mukundan, K. K.; Shenoy, K. S. V.

1990-04-01

A novel concept is described for feeding and phasing a large linear array of N antenna elements using only three or five feed points and phase shifters and still achieving beam switching. The idea consists of drastically reducing the number of input points by interlacing a small number of serially fed subarrays which are suitably phased. This so-called interlaced phased array (IPA) concept was tested using an array of 15 four-element Yagi antennas with a spacing equal to 0.8 wavelengths and found feasible. Some of the distinct advantages of the IPA in comparison with a conventional system of beam switching are reduced power loss, reduced phasing errors, reduced cost, increased reliability resulting from greatly reduced number of phase shifters, and better symmetry of off-zenith beams.

Nanohole Arrays of Mixed Designs and Microwriting for Simultaneous and Multiple Protein Binding Studies

PubMed Central

Ji, Jin; Yang, Jiun-Chan; Larson, Dale N.

2009-01-01

We demonstrate using nanohole arrays of mixed designs and a microwriting process based on dip-pen nanolithography to monitor multiple, different protein binding events simultaneously in real time based on the intensity of Extraordinary Optical Transmission of nanohole arrays. The microwriting process and small footprint of the individual nanohole arrays enabled us to observe different binding events located only 16μm apart, achieving high spatial resolution. We also present a novel concept that incorporates nanohole arrays of different designs to improve confidence and accuracy of binding studies. For proof of concept, two types of nanohole arrays, designed to exhibit opposite responses to protein bindings, were fabricated on one transducer. Initial studies indicate that the mixed designs could help to screen out artifacts such as protein intrinsic signals, providing improved accuracy of binding interpretation. PMID:19297143

Magnetization reversal in ferromagnetic wires patterned with antiferromagnetic gratings

NASA Astrophysics Data System (ADS)

Sani, S. R.; Liu, F.; Ross, C. A.

2017-04-01

The magnetic reversal behavior is examined for exchange-biased ferromagnetic/antiferromagnetic nanostructures consisting of an array of 10 nm thick Ni80Fe20 stripes with width 200 nm and periodicity 400 nm, underneath an orthogonal array of 10 nm thick IrMn stripes with width ranging from 200 nm to 500 nm and periodicity from 400 nm to 1 μm. The Ni80Fe20 stripes show a hysteresis loop with one step when the IrMn width and spacing are small. However, upon increasing the IrMn width and spacing, the hysteresis loops showed two steps as the pinned and unpinned sections of the Ni80Fe20 stripes switch at different fields. Micromagnetic modeling reveals the influence of geometry on the reversal behavior.

Comparison between beamforming and super resolution imaging algorithms for non-destructive evaluation

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

Fan, Chengguang; Drinkwater, Bruce W.

In this paper the performance of total focusing method is compared with the widely used time-reversal MUSIC super resolution technique. The algorithms are tested with simulated and experimental ultrasonic array data, each containing different noise levels. The simulated time domain signals allow the effects of array geometry, frequency, scatterer location, scatterer size, scatterer separation and random noise to be carefully controlled. The performance of the imaging algorithms is evaluated in terms of resolution and sensitivity to random noise. It is shown that for the low noise situation, time-reversal MUSIC provides enhanced lateral resolution when compared to the total focusing method.more » However, for higher noise levels, the total focusing method shows robustness, whilst the performance of time-reversal MUSIC is significantly degraded.« less

Supercritical fluid reverse micelle separation

DOEpatents

Fulton, John L.; Smith, Richard D.

1993-01-01

A method of separating solute material from a polar fluid in a first polar fluid phase is provided. The method comprises combining a polar fluid, a second fluid that is a gas at standard temperature and pressure and has a critical density, and a surfactant. The solute material is dissolved in the polar fluid to define the first polar fluid phase. The combined polar and second fluids, surfactant, and solute material dissolved in the polar fluid is maintained under near critical or supercritical temperature and pressure conditions such that the density of the second fluid exceeds the critical density thereof. In this way, a reverse micelle system defining a reverse micelle solvent is formed which comprises a continuous phase in the second fluid and a plurality of reverse micelles dispersed in the continuous phase. The solute material is dissolved in the polar fluid and is in chemical equilibrium with the reverse micelles. The first polar fluid phase and the continuous phase are immiscible. The reverse micelles each comprise a dynamic aggregate of surfactant molecules surrounding a core of the polar fluid. The reverse micelle solvent has a polar fluid-to-surfactant molar ratio W, which can vary over a range having a maximum ratio W.sub.o that determines the maximum size of the reverse micelles. The maximum ratio W.sub.o of the reverse micelle solvent is then varied, and the solute material from the first polar fluid phase is transported into the reverse micelles in the continuous phase at an extraction efficiency determined by the critical or supercritical conditions.

Supercritical fluid reverse micelle separation

DOEpatents

Fulton, J.L.; Smith, R.D.

1993-11-30

A method of separating solute material from a polar fluid in a first polar fluid phase is provided. The method comprises combining a polar fluid, a second fluid that is a gas at standard temperature and pressure and has a critical density, and a surfactant. The solute material is dissolved in the polar fluid to define the first polar fluid phase. The combined polar and second fluids, surfactant, and solute material dissolved in the polar fluid is maintained under near critical or supercritical temperature and pressure conditions such that the density of the second fluid exceeds the critical density thereof. In this way, a reverse micelle system defining a reverse micelle solvent is formed which comprises a continuous phase in the second fluid and a plurality of reverse micelles dispersed in the continuous phase. The solute material is dissolved in the polar fluid and is in chemical equilibrium with the reverse micelles. The first polar fluid phase and the continuous phase are immiscible. The reverse micelles each comprise a dynamic aggregate of surfactant molecules surrounding a core of the polar fluid. The reverse micelle solvent has a polar fluid-to-surfactant molar ratio W, which can vary over a range having a maximum ratio W[sub o] that determines the maximum size of the reverse micelles. The maximum ratio W[sub o] of the reverse micelle solvent is then varied, and the solute material from the first polar fluid phase is transported into the reverse micelles in the continuous phase at an extraction efficiency determined by the critical or supercritical conditions. 27 figures.

Cytoskeletal defects in Bmpr2-associated pulmonary arterial hypertension.

PubMed

Johnson, Jennifer A; Hemnes, Anna R; Perrien, Daniel S; Schuster, Manfred; Robinson, Linda J; Gladson, Santhi; Loibner, Hans; Bai, Susan; Blackwell, Tom R; Tada, Yuji; Harral, Julie W; Talati, Megha; Lane, Kirk B; Fagan, Karen A; West, James

2012-03-01

The heritable form of pulmonary arterial hypertension (PAH) is typically caused by a mutation in bone morphogenic protein receptor type 2 (BMPR2), and mice expressing Bmpr2 mutations develop PAH with features similar to human disease. BMPR2 is known to interact with the cytoskeleton, and human array studies in PAH patients confirm alterations in cytoskeletal pathways. The goal of this study was to evaluate cytoskeletal defects in BMPR2-associated PAH. Expression arrays on our Bmpr2 mutant mouse lungs revealed cytoskeletal defects as a prominent molecular consequence of universal expression of a Bmpr2 mutation (Rosa26-Bmpr2(R899X)). Pulmonary microvascular endothelial cells cultured from these mice have histological and functional cytoskeletal defects. Stable transfection of different BMPR2 mutations into pulmonary microvascular endothelial cells revealed that cytoskeletal defects are common to multiple BMPR2 mutations and are associated with activation of the Rho GTPase, Rac1. Rac1 defects are corrected in cell culture and in vivo through administration of exogenous recombinant human angiotensin-converting enzyme 2 (rhACE2). rhACE2 reverses 77% of gene expression changes in Rosa26-Bmpr2(R899X) transgenic mice, in particular, correcting defects in cytoskeletal function. Administration of rhACE2 to Rosa26-Bmpr2(R899X) mice with established PAH normalizes pulmonary pressures. Together, these findings suggest that cytoskeletal function is central to the development of BMPR2-associated PAH and that intervention against cytoskeletal defects may reverse established disease.

Identification of selenium-containing proteins in HEK 293 kidney cells using multiple chromatographies, LC-ICPMS and nano-LC-ESIMS.

PubMed

Chitta, Karnakar R; Landero-Figueroa, Julio A; Kodali, Phanichand; Caruso, Joseph A; Merino, Edward J

2013-09-30

Our previous studies using HeLa and HEK 293 cells demonstrated that selenomethionine, SeMet, exerts more of an antagonistic effect on arsenic than other selenium species. These studies attributed the antagonistic effect of SeMet to decreased levels of reactive oxygen species, ROS, changes in protein phosphorylation and possible incorporation of SeMet into proteins. The present study employs a metallomics approach to identify the selenium-containing proteins in HEK 293 cells raised with SeMet. The proteins were screened and separated using two dimensional high performance liquid chromatography (HPLC)-inductively coupled plasma mass spectrometry (ICPMS), size exclusion chromatography (SEC) and reversed-phase chromatography (RPC). The Se-containing proteins were identified by peptide mapping using nano-HPLC-Chip-electrospray ionization mass spectrometry (ESIMS). Copyright © 2013 Elsevier B.V. All rights reserved.

