Structural aspects of inotropic bipyridine binding. Crystal structure determination to 1.9 A of the human serum transthyretin-milrinone complex.

Science.gov (United States)

Wojtczak, A; Luft, J R; Cody, V

1993-03-25

The crystal structure of human transthyretin (TTR) complexed with milrinone (2-methyl-5-cyano-3,4'-bipyridin-6(1H)-one), a positive inotropic cardiac agent, has been refined to R = 17.4% for 8-1.9-A resolution data. This report provides the first detailed description of protein interactions for an inotropic bipyridine agent which is an effective thyroid hormone binding competitor to transthyretin. Milrinone is bound along the 2-fold axis in the binding site with its substituted pyridone ring located deep within the channel of the two identical binding domains of the TTR tetramer. In this orientation the 5-cyano group occupies the same site as the 3'-iodine in the TTR complex with 3,3'-diiodothyronine (Wojtczak, A., Luft, J., and Cody, V. (1992) J. Biol. Chem. 267, 353-357), which is 3.5 A deeper in the channel than thyroxine (Blake, C. C. F., and Oately, S. J., (1977) Nature 268, 115-120). These structural results confirm computer modeling studies of milrinone structural homology with thyroxine and its TTR binding interactions and explain the effectiveness of milrinone competition for thyroxine binding to TTR. To understand the weaker binding affinity of the parent inotropic drug, amrinone (5-amino-3,4'-bipyridin-6(1H)-one), modeling studies of its TTR binding were carried out which indicate that the 5-amino group cannot participate in strong interactions with TTR and the lack of the 2-methyl further weakens amrinone binding.

Trapping of palindromic ligands within native transthyretin prevents amyloid formation

OpenAIRE

Kolstoe, Simon E.; Mangione, Palma P.; Bellotti, Vittorio; Taylor, Graham W.; Tennent, Glenys A.; Deroo, Stéphanie; Morrison, Angus J.; Cobb, Alexander J. A.; Coyne, Anthony; McCammon, Margaret G.; Warner, Timothy D.; Mitchell, Jane; Gill, Raj; Smith, Martin D.; Ley, Steven V.

2010-01-01

Transthyretin (TTR) amyloidosis is a fatal disease for which new therapeutic approaches are urgently needed. We have designed two palindromic ligands, 2,2'-(4,4'-(heptane-1,7-diylbis(oxy))bis(3,5-dichloro-4,1-phenylene)) bis(azanediyl)dibenzoic acid (mds84) and 2,2'-(4,4'-(undecane-1,11-diylbis(oxy))bis(3,5-dichloro-4,1-phenylene)) bis(azanediyl)dibenzoic acid (4ajm15), that are rapidly bound by native wild-type TTR in whole serum and even more avidly by amyloidogenic TTR variants. One to one...

A New Serum Biomarker for Lung Cancer - Transthyretin

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Liyun LIU

2009-04-01

Full Text Available Background and objective Lung cancer is the leading cause of cancer death worldwide and very few specific biomarkers could be used in clinical diagnosis at present. The aim of this study is to find novel potential serum biomarkers for lung cancer using Surface Enhanced Laser Desorption/Ionization (SELDI technique. Methods Serumsample of 227 cases including 146 lung cancer, 13 pneumonia, 28 tuberculous pleurisy and 40 normal individuals were analyzed by CM10 chips. The candidate biomarkers were identified by ESI/MS-MS and database searching, and further confirmed by immunoprecipitation. The same sets of serum sample from all groups were re-measured by ELISA assay. Results Three protein peaks with the molecular weight 13.78 kDa, 13.90 kDa and 14.07 kDa were found significantlydecreased in lung cancer serum compared to the other groups and were all automatically selected as specific biomarkers by Biomarker Wizard software. The candidate biomarkers obtained from 1-D SDS gel bands by matching the molecular weight with peaks on CM10 chips were identified by Mass spectrometry as the native transthyretin (nativeTTR, cysTTR and glutTTR, and the identity was further validated by immunoprecipitation using commercial TTR antibodies. Downregulated of TTR was found in both ELISA and SELDI analysis. Conclusion TTRs acted as the potentially useful biomarkers for lung cancer by SELDI technique.

Disruption of thyroid hormone binding to sea bream recombinant transthyretin by ioxinyl and polybrominated diphenyl ethers.

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Morgado, Isabel; Hamers, Timo; Van der Ven, Leo; Power, D M

2007-08-01

A number of chemicals released into the environment share structural similarity to the thyroid hormones (THs), thyroxine (T(4)) and triiodothyronine (T(3)) and it is thought that they may interfere with the thyroid axis and behave as endocrine disruptors (EDs). One of the ways by which such environmental contaminants may disrupt the TH axis is by binding to TH transporter proteins. Transthyretin (TTR) is one of the thyroid hormone binding proteins responsible for TH transport in the blood. TTR forms a stable tetramer that binds both T(4) and T(3) and in fish it is principally synthesized in the liver but is also produced by the brain and intestine. In the present study, we investigate the ability of some chemicals arising from pharmaceutical, industrial or agricultural production and classified as EDs, to compete with [I(125)]-T(3) for sea bream recombinant TTR (sbrTTR). Ioxinyl, a common herbicide and several polybrominated diphenyl ethers were strong inhibitors of [I(125)]-T(3) binding to TTR and some showed even greater affinity than the natural ligand T(3). The TTR competitive binding assay developed offers a quick and effective tool for preliminary risk assessment of chemicals which may disrupt the thyroid axis in teleost fish inhabiting vulnerable aquatic environments.

Neuron-derived transthyretin modulates astrocytic glycolysis in hormone-independent manner

OpenAIRE

Zawiślak, Alina; Jakimowicz, Piotr; McCubrey, James A.; Rakus, Dariusz

2017-01-01

It has been shown that neurons alter the expression of astrocytic metabolic enzymes by secretion of until now unknown molecule(s) into extracellular fluid. Here, we present evidence that neuron-derived transthyretin (TTR) stimulates expression of glycolytic enzymes in astrocytes which is reflected by an increased synthesis of ATP. The action of TTR is restricted to regulatory enzymes of glycolysis: phosphofructokinase P (PFKP) and pyruvate kinase M1/M2 isoforms (PKM1/2). The regulation of PFK...

Unwanted road to anaemia in transthyretin familial amyloid polyneuropathy may continue irrespective of tafamidis treatment.

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Ikeda, Tokunori; Masuda, Teruaki; Ueda, Mitsuharu; Yamashita, Taro; Misumi, Yohei; Shinriki, Satoru; Ando, Yukio

2018-01-01

Background This retrospective longitudinal study was performed to determine whether tafamidis treatment leads to improvements in commonly used blood data for transthyretin familial amyloid polyneuropathy (TTR-FAP). Methods Commonly used blood data (complete blood count [including a haemogram], total protein, albumin, blood urea nitrogen, creatinine, aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase, lactate dehydrogenase, γ-glutamyl transpeptidase, total bilirubin [T-Bil], creatine kinase, choline esterase, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, estimated glomerular filtration rate [eGFR], serum amyloid A protein, TTR, haemoglobin A1c, free triiodothyronine [FT3] and free thyroxine [FT4]) were investigated in 33 TTR-FAP patients. These values included longitudinal data at three time points: six months before or after tafamidis treatment and one year after tafamidis treatment. Longitudinal changes in each blood item were examined using a linear mixed model, adjusting for age at starting tafamidis, sex, TTR-FAP stage and value before tafamidis treatment. Results Our results show elevated TTR concentrations after tafamidis treatment. In contrast, haemoglobin, mean corpuscular haemoglobin, mean corpuscular haemoglobin concentration, mean platelet volume, platelet distribution width, T-Bil, eGFR, FT3 and FT4, gradually decreased through a reference range. There were no characteristic observations in any other items. TTR binds to thyroid hormone; therefore, FT3 and FT4 decreased in inverse proportion to increased TTR concentrations. Conclusion Unfortunately, progression to anaemia may occur regardless of tafamidis treatment. Because anaemia is sometimes present in TTR-FAP, attention should be paid to longitudinal changes in commonly used blood data, irrespective of tafamidis treatment.

Transthyretin Ala36Pro mutation in a Chinese pedigree of familial transthyretin amyloidosis with elevated vitreous and serum vascular endothelial growth factor.

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Zou, Xuan; Dong, Fangtian; Zhang, Shuying; Tian, Rong; Sui, Ruifang

2013-05-01

The familial transthyretin (TTR) amyloidosis (FTA) demonstrates variable penetrance of clinical features associated with mutations in the plasma thyroid hormone-binding protein TTR gene. The purpose of this study was to assess the ocular features, to analyze vitreous and serum vascular endothelial growth factor (VEGF) levels, and to identify the genetic defect in a Chinese family with TTR FTA. The pedigree of interest was a three-generation family with eleven members. The primary ocular signs were vitreous opacities, beginning from the third or fourth decade, accompanied by retinal vasculitis, hemorrhages, and widespread pinpoint deposits in the peripheral retina. Two patients underwent vitrectomy with marked improvement of visual acuity postoperatively. Vitreous and serum samples for VEGF were analyzed with an enzyme-linked immunosorbent assay (ELISA). Forty-eight healthy adult volunteers were enrolled as a control group for the analysis of serum VEGF. Eight subjects who underwent vitrectomy for a macular epiretinal membrane or macular hole were enrolled as control for the analysis of vitreous VEGF. Both serum and vitreous VEGF levels of patients were raised compared to that of controls. Venous blood was collected from family members and the genomic DNA was extracted. All exons and exon-intron boundaries of the TTR gene were sequenced. A previously-described pathogenic transversion in exon 2 (c.G106C, p.Ala36Pro) was identified. Within this family eight individuals were confirmed as affected. In conclusion, a Chinese family with TTR Ala36Pro associated FTA is characterized by early ocular involvement. Widespread pinpoint lesions indicate RPE lesions caused by TTR deposition. FTA is associated with increased VEGF levels, both in serum and vitreous. Copyright © 2013 Elsevier Ltd. All rights reserved.

Microheterogeneity of transthyretin in serum and ascitic fluid of ovarian cancer patients

International Nuclear Information System (INIS)

Gericke, Beate; Raila, Jens; Sehouli, Jalid; Haebel, Sophie; Könsgen, Dominique; Mustea, Alexander; Schweigert, Florian J

2005-01-01

Transthyretin (TTR), a traditional biomarker for nutritional and inflammatory status exists in different molecular variants of yet unknown importance. A truncated form of TTR has recently been described to be part of a set of biomarkers for the diagnosis of ovarian cancer. The main aim of the study was therefore to characterize differences in microheterogeneity between ascitic fluid and plasma of women affected with ovarian cancer and to evaluate the tumor site as the possible source of TTR. Subjects were 48 women with primary invasive epithelial ovarian cancer or recurrent ovarian carcinoma. The control group consisted of 20 postmenopausal women. TTR and retinol-binding protein (RBP) levels were measured by enzyme-linked immunoassay (ELISA) and C-reactive protein (CRP) levels by a high-sensitivity latex particle turbidimetric assay. The molecular heterogeneity of TTR was analysed using immunoprecipitation and matrix-associated laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Presence of TTR in tumor tissue was determined with indirect peroxidase immunostaining. TTR and RBP (μg/ml) levels in serum were 148.5 ± 96.7 and 22.5 ± 14.8 in affected women compared to 363.3 ± 105.5 and 55.8 ± 9.3 in healthy postmenopausal women (p < 0.01). In ascitic fluid, levels were 1.02 ± 0.24 and 4.63 ± 1.57 μg/ml, respectively. The mean levels of TTR and RBP in serum showed a tendency to decrease with the severity of the disease and were lower in affected women whose CRP levels were > 40 mg/ml (p = 0.08 for TTR; p < 0.05 for RBP). No differences in TTR microheterogeneity were observed between TTR isolated from serum of affected and healthy women or from ascitic fluid. TTR occurred rather consistently in four variants. Mass signals were at 13758 ± 7, 13876 ± 13 (greatest intensity), 13924 ± 21 and 14062 ± 24 Da, representing native, S-cysteinylated, S-cysteinglycinylated and glutathionylated TTR, respectively. Serum of healthy and affected women

Trapping of palindromic ligands within native transthyretin prevents amyloid formation

Science.gov (United States)

Kolstoe, Simon E.; Mangione, Palma P.; Bellotti, Vittorio; Taylor, Graham W.; Tennent, Glenys A.; Deroo, Stéphanie; Morrison, Angus J.; Cobb, Alexander J. A.; Coyne, Anthony; McCammon, Margaret G.; Warner, Timothy D.; Mitchell, Jane; Gill, Raj; Smith, Martin D.; Ley, Steven V.; Robinson, Carol V.; Wood, Stephen P.; Pepys, Mark B.

2010-01-01

Transthyretin (TTR) amyloidosis is a fatal disease for which new therapeutic approaches are urgently needed. We have designed two palindromic ligands, 2,2'-(4,4'-(heptane-1,7-diylbis(oxy))bis(3,5-dichloro-4,1-phenylene)) bis(azanediyl)dibenzoic acid (mds84) and 2,2'-(4,4'-(undecane-1,11-diylbis(oxy))bis(3,5-dichloro-4,1-phenylene)) bis(azanediyl)dibenzoic acid (4ajm15), that are rapidly bound by native wild-type TTR in whole serum and even more avidly by amyloidogenic TTR variants. One to one stoichiometry, demonstrable in solution and by MS, was confirmed by X-ray crystallographic analysis showing simultaneous occupation of both T4 binding sites in each tetrameric TTR molecule by the pair of ligand head groups. Ligand binding by native TTR was irreversible under physiological conditions, and it stabilized the tetrameric assembly and inhibited amyloidogenic aggregation more potently than other known ligands. These superstabilizers are orally bioavailable and exhibit low inhibitory activity against cyclooxygenase (COX). They offer a promising platform for development of drugs to treat and prevent TTR amyloidosis. PMID:21059958

Thermodynamic stability and denaturation kinetics of a benign natural transthyretin mutant identified in a Danish kindred

DEFF Research Database (Denmark)

Jensen, Minna Grønning; Campos, Raul I.; Fagerberg, Christina

2011-01-01

The disease phenotype of transthyretin (TTR) is dramatically influenced by single point mutations in the TTR gene. Herein, we report on a novel mutation D99N (Asp99Asn) in TTR found in a Danish kindred. None of the family members carrying this mutation have so far shown any clinical signs...... of amyloidosis. One carrier found compound heterozygous for TTR D99N and L111M (Leu111Met) associated with cardiac amyloid is asymptomatic (42 years). Disease severity can often be linked to both the kinetics of fibril formation and the degree of destabilisation of the native state. In this study, we show...

Hereditary Transthyretin Amyloidosis in Eight Chinese Families

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Ling-Chao Meng

2015-01-01

Full Text Available Background: Mutations of transthyretin (TTR cause the most common type of autosomal-dominant hereditary systemic amyloidosis, which occurs worldwide. To date, more and more mutations in the TTR gene have been reported. Some variations in the clinical presentation are often observed in patients with the same mutation or the patients in the same family. The purpose of this study was to find out the clinicopathologic and genetic features of Chinese patients with hereditary TTR amyloidosis. Methods: Clinical and necessary examination materials were collected from nine patients of eight families with hereditary TTR amyloidosis at Peking University First Hospital from January 2007 to November 2014. Sural nerve biopsies were taken for eight patients and skin biopsies were taken in the calf/upper arm for two patients, for light and electron microscopy examination. The TTR genes from the nine patients were analyzed. Results: The onset age varied from 23 to 68 years. The main manifestations were paresthesia, proximal and/or distal weakness, autonomic dysfunction, cardiomyopathy, vitreous opacity, hearing loss, and glossohypertrophia. Nerve biopsy demonstrated severe loss of myelinated fibers in seven cases and amyloid deposits in three. One patient had skin amyloid deposits which were revealed from electron microscopic examination. Genetic analysis showed six kinds of mutations of TTR gene, including Val30Met, Phe33Leu, Ala36Pro, Val30Ala, Phe33Val, and Glu42Gly in exon 2. Conclusions: Since the pathological examinations of sural nerve were negative for amyloid deposition in most patients, the screening for TTR mutations should be performed in all the adult patients, who are clinically suspected with hereditary TTR amyloidosis.

Plasma transthyretin. Tissue sites of degradation and turnover in the rat

International Nuclear Information System (INIS)

Makover, A.; Moriwaki, H.; Ramakrishnan, R.; Saraiva, M.J.; Blaner, W.S.; Goodman, D.S.

1988-01-01

Transthyretin (TTR) is involved in the plasma transport of both retinol and thyroid hormones. TTR is synthesized in the liver and choroid plexus, and in small amounts in several other tissues. A study was conducted to determine the tissue sites of degradation and turnover of TTR in the rat. The study employed TTR labeled with tyramine cellobiose (TC) and the trapped ligand method. Samples of purified rat TTR were labeled either with 125I-TC or directly with 131I. A mixture of the two labeled TTRs was injected intravenously into six rats. Blood samples were collected via a venous catheter for kinetic (turnover) analysis. After 24 or 48 h, the rats were killed, and 23 different tissues/organs were assayed as possible sites of TTR degradation. Derivatization of TTR with TC did not appreciably alter TTR plasma kinetics. Plasma turnover data were best fit by a three-pool model. The mean fractional turnover of plasma TTR was 0.15/h, and of total body TTR 0.04/h. The major sites of TTR degradation were the liver (36-38% of total body TTR degradation, almost all in hepatocytes), muscle (12-15%), and skin (8-10%). Tissues that were sites of 1-8% of body TTR degradation included kidneys, adipose tissue, testes, and the gastrointestinal tract. Less than 1% of total TTR degradation occurred in the other tissues examined. A second study was conducted in which labeled TTR was injected intraventricularly into the cerebrospinal fluid in order to explore the degradation of TTR of choroid plexus origin. The kinetics of the appearance and disappearance of such labeled TTR in plasma were physiologically reasonable, with an estimated turnover of cerebrospinal fluid TTR of the order of 0.33/h. The major tissue sites of degradation of labeled TTR injected into cerebrospinal fluid and into plasma were approximately the same

Identification of Transthyretin Fibril Formation Inhibitors Using Structure-Based Virtual Screening.

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Ortore, Gabriella; Martinelli, Adriano

2017-08-22

Transthyretin (TTR) is the primary carrier for thyroxine (T 4 ) in cerebrospinal fluid and a secondary carrier in blood. TTR is a stable homotetramer, but certain factors, genetic or environmental, could promote its degradation to form amyloid fibrils. A docking study using crystal structures of wild-type TTR was planned; our aim was to design new ligands that are able to inhibit TTR fibril formation. The computational protocol was thought to overcome the multiple binding modes of the ligands induced by the peculiarity of the TTR binding site and by the pseudosymmetry of the site pockets, which generally weaken such structure-based studies. Two docking steps, one that is very fast and a subsequent step that is more accurate, were used to screen the Aldrich Market Select database. Five compounds were selected, and their activity toward inhibiting TTR fibril formation was assessed. Three compounds were observed to be actives, two of which have the same potency as the positive control, and the other was found to be a promising lead compound. These results validate a computational protocol that is able to archive information on the key interactions between database compounds and TTR, which is valuable for supporting further studies. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transthyretin protects against A-beta peptide toxicity by proteolytic cleavage of the peptide: a mechanism sensitive to the Kunitz protease inhibitor.

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Rita Costa

Full Text Available Alzheimer's disease (AD is a neurodegenerative disorder characterized by the deposition of amyloid beta-peptide (A-Beta in the brain. Transthyretin (TTR is a tetrameric protein of about 55 kDa mainly produced in the liver and choroid plexus of the brain. The known physiological functions of TTR are the transport of thyroid hormone T(4 and retinol, through binding to the retinol binding protein. TTR has also been established as a cryptic protease able to cleave ApoA-I in vitro. It has been described that TTR is involved in preventing A-Beta fibrilization, both by inhibiting and disrupting A-Beta fibrils, with consequent abrogation of toxicity. We further characterized the nature of the TTR/A-Beta interaction and found that TTR, both recombinant or isolated from human sera, was able to proteolytically process A-Beta, cleaving the peptide after aminoacid residues 1, 2, 3, 10, 13, 14,16, 19 and 27, as determined by mass spectrometry, and reversed phase chromatography followed by N-terminal sequencing. A-Beta peptides (1-14 and (15-42 showed lower amyloidogenic potential than the full length counterpart, as assessed by thioflavin binding assay and ultrastructural analysis by transmission electron microscopy. A-Beta cleavage by TTR was inhibited in the presence of an alphaAPP peptide containing the Kunitz Protease Inhibitor (KPI domain but not in the presence of the secreted alphaAPP derived from the APP isoform 695 without the KPI domain. TTR was also able to degrade aggregated forms of A-Beta peptide. Our results confirmed TTR as a protective molecule in AD, and prompted A-Beta proteolysis by TTR as a protective mechanism in this disease. TTR may prove to be a useful therapeutic agent for preventing or retarding the cerebral amyloid plaque formation implicated in AD pathology.

The proteome response to amyloid protein expression in vivo.

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Ricardo A Gomes

Full Text Available Protein misfolding disorders such as Alzheimer, Parkinson and transthyretin amyloidosis are characterized by the formation of protein amyloid deposits. Although the nature and location of the aggregated proteins varies between different diseases, they all share similar molecular pathways of protein unfolding, aggregation and amyloid deposition. Most effects of these proteins are likely to occur at the proteome level, a virtually unexplored reality. To investigate the effects of an amyloid protein expression on the cellular proteome, we created a yeast expression system using human transthyretin (TTR as a model amyloidogenic protein. We used Saccharomyces cerevisiae, a living test tube, to express native TTR (non-amyloidogenic and the amyloidogenic TTR variant L55P, the later forming aggregates when expressed in yeast. Differential proteome changes were quantitatively analyzed by 2D-differential in gel electrophoresis (2D-DIGE. We show that the expression of the amyloidogenic TTR-L55P causes a metabolic shift towards energy production, increased superoxide dismutase expression as well as of several molecular chaperones involved in protein refolding. Among these chaperones, members of the HSP70 family and the peptidyl-prolyl-cis-trans isomerase (PPIase were identified. The latter is highly relevant considering that it was previously found to be a TTR interacting partner in the plasma of ATTR patients but not in healthy or asymptomatic subjects. The small ubiquitin-like modifier (SUMO expression is also increased. Our findings suggest that refolding and degradation pathways are activated, causing an increased demand of energetic resources, thus the metabolic shift. Additionally, oxidative stress appears to be a consequence of the amyloidogenic process, posing an enhanced threat to cell survival.

Characterization of little skate (Leucoraja erinacea) recombinant transthyretin: Zinc-dependent 3,3',5-triiodo-l-thyronine binding.

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Suzuki, Shunsuke; Kasai, Kentaro; Yamauchi, Kiyoshi

2015-01-01

Transthyretin (TTR) diverged from an ancestral 5-hydroxyisourate hydrolase (HIUHase) by gene duplication at some early stage of chordate evolution. To clarify how TTR had participated in the thyroid system as an extracellular thyroid hormone (TH) binding protein, TH binding properties of recombinant little skate Leucoraja erinacea TTR was investigated. At the amino acid level, skate TTR showed 37-46% identities with the other vertebrate TTRs. Because the skate TTR had a unique histidine-rich segment in the N-terminal region, it could be purified by Ni-affinity chromatography. The skate TTR was a 46-kDa homotetramer of 14.5kDa subunits, and had one order of magnitude higher affinity for 3,3',5-triiodo-l-thyronine (T3) and some halogenated phenols than for l-thyroxine. However, the skate TTR had no HIUHase activity. Ethylenediaminetetraacetic acid (EDTA) treatment inhibited [(125)I]T3 binding activity whereas the addition of Zn(2+) to the EDTA-treated TTR recovered [(125)I]T3 binding activity in a Zn(2+) concentration-dependent manner. Scatchard analysis revealed the presence of two classes of binding site for T3, with dissociation constants of 0.24 and 17nM. However, the high-affinity sites were completely abolished with 1mM EDTA, whereas the remaining low-affinity sites decreased binding capacity. The number of zinc per TTR was quantified to be 4.5-6.3. Our results suggest that skate TTR has tight Zn(2+)-binding sites, which are essential for T3 binding to at least the high-affinity sites. Zn(2+) binding to the N-terminal histidine-rich segment may play an important role in acquisition or reinforcement of TH binding ability during early evolution of TTR. Copyright © 2015 Elsevier Inc. All rights reserved.

Mobile and cordless telephones, serum transthyretin and the blood-cerebrospinal fluid barrier: a cross-sectional study

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Carlberg Michael

2009-04-01

Full Text Available Abstract Background Whether low-intensity radiofrequency radiation damages the blood-brain barrier has long been debated, but little or no consideration has been given to the blood-cerebrospinal fluid barrier. In this cross-sectional study we tested whether long-term and/or short-term use of wireless telephones was associated with changes in the serum transthyretin level, indicating altered transthyretin concentration in the cerebrospinal fluid, possibly reflecting an effect of radiation. Methods One thousand subjects, 500 of each sex aged 18–65 years, were randomly recruited using the population registry. Data on wireless telephone use were assessed by a postal questionnaire and blood samples were analyzed for serum transthyretin concentrations determined by standard immunonephelometric techniques on a BN Prospec® instrument. Results The response rate was 31.4%. Logistic regression of dichotomized TTR serum levels with a cut-point of 0.31 g/l on wireless telephone use yielded increased odds ratios that were statistically not significant. Linear regression of time since first use overall and on the day that blood was withdrawn gave different results for males and females: for men significantly higher serum concentrations of TTR were seen the longer an analogue telephone or a mobile and cordless desktop telephone combined had been used, and in contrast, significantly lower serum levels were seen the longer an UMTS telephone had been used. Adjustment for fractions of use of the different telephone types did not modify the effect for cumulative use or years since first use for mobile telephone and DECT, combined. For women, linear regression gave a significant association for short-term use of mobile and cordless telephones combined, indicating that the sooner blood was withdrawn after the most recent telephone call, the higher the expected transthyretin concentration. Conclusion In this hypothesis-generating descriptive study time since first

Transthyretin-binding activity of contaminants in blood from polar bear (Ursus maritimus) cubs.

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Bytingsvik, Jenny; Simon, Eszter; Leonards, Pim E G; Lamoree, Marja; Lie, Elisabeth; Aars, Jon; Derocher, Andrew E; Wiig, Oystein; Jenssen, Bjørn M; Hamers, Timo

2013-05-07

We determined the transthyretin (TTR)-binding activity of blood-accumulating contaminants in blood plasma samples of approximately 4-months-old polar bear (Ursus maritimus) cubs from Svalbard sampled in 1998 and 2008. The TTR-binding activity was measured as thyroxine (T4)-like equivalents (T4-EQMeas). Our findings show that the TTR-binding activity related to contaminant levels was significantly lower (45%) in 2008 than in 1998 (mean ± standard error of mean: 1998, 2265 ± 231 nM; 2008, 1258 ± 170 nM). Although we cannot exclude a potential influence of between-year differences in capture location and cub body mass, our findings most likely reflect reductions of TTR-binding contaminants or their precursors in the arctic environment (e.g., polychlorinated biphenyls [PCBs]). The measured TTR-binding activity correlated positively with the cubs' plasma levels of hydroxylated PCBs (OH-PCBs). No such association was found between TTR-binding activity and the plasma levels of perfluoroalkyl substances (PFASs). The OH-PCBs explained 60 ± 7% and 54 ± 4% of the TTR-binding activity in 1998 and 2008, respectively, and PFASs explained ≤1.2% both years. Still, almost half the TTR-binding activity could not be explained by the contaminants we examined. The considerable levels of TTR-binding contaminants warrant further effect directed analysis (EDA) to identify the contaminants responsible for the unexplained part of the observed TTR-binding activity.

Establishing and validating the fluorescent amyloid ligand h-FTAA (heptamer formyl thiophene acetic acid) to identify transthyretin amyloid deposits in carpal tunnel syndrome.

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Hahn, Katharina; Nilsson, K Peter R; Hammarström, Per; Urban, Peter; Meliss, Rolf Rüdiger; Behrens, Hans-Michael; Krüger, Sandra; Röcken, Christoph

2017-06-01

Transthyretin-derived (ATTR) amyloidosis is a frequent finding in carpal tunnel syndrome. We tested the following hypotheses: the novel fluorescent amyloid ligand heptameric formic thiophene acetic acid (h-FTAA) has a superior sensitivity for the detection of amyloid compared with Congo red-staining; Amyloid load correlates with patient gender and/or patient age. We retrieved 208 resection specimens obtained from 184 patients with ATTR amyloid in the carpal tunnel. Serial sections were stained with Congo red, h-FTAA and an antibody directed against transthyretin (TTR). Stained sections were digitalized and forwarded to computational analyses. The amount of amyloid was correlated with patient demographics. Amyloid stained intensely with h-FTAA and an anti-TTR-antibody. Congo red-staining combined with fluorescence microscopy was significantly less sensitive than h-FTAA-fluorescence and TTR-immunostaining: the highest percentage area was found in TTR-immunostained sections, followed by h-FTAA and Congo red. The Pearson correlation coefficient was .8 (Congo red vs. h-FTAA) and .9 (TTR vs. h-FTAA). Amyloid load correlated with patient gender, anatomical site and patient age. h-FTAA is a highly sensitive method to detect even small amounts of ATTR amyloid in the carpal tunnel. The staining protocol is easy and h-FTAA may be a much more sensitive procedure to detect amyloid at an earlier stage.

Transthyretin as a potential CSF biomarker for Alzheimer's disease and dementia with Lewy bodies: effects of treatment with cholinesterase inhibitors

DEFF Research Database (Denmark)

Schultz, K; Nilsson, K; Nielsen, Jørgen Erik

2010-01-01

BACKGROUND: Previous studies have indicated that transthyretin (TTR) levels in cerebrospinal fluid (CSF) are altered in depression and dementia. The present study aimed to investigate whether CSF TTR can be used to discriminate between patients with Alzheimer's disease (AD) and patients...... with dementia with Lewy bodies (DLB) with or without medication, as well as to reveal whether CSF TTR correlates with depression in dementia. METHODS: CSF samples from 59 patients with AD, 13 patients with DLB and 13 healthy controls were collected, and biochemical analysis was performed. Subjects were assessed...... for the presence of depression. RESULTS: No significant differences in CSF TTR were found between AD, DLB, and control subjects or between depressed and non-depressed dementia patients. Interestingly, we found a significant reduction in CSF TTR (14%) in AD patients who were medicated with cholinesterase inhibitors...

Negative effects of transthyretin in high myopic vitreous on diabetic retinopathy

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Jun Shao

2017-12-01

Full Text Available AIM: To analyze the relationship between vitreous transthyretin (TTR levels, high myopia and diabetic retinopathy (DR. METHODS: We selected 6722 individuals from the southern Jiangsu Province for diabetes and ophthalmic examinations. The TTR concentration in the vitreous of 50 patients with high myopia and diabetes, 50 patients with only DR, and 20 healthy controls were determined by ELISA. Key factors in Tie2 pathway in DR development including vascular endothecial growth factor (VEGF, Tie2, Angpt1, Angpt2, vascular endothelial growth factor receptor (VEGFR 1 and VEGFR2 were also detected by ELISA. RESULTS: The prevalence of DR in patients with diabetes and myopia [6.00 D, and diabetes without myopia were 11.1%, 2.5%, and 60.0%, respectively. The vitreous TTR concentration of patients with diabetes and high myopia was approximately 6.5- and 4.2-times higher than those of patients with DR and healthy controls, respectively (P<0.05. Following the vitreous TTR concentration, the levels of VEGF, Tie2, Angpt1, Angpt2, VEGFR1 and VEGFR2 in vitreous of diabetes and high myopia patients, DR patients and healthy controls were detected as dramatically fluctuated. CONCLUSION: The results suggest that TTR can affect the vitreous contents of key factors in Tie2 pathway for neovascularization, and there should be a protective association between abundant TTR levels in the vitreous of highly myopic patients and a decreased risk of DR.

Familial amyloidotic polyneuropathy with severe renal involvement in association with transthyretin Gly47Glu in Dutch, British and American-Finnish families

NARCIS (Netherlands)

Haagsma, EB; Hawkins, PN; Benson, MD; Lachmann, HJ; Bybee, A; Hazenberg, BPC

Familial amyloidotic polyneuropathy (FAP) is an autosomal dominant disorder associated with more than 80 different transthyretin (TTR) mutations. The clinical features of FAP are broad and variable, but knowledge of the pattern and natural history of disease associated with particular mutations

On-line immunoaffinity solid-phase extraction capillary electrophoresis mass spectrometry using Fab´antibody fragments for the analysis of serum transthyretin.

Science.gov (United States)

Pont, Laura; Benavente, Fernando; Barbosa, José; Sanz-Nebot, Victoria

2017-08-01

This paper describes an on-line immunoaffinity solid-phase extraction capillary electrophoresis mass spectrometry (IA-SPE-CE-MS) method using an immunoaffinity sorbent with Fab' antibody fragments (Fab'-IA) for the analysis of serum transthyretin (TTR), a homotetrameric protein (M r ~56,000) involved in different types of amyloidosis. The IA sorbent was prepared by covalent attachment of Fab' fragments obtained from a polyclonal IgG antibody against TTR to succinimidyl silica particles. The Fab'-IA-SPE-CE-MS methodology was first established analyzing TTR standard solutions. Under optimized conditions, repeatability and reproducibility were acceptable, the method was linear between 1 and 25µgmL -1 , limits of detection (LODs) were around 0.5µgmL -1 (50-fold lower than by CE-MS, ~25µgmL -1 ) and different TTR conformations were observed (folded and unfolded). The applicability of the developed method to screen for familial amyloidotic polyneuropathy type I (FAP-I), which is the most common hereditary systemic amyloidosis, was evaluated analyzing serum samples from healthy controls and FAP-I patients. For the analysis of sera, the most abundant proteins were precipitated with 5% (v/v) of phenol before Fab'-IA-SPE-CE-MS. The current method enhanced our previous results for the analysis of TTR using intact antibodies immobilized on magnetic beads. It allowed a slight improvement on LODs (2-fold), the detection of proteoforms found at lower concentrations and the preparation of microcartridges with extended durability. Copyright © 2017. Published by Elsevier B.V.

Synovial deposition of wild-type transthyretin-derived amyloid in knee joint osteoarthritis patients.

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Takanashi, Tetsuo; Matsuda, Masayuki; Yazaki, Masahide; Yamazaki, Hideshi; Nawata, Masashi; Katagiri, Yoshiki; Ikeda, Shu-Ichi

2013-09-01

To investigate histological features of deposited amyloid in the synovial tissue and its clinical significance in knee joint osteoarthritis (OA) patients. We prospectively enrolled 232 consecutive patients who underwent arthroplasty or total replacement of the knee joint for treatment of OA. Congo red staining and immunohistochemistry were performed in the synovial tissue obtained at surgery. When transthyretin (TTR)-derived amyloid was positive, we analyzed all 4 exons of the TTR gene using the direct DNA sequencing method in order to detect mutations. We analyzed 322 specimens in this study. Twenty-six specimens (8.1%) obtained from 21 patients (5 men and 16 women; mean, 79.0 ± 4.6 years) showed deposition of amyloid, which was positively stained with the anti-TTR antibody. Eighteen patients showed inhomogeneous accumulations of amyloid in the loose connective tissue under the synovial epithelia sometimes with nodule formation, while in the remaining three, small vessels in the adipose tissue were involved. Medical records of these patients revealed nothing remarkable in the clinical course, laboratory data or macroscopic intraarticular findings at surgery. No mutations were detectable in the TTR gene analysis. Wild-type TTR-derived amyloid may affect the synovial tissue as a result of long-term mechanical stress or as a part of senile systemic amyloidosis in approximately 8% of knee joint OA patients. No obvious clinical significance was found in synovial deposition of amyloid.

Sensory nerve degeneration in a mouse model mimicking early manifestations of familial amyloid polyneuropathy due to transthyretin Ala97Ser.

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Kan, H-W; Chiang, H; Lin, W-M; Yu, I-S; Lin, S-W; Hsieh, S-T

2018-02-08

Sensory nerve degeneration and consequent abnormal sensations are the earliest and most prevalent manifestations of familial amyloid polyneuropathy (FAP) due to amyloidogenic transthyretin (TTR). FAP is a relentlessly progressive degenerative disease of the peripheral nervous system. However, there is a lack of mouse models to replicate the early neuropathic manifestations of FAP. We established human TTR knock-in mice by replacing one allele of the mouse Ttr locus with human wild-type TTR (hTTR wt ) or human TTR with the A97S mutation (hTTR A97S ). Given the late onset of neuropathic manifestations in A97S-FAP, we investigated nerve pathology, physiology, and behavioural tests in these mice at two age points: the adult group (8 - 56 weeks) and the ageing group (> 104 weeks). In the adult group, nerve profiles, neurophysiology and behaviour were similar between hTTR wt and hTTR A97S mice. By contrast, ageing hTTR A97S mice showed small fibre neuropathy with decreased intraepidermal nerve fibre density and behavioural signs of mechanical allodynia. Furthermore, significant reductions in sural nerve myelinated nerve fibre density and sensory nerve action potential amplitudes in these mice indicated degeneration of large sensory fibres. The unaffected motor nerve physiology replicated the early symptoms of FAP patients, that is, sensory nerves were more vulnerable to mutant TTR than motor nerves. These results demonstrate that the hTTR A97S mouse model develops sensory nerve pathology and corresponding physiology mimicking A97S-FAP and provides a platform to develop new therapies for the early stage of A97S-FAP. © 2018 British Neuropathological Society.

Age-dependent cognitive dysfunction in untreated hereditary transthyretin amyloidosis.

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Martins da Silva, Ana; Cavaco, Sara; Fernandes, Joana; Samões, Raquel; Alves, Cristina; Cardoso, Márcio; Kelly, Jeffery W; Monteiro, Cecília; Coelho, Teresa

2018-02-01

Central nervous system (CNS) involvement in hereditary transthyretin (TTR) amyloidosis has been described in patients whose disease course was modified by liver transplant. However, cognitive dysfunction has yet to be investigated in those patients. Moreover, CNS involvement in untreated patients or asymptomatic mutation carriers remains to be studied. A series of 340 carriers of the TTRVal30Met mutation (180 symptomatic and 160 asymptomatic) underwent a neuropsychological assessment, which included the Dementia Rating Scale-2 (DRS-2), auditory verbal learning test, semantic fluency, phonemic fluency, and trail making test. Cognitive deficits were identified at the individual level, after adjusting the neuropsychological test scores for demographic characteristics (sex, age, and education), based on large national normative data. The presence of cognitive dysfunction was determined by deficit in DRS-2 and/or multiple cognitive domains. Participants were also screened for depression based on a self-report questionnaire. The frequency of cognitive dysfunction was higher (p = 0.003) in symptomatic (9%) than in asymptomatic (2%) carriers. Among older carriers (≥ 50 years), the frequency of cognitive dysfunction was higher (p hereditary TTR amyloidosis patients with peripheral polyneuropathy, even in the early stages of the disease.

Levels and distributions of organic pollutants in subtidal sediments from the Loire estuary: Are there any relationships with TTR-binding activity?

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Couderc, M.; Gandolfi, F.; Zalouk-Vergnoux, A.; Beyeler, N.; Malleret, L.; Ambidina, I.; Kamari, A.; Blanchet-Letrouvé, I.; Mouneyrac, C.; Hamers, T.; Poirier, L.

2016-12-01

The Loire estuary runs through important urban sites with shipping, industrial and agricultural activities, being the receptacle of diffusive pollutants comprising, a mixture of contaminants such as persistent organic pollutants (POPs). This work was set out to evaluate the occurrence of thyroid endocrine disruptors in sediments of this estuary. Sediments were collected in September 2012 and April 2013, in subtidal zones along the estuary. Targeted chemical analyses of five classes of pollutants, i.e. polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), polycyclic aromatic hydrocarbons (PAHs), alkylphenols (APs), and bisphenol A (BPA) were performed in sediment extracts. Extracts were further tested for their thyroid hormone (TH) disrupting potency to compete with TH for binding to its transporter protein transthyretin (TTR). The Haute-Indre site was characterized by a significant PAH contamination whereas Saint-Nazaire, Bellevue and Rezé would be particularly contaminated by PCBs. These observations could be linked to the different type of anthropogenic activities taking place close to these sites. Donges, Mindin and Paimboeuf were the sampling sites displaying the lowest contamination in PAHs, APs, PCBs and PBDEs. No inter-site difference could be observed for TTR-binding activity, which should be attributed to different compounds than the chemically analyzed compounds, as confirmed by PCA analyses. Furthermore, the TTR-binding potencies of the extracts were relatively low compared to data from literature. More investigations on the quantification of PCB and PBDE hydroxylated metabolites and other known endocrine disruptors such as pesticides or perfluorinated compounds could be considered, as well as bioassays highlighting other endocrine disrupting effects.

Genetic differences in the serum proteome of horses, donkeys and mules are detectable by protein profiling.