Isolation and Preparation of Extracellular Proteins from Lignocellulose Degrading Fungi for Comparative Proteomic Studies Using Mass Spectrometry.

PubMed

Gruninger, Robert J; Tsang, Adrian; McAllister, Tim A

2017-01-01

Fungi utilize a unique mechanism of nutrient acquisition involving extracellular digestion. To understand the biology of these microbes, it is important to identify and characterize the function of proteins that are secreted and involved in this process. Mass spectrometry-based proteomics is a powerful tool to study complex mixtures of proteins and understand how the proteins produced by an organism change in response to different conditions. Many fungi are efficient decomposers of plant cell wall, and anaerobic fungi are well recognized for their ability to digest lignocellulose. Here, we outline a protocol for the enrichment and isolation of proteins secreted by anaerobic fungi after growth on simple (glucose) and complex (straw and alfalfa hay) carbon sources. We provide detailed instruction on generating protein fragments and preparing these for proteomic analysis using reversed phase chromatography and mass spectrometry.

Floral reversion mechanism in longan (Dimocarpus longan Lour.) revealed by proteomic and anatomic analyses.

PubMed

You, Xiangrong; Wang, Lingxia; Liang, Wenyu; Gai, Yonghong; Wang, Xiaoyan; Chen, Wei

2012-02-02

Two-dimensional gel electrophoresis (2-DE) was used to analyze the proteins related to floral reversion in Dimocarpus longan Lour. Proteins were extracted from buds undergoing the normal process of flowering and from those undergoing floral reversion in three developing stages in D. longan. Differentially expressed proteins were identified from the gels after 2-DE analysis, which were confirmed using matrix-assisted laser desorption/ionization-time of flying-mass spectroscopy and protein database search. A total of 39 proteins, including 18 up-regulated and 21 down-regulated proteins, were classified into different categories, such as energy and substance metabolism, protein translation, secondary metabolism, phytohormone, cytoskeleton structure, regulation, and stress tolerance. Among these, the largest functional class was associated with primary metabolism. Down-regulated proteins were involved in photosynthesis, transcription, and translation, whereas up-regulated proteins were involved in respiration. Decreased flavonoid synthesis and up-regulated GA20ox might be involved in the floral reversion process. Up-regulated 14-3-3 proteins played a role in the regulation of floral reversion in D. longan by responding to abiotic stress. Observations via transmission electron microscopy revealed the ultrastructure changes in shedding buds undergoing floral reversion. Overall, the results provided insights into the molecular basis for the floral reversion mechanism in D. longan. Copyright © 2011 Elsevier B.V. All rights reserved.

A 24-GHz portable FMCW radar with continuous beam steering phased array (Conference Presentation)

NASA Astrophysics Data System (ADS)

Peng, Zhengyu; Li, Changzhi

2017-05-01

A portable 24-GHz frequency-modulated continuous-wave (FMCW) radar with continuous beam steering phased array is presented. This board-level integrated radar system consists of a phased array antenna, a radar transceiver and a baseband. The phased array used by the receiver is a 4-element linear array. The beam of the phased array can be continuously steered with a range of ±30° on the H-plane through an array of vector controllers. The vector controller is based on the concept of vector sum with binary-phase-shift attenuators. Each vector controller is capable of independently controlling the phase and the amplitude of each element of the linear array. The radar transceiver is based on the six-port technique. A free-running voltage controlled oscillator (VCO) is controlled by an analog "sawtooth" voltage generator to produce frequency-modulated chirp signal. This chirp signal is used as the transmitter signal, as well as the local oscillator (LO) signal to drive the six-port circuit. The transmitter antenna is a single patch antenna. In the baseband, the beat signal of the FMCW radar is detected by the six-port circuit and then processed by a laptop in real time. Experiments have been performed to reveal the capabilities of the proposed radar system for applications including indoor inverse synthetic aperture radar (ISAR) imaging, vital sign detection, and short-range navigation, etc. (This abstract is for the profiles session.)

Designing of a small wearable conformal phased array antenna for wireless communications

NASA Astrophysics Data System (ADS)

Roy, Sayan

In this thesis, a unique design of a self-adapting conformal phased-array antenna system for wireless communications is presented. The antenna system is comprised of one microstrip antenna array and a sensor circuit. A 1x4 printed microstrip patch antenna array was designed on a flexible substrate with a resonant frequency of 2.47 GHz. However, the performance of the antenna starts to degrade as the curvature of the surface of the substrate changes. To recover the performance of the system, a flexible sensor circuitry was designed. This sensor circuitry uses analog phase shifters, a flexible resistor and operational-amplifier circuitry to compensate the phase of each array element of the antenna. The proposed analytical method for phase compensation has been first verified by designing an RF test platform consisting of a microstrip antenna array, commercially available analog phase shifters, analog voltage attenuators, 4-port power dividers and amplifiers. The platform can be operated through a LabVIEW GUI interface using a 12-bit digital-to-analog converter. This test board was used to design and calibrate the sensor circuitry by observing the behavior of the antenna array system on surfaces with different curvatures. In particular, this phased array antenna system was designed to be used on the surface of a spacesuit or any other flexible prototype. This work was supported in part by the Defense Miroelectronics Activity (DMEA), NASA ND EPSCoR and DARPA/MTO.

TGEV nucleocapsid protein induces cell cycle arrest and apoptosis through activation of p53 signaling

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

Ding, Li; College of Life Sciences, Hainan Normal University, Haikou, Hainan 571158; Huang, Yong

2014-03-07

Highlights: • TGEV N protein reduces cell viability by inducing cell cycle arrest and apoptosis. • TGEV N protein induces cell cycle arrest and apoptosis by regulating p53 signaling. • TGEV N protein plays important roles in TGEV-induced cell cycle arrest and apoptosis. - Abstract: Our previous studies showed that TGEV infection could induce cell cycle arrest and apoptosis via activation of p53 signaling in cultured host cells. However, it is unclear which viral gene causes these effects. In this study, we investigated the effects of TGEV nucleocapsid (N) protein on PK-15 cells. We found that TGEV N protein suppressedmore » cell proliferation by causing cell cycle arrest at the S and G2/M phases and apoptosis. Characterization of various cellular proteins that are involved in regulating cell cycle progression demonstrated that the expression of N gene resulted in an accumulation of p53 and p21, which suppressed cyclin B1, cdc2 and cdk2 expression. Moreover, the expression of TGEV N gene promoted translocation of Bax to mitochondria, which in turn caused the release of cytochrome c, followed by activation of caspase-3, resulting in cell apoptosis in the transfected PK-15 cells following cell cycle arrest. Further studies showed that p53 inhibitor attenuated TGEV N protein induced cell cycle arrest at S and G2/M phases and apoptosis through reversing the expression changes of cdc2, cdk2 and cyclin B1 and the translocation changes of Bax and cytochrome c induced by TGEV N protein. Taken together, these results demonstrated that TGEV N protein might play an important role in TGEV infection-induced p53 activation and cell cycle arrest at the S and G2/M phases and apoptosis occurrence.« less

Brazilian Decimetric Array (BDA) project - Phase II

NASA Astrophysics Data System (ADS)

Faria, C.; Stephany, S.; Sawant, H. S.; Cecatto, J. R.; Fernandes, F. C. R.

2010-02-01

The configuration of the second phase of the Brazilian Decimetric Array (BDA), installed at Cachoeira Paulista, Brazil (Longitude 45° 0‧ 20″ W and Latitude 22° 41‧ 19″ S), is a T-shaped array where 21 antennas are being added to existing 5 antennas of the first phase. In the third phase, in each arm of the T array, four more antennas will be added and baselines will be increased to 2.5 × 1.25 km in east-west and south directions, respectively. The antennas will be equally spaced at the distances of 250 meters from the central antenna of the T-array. Also, the frequency range will be increased to 1.2-1.7, 2.8 and 5.6 GHz. The Second phase of the BDA should be operational by the middle of 2010 and will operate in the frequency range of (1.2-1.7) GHz for solar and non solar observations. Here, we present the characteristics of the second phase of the BDA project, details of the array configuration, the u-v coverage, the synthesized beam obtained for the proposed configuration.

Development of a 20-MHz wide-bandwidth PMN-PT single crystal phased-array ultrasound transducer.