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Henze, Andrea; Aumer, Franziska; Grabner, Arthur; Raila, Jens; Schweigert, Florian J

2011-10-01

Although horses and donkeys belong to the same genus, their genetic characteristics probably result in specific proteomes and post-translational modifications (PTM) of proteins. Since PTM can alter protein properties, specific PTM may contribute to species-specific characteristics. Therefore, the aim of the present study was to analyse differences in serum protein profiles of horses and donkeys as well as mules, which combine the genetic backgrounds of both species. Additionally, changes in PTM of the protein transthyretin (TTR) were analysed. Serum protein profiles of each species (five animals per species) were determined using strong anion exchanger ProteinChips® (Bio-Rad, Munich, Germany) in combination with surface-enhanced laser desorption ionisation-time of flight MS. The PTM of TTR were analysed subsequently by immunoprecipitation in combination with matrix-assisted laser desorption ionisation-time of flight MS. Protein profiling revealed species-specific differences in the proteome, with some protein peaks present in all three species as well as protein peaks that were unique for donkeys and mules, horses and mules or for horses alone. The molecular weight of TTR of horses and donkeys differed by 30 Da, and both species revealed several modified forms of TTR besides the native form. The mass spectra of mules represented a merging of TTR spectra of horses and donkeys. In summary, the present study indicated that there are substantial differences in the proteome of horses and donkeys. Additionally, the results probably indicate that the proteome of mules reveal a higher similarity to donkeys than to horses.

Beyond genetic factors in familial amyloidotic polyneuropathy: protein glycation and the loss of fibrinogen's chaperone activity.

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Gonçalo da Costa

Full Text Available Familial amyloidotic polyneuropathy (FAP is a systemic conformational disease characterized by extracellular amyloid fibril formation from plasma transthyretin (TTR. This is a crippling, fatal disease for which liver transplantation is the only effective therapy. More than 80 TTR point mutations are associated with amyloidotic diseases and the most widely accepted disease model relates TTR tetramer instability with TTR point mutations. However, this model fails to explain two observations. First, native TTR also forms amyloid in systemic senile amyloidosis, a geriatric disease. Second, age at disease onset varies by decades for patients bearing the same mutation and some mutation carrier individuals are asymptomatic throughout their lives. Hence, mutations only accelerate the process and non-genetic factors must play a key role in the molecular mechanisms of disease. One of these factors is protein glycation, previously associated with conformational diseases like Alzheimer's and Parkinson's. The glycation hypothesis in FAP is supported by our previous discovery of methylglyoxal-derived glycation of amyloid fibrils in FAP patients. Here we show that plasma proteins are differentially glycated by methylglyoxal in FAP patients and that fibrinogen is the main glycation target. Moreover, we also found that fibrinogen interacts with TTR in plasma. Fibrinogen has chaperone activity which is compromised upon glycation by methylglyoxal. Hence, we propose that methylglyoxal glycation hampers the chaperone activity of fibrinogen, rendering TTR more prone to aggregation, amyloid formation and ultimately, disease.

Experience of TTR-1 decommissioning

International Nuclear Information System (INIS)

Kato, Hiroaki; Nobuoka, Yoshishige; Yoshimura, Yukio; Homma, Hitoshi; Nakai, Masaru

2005-01-01

Toshiba Training Reactor-1 (TTR-1) was planned for improvement of technical level from the standpoint of nuclear reactor manufacturer, training of a nuclear engineer, and research of nuclear physics, radiochemistry, radiation shielding and others. TTR-1 was permitted for construction in May 1960, attained at the first criticality in March 1962 and has continued to operate over 40 years. TTR-1 was permanently shut down in March 2001, accomplishing the planned target. From the initial criticality to the shut down, total operating time amounts to 15,300 hours and 31 MWds. Decommissioning plan was submitted to the Ministry of Education, Culture, Sports, Science and Technology on August 8, 2001 and dismantling work was started. The spent fuel was transported outside the laboratory, and the first phase and the second phase dismantling work were completed at the end of February 2004. Some of the reactor equipments continue maintaining their performance, and waste materials generated from dismantling work are under the state of managed storage, until disposal of the dismantling radioactive waste becomes clear, when the third phase of dismantling work will be started. At the end of the third phase work, all the TTR-1 equipments are dismantled and all waste materials are removed from TTR-1, then decommissioning of TTR-1 is completed. The outline of the decommissioning plan, the actually performed dismantling work, and spent fuel transportation work is briefly described. (author)

Positive Effectiveness of Tafamidis in Delaying Disease Progression in Transthyretin Familial Amyloid Polyneuropathy up to 2 Years: An Analysis from the Transthyretin Amyloidosis Outcomes Survey (THAOS).

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Mundayat, Rajiv; Stewart, Michelle; Alvir, Jose; Short, Sarah; Ong, Moh-Lim; Keohane, Denis; Rill, Denise; Sultan, Marla B

2018-04-09

The effectiveness of tafamidis for the treatment of transthyretin familial amyloid polyneuropathy (TTR-FAP) was evaluated using data from the Transthyretin Amyloidosis Outcomes Survey (THAOS) registry. Subjects receiving tafamidis (n = 252) were compared with untreated subjects in a non-randomized, matched cohort analysis. Subjects were matched with up to four untreated controls by genetic mutation, region of birth, and mean treatment propensity score. The matched, treated sample consisted predominantly of subjects with the Val30Met genotype (92.5%), from Portugal, and with a mean age of 40.4 years. Over the course of the 2-year follow-up period, subjects treated with tafamidis showed significantly less deterioration on the Neuropathy Impairment Score for Lower Limbs (p < 0.001) and its subscales (p < 0.023) compared with untreated subjects. There was significantly less deterioration among tafamidis-treated subjects compared with untreated subjects on the Norfolk Quality of Life scale (p < 0.001). There were no significant differences observed in functional (assessed by Karnofsky Performance Status Scale score) or nutritional (assessed by modified body mass index) status between the treated and untreated groups. The primary model which examined survival from baseline using the matched cohort was not able to yield estimates of the hazard ratio, as there were no deaths in the tafamidis-treated subjects. These findings support the results from clinical trials and strengthen evidence of the effectiveness of tafamidis beyond conventional clinical trials. ClinicalTrials.gov: NCT00628745 FUNDING: Pfizer.

Strong transthyretin immunostaining: potential pitfall in cardiac amyloid typing.

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Satoskar, Anjali A; Efebera, Yvonne; Hasan, Ayesha; Brodsky, Sergey; Nadasdy, Gyongyi; Dogan, Ahmet; Nadasdy, Tibor

2011-11-01

Although systemic amyloidosis commonly presents with renal disease, cardiac involvement usually determines the patient's prognosis. Cardiac involvement is seen in light chain amyloid and transthyretin amyloidosis. Distinguishing between these two is critical because prognosis and treatment differ. Our study demonstrates the unreliability of transthyretin immunostaining in subtyping cardiac amyloid. Between January 2003 and August 2010, we retrieved 229 native endomyocardial biopsies, of which 24 had amyloid. Immunohistochemistry for κ, λ, transthyretin, and serum amyloid A protein was performed on formalin-fixed, paraffin-embedded sections. Staining was graded as weak (trace to 1+) or strong (2 to 3+). Mass spectrometry (MS)-based proteomic typing of microdissected amyloid material was performed on selected cases. Fifteen patients had monoclonal gammopathy/plasma cell dyscrasia with cardiac amyloid. Eight of them (53%) showed strong transthyretin staining in the cardiac amyloid deposits. MS was performed in 5 of these 8 biopsies, and all 5 biopsies revealed light chain amyloid-type amyloid. Two of these 5 light chain amyloid biopsies did not even have concomitant strong staining for the appropriate light chain. Among the 15 cases with plasma cell dyscrasia, only 7 biopsies showed strong staining for the corresponding monoclonal light chain. Strong, false-positive immunostaining for transthyretin in cardiac amyloid is a potential pitfall, augmented by the frequent lack of staining for immunoglobulin light chains. Therefore, the presence of amyloid in the cardiac biopsy should prompt a search for plasma cell dyscrasia irrespective of transthyretin staining. Confirmation with MS should be sought, particularly if there is any discrepancy between κ/λ staining and serum immunofixation results.

Parenteral nutrition improves nutritional status, autonomic symptoms and quality of life in transthyretin amyloid polyneuropathy.

Science.gov (United States)

Russo, Massimo; Vita, Gian Luca; Stancanelli, Claudia; Mazzeo, Anna; Vita, Giuseppe; Messina, Sonia

2016-06-01

Transthyretin familial amyloid polyneuropathy (TTR-FAP) is an inherited amyloidosis, leading to death in about ten years in most cases due to cardiac failure or wasting syndrome. Previous studies showed that modified body mass index was related to time before death, duration of gastrointestinal disturbances, malabsorption and functional capacity. We report two patients in whom nutritional status worsened despite diet modification, hypercaloric supplement and two relevant therapeutic approaches such as liver transplant and tafamidis meglumine, respectively. The first patient, a 52-year-old lady carrying Thr49Ala mutation, had a disease duration of twelve years and had lost weight up to 35 kg because of daily diarrhea. The second patient, a 63-year-old man with Glu89Gln mutation and a disease duration of fifteen years, was in the New York Heart Association (NYHA) Functional Classification class III and his weight was 39 kg. In both cases, a peripherally inserted central catheter was placed for parenteral nutrition. It allowed to improve their nutritional status and clinical conditions, with body weight gains of 11 and 8 kg in a one year follow-up, respectively. Moreover, reduction of autonomic symptoms including postural hypotension, nausea and diarrhoea was recorded with ameliorated quality of life. Our experience suggests that parenteral nutrition may be useful in reducing complications and disabilities in TTR-FAP patients, even when all dietary adjustments have been ineffective. Reasonably, the improvement in nutritional status may prolong survival in TTR-FAP patients. Copyright © 2016 Elsevier B.V. All rights reserved.

Serum Transthyretin Level as a Plausible Marker for Diagnosis of Child Acute Malnutrition

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Behailu Tsegaye

2017-01-01

Full Text Available Malnutrition is a major underlying condition for mortality in children under five years of age in developing countries, particularly in Ethiopia. The most important forms of malnutrition in Ethiopia are protein and energy deficiencies. There is no reliable laboratory method at present to assess acute malnutrition. Transthyretin is a homotetrameric serum protein with half-life of two days. The main objective of this study was to assess the estimation of serum transthyretin level as a useful diagnostic method to evaluate nutritional status of children. We used a newly designed transthyretin test kit to evaluate nutritional status of children admitted to our hospital. There is no national reference standard; hence we made a comparative study using anthropometric measurements and measurement of serum albumin level. A total of 102 children (51 controls and 51 study subjects were included in this study. Transthyretin was found to be more sensitive to changes in acute malnutrition than albumin, and its level reflects recent dietary intake compared to overall nutritional status. The method is more sensitive and reliable for detection of acute malnutrition, along with anthropometric methods. Measurement of serum transthyretin level can be used as a valuable diagnostic method for assessment of acute malnutrition among children.

Diagnosis and management of transthyretin familial amyloid polyneuropathy in Japan: red-flag symptom clusters and treatment algorithm.

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Sekijima, Yoshiki; Ueda, Mitsuharu; Koike, Haruki; Misawa, Sonoko; Ishii, Tomonori; Ando, Yukio

2018-01-17

Hereditary ATTR (ATTRm) amyloidosis (also called transthyretin-type familial amyloid polyneuropathy [ATTR-FAP]) is an autosomal-dominant, adult-onset, rare systemic disorder predominantly characterized by irreversible, progressive, and persistent peripheral nerve damage. TTR gene mutations (e.g. replacement of valine with methionine at position 30 [Val30Met (p.Val50Met)]) lead to destabilization and dissociation of TTR tetramers into variant TTR monomers, which form amyloid fibrils that deposit in peripheral nerves and various organs, giving rise to peripheral and autonomic neuropathy and several non-disease specific symptoms.Phenotypic and genetic variability and non-disease-specific symptoms often delay diagnosis and lead to misdiagnosis. Red-flag symptom clusters simplify diagnosis globally. However, in Japan, types of TTR variants, age of onset, penetrance, and clinical symptoms of Val30Met are more varied than in other countries. Hence, development of a Japan-specific red-flag symptom cluster is warranted. Presence of progressive peripheral sensory-motor polyneuropathy and ≥1 red-flag sign/symptom (e.g. family history, autonomic dysfunction, cardiac involvement, carpal tunnel syndrome, gastrointestinal disturbances, unexplained weight loss, and immunotherapy resistance) suggests ATTR-FAP. Outside of Japan, pharmacotherapeutic options are first-line therapy. However, because of positive outcomes (better life expectancy and higher survival rates) with living donor transplant in Japan, liver transplantation remains first-line treatment, necessitating a Japan-specific treatment algorithm.Herein, we present a consolidated review of the ATTR-FAP Val30Met landscape in Japan and summarize findings from a medical advisory board meeting held in Tokyo on 18th August 2016, at which a Japan-specific ATTR-FAP red-flag symptom cluster and treatment algorithm was developed. Beside liver transplantation, a TTR-stabilizing agent (e.g. tafamidis) is a treatment option. Early

An amyotrophic lateral sclerosis-like syndrome revealing an amyloid polyneuropathy associated with a novel transthyretin mutation.

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Lozeron, Pierre; Lacroix, Catherine; Theaudin, Marie; Richer, Anne; Gugenheim, Michel; Adams, David; Misrahi, Micheline

2013-09-01

Familial amyloid polyneuropathy (FAP) is typically a predominantly sensory and autonomic neuropathy with progressive and late motor involvement leading to death within 10 years. Recently, prognosis was transformed with liver transplantation. We report an atypical sporadic pure motor and bulbar neuropathy initially mistaken for amyotrophic lateral sclerosis (ALS) in a 50-year-old Malian man. The diagnostic procedure of this clinical purely motor and bulbar neuropathy disclosed amyloid deposits on nerve biopsy which led to the identification of a new Val93Met mutation of transthyretin. This case was also remarkable by its slow progression. This report confirms the motor phenotype of TTR-FAP. That should be considered in the differential diagnosis of motor neuron diseases in order to start accurate therapy.

Comparative study on 2,2′,4,5,5′-pentachlorobiphenyl-mediated decrease in serum thyroxine level between C57BL/6 and its transthyretin-deficient mice

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Kato, Yoshihisa, E-mail: kato@kph.bunri-u.ac.jp [Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, Sanuki, Kagawa 769-2193 (Japan); Tamaki, Sekihiro [School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526 (Japan); Haraguchi, Koichi [Daiichi College of Pharmaceutical Sciences, Fukuoka 815-8511 (Japan); Ikushiro, Shin-ichi [Faculty of Engineering, Toyama Prefectural University, Toyama 939-0398 (Japan); Sekimoto, Masashi [School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526 (Japan); Ohta, Chiho [Faculty of Nutritional Sciences, Nakamura Gakuen University, Fukuoka 814-0198 (Japan); Endo, Tetsuya [Faculty of Pharmaceutical Sciences, Health Science University of Hokkaido, Hokkaido 061-0293 (Japan); Koga, Nobuyuki [Faculty of Nutritional Sciences, Nakamura Gakuen University, Fukuoka 814-0198 (Japan); Yamada, Shizuo; Degawa, Masakuni [School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526 (Japan)

2012-09-15

The relationships between the changes in the levels of serum total thyroxine (T{sub 4}), serum T{sub 4}-transthyretin (TTR) complex, and accumulation of T{sub 4} in tissues by 2,2′,4,5,5′-pentachlorobiphenyl (PentaCB) were examined using wild-type C57BL/6 (WT) and its TTR-deficient (TTR-null) mice. The constitutive level of serum total T{sub 4} was much higher in WT mice than in TTR-null mice. In WT mice 4 days after a single intraperitoneal injection with PentaCB (112 mg/kg), serum total T{sub 4} level was significantly decreased along with a decrease in serum T{sub 4}–TTR complex, and the levels of serum total T{sub 4} in the PentaCB-treated WT mice were almost the same to those in PentaCB-untreated (control) TTR-null mice. In addition, a slight decrease in serum total T{sub 4} by PentaCB treatment was observed in TTR-null mice. Furthermore, clearance of [{sup 125}I]T{sub 4} from the serum after [{sup 125}I]T{sub 4}-administration was promoted by the PentaCB-pretreatment in either strain of mice, especially WT mice. On the other hand, accumulation level of [{sup 125}I]T{sub 4} in the liver, but not in extrahepatic tissues, was strikingly enhanced in the PentaCB-pretreated WT and TTR-null mice. Furthermore, in both strains of mice, PentaCB-pretreatment led to significant increases in the steady-state distribution volume of [{sup 125}I]T{sub 4} and the concentration ratio of the liver to serum. The present findings demonstrate that PentaCB-mediated decrease in serum T{sub 4} level occurs mainly through increase in accumulation level of T{sub 4} in the liver and further indicate that the increased accumulation of T{sub 4} in the liver of WT mice is primarily dependent on the PentaCB-mediated inhibition of serum T{sub 4}–TTR complex formation.

Activated microglia mediate synapse loss and short-term memory deficits in a mouse model of transthyretin-related oculoleptomeningeal amyloidosis.

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Azevedo, E P; Ledo, J H; Barbosa, G; Sobrinho, M; Diniz, L; Fonseca, A C C; Gomes, F; Romão, L; Lima, F R S; Palhano, F L; Ferreira, S T; Foguel, D

2013-09-05

Oculoleptomeningeal amyloidosis (OA) is a fatal and untreatable hereditary disease characterized by the accumulation of transthyretin (TTR) amyloid within the central nervous system. The mechanisms underlying the pathogenesis of OA, and in particular how amyloid triggers neuronal damage, are still unknown. Here, we show that amyloid fibrils formed by a mutant form of TTR, A25T, activate microglia, leading to the secretion of tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and nitric oxide. Further, we found that A25T amyloid fibrils induce the activation of Akt, culminating in the translocation of NFκB to the nucleus of microglia. While A25T fibrils were not directly toxic to neurons, the exposure of neuronal cultures to media conditioned by fibril-activated microglia caused synapse loss that culminated in extensive neuronal death via apoptosis. Finally, intracerebroventricular (i.c.v.) injection of A25T fibrils caused microgliosis, increased brain TNF-α and IL-6 levels and cognitive deficits in mice, which could be prevented by minocycline treatment. These results indicate that A25T fibrils act as pro-inflammatory agents in OA, activating microglia and causing neuronal damage.

Transthyretin Concentrations in Acute Stroke Patients Predict Convalescent Rehabilitation.

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Isono, Naofumi; Imamura, Yuki; Ohmura, Keiko; Ueda, Norihide; Kawabata, Shinji; Furuse, Motomasa; Kuroiwa, Toshihiko

2017-06-01

For stroke patients, intensive nutritional management is an important and effective component of inpatient rehabilitation. Accordingly, acute care hospitals must detect and prevent malnutrition at an early stage. Blood transthyretin levels are widely used as a nutritional monitoring index in critically ill patients. Here, we had analyzed the relationship between the transthyretin levels during the acute phase and Functional Independence Measure in stroke patients undergoing convalescent rehabilitation. We investigated 117 patients who were admitted to our hospital with acute ischemic or hemorrhagic stroke from February 2013 to October 2015 and subsequently transferred to convalescent hospitals after receiving acute treatment. Transthyretin concentrations were evaluated at 3 time points as follows: at admission, and 5 and 10 days after admission. After categorizing patients into 3 groups according to the minimum transthyretin level, we analyzed the association between transthyretin and Functional Independence Measure. In our patients, transthyretin levels decreased during the first 5 days after admission and recovered slightly during the subsequent 5 days. Notably, Functional Independence Measure efficiency was significantly associated with the decrease in transthyretin levels during the 5 days after admission. Patients with lower transthyretin levels had poorer Functional Independence Measure outcomes and tended not to be discharged to their own homes. A minimal transthyretin concentration (stroke patients undergoing convalescent rehabilitation. In particular, an early decrease in transthyretin levels suggests restricted rehabilitation efficiency. Accordingly, transthyretin levels should be monitored in acute stroke patients to indicate mid-term rehabilitation prospects. Copyright © 2017 National Stroke Association. Published by Elsevier Inc. All rights reserved.

Considerably Unfolded Transthyretin Monomers Preceed and Exchange with Dynamically Structured Amyloid Protofibrils

DEFF Research Database (Denmark)

Groenning, Minna; Campos, Raul I; Hirschberg, Daniel

2015-01-01

describe an unexpectedly dynamic TTR protofibril structure which exchanges protomers with highly unfolded monomers in solution. The protofibrils only grow to an approximate final size of 2,900 kDa and a length of 70 nm and a comparative HXMS analysis of native and aggregated samples revealed a much higher...... average solvent exposure of TTR upon fibrillation. With SAXS, we reveal the continuous presence of a considerably unfolded TTR monomer throughout the fibrillation process, and show that a considerable fraction of the fibrillating protein remains in solution even at a late maturation state. Together......, these data reveal that the fibrillar state interchanges with the solution state. Accordingly, we suggest that TTR fibrillation proceeds via addition of considerably unfolded monomers, and the continuous presence of amyloidogenic structures near the protofibril surface offers a plausible explanation...

Potential Role of In Vivo Confocal Microscopy for Imaging Corneal Nerves in Transthyretin Familial Amyloid Polyneuropathy.

Science.gov (United States)

Rousseau, Antoine; Cauquil, Cecile; Dupas, Benedicte; Labbé, Antoine; Baudouin, Christophe; Barreau, Emmanuel; Théaudin, Marie; Lacroix, Catherine; Guiochon-Mantel, Anne; Benmalek, Anouar; Labetoulle, Marc; Adams, David

2016-09-01

Small fiber neuropathy (SFN) is an important feature of transthyretin familial amyloid polyneuropathy (TTR-FAP). A practical and objective method for the clinical evaluation of SFN is needed to improve the management of this disease. In vivo confocal microscopy (IVCM) of the corneal nerves, a rapid noninvasive technique, may be used as a surrogate marker of SFN. To determine the correlation of SFN with IVCM in patients with TTR-FAP. A prospective, single-center, cross-sectional controlled study was conducted at the French National Reference Center for TTR-FAP from June 1, 2013, to June 30, 2014. Fifteen patients with TTR-FAP underwent a complete neurologic examination, including Neuropathy Impairment Score of the Lower Limbs, hand grip strength, and evaluation of vegetative dysfunction, as well as electrophysiologic studies (nerve conduction and electrochemical skin conductance) and intraepidermal nerve fiber density quantification. Patients and 15 controls (matched for age and sex) underwent ophthalmologic assessments, including corneal esthesiometry and IVCM. Correlation of corneal nerve fiber length (CNFL) with the severity of SFN. Of the 15 patients enrolled in the study, 6 were women (40%); mean (SD) age was 54.4 [13.7] years. The CNFL was shorter in the patients than in controls (13.08 vs 17.57 mm/mm2; difference of 4.49 [95% CI, 0.72 to 8.27]; P = .02). The patients' CNFL correlated with the severity of both autonomic neuropathy assessed by the Compound Autonomic Dysfunction Test (rs = 0.66 [95% CI, 0.22 to 0.87]; P = .008) or electrochemical skin conductance (rs = 0.80 [95% CI, 0.50 to 0.93]; P < .001) and sensorimotor neuropathy assessed using the Neuropathy Impairment Score of the Lower Limbs (rs = -0.58 [95% CI, -0.84 to -0.11]; P = .02). Patients with altered sensory nerve action potentials and intraepidermal nerve fiber density had a shorter CNFL (P = .04 and P = .02, respectively). The CNFL could be measured in all

Towards data warehousing and mining of protein unfolding simulation data.

Science.gov (United States)

Berrar, Daniel; Stahl, Frederic; Silva, Candida; Rodrigues, J Rui; Brito, Rui M M; Dubitzky, Werner

2005-10-01

The prediction of protein structure and the precise understanding of protein folding and unfolding processes remains one of the greatest challenges in structural biology and bioinformatics. Computer simulations based on molecular dynamics (MD) are at the forefront of the effort to gain a deeper understanding of these complex processes. Currently, these MD simulations are usually on the order of tens of nanoseconds, generate a large amount of conformational data and are computationally expensive. More and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. To adequately organize, manage, and analyze the data generated by unfolding simulation studies, we designed a data warehouse system that is embedded in a grid environment to facilitate the seamless sharing of available computer resources and thus enable many groups to share complex molecular dynamics simulations on a more regular basis. To gain insight into the conformational fluctuations and stability of the monomeric forms of the amyloidogenic protein transthyretin (TTR), molecular dynamics unfolding simulations of the monomer of human TTR have been conducted. Trajectory data and meta-data of the wild-type (WT) protein and the highly amyloidogenic variant L55P-TTR represent the test case for the data warehouse. Web and grid services, especially pre-defined data mining services that can run on or 'near' the data repository of the data warehouse, are likely to play a pivotal role in the analysis of molecular dynamics unfolding data.

[Is plasma selenium correlated to transthyretin levels in critically ill patients?

Science.gov (United States)

Freitas, Renata G B O N; Nogueira, Roberto Jose Negrão; Cozzolino, Silvia Maria Franciscato; Vasques, Ana Carolina Junqueira; Ferreira, Matthew Thomas; Hessel, Gabriel

2017-06-05

Selenium is an essential trace element, but critically ill patients using total parenteral nutrition (PN) do not receive selenium because this mineral is not commonly offered. Threfore, the eval uation of plasma selenium levels is very important for treating or preventing this deficiency. Recent studies have shown that transthyretin may reflect the selenium intake and could be considered a biomarker. However, this issue is still little explored in the literature. This study aims to investigate the correlation of transthyretin with the plasma selenium of critically ill patients receiving PN. This was a prospective cohort study with 44 patients using PN without selenium. Blood samples were carried out in 3 stages: initial, 7th and 14th day of PN. In order to evaluate the clinical condition and the inflammatory process, albumin, C-reactive protein (CRP), transthyretin, creatinine and HDL cholesterol levels were observed. To assess the selenium status, plasma selenium and glutathione peroxidase (GPx) in whole blood were measured. Descriptive analyses were performed and the ANOVA, Mann-Whitney and Spearman's coefficient tests were conducted; we assumed a significance level of 5%. A positive correlation of selenium with the GPx levels (r = 0.46; p = 0.03) was identified. During two weeks, there was a positive correlation of transthyretin with plasma selenium (r = 0.71; p = 0.05) regardless of the CRP values. Transthyretin may have reflected plasma selenium, mainly because the correlation was verified after the acute phase.

Transthyretin levels: Potential biomarker for monitoring nutritional support efficacy and clinical complications risk in patients receiving parenteral nutrition.

Science.gov (United States)

Borges de Oliveira Nascimento Freitas, Renata Germano; Hessel, Gabriel; Junqueira Vasques, Ana Carolina; Negrão Nogueira, Roberto José

2018-04-01

Nutritional support is an effective strategy to restore or maintain nutritional status, to reduce clinical complications, hospitalization period and the morbidity/mortality risk of hospitalized patients. So, a good marker is important to evaluate the nutritional support. This study aims to evaluate the evolution of transthyretin levels in patients receiving parenteral nutrition (PN) during 14 days. Longitudinal study of 88 hospitalized patients. The assessments and samples were taken during the first 72 h (T0), on the 7th day (T7) and 14th day (T14) of PN. This study was approved by the Ethics Committee of the School of Medical Sciences at UNICAMP (No 538/2011). The C-reactive protein (CRP) levels were high and albumin and transthyretin levels were low at baseline. From T0 to T14, only transthyretin increased (p = 0.03). According to the receiver operation characteristic (ROC) curve, we found that the transthyretin had some improvement when the CRP levels were less than 10.4 mg/dl (T7). According to the CRP/albumin ratio, all patients classified as without risk for complications were discharged from the hospital. In addition, we observed that patients with transthyretin reduction had a concomitant higher risk for complications according to their ratio CRP/albumin (p = 0.03). CRP/albumin ratio was associated with the evolution of transthyretin levels. Transthyretin values showed significant improvement in the 14 days of PN. Especially, less inflamed patients (ie CRP less than 10.4 mg/dl) improved their transthyretin levels. So, CRP value at day 7 that predicts the transthyretin and transthyretin is a good biomarker for classification of nutritional support and clinical complications risk in patients receiving PN. Copyright © 2017 European Society for Clinical Nutrition and Metabolism. Published by Elsevier Ltd. All rights reserved.

Serum proteomic analysis reveals potential serum biomarkers for occupational medicamentosa-like dermatitis caused by trichloroethylene.

Science.gov (United States)

Huang, Peiwu; Ren, Xiaohu; Huang, Zhijun; Yang, Xifei; Hong, Wenxu; Zhang, Yanfang; Zhang, Hang; Liu, Wei; Huang, Haiyan; Huang, Xinfeng; Wu, Desheng; Yang, Linqing; Tang, Haiyan; Zhou, Li; Li, Xuan; Liu, Jianjun

2014-08-17

Trichloroethylene (TCE) is an industrial solvent with widespread occupational exposure and also a major environmental contaminant. Occupational medicamentosa-like dermatitis induced by trichloroethylene (OMLDT) is an autoimmune disease and it has become one major hazard in China. In this study, sera from 3 healthy controls and 3 OMLDT patients at different disease stages were used for a screening study by 2D-DIGE and MALDI-TOF-MS/MS. Eight proteins including transthyretin (TTR), retinol binding protein 4 (RBP4), haptoglobin, clusterin, serum amyloid A protein (SAA), apolipoprotein A-I, apolipoprotein C-III and apolipoprotein C-II were found to be significantly altered among the healthy, acute-stage, healing-stage and healed-stage groups. Specifically, the altered expression of TTR, RBP4 and haptoglobin were further validated by Western blot analysis and ELISA. Our data not only suggested that TTR, RBP4 and haptoglobin could serve as potential serum biomarkers of OMLDT, but also indicated that measurement of TTR, RBP4 and haptoglobin or their combination could help aid in the diagnosis, monitoring the progression and therapy of the disease. Copyright © 2014. Published by Elsevier Ireland Ltd.

Guideline of transthyretin-related hereditary amyloidosis for clinicians

Directory of Open Access Journals (Sweden)

Ando Yukio

2013-02-01

Full Text Available Abstract Transthyretin amyloidosis is a progressive and eventually fatal disease primarily characterized by sensory, motor, and autonomic neuropathy and/or cardiomyopathy. Given its phenotypic unpredictability and variability, transthyretin amyloidosis can be difficult to recognize and manage. Misdiagnosis is common, and patients may wait several years before accurate diagnosis, risking additional significant irreversible deterioration. This article aims to help physicians better understand transthyretin amyloidosis—and, specifically, familial amyloidotic polyneuropathy—so they can recognize and manage the disease more easily and discuss it with their patients. We provide guidance on making a definitive diagnosis, explain methods for disease staging and evaluation of disease progression, and discuss symptom mitigation and treatment strategies, including liver transplant and several pharmacotherapies that have shown promise in clinical trials.

Speckle Tracking and Transthyretin Amyloid Cardiomyopathy

Directory of Open Access Journals (Sweden)

Alexandre Marins Rocha

Full Text Available Abstract Background: Amyloidosis is a disease caused by deposits of insoluble fibrils in extracellular spaces. The most common type of familial amyloidosis is mediated by mutation of transthyretin, especially Val30Met. Symptoms and ejection fraction decrease may occur in cardiac amyloidosis only in case of poor prognosis. Myocardial strain detected by two-dimensional speckle tracking echocardiography can indicate changes in myocardial function at early stages of the disease. Objective: To determine the accuracy of left ventricular longitudinal strain by two-dimensional speckle tracking echocardiography in patients with familial amyloidosis caused by Val30Met transthyretin mutation. Methods: Eighteen consecutive patients, carriers of transthyretin mutation, were evaluated by two-dimensional speckle tracking echocardiography, by which myocardial strain curves were obtained, following the American Society of Echocardiography recommendations. Results: Patients were divided into three groups: 1- Val30Met with cardiac amyloidosis; 2-Val30Met with extracardiac amyloidosis; 3 - Val30Met without evidence of disease. As the three groups were compared by the Mann-Whitney test, we found a statistically significant difference between groups 1 and 2 in the mean longitudinal tension (p=0.01, mean basal longitudinal strain (p=0.014; in mean longitudinal tension and mean longitudinal strain between groups 1 and 3 (p=0.005; and in the ratio of longitudinal strain of apical septum segment to longitudinal strain of basal septum (p=0.041 between groups 2 and 3. Conclusion: Left ventricular longitudinal strain detected by two-dimensional speckle tracking echocardiography is able to diagnose left ventricular dysfunction in early stages of familial amyloidosis caused by transthyretin Val30Met mutation.

Downsizing of lean body mass is a key determinant of Alzheimer's disease.

Science.gov (United States)

Ingenbleek, Yves; Bernstein, Larry H

2015-01-01

Lean body mass (LBM) encompasses all metabolically active organs distributed into visceral and structural tissue compartments and collecting the bulk of N and K stores of the human body. Transthyretin (TTR) is a plasma protein mainly secreted by the liver within a trimolecular TTR-RBP-retinol complex revealing from birth to old age strikingly similar evolutionary patterns with LBM in health and disease. TTR is also synthesized by the choroid plexus along distinct regulatory pathways. Chronic dietary methionine (Met) deprivation or cytokine-induced inflammatory disorders generates LBM downsizing following differentiated physiopathological processes. Met-restricted regimens downregulate the transsulfuration cascade causing upstream elevation of homocysteine (Hcy) safeguarding Met homeostasis and downstream drop of hydrogen sulfide (H2S) impairing anti-oxidative capacities. Elderly persons constitute a vulnerable population group exposed to increasing Hcy burden and declining H2S protection, notably in plant-eating communities or in the course of inflammatory illnesses. Appropriate correction of defective protein status and eradication of inflammatory processes may restore an appropriate LBM size allowing the hepatic production of the retinol circulating complex to resume, in contrast with the refractory choroidal TTR secretory process. As a result of improved health status, augmented concentrations of plasma-derived TTR and retinol may reach the cerebrospinal fluid and dismantle senile amyloid plaques, contributing to the prevention or the delay of the onset of neurodegenerative events in elderly subjects at risk of Alzheimer's disease.

Low serum levels of prohepcidin, but not hepcidin-25, are related to anemia in familial amyloidosis TTR V30M.

NARCIS (Netherlands)

Beirao, I.; Almeida, S.; Swinkels, D.W.; Costa, P.M.; Moreira, L.; Fonseca, I.; Freitas, C.; Cabrita, A.; Porto, G.

2008-01-01

Familial amyloidosis TTR V30M (FAP-I) usually presents as a sensorimotor and autonomic neuropathy. Anemia was first described in this disease more than 20 years ago and classified as an anemia of chronic disease. However, so far no studies have addressed the role of inflammatory proteins in this

Transthyretin Predicts Cardiovascular Outcome In Hemodialysis Patients With Diabetes Mellitus Type 2

Directory of Open Access Journals (Sweden)

Andrea Henze

2012-06-01

A low TTR concentration was associated with an increased risk for CVE for the total study cohort (HR 1.65; 95% CI 1.27-2.14, patients with BMI ≥23kg/m² (HR 1.70; 95% CI 1.22–2.37, albumin ≥3.8g/dL (HR 1.68; 95% CI 1.17–2.42 and the combination of both (HR 1.69; 95% CI 1.13-2.53. Additionally, a low TTR concentration predicted all-cause mortality for the total study cohort (HR 1.79; 95% CI 1.43–2.24 and patients with BMI ≥23kg/m² (HR 1.46; 95% CI 1.09–1.95. In conclusion, the present study demonstrated that TTR is a useful predictor for cardiovascular outcome and mortality in hemodialysis patients. TTR was particularly useful in patients who were not identified to be at risk by BMI or albumin status.

Discordant results between biochemical and molecular transthyretin

Indian Academy of Sciences (India)

Discordant results between biochemical and molecular transthyretin assays: lessons learned from a unique testing algorithm at the Mayo Clinic. Honey V. Reddi Brittany C. Thomas Kurt S. Willkomm Matthew J. Ferber Kandelaria M. Rumilla Kimiyo M. Raymond John F. O'Brien W. Edward Highsmith. Research Note Volume ...

Effect-Directed Analysis to Explore the Polar Bear Exposome: the Identification of Thyroid Hormone Disrupting Compounds in Plasma

NARCIS (Netherlands)

Simon, E.; van Velzen, M.J.M.; Brandsma, S.H.; Lie, E.; Loken, K.; de Boer, J.; Bytingsvik, J.; Jenssen, B.M.; Aars, J.; Hamers, T.; Lamoree, M.H.

2013-01-01

Compounds with transthyretin (TTR)-binding potency in the blood plasma of polar bear cubs were identified with effect-directed analysis (EDA). This approach contributes to the understanding of the thyroid disrupting exposome of polar bears. The selection of these samples for in-depth EDA was based

Closure Letter Report for Corrective Action Unit 496: Buried Rocket Site - Antelope Lake (TTR)

International Nuclear Information System (INIS)

NSTec Environmental Restoration

2007-01-01

A Streamlined Approach for Environmental Restoration (SAFER) Plan for investigation and closure of CAU 496, Corrective Action Site (CAS) TA-55-008-TAAL (Buried Rocket), at the Tonopah Test Range (TTR), was approved by the Nevada Department of Environmental Protection (NDEP) on July 21,2004. Approval to transfer CAS TA-55-008-TAAL from CAU 496 to CAU 4000 (No Further Action Sites) was approved by NDEP on December 21, 2005, based on the assumption that the rocket did not present any environmental concern. The approval letter included the following condition: ''NDEP understands, from the NNSA/NSO letter dated November 30,2005, that a search will be conducted for the rocket during the planned characterization of other sites at the Tonopah Test Range and, if found, the rocket will be removed as a housekeeping measure''. NDEP and U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office personnel located the rocket on Mid Lake during a site visit to TTR, and a request to transfer CAS TA-55-008-TAAL from CAU 4000 back to CAU 496 was approved by NDEP on September 11,2006. CAS TA-55-008-TAAL was added to the ''Federal Facility Agreement and Consent Order'' of 1996, based on an interview with a retired TTR worker in 1993. The original interview documented that a rocket was launched from Area 9 to Antelope Lake and was never recovered due to the high frequency of rocket tests being conducted during this timeframe. The interviewee recalled the rocket being an M-55 or N-55 (the M-50 ''Honest John'' rocket was used extensively at TTR from the 1960s to early 1980s). A review of previously conducted interviews with former TTR personnel indicated that the interviewees confused information from several sites. The location of the CAU 496 rocket on Mid Lake is directly south of the TTR rocket launch facility in Area 9 and is consistent with information gathered on the lost rocket during recent interviews. Most pertinently, an interview in 2005 with a

Diagnóstico de polineuropatía amiloidótica familiar tipo I en la Argentina Diagnosis of familial amyloid polyneuropathy type I in Argentina

Directory of Open Access Journals (Sweden)

Gladys Pérez

2008-08-01

transthyretin (TTR the principal component of amyloid fibrils. TTR is a normal plasma protein (previously called prealbumin that functions as a transport protein binding tiroxine and retinol. Among many mutations that have been found in the TTR gene, the variant with a single amino acid substitution of methionine for valine at position 30 (TTR Val30Met is the responsible of the Portuguese-type Familial Amyloidotic Polyneuropathy (FAP Type I. Interest in this pathology has arisen in Argentina because of the finding of an endemic area where a group of Portuguese immigrant families is localized. Since liver transplantation is a widely accepted treatment because it results in the disappearance of variant transthyretin from plasma, an early detection of the altered gene is essential. Thus, the objective of the present work was to optimize a methodology to detect the Val30Met mutation introducing modifications into techniques that were previously developed. The simple method here described is useful to confirm the diagnosis of the potential disease and, therefore, make it possible for patients to gain access to early liver transplantation.

CSF transthyretin neuroprotection in a mouse model of brain ischemia

DEFF Research Database (Denmark)

Santos, Sofia Duque; Lambertsen, Kate Lykke; Clausen, Bettina Hjelm

2010-01-01

Brain injury caused by ischemia is a major cause of human mortality and physical/cognitive disability worldwide. Experimentally, brain ischemia can be induced surgically by permanent middle cerebral artery occlusion. Using this model, we studied the influence of transthyretin in ischemic stroke. ...

Hsf-1 affects podocyte markers NPHS1, NPHS2 and WT1 in a transgenic mouse model of TTRVal30Met-related amyloidosis.

Science.gov (United States)

Petrakis, Ioannis; Mavroeidi, Vasiliki; Stylianou, Kostas; Andronikidi, Eva; Lioudaki, Eirini; Perakis, Kostas; Stratigis, Spyridon; Vardaki, Eleftheria; Zafeiri, Maria; Giannakakis, Kostantinos; Plaitakis, Andreas; Amoiridis, George; Saraiva, Maria Joao; Daphnis, Eugene

2013-09-01

Familial amyloid polyneuropathy is characterized by transthyretin (TTR) deposition in various tissues, including the kidneys. While deposition induces organ dysfunction, renal involvement in TTR-related amyloidosis could manifest from proteinuria to end-stage kidney failure. As proteinuria is considered result of glomerular filtration barrier injury we investigated whether TTR deposition affects either glomerular basement membrane (GBM) or podocytes. Immunohistochemistry, immunoblot and gene expression studies for nephrin, podocin and WT1 were run on renal tissue from human-TTRV30M transgenic mice hemizygous or homozygous for heat shock factor one (Hsf-1). Transmission electron microscopy was used for evaluation of podocyte foot process width (PFW) and GBM thickness in Hsf-1 hemizygous mice with or without TTRV30M or amyloid deposition. Glomeruli of hsf-1 hemizygous transgenic mice showed lower nephrin and podocin protein levels but an increased podocyte number when compared to Hsf-1 homozygous transgenic mice. Nephrin, podocin and WT1 gene expression levels were unaffected by the Hsf-1 carrier status. TTRV30M deposition was associated with increased PFW and GBM thickness. Under the effect of Hsf-1 hemizygosity, TTRV30M deposition has deleterious effects on GBM thickness, PFW and slit diaphragm composition, without affecting nephrin and podocin gene expression.