PubMed

Wong, Chi-Man; Chen, Yan; Luo, Haosu; Dai, Jiyan; Lam, Kwok-Ho; Chan, Helen Lai-Wa

2017-01-01

In this study, a 20-MHz 64-element phased-array ultrasound transducer with a one-wavelength pitch is developed using a PMN-30%PT single crystal and double-matching layer scheme. High piezoelectric (d 33 >1000pC/N) and electromechanical coupling (k 33 >0.8) properties of the single crystal with an optimized fabrication process involving the photolithography technique have been demonstrated to be suitable for wide-bandwidth (⩾70%) and high-sensitivity (insertion loss ⩽30dB) phased-array transducer application. A -6dBbandwidth of 91% and an insertion loss of 29dBfor the 20-MHz 64-element phased-array transducer were achieved. This result shows that the bandwidth is improved comparing with the investigated high-frequency (⩾20MHz) ultrasound transducers using piezoelectric ceramic and single crystal materials. It shows that this phased-array transducer has potential to improve the resolution of biomedical imaging, theoretically. Based on the hypothesis of resolution improvement, this phased-array transducer is capable for small animal (i.e. mouse and zebrafish) studies. Copyright © 2016 Elsevier B.V. All rights reserved.

Intracavitary ultrasound phased arrays for thermal therapies

NASA Astrophysics Data System (ADS)

Hutchinson, Erin

Currently, the success of hyperthermia and thermal surgery treatments is limited by the technology used in the design and fabrication of clinical heating devices and the completeness of the thermometry systems used for guidance. For both hyperthermia and thermal surgery, electrically focused ultrasound generated by phased arrays provides a means of controlling localized energy deposition in body tissues. Intracavitary applicators can be used to bring the energy source close to a target volume, such as the prostate, thereby minimizing normal tissue damage. The work performed in this study was aimed at improving noninvasive prostate thermal therapies and utilized three research approaches: (1) Acoustic, thermal and optimization simulations, (2) Design and fabrication of multiple phased arrays, (3) Ex vivo and in vivo experimental testing of the heating capabilities of the phased arrays. As part of this study, a novel aperiodic phased array design was developed which resulted in a 30- 45% reduction in grating lobe levels when compared to conventional phased arrays. Measured acoustic fields generated by the constructed aperiodic arrays agreed closely with the fields predicted by the theoretical simulations and covered anatomically appropriate ranges. The power capabilities of these arrays were demonstrated to be sufficient for the purposes of hyperthermia and thermal surgery. The advantage of using phased arrays in place of fixed focus transducers was shown by demonstrating the ability of electronic scanning to increase the size of the necrosed tissue volume while providing a more uniform thermal dose, which can ultimately reduce patient treatment times. A theoretical study on the feasibility of MRI (magnetic resonance imaging) thermometry for noninvasive temperature feedback control was investigated as a means to improve transient and steady state temperature distributions achieved in hyperthermia treatments. MRI guided ex vivo and in vivo experiments demonstrated that the heating capabilities of the constructed phased arrays were adequate for hyperthermia and thermal surgery treatments. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253- 1690.)

C18 solid-phase isolation and high-performance liquid chromatography/ultraviolet diode array determination of fully methoxylated flavones in citrus juices.

PubMed

Sendra, J M; Navarro, J L; Izquierdo, L

1988-09-01

A new analytical methodology for the determination of fully methoxylated flavones (FMFs) in citrus juices is described. Isolation of the FMFs is carried out by percolation of 30 mL of clarified citrus juice (to which tetramethyl-o-kaempferol is previously added as internal standard) through a C18 Sep-Pak cartridge, washing with 3 mL of water followed by 5 mL of water/acetonitrile (3:1), and selective elution of the retained FMFs with 5 mL of water/acetonitrile (9:11). Determination of the isolated FMFs is carried out by reversed-phase high-performance liquid chromatography (HPLC) and UV diode array detection (DAD). Signals at wavelengths 320, 335, and 345 nm (bandwidth 4 nm) are simultaneously acquired, stored, plotted, and integrated. The column used is a microbore (200 x 2.1-mm) Hypersil ODS 5 microns. Elution is in gradient mode, using a ternary mobile phase (water/acetonitrile/tetrahydrofuran). Column temperature is 40 degrees C. Recovery yields are nearly 100% for all the FMFs detected and identified: isosinensetin, hexamethyl-o-gossypetin, sinensetin, tetramethyl-o-isoscutellarein, hexamethyl-o-quercetagetin, nobiletin, tetramethyl-o-scutellarein, heptamethoxyflavone, and tangeretin. Chromatographic separation of the FMFs is extremely dependent upon the minor changes of the mobile phase composition and percentages, gradient rate, and temperature. The UV spectra (230 to 400 nm) of the FMFs obtained under chromatographic conditions are given. The FMFs relative response factors at 320, 335, and 345 nm and their concentrations in hand-squeezed and commercial concentrated orange and mandarin juices are tabulated. The FMF concentration differences found among samples are discussed.

Two-dimensional beam steering using a thermo-optic silicon photonic optical phased array

NASA Astrophysics Data System (ADS)

Rabinovich, William S.; Goetz, Peter G.; Pruessner, Marcel W.; Mahon, Rita; Ferraro, Mike S.; Park, Doe; Fleet, Erin; DePrenger, Michael J.

2016-11-01

Many components for free-space optical (FSO) communication systems have shrunken in size over the last decade. However, the steering systems have remained large and power hungry. Nonmechanical beam steering offers a path to reducing the size of these systems. Optical phased arrays can allow integrated beam steering elements. One of the most important aspects of an optical phased array technology is its scalability to a large number of elements. Silicon photonics can potentially offer this scalability using CMOS foundry techniques. A phased array that can steer in two dimensions using the thermo-optic effect is demonstrated. No wavelength tuning of the input laser is needed and the design allows a simple control system with only two inputs. A benchtop FSO link with the phased array in both transmit and receive mode is demonstrated.

The use of native cation-exchange chromatography to study aggregation and phase separation of monoclonal antibodies

PubMed Central

Chen, Shuang; Lau, Hollis; Brodsky, Yan; Kleemann, Gerd R; Latypov, Ramil F

2010-01-01

This study introduces a novel analytical approach for studying aggregation and phase separation of monoclonal antibodies (mAbs). The approach is based on using analytical scale cation-exchange chromatography (CEX) for measuring the loss of soluble monomer in the case of individual and mixed protein solutions. Native CEX outperforms traditional size-exclusion chromatography in separating complex protein mixtures, offering an easy way to assess mAb aggregation propensity. Different IgG1 and IgG2 molecules were tested individually and in mixtures consisting of up to four protein molecules. Antibody aggregation was induced by four different stress factors: high temperature, low pH, addition of fatty acids, and rigorous agitation. The extent of aggregation was determined from the amount of monomeric protein remaining in solution after stress. Consequently, it was possible to address the role of specific mAb regions in antibody aggregation by co-incubating Fab and Fc fragments with their respective full-length molecules. Our results revealed that the relative contribution of Fab and Fc regions in mAb aggregation is strongly dependent on pH and the stress factor applied. In addition, the CEX-based approach was used to study reversible protein precipitation due to phase separation, which demonstrated its use for a broader range of protein–protein association phenomena. In all cases, the role of Fab and Fc was clearly dissected, providing important information for engineering more stable mAb-based therapeutics. PMID:20512972

Unique Features of Halophilic Proteins.

PubMed

Arakawa, Tsutomu; Yamaguchi, Rui; Tokunaga, Hiroko; Tokunaga, Masao

2017-01-01

Proteins from moderate and extreme halophiles have unique characteristics. They are highly acidic and hydrophilic, similar to intrinsically disordered proteins. These characteristics make the halophilic proteins soluble in water and fold reversibly. In addition to reversible folding, the rate of refolding of halophilic proteins from denatured structure is generally slow, often taking several days, for example, for extremely halophilic proteins. This slow folding rate makes the halophilic proteins a novel model system for folding mechanism analysis. High solubility and reversible folding also make the halophilic proteins excellent fusion partners for soluble expression of recombinant proteins.

An Agile Beam Transmit Array Using Coupled Oscillator Phase Control

NASA Technical Reports Server (NTRS)

Pogorzelski, Ronald S.; Scaramastra, Rocco P.; Huang, John; Beckon, Robert J.; Petree, Steve M.; Chavez, Cosme

1993-01-01

A few years ago York and colleagues suggested that injection locking of voltage controlled oscillators could be used to implement beam steering in a phased array [I]. The scheme makes use of the fact that when an oscillator is injection locked to an external signal, the phase difference between the output of the oscillator and the injection signal is governed by the difference between the injection frequency and the free running frequency of the oscillator (the frequency to which the oscillator is tuned). Thus, if voltage controlled oscillators (VCOs) are used, this phase difference is controlled by an applied voltage. Now, if a set of such oscillators are coupled to nearest neighbors, they can be made to mutually injection lock and oscillate as an ensemble. If they are all tuned to the same frequency, they will all oscillate in phase. Thus, if the outputs are connected to radiating elements forming a linear array, the antenna will radiate normal to the line of elements. Scanning is accomplished by antisymmetrically detuning the end oscillators in the array by application of a pair of appropriate voltages to their tuning ports. This results in a linear phase progression across the array which is just the phasing required to scan the beam. The scan angle is determined by the degree of detuning. We have constructed a seven element one dimensional agile beam array at S-band based on the above principle. Although, a few such arrays have been built in the past, this array possesses two unique features. First, the VCO MMICs have buffer amplifiers which isolate the output from the tuning circuit, and second, the oscillators are weakly coupled to each other at their resonant circuits rather than their outputs. This results in a convenient isolation between the oscillator array design and the radiating aperture design. An important parameter in the design is the so called coupling phase which determines the phase shift of the signals passing from one oscillator to its neighbors. Using this array, we have been able to verify the theoretical predictions concerning the effect of this phase on both the locking range and ensemble frequency of the array. However, the scan range achieved fell somewhat short of the theoretical value because of the amplitude variation of the oscillator outputs with tuning.