Ecological studies of small vertebrates in Pu-contaminated study areas of NTS and TTR

International Nuclear Information System (INIS)

Bradley, W.G.; Moor, K.S.

1975-01-01

Ecological studies of vertebrates in plutonium-contaminated areas of the Nevada Test Site (NTS) were initiated in March 1972, and have continued to date. In September 1973, standard census methods were also employed to derive a qualitative and quantitative inventory of vertebrate biota of four Nevada Applied Ecology Group (NAEG) study areas of the Tonopah Test Range (TTR). A checklist of vertebrates of NAEG study areas of NTS and TTR is presented. Data are presented on vertebrate composition, relative abundance, and seasonal status in the study areas. Concentrations of 239 Pu and 241 Am were determined in pelt or skin, GI tract, and carcass of 13 lizards and 16 mammals resident on Clean Slate 2, TTR, and Area 11, NTS. A total of 71 animals were collected for radioanalysis. However, the data were not available at the time this report was written. Pu tissue burdens were highest in lizards from Area 11 GZ. Maximum values obtained in nCi/g ash were 30.9, 42.2, and 0.43 for the pelt, GI tract, and carcass, respectively. Maximum 239 Pu values in tissues of small rodents from Area 11 (not from GZ) were 11.4, 6.49, and 0.20 nCi/g ash for pelt, GI tract, and carcass, respectively. Pu/Am ratios were relatively consistent in tissue samples of lizards and small mammals from Area 11 (approximately 6:1, Pu/Am). Pu/Am ratios were not consistent in vertebrates of Clean Slate 2, TTR, and appeared to be lower in carcass (28:1, Pu/Am in mammals) than GI tract (9:1, Pu/Am in mammals). Although this trend was more conspicuous in mammals, it was also evident in reptiles. (auth)

Biosensor discovery of thyroxine transport disrupting chemicals

International Nuclear Information System (INIS)

Marchesini, Gerardo R.; Meimaridou, Anastasia; Haasnoot, Willem; Meulenberg, Eline; Albertus, Faywell; Mizuguchi, Mineyuki; Takeuchi, Makoto; Irth, Hubertus; Murk, Albertinka J.

2008-01-01

Ubiquitous chemicals may interfere with the thyroid system that is essential in the development and physiology of vertebrates. We applied a surface plasmon resonance (SPR) biosensor-based screening method for the fast screening of chemicals with thyroxine (T4) transport disrupting activity. Two inhibition assays using the main thyroid hormone transport proteins, T4 binding globulin (TBG) and transthyretin (TTR), in combination with a T4-coated biosensor chip were optimized and automated for screening chemical libraries. The transport protein-based biosensor assays were rapid, high throughput and bioeffect-related. A library of 62 chemicals including the natural hormones, polychlorinated biphenyls (PCBs), polybrominated diphenylethers (PBDEs) and metabolites, halogenated bisphenol A (BPA), halogenated phenols, pharmaceuticals, pesticides and other potential environmentally relevant chemicals was tested with the two assays. We discovered ten new active compounds with moderate to high affinity for TBG with the TBG assay. Strikingly, the most potent binding was observed with hydroxylated metabolites of the brominated diphenyl ethers (BDEs) BDE 47, BDE 49 and BDE 99, that are commonly found in human plasma. The TTR assay confirmed the activity of previously identified hydroxylated metabolites of PCBs and PBDEs, halogenated BPA and genistein. These results show that the hydroxylated metabolites of the ubiquitous PBDEs not only target the T4 transport at the TTR level, but also, and to a great extent, at the TBG level where most of the T4 in humans is circulating. The optimized SPR biosensor-based transport protein assay is a suitable method for high throughput screening of large libraries for potential thyroid hormone disrupting compounds

Biosensor discovery of thyroxine transport disrupting chemicals.

Science.gov (United States)

Marchesini, Gerardo R; Meimaridou, Anastasia; Haasnoot, Willem; Meulenberg, Eline; Albertus, Faywell; Mizuguchi, Mineyuki; Takeuchi, Makoto; Irth, Hubertus; Murk, Albertinka J

2008-10-01

Ubiquitous chemicals may interfere with the thyroid system that is essential in the development and physiology of vertebrates. We applied a surface plasmon resonance (SPR) biosensor-based screening method for the fast screening of chemicals with thyroxine (T4) transport disrupting activity. Two inhibition assays using the main thyroid hormone transport proteins, T4 binding globulin (TBG) and transthyretin (TTR), in combination with a T4-coated biosensor chip were optimized and automated for screening chemical libraries. The transport protein-based biosensor assays were rapid, high throughput and bioeffect-related. A library of 62 chemicals including the natural hormones, polychlorinated biphenyls (PCBs), polybrominated diphenylethers (PBDEs) and metabolites, halogenated bisphenol A (BPA), halogenated phenols, pharmaceuticals, pesticides and other potential environmentally relevant chemicals was tested with the two assays. We discovered ten new active compounds with moderate to high affinity for TBG with the TBG assay. Strikingly, the most potent binding was observed with hydroxylated metabolites of the brominated diphenyl ethers (BDEs) BDE 47, BDE 49 and BDE 99, that are commonly found in human plasma. The TTR assay confirmed the activity of previously identified hydroxylated metabolites of PCBs and PBDEs, halogenated BPA and genistein. These results show that the hydroxylated metabolites of the ubiquitous PBDEs not only target the T4 transport at the TTR level, but also, and to a great extent, at the TBG level where most of the T4 in humans is circulating. The optimized SPR biosensor-based transport protein assay is a suitable method for high throughput screening of large libraries for potential thyroid hormone disrupting compounds.

In vitro assay shows that PCB metabolites completely saturate thyroid hormone transport capacity in blood of wild polar bears (Ursus maritimus).

Science.gov (United States)

Gutleb, Arno C; Cenijn, Peter; Velzen, Martin van; Lie, Elisabeth; Ropstad, Erik; Skaare, Janneche Utne; Malmberg, Tina; Bergman, Ake; Gabrielsen, Geir W; Legler, Juliette

2010-04-15

Persistent chemicals accumulate in the arctic environment due to their chemical reactivity and physicochemical properties and polychlorinated biphenyls (PCBs) are the most concentrated pollutant class in polar bears (Ursus maritimus). Metabolism of PCB and polybrominated biphenyl ether (PBDE) flame-retardants alter their toxicological properties and these metabolites are known to interfere with the binding of thyroid hormone (TH) to transthyretin (TTR) in rodents and humans. In polar bear plasma samples no binding of [125I]-T(4) to TTR was observed after incubation and PAGE separation. Incubation of the plasma samples with [14C]-4-OH-CB107, a compound with a higher binding affinity to TTR than the endogenous ligand T(4) resulted in competitive binding as proven by the appearance of a radio labeled TTR peak in the gel. Plasma incubation with T(4) up to 1 mM, a concentration that is not physiologically relevant anymore did not result in any visible competition. These results give evidence that the binding sites on TTR for T(4) in wild living polar bears are completely saturated. Such saturation of binding sites can explain observed lowered levels of THs and could lead to contaminant transport into the developing fetus.

Apolipoproteins C-II and C-III as nutritional markers unaffected by inflammation.

Science.gov (United States)

Isshiki, Miwa; Hirayama, Satoshi; Ueno, Tsuyoshi; Ito, Masayuki; Furuta, Ayaka; Yano, Kouji; Yamatani, Kotoko; Sugihara, Masami; Idei, Mayumi; Miida, Takashi

2018-06-01

Rapid turnover proteins (RTPs), such as transthyretin (TTR), retinol binding protein (RBP), and transferrin (Tf), provide an accurate assessment of nutritional status but are susceptible to inflammation. Lipid-related markers, which have short half-lives in serum, may be better suited for nutritional assessment. We sought to identify sensitive nutritional markers unaffected by inflammation. Fasting serum samples were collected from 30 malnourished inpatients and 25 healthy volunteers. Malnourished inpatients were divided into 2 groups: a low-C-reactive protein (CRP) group (CRP group (CRP ≥ 20 mg/l, n = 15). Lipid-related markers, traditional nutritional markers, RTPs, micronutrients, and ketone bodies were measured and compared among the groups. Apolipoprotein (Apo)C-II and ApoC-III concentrations were lower in malnourished inpatients than in the control group. There was no significant difference in ApoC-II and ApoC-III between the low- and high-CRP groups. Carnitine transporters and ketone bodies did not show a significant difference among the three groups. Albumin, TTR, RBP, and Tf concentrations were lowest in the high-CRP group, intermediate in the low-CRP group, and highest in the control group. These results indicate that ApoC-II and ApoC-III are appropriate nutritional biomarkers unaffected by inflammation. Copyright © 2018 Elsevier B.V. All rights reserved.

Maternal serum protein profile and immune response protein subunits as markers for non-invasive prenatal diagnosis of trisomy 21, 18, and 13

KAUST Repository

Narasimhan, Kothandaraman; Lin, SuLin; Tong, Terry; Baig, Sonia; Ho, Sherry; Sukumar, Ponnusamy; Biswas, Arijit; Hahn, Sinuhe; Bajic, Vladimir B.; Choolani, Mahesh A.

2013-01-01

(MALDI-TOF/TOF) and western blot, glyco proteins such as alpha-1-antitrypsin, apolipoprotein E, apolipoprotein H, and serum carrier protein transthyretin were identified as potential maternal serum markers for fetal trisomy condition. The identified

Biomarkers in volunteers exposed to mobile phone radiation.

Science.gov (United States)

Söderqvist, Fredrik; Carlberg, Michael; Hardell, Lennart

2015-06-01

For some time it has been investigated whether low-intensity non-thermal microwave radiation from mobile phones adversely affects the mammalian blood-brain barrier (BBB). All such studies except one have been either in vitro or experimental animal studies. The one carried out on humans showed a statistically significant increase in serum transthyretin (TTR) 60 min after finishing of a 30-min microwave exposure session. The aim of the present study was to follow up on the finding of the previous one using a better study design. Using biomarkers analyzed in blood serum before and after the exposure this single blinded randomized counterbalanced study, including 24 healthy subjects aged 18-30 years that all underwent three exposure conditions (SAR(10G)=2 W/kg, SAR(10G)=0.2 W/kg, sham), tested whether microwaves from an 890-MHz phone-like signal give acute effects on the integrity of brain-shielding barriers. Over time, statistically significant variations were found for two of the three biomarkers (TTR; β-trace protein); however, no such difference was found between the different exposure conditions nor was there any interaction between exposure condition and time of blood sampling. In conclusion this study failed to show any acute clinically or statistically significant effect of short term microwave exposure on the serum levels of S100β, TTR and β-trace protein with a follow up limited to two hours. The study was hampered by the fact that all study persons were regular wireless phone users and thus not naïve as to microwave exposure. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Autonomic Neuropathy and Albuminocytologic Dissociation in Cerebrospinal Fluid As the Presenting Features of Primary Amyloidosis: A Case Report

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Jingjing Li

2017-07-01

Full Text Available ObjectivePrimary amyloidosis is a disease with a poor prognosis and multi-organ involvement. Here, we report the clinical and pathological features of a patient with primary amyloidosis featuring autonomic neuropathy as the initial symptom and albuminocytologic dissociation in the cerebrospinal fluid (CSF.MethodsThe patient was a 60-year-old Chinese male with numbness, orthostatic hypotension, and gastrointestinal symptoms. For diagnosis, we performed an electromyogram (EMG, lumbar puncture, Bence Jones protein urine test, serum electrophoresis blood test, sural nerve and rectal membrane biopsies, transthyretin (TTR gene sequencing, and bone marrow puncture.ResultsCongo red staining of sural nerve and rectal membrane biopsies showed amyloid deposition and apple-green birefringence was visualized under polarized light microscopy. TTR gene sequencing showed no causative mutation. Following lumbar puncture, normal CSF cell counts and elevated CSF protein concentration (1,680 mg/L were detected. Bone marrow puncture showed that out of the total number of whole blood cells, 0.56% were abnormal plasma cells and that 87.4% of the total number of plasma cells were abnormal. EMG results showed mixed peripheral nerve damage predominately in the sensory nerve fibers.ConclusionObvious symptoms of neuropathy, particularly autonomic neuropathy, albuminocytologic dissociation, and organ function damage suggested a diagnosis of amyloidosis. In such patients, neurologists should use caution to differentiate between chronic inflammatory demyelinating polyneuropathy, primary amyloidosis, and familial amyloid neuropathy.

A Dutch kindred with familial amyloidotic polyneuropathy associated with the transthyretin Cys 114 mutant

NARCIS (Netherlands)

Haagsma, EB; Post, JG; DeJager, AEJ; Nikkels, PGJ; Hamel, BCJ; Hazenberg, BPC

A Dutch kindred with transthyretin Cys 114 related familial amyloidotic polyneuropathy is reported. The finding of early involvement of the heart is of great concern and of special relevance to the optimal timing for liver transplantation. To date, the variant had only been reported to be present in

In vitro fluorescence displacement investigation of thyroxine transport disruption by bisphenol A

Institute of Scientific and Technical Information of China (English)

Jie Cao; Liang-Hong Guo; Bin Wan; Yin Wei

2011-01-01

Bisphenol A (BPA) is a chemical with high production volume and wide applications in many industries.Although BPA is known as an endocrine disruptor, its toxic mechanisms have not been fully characterized.Due to its structural similarity to thyroid hormones thyroxine (T4) and triiodothyronine (T3), one possible mechanism of BPA toxicity is disruption of hormone transport by competitive binding with the transport proteins.In this study, the binding interactions of BPA, T4, and T3 with three thyroid hormone transport proteins, human serum albumin (HSA), transthyretin (TTR), and thyroxine-binding globulin (TBG) were investigated by fluorescence measurement.Using two site-specific fluorescence probes dansylamide and dansyl-L-proline, the binding constants of BPA with HSA at drug site I and site Ⅱ were determined as 2.90 × 104 and 3.14 × 104 L/mol, respectively.By monitoring the intrinsic fluorescence of tryptophan, a binding constant of 4.70 × 103 L/mol was obtained.Similarly, by employing 8-anilino-1-naphthalenesulfonic acid as fluorescence probe, the binding affinity of BPA with TTR and TBG was measured to be 3.10 × 105 and 5.90 × 105 L/mol, respectively.In general, BPA showed lower binding affinity with the proteins than T3 did, and even lower affinity than T4.Using these binding constants, the amount of BPA which would bind to the transport proteins in human plasma was estimated.These results suggest that the concentrations of BPA commonly found in human plasma are probably not high enough to interfere with T4 transport.

Validation of Candidate Serum Ovarian Cancer Biomarkers for Early Detection

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Feng Su

2007-01-01

Full Text Available Objective: We have previously analyzed protein profi les using Surface Enhanced Laser Desorption and Ionization Time-Of-Flight Mass Spectroscopy (SELDI-TOF-MS [Kozak et al. 2003, Proc. Natl. Acad. Sci. U.S.A. 100:12343–8] and identified 3 differentially expressed serum proteins for the diagnosis of ovarian cancer (OC [Kozak et al. 2005, Proteomics, 5:4589–96], namely, apolipoprotein A-I (apoA-I, transthyretin (TTR and transferin (TF. The objective of the present study is to determine the efficacy of the three OC biomarkers for the detection of early stage (ES OC, in direct comparison to CA125.Methods: The levels of CA125, apoA-I, TTR and TF were measured in 392 serum samples [82 women with normal ovaries (N, 24 women with benign ovarian tumors (B, 85 women with ovarian tumors of low malignant potential (LMP, 126 women with early stage ovarian cancer (ESOC, and 75 women with late stage ovarian cancer (LSOC], obtained through the GOG and Cooperative Human Tissue Network. Following statistical analysis, multivariate regression models were built to evaluate the utility of the three OC markers in early detection.Results: Multiple logistic regression models (MLRM utilizing all biomarker values (CA125, TTR, TF and apoA-I from all histological subtypes (serous, mucinous, and endometrioid adenocarcinoma distinguished normal samples from LMP with 91% sensitivity (specifi city 92%, and normal samples from ESOC with a sensitivity of 89% (specifi city 92%. MLRM, utilizing values of all four markers from only the mucinous histological subtype showed that collectively, CA125, TTR, TF and apoA-I, were able to distinguish normal samples from mucinous LMP with 90% sensitivity, and further distinguished normal samples from early stage mucinous ovarian cancer with a sensitivity of 95%. In contrast, in serum samples from patients with mucinous tumors, CA125 alone was able to distinguish normal samples from LMP and early stage ovarian cancer with a sensitivity of

Applying an artificial neural network model for developing a severity score for patients with hereditary amyloid polyneuropathy.

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Novis, Shenia; Machado, Felipe; Costa, Victor B; Foguel, Debora; Cruz, Marcia W; de Seixas, José Manoel

2017-09-01

Hereditary (familial) amyloid polyneuropathy (FAP) is a systemic disease that includes a sensorimotor polyneuropathy related to transthyretin (TTR) mutations. So far, a scale designed to classify the severity of this disease has not yet been validated. This work proposes the implementation of an artificial neural network (ANN) in order to develop a severity scale for monitoring the disease progression in FAP patients. In order to achieve this goal, relevant symptoms and laboratory findings were collected from 98 Brazilian patients included in THAOS - the Transthyretin Amyloidosis Outcomes Survey. Ninety-three percent of them bore Val30Met, the most prevalent variant of TTR worldwide; 63 were symptomatic and 35 were asymptomatic. These data were numerically codified for the purpose of constructing a Self-Organizing Map (SOM), which maps data onto a grid of artificial neurons. Mapped data could be clustered by similarity into five groups, based on increasing FAP severity (from Groups 1 to 5). Most symptoms were virtually absent from patients who mapped to Group 1, which also includes the asymptomatic patients. Group 2 encompasses the patients bearing symptoms considered to be initial markers of FAP, such as first signs of walking disabilities and lack of sensitivity to temperature and pain. Interestingly, the patients with cardiac symptoms, which also carry cardiac-associated mutations of the TTR gene (such as Val112Ile and Ala19Asp), were concentrated in Group 3. Symptoms such as urinary and fecal incontinence and diarrhea characterized particularly Groups 4 and 5. Renal impairment was found almost exclusively in Group 5. Model validation was accomplished by considering the symptoms from a sample with 48 additional Brazilian patients. The severity scores proposed here not only identify the current stage of a patient's disease but also offer to the physician an easy-to-read, 2D map that makes it possible to track disease progression.

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring.

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Durston, Kirk K; Chiu, David Ky; Wong, Andrew Kc; Li, Gary Cl

2012-07-13

Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Our results

Molecular Basis for Certain Neuroprotective Effects of Thyroid Hormone

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Paul eDavis

2011-10-01

Full Text Available The pathophysiology of brain damage that is common to ischemia-reperfusion inury and brain trauma includes disordered neuronal and glial cell energetics, intracellular acidosis, calcium toxicity, extracellular excitotoxic glutamate accumulation and dysfunction of the cytoskeleton and endoplasmic reticulum. Thyroid hormone isoforms, 3, 5, 3'-triiodo-L-thyronine (T3 and L-thyroxine (T4, have nongenomic and genomic actions that are relevant to repair of certain features of the pathophysiology of brain damage. Thyroid hormone can nongenomically repair intracullar H+ accumulation by stimulation of the Na+/H+ exchanger and can support desirably low [Ca2+]i.c. by activation of plasma membrane Ca2+-ATPase. Thyroid hormone nongenomically stimulates astrocyte glutamate uptake, an action that protects both glial cells and neurons. The hormone supports the integrity of the cytoskeleton by its effect on actin. Several proteins linked to thyroid hormone action are also neuroprotective. For example, the hormone stimulates expression of the seladin-1 gene whose gene product is anti-apoptotic and is potentially protection in the setting of neurodegeneration. Transthyretin (TTR is a serum transport protein for T4 that is important to blood-brain barrier transfer of the hormone and TTR has also been found to be neuroprotective in the setting of ischemia. Finally, the interesting thyronamine derivatives of T4 have been shown to protect against ischemic brain damage through their ability to induce hypothermia in the intact organism. Thus, thyroid hromone or hormone derivatives have experimental promise as neuroprotective agents.

Crystal structure of tabtoxin resistance protein complexed with acetyl coenzyme A reveals the mechanism for beta-lactam acetylation.

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He, Hongzhen; Ding, Yi; Bartlam, Mark; Sun, Fei; Le, Yi; Qin, Xincheng; Tang, Hong; Zhang, Rongguang; Joachimiak, Andrzej; Liu, Jinyuan; Zhao, Nanming; Rao, Zihe

2003-01-31

Tabtoxin resistance protein (TTR) is an enzyme that renders tabtoxin-producing pathogens, such as Pseudomonas syringae, tolerant to their own phytotoxins. Here, we report the crystal structure of TTR complexed with its natural cofactor, acetyl coenzyme A (AcCoA), to 1.55A resolution. The binary complex forms a characteristic "V" shape for substrate binding and contains the four motifs conserved in the GCN5-related N-acetyltransferase (GNAT) superfamily, which also includes the histone acetyltransferases (HATs). A single-step mechanism is proposed to explain the function of three conserved residues, Glu92, Asp130 and Tyr141, in catalyzing the acetyl group transfer to its substrate. We also report that TTR possesses HAT activity and suggest an evolutionary relationship between TTR and other GNAT members.

Effect-directed analysis to explore the polar bear exposome: identification of thyroid hormone disrupting compounds in plasma.

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Simon, Eszter; van Velzen, Martin; Brandsma, Sicco H; Lie, Elisabeth; Løken, Katharina; de Boer, Jacob; Bytingsvik, Jenny; Jenssen, Bjørn M; Aars, Jon; Hamers, Timo; Lamoree, Marja H

2013-08-06

Compounds with transthyretin (TTR)-binding potency in the blood plasma of polar bear cubs were identified with effect-directed analysis (EDA). This approach contributes to the understanding of the thyroid disrupting exposome of polar bears. The selection of these samples for in-depth EDA was based on the difference between the observed TTR-binding potency on the one hand and the calculated potency (based on known concentrations of TTR-binding compounds and their relative potencies) on the other. A library-based identification was applied to the liquid chromatography-time-of-flight-mass spectrometry (LC-ToF-MS) data by screening for matches between compound lists and the LC-ToF-MS data regarding accurate mass and isotope pattern. Then, isotope cluster analysis (ICA) was applied to the LC-ToF-MS data allowing specific screening for halogen isotope patterns. The presence of linear and branched nonylphenol (NP) was observed for the first time in polar bears. Furthermore, the presence of one di- and two monohydroxylated octachlorinated biphenyls (octaCBs) was revealed in the extracts. Linear and branched NP, 4'-OH-CB201 and 4,4'-OH-CB202 could be successfully confirmed with respect to their retention time in the analytical system. In addition, branched NP, mono- and dihydroxylated-octaCBs showed TTR-binding potencies and could explain another 32 ± 2% of the total measured activities in the extracts.

The evaluation of preoperative nutritional status in patients undergoing thoracic surgery.

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Trufă, D I; Arhire, Lidia Iuliana; Niţă, Otilia; Gherasim, Andreea; Niţă, G; Graur, Mariana

2014-01-01

The aim of this study was to assess the preoperative nutritional status of patients undergoing thoracic surgery using different nutritional tools. . We conducted a prospective study on a sample of 43 thoracic patients, including 23 with neoplasms and 20 with non-neoplastic pathology who underwent thoracic surgery procedures between July-September 2011, in the Thoracic Surgery Clinic in Iaşi. Weight and height were measured and body mass index (BMI) was calculated. WHO classification for BMI categories was used. Preoperative serum level of transthyretin (TTR) and demographic data (gender, age) were also assessed. All patients were examined by the Subjective Global Assessment (SGA) and the Nutritional Risk Screening 2002 (NRS 2002). After performing SGA, 67.9% of the patients were well-nourished, 21.4% were moderately or suspected of being malnourished and 10.7% were severely malnourished. The level of TTR was significantly lower in the moderately or severely malnourished group, compared to those considered well-nourished. According to NRS-2002, 42.9% of the patients were considered at nutritional risk. The level of TTR of these patients was lower than the level of TTR of the patients without nutritional risk, but without statistical significance. Subjective Global Assessment (SGA) and the Nutritional Risk Screening 2002 (NRS 2002) are useful in identifying patients with nutritional risk, so that appropriate nutritional management could be initialised even before surgery.

Crystal structure of tabtoxin resistance protein complexed with acetyl coenzyme A reveals the mechanism for {beta}-lactam acetylation.

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He, H.; Ding, Y.; Bartlam, M.; Sun, F.; Le, Y.; Qin, X.; Tang, H.; Zhang, R.; Joachimiak, A.; Liu, J.; Zhao, N.; Rao, Z.; Biosciences Division; Tsinghua Univ.; Chinese Academy of Science

2003-01-31

Tabtoxin resistance protein (TTR) is an enzyme that renders tabtoxin-producing pathogens, such as Pseudomonas syringae, tolerant to their own phytotoxins. Here, we report the crystal structure of TTR complexed with its natural cofactor, acetyl coenzyme A (AcCoA), to 1.55 {angstrom} resolution. The binary complex forms a characteristic 'V' shape for substrate binding and contains the four motifs conserved in the GCN5-related N-acetyltransferase (GNAT) superfamily, which also includes the histone acetyltransferases (HATs). A single-step mechanism is proposed to explain the function of three conserved residues, Glu92, Asp130 and Tyr141, in catalyzing the acetyl group transfer to its substrate. We also report that TTR possesses HAT activity and suggest an evolutionary relationship between TTR and other GNAT members.

Lumbosacral stenosis in Labrador retriever military working dogs - an exomic exploratory study.

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Mukherjee, Meenakshi; Jones, Jeryl C; Yao, Jianbo

2017-01-01

Canine lumbosacral stenosis is defined as narrowing of the caudal lumbar and/or sacral vertebral canal. A risk factor for neurologic problems in many large sized breeds, lumbosacral stenosis can also cause early retirement in Labrador retriever military working dogs. Though vital for conservative management of the condition, early detection is complicated by the ambiguous nature of clinical signs of lumbosacral stenosis in stoic and high-drive Labrador retriever military working dogs. Though clinical diagnoses of lumbosacral stenosis using CT imaging are standard, they are usually not performed unless dogs present with clinical symptoms. Understanding the underlying genomic mechanisms would be beneficial in developing early detection methods for lumbosacral stenosis, which could prevent premature retirement in working dogs. The exomes of 8 young Labrador retriever military working dogs (4 affected and 4 unaffected by lumbosacral stenosis, phenotypically selected by CT image analyses from 40 dogs with no reported clinical signs of the condition) were sequenced to identify and annotate exonic variants between dogs negative and positive for lumbosacral stenosis. Two-hundred and fifty-two variants were detected to be homozygous for the wild allele and either homozygous or heterozygous for the variant allele. Seventeen non-disruptive variants were detected that could affect protein effectiveness in 7 annotated (SCN1B, RGS9BP, ASXL3, TTR, LRRC16B, PTPRO, ZBBX) and 3 predicted genes (EEF1A1, DNAJA1, ZFX). No exonic variants were detected in any of the canine orthologues for human lumbar spinal stenosis candidate genes. TTR (transthyretin) gene could be a possible candidate for lumbosacral stenosis in Labrador retrievers based on previous human studies that have reported an association between human lumbar spinal stenosis and transthyretin protein amyloidosis. Other genes identified with exonic variants in this study but with no known published association with lumbosacral

Frequency of and Prognostic Significance of Cardiac Involvement at Presentation in Hereditary Transthyretin-Derived Amyloidosis and the Value of N-Terminal Pro-B-Type Natriuretic Peptide.

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Klaassen, Sebastiaan H C; Tromp, Jasper; Nienhuis, Hans L A; van der Meer, Peter; van den Berg, Maarten P; Blokzijl, Hans; van Veldhuisen, Dirk J; Hazenberg, Bouke P C

2018-01-01

The aim of this study is to assess the prevalence of cardiac involvement in hereditary transthyretin-derived (ATTRm) amyloidosis at the time of diagnosis and to determine the diagnostic and clinical value of N-terminal pro-B-type natriuretic peptide (NT-proBNP). The University Medical Center Groningen is the national center of expertise for amyloidosis. All consecutive patients between 1994 and 2016 with ATTRm amyloidosis were followed prospectively. Baseline was set at the time of the first positive biopsy. All patients underwent a standard cardiac and neurologic work-up. Cardiac involvement was defined by otherwise unexplained left and/or right ventricular wall hypertrophy on cardiac ultrasound and/or advanced conduction disturbances. Seventy-seven patients had ATTRm amyloidosis and were included in the study. The TTR V30M mutation was present in 30 patients (39%). In both the V30M and the non-V30M groups, the neurologic presentation dominated (77% vs 51%), whereas cardiac presentation was infrequent (7% vs 15%). Clinical work-up showed that cardiac involvement was present at baseline in 51% of all patients irrespective of genotype and was associated with increased overall mortality (hazard ratio 5.95, 95% confidence interval 2.12 to 16.7), independent from clinical confounders. At a cutoff level of 125 ng/L, NT-proBNP had a sensitivity of 92% for establishing cardiac involvement. In conclusion, irrespective of the frequent noncardiac presentation of ATTRm amyloidosis, cardiac involvement is already present at diagnosis in half of the patients and is associated with increased mortality. NT-proBNP is a useful marker to determine cardiac involvement in this disease. Copyright © 2017 Elsevier Inc. All rights reserved.

Proteomic biomarkers apolipoprotein A1, truncated transthyretin and connective tissue activating protein III enhance the sensitivity of CA125 for detecting early stage epithelial ovarian cancer.

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Clarke, Charlotte H; Yip, Christine; Badgwell, Donna; Fung, Eric T; Coombes, Kevin R; Zhang, Zhen; Lu, Karen H; Bast, Robert C

2011-09-01

The low prevalence of ovarian cancer demands both high sensitivity (>75%) and specificity (99.6%) to achieve a positive predictive value of 10% for successful early detection. Utilizing a two stage strategy where serum marker(s) prompt the performance of transvaginal sonography (TVS) in a limited number (2%) of women could reduce the requisite specificity for serum markers to 98%. We have attempted to improve sensitivity by combining CA125 with proteomic markers. Sera from 41 patients with early stage (I/II) and 51 with late stage (III/IV) epithelial ovarian cancer, 40 with benign disease and 99 healthy individuals, were analyzed to measure 7 proteins [Apolipoprotein A1 (Apo-A1), truncated transthyretin (TT), transferrin, hepcidin, ß-2-microglobulin (ß2M), Connective Tissue Activating Protein III (CTAPIII), and Inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4)]. Statistical models were fit by logistic regression, followed by optimization of factors retained in the models determined by optimizing the Akaike Information Criterion. A validation set included 136 stage I ovarian cancers, 140 benign pelvic masses and 174 healthy controls. In a training set analysis, the 3 most effective biomarkers (Apo-A1, TT and CTAPIII) exhibited 54% sensitivity at 98% specificity, CA125 alone produced 68% sensitivity and the combination increased sensitivity to 88%. In a validation set, the marker panel plus CA125 produced a sensitivity of 84% at 98% specificity (P=0.015, McNemar's test). Combining a panel of proteomic markers with CA125 could provide a first step in a sequential two-stage strategy with TVS for early detection of ovarian cancer. Copyright © 2011. Published by Elsevier Inc.

3,3',5-Triiodo-L-thyronine-like activity in effluents from domestic sewage treatment plants detected by in vitro and in vivo bioassays

International Nuclear Information System (INIS)

Murata, Tomonori; Yamauchi, Kiyoshi

2008-01-01

Thyroid system-disrupting activity in effluents from municipal domestic sewage treatment plants was detected using three in vitro assays and one in vivo assay. Contaminants in the effluents were extracted by solid-phase extraction (SPE) and eluted stepwise with different organic solvents. The majority of the thyroid system-disrupting activity was detected in the dichloromethane/methanol (1/1) fraction after SPE in all three in vitro assays: competitive assays of 3,3',5-[ 125 I]triiodo-L-thyronine ([ 125 I]T 3 ) binding to the plasma protein transthyretin (TTR assay) and thyroid hormone receptor (TR assay) and T 3 -dependent luciferase assay (Luc assay). Subsequent reverse-phase high-performance liquid chromatography (RP-HPLC) of the dichloromethane/methanol (1/1) fraction separated contaminants potent in the TR and Luc assays from those potent in the TTR assay. The contaminants potent in the TR and Luc assays were also potent in an in vivo short-term gene expression assay in Xenopus laevis (Tadpole assay). The present study demonstrated that the effluents from domestic sewage treatment plants contain contaminants with T 3 -like activity of ∼ 10 -10 M T 3 -equivalent concentration (T 3 EQ) and that the TR and Luc assays are powerful in vitro bioassays for detecting thyroid system-disrupting activity in effluents. The availability and applicability of these bioassays for screening contaminants with thyroid system-disrupting activity in the water environment are discussed

Randomized controlled trial of a protein substitute with prolonged release on the protein status of children with phenylketonuria.

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Giovannini, Marcello; Riva, Enrica; Salvatici, Elisabetta; Cefalo, Graziella; Radaelli, Giovanni

2014-01-01

To examine whether a phenylalanine-free protein substitute with prolonged release may be beneficial to the protein status of children with phenylketonuria (PKU) compared to conventional substitutes. Sixty children with PKU, 7 to 16 years of age, were randomly allocated to receive either a prolonged-release (test) or the current conventional protein substitute for 30 days. Subjects were additionally sex and age matched with 60 subjects with mild hyperphenylalaninemia and 60 unaffected subjects. The protein status in children with PKU was assessed by albumin, transthyretin, and retinol-binding protein (RBP), and changes throughout the trial period were the primary outcome measures. Children with PKU did not differ in anthropometry from children with mild hyperphenylalaninemia or unaffected children but they ingested lower amounts of proteins (p phenylketonuria.

Up-Regulation of Antioxidant Proteins in the Plasma Proteome during Saturation Diving: Unique Coincidence under Hypobaric Hypoxia.

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Domoto, Hideharu; Iwaya, Keiichi; Ikomi, Fumitaka; Matsuo, Hirotaka; Tadano, Yutaka; Fujii, Shigenori; Tachi, Kazuyoshi; Itoh, Yoshiyuki; Sato, Michiya; Inoue, Kimitoshi; Shinomiya, Nariyoshi

2016-01-01

Saturation diving (SD) is one of the safest techniques for tolerating hyperbaric conditions for long durations. However, the changes in the human plasma protein profile that occur during SD are unknown. To identify differential protein expression during or after SD, 65 blood samples from 15 healthy Japanese men trained in SD were analyzed by two-dimensional fluorescence difference gel electrophoresis. The expression of two proteins, one 32.4 kDa with an isoelectric point (pI) of 5.8 and the other 44.8 kDa with pI 4.0, were elevated during SD to 60, 100, and 200 meters sea water (msw). The expression of these proteins returned to pre-diving level when the SD training was completed. The two proteins were identified using in-gel digestion and mass spectrometric analysis; the 32.4 kDa protein was transthyretin and the 44.8 kDa protein was alpha-1-acid glycoprotein 1. Oxidation was detected at methionine 13 of transthyretin and at methionine 129 of alpha-1-acid glycoprotein 1 by tandem mass spectrometry. Moreover, haptoglobin was up-regulated during the decompression phase of 200 msw. These plasma proteins up-regulated during SD have a common function as anti-oxidants. This suggests that by coordinating their biological effects, these proteins activate a defense mechanism to counteract the effects of hyperbaric-hyperoxic conditions during SD.

Up-Regulation of Antioxidant Proteins in the Plasma Proteome during Saturation Diving: Unique Coincidence under Hypobaric Hypoxia.

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Hideharu Domoto

Full Text Available Saturation diving (SD is one of the safest techniques for tolerating hyperbaric conditions for long durations. However, the changes in the human plasma protein profile that occur during SD are unknown. To identify differential protein expression during or after SD, 65 blood samples from 15 healthy Japanese men trained in SD were analyzed by two-dimensional fluorescence difference gel electrophoresis. The expression of two proteins, one 32.4 kDa with an isoelectric point (pI of 5.8 and the other 44.8 kDa with pI 4.0, were elevated during SD to 60, 100, and 200 meters sea water (msw. The expression of these proteins returned to pre-diving level when the SD training was completed. The two proteins were identified using in-gel digestion and mass spectrometric analysis; the 32.4 kDa protein was transthyretin and the 44.8 kDa protein was alpha-1-acid glycoprotein 1. Oxidation was detected at methionine 13 of transthyretin and at methionine 129 of alpha-1-acid glycoprotein 1 by tandem mass spectrometry. Moreover, haptoglobin was up-regulated during the decompression phase of 200 msw. These plasma proteins up-regulated during SD have a common function as anti-oxidants. This suggests that by coordinating their biological effects, these proteins activate a defense mechanism to counteract the effects of hyperbaric-hyperoxic conditions during SD.

Comparação entre a relação PCR/albumina e o índice prognóstico inflamatório nutricional (IPIN Comparison of PCR/albumin ratio with prognostic inflammatory nutritional index (PINI

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Camila Renata Corrêa

2002-07-01

diferenciação G3 > (G1 = G2 e G3 > G3A. Entre todas as proteínas dosadas apenas PCR, Alb e TTR discriminaram os grupos: sendo G3 > (G1= G2 para PCR e G3 G3A (para PCR e G3D The inflammatory stress of hospitalyzed patients was quantified according to their plasma levels of acute-phase proteins (APP. The data from 54 adult (48 ± 20 yrs patients were retrospectively (1994-1998 analysed along with other 12 healthy controls. The major pathologies were peripheral vascular disease (22 , penphigus pholiaceos (7, inflammatory bowel disease (7, trauma (6 and orthognatic post surgery (3. Samples of fasting venous blood were drawn and their plasma used for positive (+ and negative (- APP by nephelometric assays. Among assayed APP+ were C-reactive protein (CRP, acid alpha-1-glycoprotein (AAG, alpha-1-antitrypsin (AAT and ceruloplasmim (CER while albumin (Alb, transthyretin (TTR, transferrin (TF and retinol-binding protein (RBP were the APP- representatives. A significant relationship (Spearman test was found between the variables CRP ´ AAG (r = 0.49, Alb ´ TTR (r = 0.60, Alb ´ RBP (0.58, Alb ´ TF (r = 0.39, TTR ´ RBP (r = 0.56 and TTR ´TF (r = 0.43. The stronger relationships between APP+ ´ APP- were found for CRP ´ Alb (r = - 0.71, CRP ´ TTR (- 0.54, CRP ´ TF (r = - 0.39 and AAG ´ Alb (r = - 0.35. By assembling the APP according to the prognostic inflammatory nutritional index (PINI proposed by Ingenbleek & Carpentier (Int. J. Vitam. Nutr. Res., 55: 91, 1985 the obtained data allowed a group distribution as healthy controls (G1, patients without (PINI 1, G3. The later was split as lower (G3A, n =16 medium (G3B, n =10 and high (G3C, n = 6 risk and mortality-risk (G3D, n =11. The PINI values differentiated (non-parametric Kruskall-Wallis test G3 > (G1= G2 and G3 > G3A. Among all assayed proteins only CRP, Alb and TTR discriminated groups as G3 > (G1= G2 for CRP or G3 G3A (for CRP and G3D < G3A (for TTR and TF. The correlation coeficient allowed only APP-- substitutions at

Transplacental transport and fetal localization of bispehnol A, tetrabromobisphenol A and 2,4,6-tribromophenol in mice

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Sundberg, A.; Brunstroem, B.; Brandt, I. [Uppsala Univ. (Sweden). Dept. of Environmental Toxicology; Cantillana, T.; Bergman, Aa. [Stockholm Univ. (Sweden). Dept. of Environmental Chemistry

2004-09-15

Bisphenol A (BPA) is an intermediate in the production of epoxy resins, while its brominated derivative tetrabromobishenol A (TBBPA) and its photolysis degradation product 2,4,6-tribromophenol (TBP) are widely used flame retardants. These brominated compounds have been identified in human blood. TBBPA, TBP and a number of 4-hydroxy-PCBs (e.g. 4-OH-CB107) are high affinity ligands for the thyroxin (T4) transporter transthyretin (TTR) in rodents and other species. Displacement of T4 from the TTR binding site has been proposed as an important mechanism of endocrine disruption by certain halogenated phenolic environmental pollutants. BPA is a fairly potent environmental estrogen receptor agonist that can induce an array of estrogenic effects in several species including mammals, birds and fish. Although the estrogenic activity of TBBPA is less obvious, this brominated BPA analog has been reported to interact with the estrogen receptor and induce estrogenic effects in some in vitro test systems. While the reproductive and developmental toxicity of BPA is well documented, there is evidence that also halogenated phenolic compounds can pass the placental barrier and induce such toxicity. Within the objectives of the COMPARE EU project we study the fetal and maternal kinetics and transplacental transport of phenolic environmental pollutants in pregnant mice. To explore the role of TTR in the placental and blood-brain barrier transport, we employ TTR-deficient mice. For comparative reasons, we also explore the transfer to bird embryos following injection into the yolk or administration to the egg-laying bird. In the present communication, we report on the disposition of BPA, TBBPA and TBP in the fetoplacental unit in pregnant wild-type mice.