Indications for an inducible component of error-prone DNA repair in yeast.

PubMed

Siede, W; Eckardt, F

1984-01-01

In a thermoconditional mutant of mutagenic DNA repair (rev 2ts = rad 5-8) of Saccharomyces cerevisiae recovery of survival and mutation frequencies can be monitored by incubating UV-irradiated cells in growth medium at a permissive temperature (23 degrees C) before plating and a shift to restrictive temperature (36 degrees C). Inhibition of protein synthesis with cycloheximide during incubation at permissive conditions blocks this REV 2 dependent recovery process in stationary phase rev 2ts cells, whereas it can be reduced but not totally abolished in exponentially growing cells. These results indicate a strict dependence on post-irradiation protein synthesis in stationary phase cells and argue for a considerable constitutive level and only limited inducibility in logarithmic phase cells. The UV inducibility of the REV 2 coded function in stationary phase cells could be confirmed by analysis of the dose-response pattern of the his 5-2 reversion: in stationary phase rev 2ts cells, the quadratic component of the biphasic linear-quadratic induction kinetics found at 23 degrees C, which is interpreted as the consequence of induction of mutagenic repair, is eliminated at 36 degrees C.

Mapping protein-protein interactions using yeast two-hybrid assays.

PubMed

Mehla, Jitender; Caufield, J Harry; Uetz, Peter

2015-05-01

Yeast two-hybrid (Y2H) screens are an efficient system for mapping protein-protein interactions and whole interactomes. The screens can be performed using random libraries or collections of defined open reading frames (ORFs) called ORFeomes. This protocol describes both library and array-based Y2H screening, with an emphasis on array-based assays. Array-based Y2H is commonly used to test a number of "prey" proteins for interactions with a single "bait" (target) protein or pool of proteins. The advantage of this approach is the direct identification of interacting protein pairs without further downstream experiments: The identity of the preys is known and does not require further confirmation. In contrast, constructing and screening a random prey library requires identification of individual prey clones and systematic retesting. Retesting is typically performed in an array format. © 2015 Cold Spring Harbor Laboratory Press.

Selective deposition and self-assembly of triblock copolymers into matrix arrays for membrane protein production.

PubMed

Andreasson-Ochsner, Mirjam; Fu, Zhikang; May, Sylvia; Xiu, Low Ying; Nallani, Madhavan; Sinner, Eva-Kathrin

2012-01-31

To improve the stability of cell membrane mimics, there has been growing interest in the use of block copolymers. Here, we present an easy approach to create an array of planar polymeric matrices capable of hosting membrane proteins. The array of polymeric matrices was formed by the selective deposition of triblock copolymers onto an array of hydrophilic islands situated within a hydrophobic background. The thickness of these matrices corresponds to the length of a single polymer chain. These polymeric matrices were used to host cell-free expressed membrane proteins, and offers a prototype from which a membrane protein array can be created for diagnostics or drug discovery purposes. © 2011 American Chemical Society

Electrowetting lenses for compensating phase and curvature distortion in arrayed laser systems.

PubMed

Niederriter, Robert D; Watson, Alexander M; Zahreddine, Ramzi N; Cogswell, Carol J; Cormack, Robert H; Bright, Victor M; Gopinath, Juliet T

2013-05-10

We have demonstrated a one-dimensional array of individually addressable electrowetting tunable liquid lenses that compensate for more than one wave of phase distortion across a wavefront. We report a scheme for piston control using tunable liquid lens arrays in volume-bound cavities that alter the optical path length without affecting the wavefront curvature. Liquid lens arrays with separately tunable focus or phase control hold promise for laser communication systems and adaptive optics.

Identification of avocado (Persea americana) pulp proteins by nano-LC-MS/MS via combinatorial peptide ligand libraries.

PubMed

Esteve, Clara; D'Amato, Alfonsina; Marina, María Luisa; García, María Concepción; Righetti, Pier Giorgio

2012-09-01

Avocado (Persea americana) proteins have been scarcely studied despite their importance, especially in food related allergies. The proteome of avocado pulp was explored in depth by extracting proteins with capture by combinatorial peptide ligand libraries at pH 7.4 and under conditions mimicking reverse-phase capture at pH 2.2. The total number of unique gene products identified amounts to 1012 proteins, of which 174 are in common with the control, untreated sample, 190 are present only in the control and 648 represent the new species detected via combinatorial peptide ligand libraries of all combined eluates and likely represent low-abundance proteins. Among the 1012 proteins, it was possible to identify the already known avocado allergen Pers a 1 and different proteins susceptible to be allergens such as a profilin, a polygalacturonase, a thaumatin-like protein, a glucanase, and an isoflavone reductase like protein. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

In Vitro Proliferation and Anti-Apoptosis of the Papain-Generated Casein and Soy Protein Hydrolysates towards Osteoblastic Cells (hFOB1.19).

PubMed

Pan, Xiao-Wen; Zhao, Xin-Huai

2015-06-17

Casein and soy protein were digested by papain to three degrees of hydrolysis (DH) 7.3%-13.3%, to obtain respective six casein and soy protein hydrolysates, aiming to clarify their in vitro proliferation and anti-apoptosis towards a human osteoblastic cell line (hFOB1.19 cells). Six casein and soy protein hydrolysates at five levels (0.01-0.2 mg/mL) mostly showed proliferation as positive 17β-estradiol did, because they conferred the osteoblasts with cell viability of 100%-114% and 104%-123%, respectively. The hydrolysates of higher DH values had stronger proliferation. Casein and soy protein hydrolysates of the highest DH values altered cell cycle progression, and enhanced cell proportion of S-phase from 50.5% to 56.5% and 60.5%. The two also antagonized etoposide- and NaF-induced osteoblast apoptosis. In apoptotic prevention, apoptotic cells were decreased from 31.6% to 22.6% and 15.6% (etoposide treatment), or from 19.5% to 17.7% and 12.4% (NaF treatment), respectively. In apoptotic reversal, soy protein hydrolysate decreased apoptotic cells from 13.3% to 11.7% (etoposide treatment), or from 14.5% to 11.0% (NaF treatment), but casein hydrolysate showed no reversal effect. It is concluded that the hydrolysates of two kinds had estradiol-like action on the osteoblasts, and soy protein hydrolysates had stronger proliferation and anti-apoptosis on the osteoblasts than casein hydrolysates.

5-ASA Affects Cell Cycle Progression in Colorectal Cells by Reversibly Activating a Replication Checkpoint

PubMed Central

LUCIANI, M. GLORIA; CAMPREGHER, CHRISTOPH; FORTUNE, JOHN M.; KUNKEL, THOMAS A.; GASCHE, CHRISTOPH

2007-01-01

Background & Aims Individuals with inflammatory bowel disease are at risk of developing colorectal cancer (CRC). Epidemiologic, animal, and laboratory studies suggest that 5-amino-salicylic acid (5-ASA) protects from the development of CRC by altering cell cycle progression and by inducing apoptosis. Our previous results indicate that 5-ASA improves replication fidelity in colorectal cells, an effect that is active in reducing mutations. In this study, we hypothesized that 5-ASA restrains cell cycle progression by activating checkpoint pathways in colorectal cell lines, which would prevent tumor development and improve genomic stability. Methods CRC cells with different genetic backgrounds such as HT29, HCT116, HCT116p53−/−, HCT116+chr3, and LoVo were treated with 5-ASA for 2–96 hours. Cell cycle progression, phosphorylation, and DNA binding of cell cycle checkpoint proteins were analyzed. Results We found that 5-ASA at concentrations between 10 and 40 mmol/L affects cell cycle progression by inducing cells to accumulate in the S phase. This effect was independent of the hMLH1, hMSH2, and p53 status because it was observed to a similar extent in all cell lines under investigation. Moreover, wash-out experiments demonstrated reversibility within 48 hours. Although p53 did not have a causative role, p53 Ser15 was strongly phosphorylated. Proteins involved in the ATM-and-Rad3-related kinase (ATR)-dependent S-phase checkpoint response (Chk1 and Rad17) were also phosphorylated but not ataxia telengectasia mutated kinase. Conclusions Our data demonstrate that 5-ASA causes cells to reversibly accumulate in S phase and activate an ATR-dependent checkpoint. The activation of replication checkpoint may slow down DNA replication and improve DNA replication fidelity, which increases the maintenance of genomic stability and counteracts carcinogenesis. PMID:17241873

Pulse-Echo Phased Array Ultrasonic Inspection of Pultruded Rod Stitched Efficient Unitized Structure (PRSEUS)

NASA Technical Reports Server (NTRS)

Johnston, Pat H.

2010-01-01

A PRSEUS test article was subjected to controlled impact on the skin face followed by static and cyclic axial compressions. Phased array ultrasonic inspection was conducted before impact, and after each of the test conditions. A linear phased array probe with a manual X-Y scanner was used for interrogation. Ultrasound showed a delamination between the skin and stringer flange adjacent to the impact. As designed, the stitching in the flange arrested the lateral flaw formation. Subsequent ultrasonic data showed no delamination growth due to continued loading. Keywords: Phased Array, Ultrasonics, Composites, Out-of-Autoclave

Enhanced sensitivity of surface acoustic wave-based rate sensors incorporating metallic dot arrays.

PubMed

Wang, Wen; Shao, Xiuting; Liu, Xinlu; Liu, Jiuling; He, Shitang

2014-02-26

A new surface acoustic wave (SAW)-based rate sensor pattern incorporating metallic dot arrays was developed in this paper. Two parallel SAW delay lines with a reverse direction and an operation frequency of 80 MHz on a same X-112°Y LiTaO3 wafer are fabricated as the feedback of two SAW oscillators, and mixed oscillation frequency was used to characterize the external rotation. To enhance the Coriolis force effect acting on the SAW propagation, a copper (Cu) dot array was deposited along the SAW propagation path of the SAW devices. The approach of partial-wave analysis in layered media was referred to analyze the response mechanisms of the SAW based rate sensor, resulting in determination of the optimal design parameters. To improve the frequency stability of the oscillator, the single phase unidirectional transducers (SPUDTs) and combed transducer were used to form the SAW device to minimize the insertion loss and accomplish the single mode selection, respectively. Excellent long-term (measured in hours) frequency stability of 0.1 ppm/h was obtained. Using the rate table with high precision, the performance of the developed SAW rate sensor was evaluated experimentally; satisfactory detection sensitivity (16.7 Hz∙deg∙s(-1)) and good linearity were observed.

Enhanced Sensitivity of Surface Acoustic Wave-Based Rate Sensors Incorporating Metallic Dot Arrays

PubMed Central

Wang, Wen; Shao, Xiuting; Liu, Xinlu; Liu, Jiuling; He, Shitang

2014-01-01

A new surface acoustic wave (SAW)-based rate sensor pattern incorporating metallic dot arrays was developed in this paper. Two parallel SAW delay lines with a reverse direction and an operation frequency of 80 MHz on a same X-112°Y LiTaO3 wafer are fabricated as the feedback of two SAW oscillators, and mixed oscillation frequency was used to characterize the external rotation. To enhance the Coriolis force effect acting on the SAW propagation, a copper (Cu) dot array was deposited along the SAW propagation path of the SAW devices. The approach of partial-wave analysis in layered media was referred to analyze the response mechanisms of the SAW based rate sensor, resulting in determination of the optimal design parameters. To improve the frequency stability of the oscillator, the single phase unidirectional transducers (SPUDTs) and combed transducer were used to form the SAW device to minimize the insertion loss and accomplish the single mode selection, respectively. Excellent long-term (measured in hours) frequency stability of 0.1 ppm/h was obtained. Using the rate table with high precision, the performance of the developed SAW rate sensor was evaluated experimentally; satisfactory detection sensitivity (16.7 Hz·deg·s−1) and good linearity were observed. PMID:24577520

Evaluation of ultrasonic array imaging algorithms for inspection of a coarse grained material

NASA Astrophysics Data System (ADS)

Van Pamel, A.; Lowe, M. J. S.; Brett, C. R.

2014-02-01

Improving the ultrasound inspection capability for coarse grain metals remains of longstanding interest to industry and the NDE research community and is expected to become increasingly important for next generation power plants. A test sample of coarse grained Inconel 625 which is representative of future power plant components has been manufactured to test the detectability of different inspection techniques. Conventional ultrasonic A, B, and C-scans showed the sample to be extraordinarily difficult to inspect due to its scattering behaviour. However, in recent years, array probes and Full Matrix Capture (FMC) imaging algorithms, which extract the maximum amount of information possible, have unlocked exciting possibilities for improvements. This article proposes a robust methodology to evaluate the detection performance of imaging algorithms, applying this to three FMC imaging algorithms; Total Focusing Method (TFM), Phase Coherent Imaging (PCI), and Decomposition of the Time Reversal Operator with Multiple Scattering (DORT MSF). The methodology considers the statistics of detection, presenting the detection performance as Probability of Detection (POD) and probability of False Alarm (PFA). The data is captured in pulse-echo mode using 64 element array probes at centre frequencies of 1MHz and 5MHz. All three algorithms are shown to perform very similarly when comparing their flaw detection capabilities on this particular case.

A new approach to phosphoserine and phosphothreonine analysis in peptides and proteins: chemical modification, enrichment via solid-phase reversible binding, and analysis by mass spectrometry.

PubMed

Thaler, Florian; Valsasina, Barbara; Baldi, Rosario; Xie, Jin; Stewart, Albert; Isacchi, Antonella; Kalisz, Henryk M; Rusconi, Luisa

2003-06-01

beta-Elimination of the phosphate group on phosphoserine and phosphothreonine residues and addition of an alkyldithiol is a useful tool for analysis of the phosphorylation states of proteins and peptides. We have explored the influence of several conditions on the efficiency of this PO(4)(3-) elimination reaction upon addition of propanedithiol. In addition to the described influence of different bases, the solvent composition was also found to have a major effect on the yield of the reaction. In particular, an increase in the percentage of DMSO enhances the conversion rate, whereas a higher amount of protic polar solvents, such as water or isopropanol, induces the opposite effect. We have also developed a protocol for enrichment of the modified peptides, which is based on solid-phase covalent capture/release with a dithiopyridino-resin. The procedure for beta-elimination and isolation of phosphorylated peptides by solid-phase capture/release was developed with commercially available alpha-casein. Enriched peptide fragments were characterized by MALDI-TOF mass spectrometric analysis before and after alkylation with iodoacetamide, which allowed rapid confirmation of the purposely introduced thiol moiety. Sensitivity studies, carried out in order to determine the detection limit, demonstrated that samples could be detected even in the low picomolar range by mass spectrometry. The developed solid-phase enrichment procedure based on reversible covalent binding of the modified peptides is more effective and significantly simpler than methods based on the interaction between biotin and avidin, which require additional steps such as tagging the modified peptides and work-up of the samples prior to the affinity capture step.

A Tikhonov Regularization Scheme for Focus Rotations with Focused Ultrasound Phased Arrays

PubMed Central

Hughes, Alec; Hynynen, Kullervo

2016-01-01

Phased arrays have a wide range of applications in focused ultrasound therapy. By using an array of individually-driven transducer elements, it is possible to steer a focus through space electronically and compensate for acoustically heterogeneous media with phase delays. In this paper, the concept of focusing an ultrasound phased array is expanded to include a method to control the orientation of the focus using a Tikhonov regularization scheme. It is then shown that the Tikhonov regularization parameter used to solve the ill-posed focus rotation problem plays an important role in the balance between quality focusing and array efficiency. Finally, the technique is applied to the synthesis of multiple foci, showing that this method allows for multiple independent spatial rotations. PMID:27913323

A Tikhonov Regularization Scheme for Focus Rotations With Focused Ultrasound-Phased Arrays.

PubMed

Hughes, Alec; Hynynen, Kullervo

2016-12-01

Phased arrays have a wide range of applications in focused ultrasound therapy. By using an array of individually driven transducer elements, it is possible to steer a focus through space electronically and compensate for acoustically heterogeneous media with phase delays. In this paper, the concept of focusing an ultrasound-phased array is expanded to include a method to control the orientation of the focus using a Tikhonov regularization scheme. It is then shown that the Tikhonov regularization parameter used to solve the ill-posed focus rotation problem plays an important role in the balance between quality focusing and array efficiency. Finally, the technique is applied to the synthesis of multiple foci, showing that this method allows for multiple independent spatial rotations.

Large Phased Array Radar Using Networked Small Parabolic Reflectors

NASA Technical Reports Server (NTRS)

Amoozegar, Farid

2006-01-01

Multifunction phased array systems with radar, telecom, and imaging applications have already been established for flat plate phased arrays of dipoles, or waveguides. In this paper the design trades and candidate options for combining the radar and telecom functions of the Deep Space Network (DSN) into a single large transmit array of small parabolic reflectors will be discussed. In particular the effect of combing the radar and telecom functions on the sizes of individual antenna apertures and the corresponding spacing between the antenna elements of the array will be analyzed. A heterogeneous architecture for the DSN large transmit array is proposed to meet the radar and telecom requirements while considering the budget, scheduling, and strategic planning constrains.

Reversible inactivation of interpeduncular nucleus impairs memory consolidation and retrieval but not learning in rats: A behavioral and molecular study.