Use of electrophoretically separated serum protein fractions for the diagnosis of cardiomyopathy

International Nuclear Information System (INIS)

Siddiqui, Z.H.; Cheema, A.M.

2011-01-01

In an investigation of molecular pathogenesis in cardiovascular diseases, the blood samples of the patients diagnosed for cardiomyopathy (CMP) were obtained from the Punjab Institute of Cardiology, Lahore. Blood samples of the healthy subjects of comparable age group without any history of cardiac ailment were also collected for the control comparisons. The sera of CMP were separated and used for the study of the protein profiles with sodium dodecyle sulfate polyacrylamide gel electrophoresis (SDS-PAGE) in first dimension. Quantification of various protein fractions done by Gene Genius Bio-imaging Gel Documentation System that provide the data of molecular weights and the percent raw volume covered by each of the fractions. The protein fractions that showed significant variation were separated by using the technique of electro blotting and electro elution and run on isoelectric focusing (IEF) in second dimension to determine their isoelectric points. The most pertinent results in the comparison were the significant increase in apolipoprotein B, Ceruloplasmin, apolipoprotein A-I and transthyretin in the sera of patients of CMP compared to healthy subjects. These results show that level of apolipoprotein B, Ceruloplasmin, apolipoprotein A-I and transthyretin are strong predictor of CMP and can also be used for the diagnosis of CMP. (author)

Effects of low dose radiation on differential expression of serum protein in mice

International Nuclear Information System (INIS)

Chen Wei; He Ying; Shen Xianrong

2014-01-01

The aim is to find out the key proteins related with low dose radiation (Ld) by parametric technology, which provided the theory foundation for LDR protection Two-dimensional electrophoresis (2-DE) was performed on serum protein Differential expression proteins were identified by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and database analysis Compared with the control group, 7 altered proteins was definite in terms of apolipoprotein C-Ⅲ, beta-globin parotid secretory protein alpha-2-macroglobulin precursor, mouse transthyretin, C1qc protein and clusterin. Some proteins related with LDR are found. It may provide some new explanations for the mechanism of LDR. (authors)

An attempt to validate serum and plasma as sample matrices for analyses of polychlorobiphenylols

Energy Technology Data Exchange (ETDEWEB)

Weiss, J.; Bergman, Aa. [Stockholm Univ. (Sweden). Dept. of Environmental Chemistry; Bignert, A. [Museum of Natural History (Sweden)

2004-09-15

Polychlorinated biphenyls (PCBs) form hydroxylated metabolites (OH-PCBs), as reported both from wildlife and from experimental animal studies already in the early 1970s'. However, the interest increased in OH-PCBs from the mid 1990s' depending on the discovery that some OHPCB congeners are strongly retained in the blood of birds, fish and mammals, including humans. The interest is linked to the fact that OH-PCBs is strongly, but reversibly, bound to the blood protein transthyretin (TTR). It is reasonable to believe that the strong TTR binding may have toxicological impact, probably related to endocrine type effects. Importantly, OH-PCBs are present in blood at far higher concentrations than in any other compartment in the body, which is dependent on the physico-chemical characteristics of the phenols. Analyses of OH-PCBs have thus been concentrated to whole blood, plasma or serum. Still there is no comparison between the three sample types even though it is clear that whole blood is not optimal due to the large proportion of haemoglobin in the sample that make the clean up more difficult than if plasma or serum is selected for analysis. In the present study we have addressed two questions: First we have looked at any potential differences in the analytical results of OH-PCBs when using serum and plasma for extraction and clean up; Second, the serum and plasma applied in the validation has been unfrozen, frozen (at -20 C) for two months and frozen for twenty months, respectively.

Estimating the global prevalence of transthyretin familial amyloid polyneuropathy

Science.gov (United States)

Waddington‐Cruz, Márcia; Botteman, Marc F.; Carter, John A.; Chopra, Avijeet S.; Hopps, Markay; Stewart, Michelle; Fallet, Shari; Amass, Leslie

2018-01-01

ABSTRACT Introduction: This study sought to estimate the global prevalence of transthyretin familial amyloid polyneuropathy (ATTR‐FAP). Methods: Prevalence estimates and information supporting prevalence calculations was extracted from records yielded by reference‐database searches (2005–2016), conference proceedings, and nonpeer reviewed sources. Prevalence was calculated as prevalence rate multiplied by general population size, then extrapolated to countries without prevalence estimates but with reported cases. Results: Searches returned 3,006 records; 1,001 were fully assessed and 10 retained, yielding prevalence for 10 “core” countries, then extrapolated to 32 additional countries. ATTR‐FAP prevalence in core countries, extrapolated countries, and globally was 3,762 (range 3639–3884), 6424 (range, 1,887–34,584), and 10,186 (range, 5,526–38,468) persons, respectively. Discussion: The mid global prevalence estimate (10,186) approximates the maximum commonly accepted estimate (5,000–10,000). The upper limit (38,468) implies potentially higher prevalence. These estimates should be interpreted carefully because contributing evidence was heterogeneous and carried an overall moderate risk of bias. This highlights the requirement for increasing rare‐disease epidemiological assessment and clinician awareness. Muscle Nerve 57: 829–837, 2018 PMID:29211930

Cytotoxic effects of TBBPA and its interactions with signalling pathways in mammalian cells

Energy Technology Data Exchange (ETDEWEB)

Strack, S.; Sander, M.; Detzel, T.; Krug, H.F. [Forschungszentrum Kalsruhe (Germany). Inst. fuer Toxikologie und Genetik; Kuch, B. [Stuttgart Univ. (Germany). Inst. fuer Siedlungswasserbau und Wasserguetewirtschaft

2004-09-15

Toxic effects of TBBPA published so far have been recently reviewed by Birnbaum and Staskal The LC{sub 50} indicating the acute toxicity in vivo due to a single oral dose in mice and rats were higher than 4 to 5 g/kg, however, systematically long-term in vivo studies are missing. Weak estrogenic effects have been described by Meerts et al., demonstrating for TBBPA less pronounced activity than for other brominated bisphenols. The same group described competitive interactions in vitro with human transthyretin (TTR). In binding affinity assays they could demonstrate that TBBPA binds to TTR ten times more effectively than T{sub 4}. However, the available toxicological data are still extremely limited. For a comprehensive risk assessment valid data are insufficient. The aim of this study was to evaluate possible cytotoxic effects, and to gain insights into the underlying molecular mechanisms respectively the corresponding cellular signalling processes. This approach would allow to identify sensitive end-points of cellular toxicological responses. For these molecular toxicological investigations established cell lines should be used, in order to have a suitable model for appropriate toxicological studies.

Frequency of and Prognostic Significance of Cardiac Involvement at Presentation in Hereditary Transthyretin-Derived Amyloidosis and the Value of N-Terminal Pro-B-Type Natriuretic Peptide

NARCIS (Netherlands)

Klaassen, Sebastiaan H C; Tromp, Jasper; Nienhuis, Hans L A; van der Meer, Peter; van den Berg, Maarten P; Blokzijl, Hans; van Veldhuisen, Dirk J; Hazenberg, Bouke P C

2018-01-01

The aim of this study is to assess the prevalence of cardiac involvement in hereditary transthyretin-derived (ATTRm) amyloidosis at the time of diagnosis and to determine the diagnostic and clinical value of N-terminal pro-B-type natriuretic peptide (NT-proBNP). The University Medical Center

FOLATE CYCLE GENE POLYMORPHISM AND ENDOGENOUS PEPTIDES IN CHILDREN WITH COW’S MILK PROTEIN ALLERGY

Directory of Open Access Journals (Sweden)

T. A. Shumatova

2016-01-01

Full Text Available Folate cycle gene polymorphisms and the levels of endogenous antimicrobial peptides and proteins in the blood and coprofiltrates were studied in 45 children aged 3 to 12 months with cow’s milk protein allergy. The polymorphic variants of the MTHFR, MTRR, and MTR genes were shown to be considered as a risk factor for the development of allergy. There was a significant increase in the levels of zonulin, β-defensin 2, transthyretin, and eosinophil cationic protein in the coprofiltrates and in those of eotaxin, fatty acidbinding proteins, and membrane permeability-increasing protein in the serum (p<0.05. The finding can improve the diagnosis of the disease for a predictive purpose for the evaluation of the efficiency of performed therapy.

Validation of serum markers for blood-brain barrier disruption in traumatic brain injury.

Science.gov (United States)

Blyth, Brian J; Farhavar, Arash; Gee, Christopher; Hawthorn, Brendan; He, Hua; Nayak, Akshata; Stöcklein, Veit; Bazarian, Jeffrey J

2009-09-01

The blood-brain barrier (BBB), which prevents the entry into the central nervous system (CNS) of most water-soluble molecules over 500 Da, is often disrupted after trauma. Post-traumatic BBB disruption may have important implications for prognosis and therapy. Assessment of BBB status is not routine in clinical practice because available techniques are invasive. The gold-standard measure, the cerebrospinal fluide (CSF)-serum albumin quotient (Q(A)), requires the measurement of albumin in CSF and serum collected contemporaneously. Accurate, less invasive techniques are necessary. The objective of this study was to evaluate the relationship between Q(A) and serum concentrations of monomeric transthyretin (TTR) or S100B. Nine subjects with severe traumatic brain injury (TBI; Glasgow Coma Scale [GCS] score < or =8) and 11 subjects with non-traumatic headache who had CSF collected by ventriculostomy or lumbar puncture (LP) were enrolled. Serum and CSF were collected at the time of LP for headache subjects and at 12, 24, and 48 h after ventriculostomy for TBI subjects. The Q(A) was calculated for all time points at which paired CSF and serum samples were available. Serum S100B and TTR levels were also measured. Pearson's correlation coefficient and area under the receiver operating characteristic (ROC) curve were used to determine the relationship between the serum proteins and QA. Seven TBI subjects had abnormal Q(A)'s indicating BBB dysfunction. The remaining TBI and control subjects had normal BBB function. No significant relationship between TTR and QA was found. A statistically significant linear correlation between serum S100B and Q(A) was present (r = 0.432, p = 0.02). ROC analysis demonstrated a significant relationship between Q(A) and serum S100B concentrations at 12 h after TBI (AUC = 0.800; SE 0.147, 95% CI 0.511-1.089). Using an S100B concentration cutoff of 0.027 ng=ml, specificity for abnormal Q(A) was 90% or higher at each time point. We conclude that

Delineation of concentration ranges and longitudinal changes of human plasma protein variants.

Directory of Open Access Journals (Sweden)

Olgica Trenchevska

Full Text Available Human protein diversity arises as a result of alternative splicing, single nucleotide polymorphisms (SNPs and posttranslational modifications. Because of these processes, each protein can exists as multiple variants in vivo. Tailored strategies are needed to study these protein variants and understand their role in health and disease. In this work we utilized quantitative mass spectrometric immunoassays to determine the protein variants concentration of beta-2-microglobulin, cystatin C, retinol binding protein, and transthyretin, in a population of 500 healthy individuals. Additionally, we determined the longitudinal concentration changes for the protein variants from four individuals over a 6 month period. Along with the native forms of the four proteins, 13 posttranslationally modified variants and 7 SNP-derived variants were detected and their concentration determined. Correlations of the variants concentration with geographical origin, gender, and age of the individuals were also examined. This work represents an important step toward building a catalog of protein variants concentrations and examining their longitudinal changes.

Closure Report for Corrective Action Unit 412: Clean Slate I Plutonium Dispersion (TTR) Tonopah Test Range, Nevada, Revision 0

International Nuclear Information System (INIS)

Matthews, Patrick

2016-01-01

This Closure Report (CR) presents information supporting the clean closure of Corrective Action Unit (CAU) 412: Clean Slate I Plutonium Dispersion (TTR), located on the Tonopah Test Range, Nevada. CAU 412 consists of a release of radionuclides to the surrounding soil from a storage-transportation test conducted on May 25, 1963. Corrective action investigation (CAI) activities were performed in April and May 2015, as set forth in the Streamlined Approach for Environmental Restoration (SAFER) Plan for Corrective Action Unit 412: Clean Slate I Plutonium Dispersion (TTR), Tonopah Test Range, Nevada; and in accordance with the Soils Activity Quality Assurance Plan. The purpose of the CAI was to fulfill data needs as defined during the data quality objectives process. The CAU 412 dataset of investigation results was evaluated based on a data quality assessment. This assessment demonstrated the dataset is complete and acceptable for use in fulfilling the data needs identified by the data quality objectives process. This CR provides documentation and justification for the clean closure of CAU 412 under the FFACO without further corrective action. This justification is based on historical knowledge of the site, previous site investigations, implementation of the 1997 interim corrective action, and the results of the CAI. The corrective action of clean closure was confirmed as appropriate for closure of CAU 412 based on achievement of the following closure objectives: Radiological contamination at the site is less than the final action level using the ground troops exposure scenario (i.e., the radiological dose is less than the final action level): Removable alpha contamination is less than the high contamination area criterion: No potential source material is present at the site, and any impacted soil associated with potential source material has been removed so that remaining soil contains contaminants at concentrations less than the final action levels: and There is

Closure Report for Corrective Action Unit 412: Clean Slate I Plutonium Dispersion (TTR) Tonopah Test Range, Nevada, Revision 0

Energy Technology Data Exchange (ETDEWEB)

Matthews, Patrick [Navarro, Las Vegas, NV (United States)

2016-08-22

This Closure Report (CR) presents information supporting the clean closure of Corrective Action Unit (CAU) 412: Clean Slate I Plutonium Dispersion (TTR), located on the Tonopah Test Range, Nevada. CAU 412 consists of a release of radionuclides to the surrounding soil from a storage–transportation test conducted on May 25, 1963. Corrective action investigation (CAI) activities were performed in April and May 2015, as set forth in the Streamlined Approach for Environmental Restoration (SAFER) Plan for Corrective Action Unit 412: Clean Slate I Plutonium Dispersion (TTR), Tonopah Test Range, Nevada; and in accordance with the Soils Activity Quality Assurance Plan. The purpose of the CAI was to fulfill data needs as defined during the data quality objectives process. The CAU 412 dataset of investigation results was evaluated based on a data quality assessment. This assessment demonstrated the dataset is complete and acceptable for use in fulfilling the data needs identified by the data quality objectives process. This CR provides documentation and justification for the clean closure of CAU 412 under the FFACO without further corrective action. This justification is based on historical knowledge of the site, previous site investigations, implementation of the 1997 interim corrective action, and the results of the CAI. The corrective action of clean closure was confirmed as appropriate for closure of CAU 412 based on achievement of the following closure objectives: Radiological contamination at the site is less than the final action level using the ground troops exposure scenario (i.e., the radiological dose is less than the final action level): Removable alpha contamination is less than the high contamination area criterion: No potential source material is present at the site, and any impacted soil associated with potential source material has been removed so that remaining soil contains contaminants at concentrations less than the final action levels: and There is

Effects of the soya isoflavone genistein in early life stages of the Senegalese sole, Solea senegalensis: Thyroid, estrogenic and metabolic biomarkers.

Science.gov (United States)

Sarasquete, Carmen; Úbeda-Manzanaro, Maria; Ortiz-Delgado, Juan Bosco

2017-09-01

This study examines the effects induced by environmentally relevant concentrations of the isoflavone genistein (3mg/L and 10mg/L) during early life stages of the Senegalese sole. Throughout the hypothalamus-pituitary-thyroid (HPT) axis, several neurohormonal regulatory thyroid signalling patterns (thyroglobulin/Tg, thyroid peroxidase/TPO, transthyretin/TTR, thyroid receptors/TRβ, and iodothrynonine deiodinases, Dio2 and Dio3) were analysed. Furthermore, the expression patterns of estrogen receptor ERβ and haemoprotein Cyp1a were also evaluated. In the control larvae, progressive increases of constitutive hormonal signalling pathways have been evidenced from the pre-metamorphosis phase onwards, reaching the highest expression basal levels at the metamorphosis (Tg, TPO, Dio2) and/or during post-metamorphosis (TTR, TRβ, ERβ). When the early larvae were exposed to both genistein concentrations (3mg/L and 10mg/L), a statistically significant down-regulation of TPO, TTR and Tg mRNA levels was clearly detected at the metamorphic stages. In addition, the Dio2 and Dio3 transcript expression levels were also down and up-regulated when exposed to both genistein concentrations. In the larvae exposed to genistein, no statistically significant responses were recorded for the TRβ expression patterns. Nevertheless, the ERβ and Cyp1a transcript levels were up-regulated at the middle metamorphic stage (S2, at 16 dph) in the larvae exposed to high genistein concentrations and, only the ERβ was down-regulated (S1, at 12dph) at the lower doses. Finally, all these pointed out imbalances were only temporarily disrupted by exposure to genistein, since most of the modulated transcriptional signals (i.e. up or down-regulation) were quickly restored to the baseline levels. Additionally, the control and genistein-exposed Senegalese sole specimens showed characteristic ontogenetic patterns and completely suitable for an optimal development, metamorphosis, and growth. Copyright © 2017

Validation of podocalyxin-like protein as a biomarker of poor prognosis in colorectal cancer

International Nuclear Information System (INIS)

Larsson, Anna; Fridberg, Marie; Gaber, Alexander; Nodin, Björn; Levéen, Per; Jönsson, Göran; Uhlén, Mathias; Birgisson, Helgi; Jirström, Karin

2012-01-01

Podocalyxin-like 1 (PODXL) is a cell-adhesion glycoprotein and stem cell marker that has been associated with an aggressive tumour phenotype and adverse outcome in several cancer types. We recently demonstrated that overexpression of PODXL is an independent factor of poor prognosis in colorectal cancer (CRC). The aim of this study was to validate these results in two additional independent patient cohorts and to examine the correlation between PODXL mRNA and protein levels in a subset of tumours. PODXL protein expression was analyzed by immunohistochemistry in tissue microarrays with tumour samples from a consecutive, retrospective cohort of 270 CRC patients (cohort 1) and a prospective cohort of 337 CRC patients (cohort 2). The expression of PODXL mRNA was measured by real-time quantitative PCR in a subgroup of 62 patients from cohort 2. Spearman´;s Rho and Chi-Square tests were used for analysis of correlations between PODXL expression and clinicopathological parameters. Kaplan Meier analysis and Cox proportional hazards modelling were applied to assess the relationship between PODXL expression and time to recurrence (TTR), disease free survival (DFS) and overall survival (OS). High PODXL protein expression was significantly associated with unfavourable clinicopathological characteristics in both cohorts. In cohort 1, high PODXL expression was associated with a significantly shorter 5-year OS in both univariable (HR = 2.28; 95% CI 1.43-3.63, p = 0.001) and multivariable analysis (HR = 2.07; 95% CI 1.25-3.43, p = 0.005). In cohort 2, high PODXL expression was associated with a shorter TTR (HR = 2.93; 95% CI 1.26-6.82, p = 0.013) and DFS (HR = 2.44; 95% CI 1.32-4.54, p = 0.005), remaining significant in multivariable analysis, HR = 2.50; 95% CI 1.05-5.96, p = 0.038 for TTR and HR = 2.11; 95% CI 1.13-3.94, p = 0.019 for DFS. No significant correlation could be found between mRNA levels and protein expression of PODXL and there was no association between mRNA levels

The structure of Serratia marcescens Lip, a membrane-bound component of the type VI secretion system

International Nuclear Information System (INIS)

Rao, Vincenzo A.; Shepherd, Sharon M.; English, Grant; Coulthurst, Sarah J.; Hunter, William N.