PubMed

Khatami, Leila; Khodagholi, Fariba; Motamedi, Fereshteh

2018-04-16

The Interpedundular nucleus (IPN) is a small midbrain structure located deeply between the two cerebral peduncles. The strategic placement of this nucleus makes it a possible relay between structures involved in the modulation of hippocampal theta rhythm activity. In this study we aimed to investigate how reversible inactivation of IPN could affect the acquisition, consolidation and retrieval phases of memory in passive avoidance (PA) and Morris water maze (MWM) tasks. To support our data, molecular studies were performed in order to detect possible changes in the expression of proteins related to learning and memory in the hippocampus. To address this issue rats' IPN was reversibly inactivated by microinjection of lidocaine hydrochloride (4%). After the behavioral studies, the phosphorylation of CREB and P70, and c-fos expression levels in the hippocampus were determined using western blotting and immunohistochemistry respectively. Our results in the PA and MWM tasks showed that IPN reversible inactivation could impair immediate post training consolidation and retrieval while it had no effect on the acquisition phase. In addition, there was a deficit in the retention of the MWM working memory. Our data showed the ratio of pCREB/CREB, pP70/P70 and c-fos expression in the hippocampus significantly decreased after IPN reversible inactivation. Collectively, the results show that behaviorally defined changes could be due to what happens molecularly in the hippocampus after IPN reversible inactivation. It is concluded that IPN not only makes part of a network involved in the modulation of hippocampal theta rhythm activity, but also is actively engaged in hippocampal memory formation. Copyright © 2018 Elsevier B.V. All rights reserved.

Differential screening and mass mapping of proteins from premalignant and cancer cell lines using nonporous reversed-phase HPLC coupled with mass spectrometric analysis.

PubMed

Chong, B E; Hamler, R L; Lubman, D M; Ethier, S P; Rosenspire, A J; Miller, F R

2001-03-15

Nonporous (NPS) RP-HPLC has been used to rapidly separate proteins from whole cell lysates of human breast cell lines. The nonporous separation involves the use of hard-sphere silica beads of 1.5-microm diameter coated with C18, which can be used to separate proteins ranging from 5 to 90 kDa. Using only 30-40 microg of total protein, the protein molecular weights are detectable on-line using an ESI-oaTOF MS. Of hundreds of proteins detected in this mass range, approxinately 75-80 are more highly expressed. The molecular weight profiles can be displayed as a mass map analogous to a virtual "1-D gel" and differentially expressed proteins can be compared by image analysis. The separated proteins can also be detected by UV absorption and differentially expressed proteins quantified. The eluting proteins can be collected in the liquid phase and the molecular weight and peptide maps determined by MALDI-TOF MS for identification. It is demonstrated that the expressed protein profiles change during neoplastic progression and that many oncoproteins are readily detected. It is also shown that the response of premalignant cancer cells to estradiol can be rapidly screened by this method, demonstrating significant changes in response to an external agent. Ultimately, the proteins can be studied by peptide mapping to search for posttranslational modifications of the oncoproteins accompanying progression.

2D-1D structural phase transformation of Co(II) 3,5-pyridinedicarboxylate frameworks with chromotropism.

PubMed

Cheansirisomboon, Achareeya; Pakawatchai, Chaveng; Youngme, Sujittra

2012-09-21

Two new metal-organic frameworks [Co(pydc)(H(2)O)(2)](n) (1) and [Co(pydc)(H(2)O)(4)](n)(H(2)O)(n) (2), (pydc = 3,5-pyridinedicarboxylate) have been synthesized by a diffusion method and characterized by single-crystal X-ray diffraction. The structure of 1 reveals an infinite 2D layer with honeycomb-like cavities in which each pydc ligand bridges three Co(II) ions. The adjacent 2D layers are orderly packed in an ABAB-type array via intermolecular interactions of the combined π-π stacking and hydrogen bonds to form a 3D supramolecular architecture. Interestingly, compound 1 exhibits a water induced crystal-to-amorphous transformation with chromotropism confirmed by spectroscopic techniques, elemental analysis, TGA and XRPD. When this amorphous phase (1A) was exposed to water vapor, it was readily converted into the second crystalline phase 1B with a color change. Moreover, a reversible process between 1A and 1B was performed. In the case of compound 2, pydc acts as didentate bridging ligand connecting two Co(II) ions, leading to a 1D zig-zag chain. Guest water molecules fill the gaps in between chains and form hydrogen bonds with the host chains stabilizing the 3D network of 2. Additionally, compound 2 also exhibits a water induced crystal-to-amorphous transformation with chromotropism and the reversible process was also performed between the dehydrated (2A) and rehydrated (2') forms. Surprisingly, the IR and UV-vis spectra, elemental analysis, TGA curve and XRPD pattern of the rehydrated second phase 1B are found to be identical to that of 2 and 2', these results confirm that 2, 2' and 1B are the same compound.

TU-E-BRA-05: Reverse Geometry Imaging with MV Detector for Improved Image Resolution.

PubMed

Ganguly, A; Abel, E; Sun, M; Fahrig, R; Virshup, G; Star-Lack, J

2012-06-01

Thick pixilated scintillators can offer significant improvements in quantum efficiency over phosphor screen megavoltage (MV) detectors. However spatial resolution can be compromised due to the spreading of light across pixels within septa. Of particular interest are the lower energy x-ray photons and associated light photons that produce higher image contrast but are stopped near the scintillator entrance surface. They suffer the most scattering in the scintillator prior to detection in the photodiodes. Reversing the detector geometry, so that the incident x-ray beam passes through the photodiode array into the scintillator, allows the light to scatter less prior to detection. This also reduces the Swank noise since now higher and lower energy x-ray photons tend to produce similar electronic signals. In this work, we present simulations and measurements of detector MTF for the conventional/forward and reverse geometries to demonstrate this phenomenon. A tabletop system consisting of a Varian CX1 1MeV linear accelerator and a modified Varian Paxscan4030 with the readout electronics moved away from the incident the beam was used. A special holder was used to press a 2.5W×5.0L×2.0Hcm 3 pixellated Cesium Iodide (CsI:Tl) scintillator array on to the detector glass. The CsI array had a pitch of 0.784mm with plastic septa between pixels and the photodiode array pitch was 0.192 mm. The MTF in the forward and reverse geometries was measured using a 0.5mm thick Tantalum slanted edge. Geant4-based Monte Carlo simulations were performed for comparison. The measured and simulated MTFs matched to within 3.4(±3.7)% in the forward and 4.4(±1.5)% in reverse geometries. The reverse geometry MTF was higher than the forward geometry MTF at all spatial frequencies and doubled to .25 at 0.3lp/mm. A novel method of improving the image resolution at MV energies was demonstrated. The improvements should be more pronounced with increased scintillator thickness. Funding support provided by NIH (grant number NIH R01 CA138426). © 2012 American Association of Physicists in Medicine.

Glutathionylation acts as a control switch for uncoupling proteins UCP2 and UCP3.

PubMed

Mailloux, Ryan J; Seifert, Erin L; Bouillaud, Frédéric; Aguer, Céline; Collins, Sheila; Harper, Mary-Ellen

2011-06-17

The mitochondrial uncoupling proteins 2 and 3 (UCP2 and -3) are known to curtail oxidative stress and participate in a wide array of cellular functions, including insulin secretion and the regulation of satiety. However, the molecular control mechanism(s) governing these proteins remains elusive. Here we reveal that UCP2 and UCP3 contain reactive cysteine residues that can be conjugated to glutathione. We further demonstrate that this modification controls UCP2 and UCP3 function. Both reactive oxygen species and glutathionylation were found to activate and deactivate UCP3-dependent increases in non-phosphorylating respiration. We identified both Cys(25) and Cys(259) as the major glutathionylation sites on UCP3. Additional experiments in thymocytes from wild-type and UCP2 null mice demonstrated that glutathionylation similarly diminishes non-phosphorylating respiration. Our results illustrate that UCP2- and UCP3-mediated state 4 respiration is controlled by reversible glutathionylation. Altogether, these findings advance our understanding of the roles UCP2 and UCP3 play in modulating metabolic efficiency, cell signaling, and oxidative stress processes.

Deriving an explicit hepatic clearance equation accounting for plasma protein binding and hepatocellular uptake.

PubMed

Yoon, Miyoung; Clewell, Harvey J; Andersen, Melvin E

2013-02-01

High throughput in vitro biochemical and cell-based assays have the promise to provide more mechanism-based assessments of the adverse effects of large numbers of chemicals. One of the most challenging hurdles for interpreting in vitro toxicity findings is the need for reverse dosimetry tools that estimate the exposures that will give concentrations in vivo similar to the active concentrations in vitro. Recent experience using IVIVE approaches to estimate in vivo pharmacokinetics (Wetmore et al., 2012) identified the need to develop a hepatic clearance equation that explicitly accounted for a broader set of protein binding and membrane transport processes and did not depend on a well-mixed description of the liver compartment. Here we derive an explicit steady-state hepatic clearance equation that includes these factors. In addition to the derivation, we provide simple computer code to calculate steady-state extraction for any combination of blood flow, membrane transport processes and plasma protein-chemical binding rates. This expanded equation provides a tool to estimate hepatic clearance for a more diverse array of compounds. Copyright © 2012 Elsevier Ltd. All rights reserved.

Dispersive liquid-liquid microextraction for the determination of vitamins D and K in foods by liquid chromatography with diode-array and atmospheric pressure chemical ionization-mass spectrometry detection.

PubMed

Viñas, Pilar; Bravo-Bravo, María; López-García, Ignacio; Hernández-Córdoba, Manuel

2013-10-15

A simple and rapid method was developed using reversed-phase liquid chromatography (LC) with both diode array (DAD) and atmospheric pressure chemical ionization mass spectrometric (APCI-MS) detection, for the simultaneous analysis of the vitamins ergocalciferol (D2), cholecalciferol (D3), phylloquinone (K1), menaquinone-4 (K2) and a synthetic form of vitamin K, menadione (K3). The Taguchi experimental method, an orthogonal array design (OAD), was used to optimize an efficient and clean preconcentration step based on dispersive liquid-liquid microextraction (DLLME). A factorial design was applied with six factors and three levels for each factor, namely, carbon tetrachloride volume, methanol volume, aqueous sample volume, pH of sample, sodium chloride concentration and time of the centrifugation step. The DLLME optimized procedure consisted of rapidly injecting 3 mL of acetonitrile (disperser solvent) containing 150 µL carbon tetrachloride (extraction solvent) into the aqueous sample, thereby forming a cloudy solution. Phase separation was performed by centrifugation, and the sedimented phase was evaporated with nitrogen, reconstituted with 50 µL of acetonitrile, and injected. The LC analyses were carried out using a mobile phase composed of acetonitrile, 2-propanol and water, under gradient elution. Quantification was carried out by the standard additions method. The APCI-MS spectra, in combination with UV spectra, permitted the correct identification of compounds in the food samples. The method was validated according to international guidelines and using a certified reference material. The validated method was applied for the analysis of vitamins D and K in infant foods and several green vegetables. There was little variability in the forms of vitamin K present in vegetables, with the most abundant vitamer in all the samples being phylloquinone, while menadione could not be detected. Conversely, cholecalciferol, which is present in food of animal origin, was the main form in infant foods, while ergocalciferol was not detected. Copyright © 2013 Elsevier B.V. All rights reserved.

The Potential of Phased Arrays for Planetary Exploration

NASA Astrophysics Data System (ADS)

Pogorzelski, Ronald J.

2000-01-01

Phased array antennas provide a set of operational capabilities which are very attractive for certain mission applications and not very attractive for others. Such antennas are by no means a panacea for telecommunications. In this paper the features of phased arrays are reviewed and their implications for space missions are considered in terms of benefits and costs. The primary capability provided by a phased array is electronic beam agility. The beam direction may be controlled at electronic speeds (vs. mechanical actuation) permitting time division multiplexing of multiple "users." Moreover, the beam direction can be varied over a full hemisphere (for a planar array). On the other hand, such antennas are typically much more complicated than the more commonly used reflectors and horns and this implies higher cost. In some applications, this increased cost must be accepted if the mission is to be carried out at all. The SIR-C radar is an example of such a case albeit not for deep space. Assuming for the sake of argument that the complexity and cost of a phased array can be significantly reduced, where can such antennas be of value in the future of planetary exploration? Potential applications to be discussed are planetary rovers, landers, and orbiters including both the areosynchronous and low orbit varieties. In addition, consideration is given to links from deep space to earth. As may be fairly obvious, the deep space link to earth would not benefit from the wide angle steering capability provided by a phase array whereas a rover could gain advantage from the capability to steer a beam anywhere in the sky. In the rover case, however, physical size of the aperture becomes a significant factor which, of course, has implications regarding the choice of frequency band. Recent research work concerning phased arrays has suggested that future phased arrays might be made less complex and, therefore, less costly. Successful realization of such phased arrays would enable many of the planetary missions discussed in this paper and significantly broaden the telecommunications capabilities available to the mission designers of the future.

PMN-PT Single-Crystal High-Frequency Kerfless Phased Array

PubMed Central

Chen, Ruimin; Cabrera-Munoz, Nestor E.; Lam, Kwok Ho; Hsu, Hsiu-sheng; Zheng, Fan; Zhou, Qifa; Shung, K. Kirk

2015-01-01

This paper reports the design, fabrication, and characterization of a miniature high-frequency kerfless phased array prepared from a PMN-PT single crystal for forward-looking intravascular or endoscopic imaging applications. After lapping down to around 40 μm, the PMN-PT material was utilized to fabricate 32-element kerfless phased arrays using micromachining techniques. The aperture size of the active area was only 1.0 × 1.0 mm. The measured results showed that the array had a center frequency of 40 MHz, a bandwidth of 34% at −6 dB with a polymer matching layer, and an insertion loss of 20 dB at the center frequency. Phantom images were acquired and compared with simulated images. The results suggest that the feasibility of developing a phased array mounted at the tip of a forward-looking intravascular catheter or endoscope. The fabricated array exhibits much higher sensitivity than PZT ceramic-based arrays and demonstrates that PMN-PT is well suited for this application. PMID:24859667

High Rate User Ka-Band Phased Array Antenna Test Results

NASA Technical Reports Server (NTRS)

Caroglanian, Armen; Perko, Kenneth; Seufert, Steve; Dod, Tom; Warshowsky, Jay; Day, John H. (Technical Monitor)

2001-01-01

The High Rate User Phased Array Antenna (HRUPAA) is a Ka-Band planar phased array designed by the Harris Corporation for the NASA Goddard Space Flight Center. The HRUPAA permits a satellite to downlink data either to a ground station or through the Tracking and Data Relay Satellite System (TDRSS). The HRUPAA is scanned electronically by ground station / user satellite command over a 120 degree cone angle. The phased array has the advantage of not imparting attitude disturbances to the user spacecraft. The 288-element transmit-only array has distributed RF amplifiers integrated behind each of the printed patch antenna elements. The array has 33 dBW EIRP and is left-hand circularly polarized. An engineering model of a partially populated array has been developed and delivered to NASA Goddard Space Flight Center. This report deals with the testing of the engineering model at the Goddard Antenna Range near-field and compact range facilities. The antenna specifications are described first, followed by the test plan and test results.

Polarimetry With Phased Array Antennas: Theoretical Framework and Definitions

NASA Astrophysics Data System (ADS)

Warnick, Karl F.; Ivashina, Marianna V.; Wijnholds, Stefan J.; Maaskant, Rob

2012-01-01

For phased array receivers, the accuracy with which the polarization state of a received signal can be measured depends on the antenna configuration, array calibration process, and beamforming algorithms. A signal and noise model for a dual-polarized array is developed and related to standard polarimetric antenna figures of merit, and the ideal polarimetrically calibrated, maximum-sensitivity beamforming solution for a dual-polarized phased array feed is derived. A practical polarimetric beamformer solution that does not require exact knowledge of the array polarimetric response is shown to be equivalent to the optimal solution in the sense that when the practical beamformers are calibrated, the optimal solution is obtained. To provide a rough initial polarimetric calibration for the practical beamformer solution, an approximate single-source polarimetric calibration method is developed. The modeled instrumental polarization error for a dipole phased array feed with the practical beamformer solution and single-source polarimetric calibration was -10 dB or lower over the array field of view for elements with alignments perturbed by random rotations with 5 degree standard deviation.

Microelectrode array recordings of cultured hippocampal networks reveal a simple model for transcription and protein synthesis-dependent plasticity

PubMed Central

Arnold, Fiona JL; Hofmann, Frank; Bengtson, C. Peter; Wittmann, Malte; Vanhoutte, Peter; Bading, Hilmar

2005-01-01

A simplified cell culture system was developed to study neuronal plasticity. As changes in synaptic strength may alter network activity patterns, we grew hippocampal neurones on a microelectrode array (MEA) and monitored their collective behaviour with 60 electrodes simultaneously. We found that exposure of the network for 15 min to the GABAA receptor antagonist bicuculline induced an increase in synaptic efficacy at excitatory synapses that was associated with an increase in the frequency of miniature AMPA receptor-mediated EPSCs and a change in network activity from uncoordinated firing of neurones (lacking any recognizable pattern) to a highly organized, periodic and synchronous burst pattern. Induction of recurrent synchronous bursting was dependent on NMDA receptor activation and required extracellular signal-regulated kinase (ERK)1/2 signalling and translation of pre-existing mRNAs. Once induced, the burst pattern persisted for several days; its maintenance phase (> 4 h) was dependent on gene transcription taking place in a critical period of 120 min following induction. Thus, cultured hippocampal neurones display a simple, transcription and protein synthesis-dependent form of plasticity. The non-invasive nature of MEA recordings provides a significant advantage over traditional assays for synaptic connectivity (i.e. long-term potentiation in brain slices) and facilitates the search for activity-regulated genes critical for late-phase plasticity. PMID:15618268

Microelectrode array recordings of cultured hippocampal networks reveal a simple model for transcription and protein synthesis-dependent plasticity.

PubMed

Arnold, Fiona J L; Hofmann, Frank; Bengtson, C Peter; Wittmann, Malte; Vanhoutte, Peter; Bading, Hilmar

2005-04-01

A simplified cell culture system was developed to study neuronal plasticity. As changes in synaptic strength may alter network activity patterns, we grew hippocampal neurones on a microelectrode array (MEA) and monitored their collective behaviour with 60 electrodes simultaneously. We found that exposure of the network for 15 min to the GABA(A) receptor antagonist bicuculline induced an increase in synaptic efficacy at excitatory synapses that was associated with an increase in the frequency of miniature AMPA receptor-mediated EPSCs and a change in network activity from uncoordinated firing of neurones (lacking any recognizable pattern) to a highly organized, periodic and synchronous burst pattern. Induction of recurrent synchronous bursting was dependent on NMDA receptor activation and required extracellular signal-regulated kinase (ERK)1/2 signalling and translation of pre-existing mRNAs. Once induced, the burst pattern persisted for several days; its maintenance phase (> 4 h) was dependent on gene transcription taking place in a critical period of 120 min following induction. Thus, cultured hippocampal neurones display a simple, transcription and protein synthesis-dependent form of plasticity. The non-invasive nature of MEA recordings provides a significant advantage over traditional assays for synaptic connectivity (i.e. long-term potentiation in brain slices) and facilitates the search for activity-regulated genes critical for late-phase plasticity.

Reconfigurable Transmission Line for a Series-Fed Ku-Band Phased Array Using a Single Feed

NASA Technical Reports Server (NTRS)

Host, Nicholas K.; Chen, Chi-Chih; Volakis, John L.; Miranda. Felix, A.

2013-01-01

The paper presents a novel approach to realize a lowcost phased array using a simple feeding mechanism. Specifically, a single coplanar stripline (CPS) transmission line is used to feed the antenna array elements. By controlling the CPS's dielectric properties using a movable dielectric plunger, scanning is achieved. Due to its simplicity, single feed, and no phase shifters, this approach leads to a dramatic reduction in cost which does not scale for larger arrays.

Solid cation exchange phase to remove interfering anthocyanins in the analysis of other bioactive phenols in red wine.

PubMed

da Silva, Letícia Flores; Guerra, Celito Crivellaro; Klein, Diandra; Bergold, Ana Maria

2017-07-15

Bioactive phenols (BPs) are often targets in red wine analysis. However, other compounds interfere in the liquid chromatography methods used for this analysis. Here, purification procedures were tested to eliminate anthocyanin interference during the determination of 19 red-wine BPs. Liquid chromatography, coupled to a diode array detector (HPLC-DAD) and a mass spectrometer (UPLC-MS), was used to compare the direct injection of the samples with solid-phase extractions: reversed-phase (C18) and strong cation-exchange (SCX). The HPLC-DAD method revealed that, out of 13BPs, only six are selectively analyzed with or without C18 treatment, whereas SCX enabled the detection of all BPs. The recovery with SCX was above 86.6% for eight BPs. Moreover, UPLC-MS demonstrated the potential of SCX sample preparation for the determination of 19BPs. The developed procedure may be extended to the analysis of other red wine molecules or to other analytical methods where anthocyanins may interfere. Copyright © 2017 Elsevier Ltd. All rights reserved.

Multi-pulse shadowgraphic RGB illumination and detection for flow tracking

NASA Astrophysics Data System (ADS)

Menser, Jan; Schneider, Florian; Dreier, Thomas; Kaiser, Sebastian A.

2018-06-01

This work demonstrates the application of a multi-color LED and a consumer color camera for visualizing phase boundaries in two-phase flows, in particular for particle tracking velocimetry. The LED emits a sequence of short light pulses, red, green, then blue (RGB), and through its color-filter array, the camera captures all three pulses on a single RGB frame. In a backlit configuration, liquid droplets appear as shadows in each color channel. Color reversal and color cross-talk correction yield a series of three frozen-flow images that can be used for further analysis, e.g., determining the droplet velocity by particle tracking. Three example flows are presented, solid particles suspended in water, the penetrating front of a gasoline direct-injection spray, and the liquid break-up region of an "air-assisted" nozzle. Because of the shadowgraphic arrangement, long path lengths through scattering media lower image contrast, while visualization of phase boundaries with high resolution is a strength of this method. Apart from a pulse-and-delay generator, the overall system cost is very low.

Experimental design for a basic mixture on a fluorinated packing. The effect of composition of the mobile phase.

PubMed

Wang, Y; Harrison, M; Clark, B J

2006-02-10

An optimization methodology is introduced for investigating the separation and the retention behavior of analytes on a new fluorinated reversed-phase packing. Ten basic compounds were selected as test probes to study the predictive models developed by using SPSS and MATLAB software. A two-level orthogonal array design (OAD) was used to extract significant parameters. The significant factors were optimised using a central composite design to obtain the quadratic relationship between the dependent and the independent variables. Using this strategy, response surfaces were derived as the 3D and contour plots, and mathematical models were defined for the separation. The models had a satisfactory coefficient (R(2) > 0.97, n = 16). For the test compounds, the best separation condition was: MeCN/30 mM phosphate buffer pH 7.1(55.5:44.5, v/v) and 10 basic solutes were resolved in 22 min. The significant influence of the concentration of buffer shows that different mechanisms of separation for basic compounds on the fluorinated packing exist compared with a common ODS stationary phase.

Ku-Band Traveling Wave Slot Array Using Simple Scanning Control

NASA Technical Reports Server (NTRS)

Host, Nicholas K.; Chen, Chi-Chih; Volakis, John L.; Miranda, Felix A.

2015-01-01

This poster introduces a feeding concept aimed at simplifying the backend (phase shifters) of traditional phased arrays. As an alternative to traditional phased arrays, we employ a traveling wave array (TWA) using a single feedline whose propagation constant is controlled via a single, small mechanical movement without a need for phase shifters to enable scanning. Specifically, a dielectric plunger is positioned within a parallel plate waveguide (PPW) transmission line (TL) that feeds the TWA. By adjusting the position of the dielectric plunger within the PPW feeding the TWA, beam steering is achieved. A 20-element array is designed at 13 gigaherz shown to give stable realized gain across the angular range of minus 25 degrees less than or equal to theta and less than or equal to 25 degrees. A proof of concept array is fabricated and measured to demonstrate and validate the concept's operation.

Ku-Band Traveling Wave Slot Array Using Simple Scanning Control

NASA Technical Reports Server (NTRS)

Host, Nicholas K.; Chen, Chi-Chih; Volakis, John L.; Miranda, Felix A.

2015-01-01

This paper introduces a feeding concept aimed at simplifying the backend (phase shifters) of traditional phased arrays. As an alternative to traditional phased arrays, we employ a traveling wave array (TWA) using a single feedline whose propagation constant is controlled via a single, small mechanical movement without a need for phase shifters to enable scanning. Specifically, a dielectric plunger is positioned within a parallel plate waveguide (PPW) transmission line (TL) that feeds the TWA. By adjusting the position of the dielectric plunger within the PPW feeding the TWA, beam steering is achieved. A 20 element array is designed at 13GHz shown to give stable realized gain across the angular range of -25 deg. less than or equal to theta less than or equal to 25 deg. A proof of concept array is fabricated and measured to demonstrate and validate the concept's operation.

Large improvement of the electrical impedance of imaging and high-intensity focused ultrasound (HIFU) phased arrays using multilayer piezoelectric ceramics coupled in lateral mode.

PubMed

Song, Junho; Lucht, Benjamin; Hynynen, Kullervo

2012-07-01

With a change in phased-array configuration from one dimension to two, the electrical impedance of the array elements is substantially increased because of their decreased width (w)-to-thickness (t) ratio. The most common way to compensate for this impedance increase is to employ electrical matching circuits at a high cost of fabrication complexity and effort. In this paper, we introduce a multilayer lateral-mode coupling method for phased-array construction. The direct comparison showed that the electrical impedance of a single-layer transducer driven in thickness mode is 1/(n²(1/(w/t))²) times that of an n-layer lateral mode transducer. A large reduction of the electrical impedance showed the impact and benefit of the lateral-mode coupling method. A one-dimensional linear 32-element 770-kHz imaging array and a 42-element 1.45-MHz high-intensity focused ultrasound (HIFU) phased array were fabricated. The averaged electrical impedances of each element were measured to be 58 Ω at the maximum phase angle of -1.2° for the imaging array and 105 Ω at 0° for the HIFU array. The imaging array had a center frequency of 770 kHz with an averaged -6-dB bandwidth of approximately 52%. For the HIFU array, the averaged maximum surface acoustic intensity was measured to be 32.8 W/cm² before failure.