2011-01-01

The high-resolution crystal structure of S. marcescens Lip reveals a new member of the transthyretin family of proteins. Lip, a core component of the type VI secretion apparatus, is localized to the outer membrane and is positioned to interact with other proteins forming this complex system. Lip is a membrane-bound lipoprotein and a core component of the type VI secretion system found in Gram-negative bacteria. The structure of a Lip construct (residues 29–176) from Serratia marcescens (SmLip) has been determined at 1.92 Å resolution. Experimental phases were derived using a single-wavelength anomalous dispersion approach on a sample cocrystallized with iodide. The membrane localization of the native protein was confirmed. The structure is that of the globular domain lacking only the lipoprotein signal peptide and the lipidated N-terminus of the mature protein. The protein fold is dominated by an eight-stranded β-sandwich and identifies SmLip as a new member of the transthyretin family of proteins. Transthyretin and the only other member of the family fold, 5-hydroxyisourate hydrolase, form homotetramers important for their function. The asymmetric unit of SmLip is a tetramer with 222 symmetry, but the assembly is distinct from that previously noted for the transthyretin protein family. However, structural comparisons and bacterial two-hybrid data suggest that the SmLip tetramer is not relevant to its role as a core component of the type VI secretion system, but rather reflects a propensity for SmLip to participate in protein–protein interactions. A relatively low level of sequence conservation amongst Lip homologues is noted and is restricted to parts of the structure that might be involved in interactions with physiological partners

The structure of Serratia marcescens Lip, a membrane-bound component of the type VI secretion system

Energy Technology Data Exchange (ETDEWEB)

Rao, Vincenzo A.; Shepherd, Sharon M.; English, Grant; Coulthurst, Sarah J.; Hunter, William N., E-mail: w.n.hunter@dundee.ac.uk [College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland (United Kingdom)

2011-12-01

The high-resolution crystal structure of S. marcescens Lip reveals a new member of the transthyretin family of proteins. Lip, a core component of the type VI secretion apparatus, is localized to the outer membrane and is positioned to interact with other proteins forming this complex system. Lip is a membrane-bound lipoprotein and a core component of the type VI secretion system found in Gram-negative bacteria. The structure of a Lip construct (residues 29–176) from Serratia marcescens (SmLip) has been determined at 1.92 Å resolution. Experimental phases were derived using a single-wavelength anomalous dispersion approach on a sample cocrystallized with iodide. The membrane localization of the native protein was confirmed. The structure is that of the globular domain lacking only the lipoprotein signal peptide and the lipidated N-terminus of the mature protein. The protein fold is dominated by an eight-stranded β-sandwich and identifies SmLip as a new member of the transthyretin family of proteins. Transthyretin and the only other member of the family fold, 5-hydroxyisourate hydrolase, form homotetramers important for their function. The asymmetric unit of SmLip is a tetramer with 222 symmetry, but the assembly is distinct from that previously noted for the transthyretin protein family. However, structural comparisons and bacterial two-hybrid data suggest that the SmLip tetramer is not relevant to its role as a core component of the type VI secretion system, but rather reflects a propensity for SmLip to participate in protein–protein interactions. A relatively low level of sequence conservation amongst Lip homologues is noted and is restricted to parts of the structure that might be involved in interactions with physiological partners.

Analysis of Serum Proteom after Intravenous Injection of cultivated wild ginseng pharmacopuncture

Directory of Open Access Journals (Sweden)

Dong-Hee,Lee

2006-06-01

inflammatory response in the lungs, was reduced after the administration of pharmacopuncture. 6. Proapolipoprotein(2013, 3010 and apolipoprotein(7104, key components of the HDL-cholesterol which plays an important role in preventing arteriosclerosis, were increased after the administration of pharmacopuncture. 7. Vitamin D binding protein(DBP, 2403, protecting the lung at the time of inflammatory response, was increased after the administration of pharmacopuncture. 8. Transthyretin(TTR, 3205, which is the main protein causing familial amyloid polyneuropathy(FAP, was decreased after the administration of pharmacopuncture. 9. Ras-related protein Ral-A(4002 that controls phospholipid metabolism, cytoskeletal formation, and membrane traffic, was increased after the administration of pharmacopuncture. 10. Testis-specific protein Y(8006, which takes part in determination of the gender, was increased by more than two-times after the administration of pharmacopuncture. 11. Transferrin(8101, which balances the iron level in the body, was increased after the administration of pharmacopuncture. Conclusion : Above results support the notion that intravenous injection of cultivated wild ginseng pharmacopuncture induce changes in serum proteins and this research can be a pioneer work in finding biomarkers.

Trojan Tour and Rendezvous (TTR): A New Frontiers Mission to Explore the Origin and Evolution of the Early Solar System

Science.gov (United States)

Bell, J. F., III; Olkin, C.; Castillo, J. C.

2015-12-01

The orbital properties, compositions, and physical properties of the diverse populations of small outer solar system bodies provide a forensic map of how our solar system formed and evolved. Perhaps the most potentially diagnostic, but least explored, of those populations are the Jupiter Trojan asteroids, which orbit at ~5 AU in the L4 and L5 Lagrange points of Jupiter. More than 6200 Jupiter Trojans are presently known, but these are predicted to be only a small fraction of the 500,000 to 1 million Trojans >1 km in size. The Trojans are hypothesized to be either former Kuiper Belt Objects (KBOs) that were scattered into the inner solar system by early giant planet migration and then trapped in the 1:1 Jupiter mean motion resonance, or bodies formed near 5 AU in a much more quiescent early solar system, and then trapped at L4 and L5. The 2011 Planetary Science Decadal Survey identified important questions about the origin and evolution of the solar system that can be addressed by studying of the Trojan asteroids, including: (a) How did the giant planets and their satellite systems accrete, and is there evidence that they migrated to new orbital positions? (b) What is the relationship between large and small KBOs? Is the small population derived by impact disruption of the large one? (c) What kinds of surface evolution, radiation chemistry, and surface-atmosphere interactions occur on distant icy primitive bodies? And (d) What are the sources of asteroid groups (Trojans and Centaurs) that remain to be explored by spacecraft? The Trojan Tour and Rendezvous (TTR) is a New Frontiers-class mission designed to answer these questions, and to test hypotheses for early giant planet migration and solar system evolution. Via close flybys of a large number of these objects,, and orbital characterization of at least one large Trojan, TTR will enable the first-time exploration of this population. Our primary mission goals are to characterize the overall surface geology

The use of the AOA TTR-4P GPS receiver in operation at the BIPM for real-time restitution of GPS time

Science.gov (United States)

Thomas, Claudine

1994-01-01

The Global Positioning System is an outstanding tool for the dissemination of time. Using mono-channel C/A-code GPS time receivers, the restitution of GPS time through the satellite constellation presents a peak-to-peak discrepancy of several tens of nanoseconds without SA but may be as high as several hundreds of nanoseconds with SA. As a consequence, civil users are more and more interested in implementing hardware and software methods for efficient restitution of GPS time, especially in the framework of the project of a real-time prediction of UTC (UTCp) which could be available in the form of time differences (UTCp - GPS time). Previous work, for improving the real-time restitution of GPS time with SA, to the level obtained without SA, focused on the implementation of a Kalman filter based on past data and updated at each new observation. An alternative solution relies upon the statistical features of the noise brought about by SA; it has already been shown that the SA noise is efficiently reduced by averaging data from numerous satellites observed simultaneously over a sufficiently long time. This method was successfully applied to data from a GPS time receiver, model AOA TTR-4P, connected to the cesium clock kept at the BIPM. This device, a multi-channel, dual frequency, P-code GPS time receiver, is one of the first TTR-4P units in operation in a civil laboratory. Preliminary comparative studies of this new equipment with conventional GPS time receivers are described in this paper. The results of an experimental restitution of GPS time, obtained in June 1993, are also detailed: 3 to 6 satellites were observed simultaneously with a sample interval of 15 s, an efficient smoothing of SA noise was realized by averaging data on all observed satellites over more than 1 hour. When the GPS system is complete in 1994, 8 satellites will be observable continuously from anywhere in the world and the same level of uncertainty will be obtained using a shorter averaging

Interest and limits of glomerular filtration rate (GFR) estimation with formulae using creatinine or cystatin C in the malnourished elderly population.

Science.gov (United States)

Fabre, Emmanuelle E; Raynaud-Simon, Agathe; Golmard, Jean-Louis; Gourgouillon, Nadège; Beaudeux, Jean-Louis; Nivet-Antoine, Valérie

2010-01-01

Renal function is often altered in elderly patients. A lot of formulae are proposed to estimate GFR to adjust drug posology. French guidelines recommend the Cockcroft-Gault formula corrected with the body surface area (cCG), but the initially described unadjusted Cockcroft-Gault equation (CG) is mainly used in geriatric clinical practice. International recommendations have proposed the modification of diet in renal disease (MDRD) formula, since several authors recommended the Rule formula using cystatin C (cystC) in particular population. To appreciate the most accurate GFR estimation for posology adaptation in an elderly polypathological population, a cross-sectional study with prospective inclusion was carried out in Charles Foix Hospital. Plasma glucose levels (PGL), creatinine (CREA) levels and serum cystC, albumin (ALB), transthyretin (TTR), C-reactive protein (CRP), orosomucoid (ORO) total cholesterol (tCHOL) levels were determined among 193 elderly patients aged 70 and older. The results showed that in a malnourished, inflamed old population, CG, MDRD and Rule formulae resulted in different estimations of GFR, depending on nutritional and inflammatory parameters. Only cCG estimation was shown to be independent from these parameters. To conclude, cCG seems to be the most accurate and appropriate formula in a polypathological elderly population to evaluate renal function in order to adapt drug posology. Copyright (c) 2009 Elsevier Ireland Ltd. All rights reserved.

Maternal serum protein profile and immune response protein subunits as markers for non-invasive prenatal diagnosis of trisomy 21, 18, and 13

KAUST Repository

Narasimhan, Kothandaraman

2013-02-01

Objectives: To use proteomics to identify and characterize proteins in maternal serum from patients at high-risk for fetal trisomy 21, trisomy 18, and trisomy 13 on the basis of ultrasound and maternal serum triple tests. Methods: We performed a comprehensive proteomic analysis on 23 trisomy cases and 85 normal cases during the early second trimester of pregnancy. Protein profiling along with conventional sodium dodecyl sulfate polyacrylamide gel electrophoresis/Tandem mass spectrometry analysis was carried out to characterize proteins associated with each trisomy condition and later validated using Western blot. Results: Protein profiling approach using surface enhanced laser desorption/ionization time-of-flight mass (SELDI-TOF/MS) spectrometry resulted in the identification of 37 unique hydrophobic proteomic features for three trisomy conditions. Using sodium dodecyl sulfate polyacrylamide gel electrophoresis followed by Matrix Assisted Laser Desorption Ionization - Time of Flight/Time of Flight (MALDI-TOF/TOF) and western blot, glyco proteins such as alpha-1-antitrypsin, apolipoprotein E, apolipoprotein H, and serum carrier protein transthyretin were identified as potential maternal serum markers for fetal trisomy condition. The identified proteins showed differential expression at the subunit level. Conclusions: Maternal serum protein profiling using proteomics may allow non-invasive diagnostic testing for the most common trisomies and may complement ultrasound-based methods to more accurately determine pregnancies with fetal aneuploidies. © 2013 John Wiley & Sons, Ltd.

Cyclodextrins as Protective Agents of Protein Aggregation: An Overview.

Science.gov (United States)

Oliveri, Valentina; Vecchio, Graziella

2016-06-06

Cyclodextrins are extensively used in different fields (e.g., catalysis, chromatography, pharma, supramolecular chemistry, bioorganic chemistry, and bioinorganic chemistry), and their applications have been widely reviewed. Their main application in the field of pharmaceutical is as a drug carrier. This review overviews, for the first time, the use of cyclodextrins and their derivatives as antiaggregant agents in a number of proteins (e.g., amyloid-β, insulin, recombinant human growth hormone, prion protein, transthyretin, and α-synuclein) and some multimeric enzymes. There are many diseases that are correlated to protein misfolding and amyloid formation processes affecting numerous organs and tissues. There are over 30 different amyloid proteins and a number of corresponding diseases. Alzheimer's disease is the most common neurodegenerative disease. Treatment of these diseases is still a goal to reach, and many molecules are studied in this perspective. Cyclodextrins have also been studied, and they show great potential; as such, further studies could be very promising. This review aims to be a stimulus for the design of new cyclodextrin derivatives to obtain multifunctional systems with antiaggregant activity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparison between (99m)Tc-diphosphonate imaging and MRI with late gadolinium enhancement in evaluating cardiac involvement in patients with transthyretin familial amyloid polyneuropathy.

Science.gov (United States)

Minutoli, Fabio; Di Bella, Gianluca; Mazzeo, Anna; Donato, Rocco; Russo, Massimo; Scribano, Emanuele; Baldari, Sergio

2013-03-01

Cardiac involvement is not rare in systemic amyloidosis and is associated with poor prognosis. Both (99m)Tc-diphosphonate imaging and cardiac MRI with late gadolinium enhancement are considered valuable tools in revealing amyloid deposition in the myocardium; however, to our knowledge, no comparative study between the two techniques exists. We compared findings of these two techniques in patients with transthyretin-familial amyloid polyneuropathy (FAP). Eighteen patients with transthyretin-FAP underwent (99m)Tc-diphosphonate imaging and MRI with late gadolinium enhancement. Images were visually evaluated by independent readers to determine the presence of radiotracer accumulation or late gadolinium enhancement-positive areas at the level of cardiac chambers. Interobserver agreement ranged from moderate to very good for (99m)Tc-diphosphonate imaging findings and was very good for findings of MRI with late gadolinium enhancement. Left ventricle (LV) radiotracer uptake was found in 10 of 18 patients, whereas LV late gadolinium enhancement-positive areas were found in eight of 18 patients (χ(2) = 0.9; p = 0.343). One hundred fifty-nine LV segments showed (99m)Tc-diphosphonate accumulation, and 57 LV segments were late gadolinium enhancement positive (p < 0.0001). Radiotracer uptake was found in the right ventricle (RV) in eight patients and in both atria in five patients, whereas MRI showed that RV was involved in three patients and both atria in six patients; the differences were not statistically significant (RV, p = 0.07; atria, p = 1). Intermodality agreement between (99m)Tc-diphosphonate imaging and MRI ranged from fair to good. Our study shows that, although (99m)Tc-diphosphonate imaging and MRI with late gadolinium enhancement have similar capabilities to identify patients with myocardial amyloid deposition, cardiac amyloid infiltration burden can be significantly underestimated by visual analysis of MRI with late gadolinium enhancement compared with (99m

Analysis of Serum proteom before and after Intravenous Injection of wild ginseng herbal acupuncture

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Tae-Sik Kang

2004-12-01

. Immunoglobulin lambda chain(3105, Alpha-Oxy, Beta-(C112gdeoxy T-State Human Hemoglobin(9001, and human hemoglobin(9003 were increased by more than two-times after the administration of herbal acupuncture. 6. Proapolipoprotein(2013, 3010 and apolipoprotein(7104, key components of the HDL-cholesterol which plays an important role in preventing arteriosclerosis, were increased after the administration of herbal acupuncture. 7. Vitamin D binding protein(DBP, 2403, protecting the lung at the time of inflammatory response, was increased after the administration of herbal acupuncture. 8. Transthyretin(TTR, 3205, which is the main protein causing familial amyloid polyneuropathy(FAP, was decreased after the administration of herbal acupuncture. 9. Ras-related protein Ral-A(4002 that controls phospholipid metabolism, cytoskeletal formation, and membrane traffic, was increased after the administration of herbal acupuncture. 10. Testis-specific protein Y(8006, which takes part in determination of the gender, was increased by more than two-times after the administration of herbal acupuncture. 11. Transferrin(8101, T-State Human Hemoblobin(9001, and Human Hemoblobin(9003 which balances the iron level in the body, were increased after the administration of herbal acupuncture. Conclusion : Above results support the notion that intravenous injection of cultivated wild ginseng herbal acupuncture induce changes in serum proteins and this research can be a pioneer work in finding biomarkers.

Pre-emptive Quality Control Protects the ER from Protein Overload via the Proximity of ERAD Components and SRP

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Hisae Kadowaki

2015-11-01

Full Text Available Cells possess ER quality control systems to adapt to ER stress and maintain their function. ER-stress-induced pre-emptive quality control (ER pQC selectively degrades ER proteins via translocational attenuation during ER stress. However, the molecular mechanism underlying this process remains unclear. Here, we find that most newly synthesized endogenous transthyretin proteins are rerouted to the cytosol without cleavage of the signal peptide, resulting in proteasomal degradation in hepatocytes during ER stress. Derlin family proteins (Derlins, which are ER-associated degradation components, reroute specific ER proteins, but not ER chaperones, from the translocon to the proteasome through interactions with the signal recognition particle (SRP. Moreover, the cytosolic chaperone Bag6 and the AAA-ATPase p97 contribute to the degradation of ER pQC substrates. These findings demonstrate that Derlins-mediated substrate-specific rerouting and Bag6- and p97-mediated effective degradation contribute to the maintenance of ER homeostasis without the need for translocation.

A multi-assay screening approach for assessment of endocrine-active contaminants in wastewater effluent samples

Energy Technology Data Exchange (ETDEWEB)

Metcalfe, Chris D., E-mail: cmetcalfe@trentu.ca [Environmental and Resource Studies, Trent University, Peterborough, ON, K9J 7B8 (Canada); Kleywegt, Sonya [Standards Development Branch, Ontario Ministry of the Environment, 40 St. Clair Ave. West, Toronto, ON, M4V 1M2 (Canada); Letcher, Robert J. [Ecotoxicology and Wildlife Health Division, Science and Technology Branch, Environment Canada, National Wildlife Research Centre, Carleton University, Ottawa, ON, K1A 0H3 (Canada); Topp, Edward [Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, ON, N5V 7T3 (Canada); Wagh, Purva; Trudeau, Vance L.; Moon, Thomas W. [Department of Biology and Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, ON, K1N 6N5 (Canada)

2013-06-01

Environmental agencies must monitor an ever increasing range of contaminants of emerging concern, including endocrine disrupting compounds (EDCs). An alternative to using ultra-trace chemical analysis of samples for EDCs is to test for biological activity using in vitro screening assays, then use these assay results to direct analytical chemistry approaches. In this study, we used both analytical approaches and in vitro bioassays to characterize the EDCs present in treated wastewater from four wastewater treatment plants (WWTPs) in Ontario, Canada. Estrogen-mediated activity was assessed using a yeast estrogenicity screening (YES) assay. An in vitro competitive binding assay was used to assess capacity to interfere with binding of the thyroid hormone, thyroxine (T4) to the recombinant human thyroid hormone transport protein, transthyretin (i.e. hTTR). An in vitro binding assay with a rat peroxisome proliferator responsive element transfected into a rainbow trout gill cell line was used to evaluate binding and subsequent gene expression via the peroxisome proliferator activated receptor (PPAR). Analyses of a suite of contaminants known to be EDCs in extracts from treated wastewater were conducted using either gas chromatography with mass spectrometry (GC-MS) or liquid chromatography with tandem mass spectrometry (LC-MS/MS). Estrogenic activity was detected in the YES assay only in those extracts that contained detectable amounts of estradiol (E2). There was a positive relationship between the degree of response in the T4-hTTR assay and the amounts of polybrominated diphenyl ether (PBDE) congeners 47 and 99, triclosan and the PBDE metabolite, 4-OH-BDE17. Several wastewater extracts gave a positive response in the PPAR assay, but these responses were not correlated with the amounts of any of the EDCs analyzed by LC-MS/MS. Overall, these data indicate that a step-wise approach is feasible using a combination of in vitro testing and instrumental analysis to monitor for

A multi-assay screening approach for assessment of endocrine-active contaminants in wastewater effluent samples

International Nuclear Information System (INIS)

Metcalfe, Chris D.; Kleywegt, Sonya; Letcher, Robert J.; Topp, Edward; Wagh, Purva; Trudeau, Vance L.; Moon, Thomas W.

2013-01-01

Environmental agencies must monitor an ever increasing range of contaminants of emerging concern, including endocrine disrupting compounds (EDCs). An alternative to using ultra-trace chemical analysis of samples for EDCs is to test for biological activity using in vitro screening assays, then use these assay results to direct analytical chemistry approaches. In this study, we used both analytical approaches and in vitro bioassays to characterize the EDCs present in treated wastewater from four wastewater treatment plants (WWTPs) in Ontario, Canada. Estrogen-mediated activity was assessed using a yeast estrogenicity screening (YES) assay. An in vitro competitive binding assay was used to assess capacity to interfere with binding of the thyroid hormone, thyroxine (T4) to the recombinant human thyroid hormone transport protein, transthyretin (i.e. hTTR). An in vitro binding assay with a rat peroxisome proliferator responsive element transfected into a rainbow trout gill cell line was used to evaluate binding and subsequent gene expression via the peroxisome proliferator activated receptor (PPAR). Analyses of a suite of contaminants known to be EDCs in extracts from treated wastewater were conducted using either gas chromatography with mass spectrometry (GC-MS) or liquid chromatography with tandem mass spectrometry (LC-MS/MS). Estrogenic activity was detected in the YES assay only in those extracts that contained detectable amounts of estradiol (E2). There was a positive relationship between the degree of response in the T4-hTTR assay and the amounts of polybrominated diphenyl ether (PBDE) congeners 47 and 99, triclosan and the PBDE metabolite, 4-OH-BDE17. Several wastewater extracts gave a positive response in the PPAR assay, but these responses were not correlated with the amounts of any of the EDCs analyzed by LC-MS/MS. Overall, these data indicate that a step-wise approach is feasible using a combination of in vitro testing and instrumental analysis to monitor for

Changes of synovial fluid protein concentrations in supra-patellar bursitis patients after the injection of different molecular weights of hyaluronic acid.

Science.gov (United States)

Chen, Carl P C; Hsu, Chih Chin; Pei, Yu-Cheng; Chen, Ruo Li; Zhou, Shaobo; Shen, Hsuan-Chen; Lin, Shih-Cherng; Tsai, Wen Chung

2014-04-01

molecular weight hyaluronic acid injection group. Transthyretin, complement 5, and matrilin 3 proteins revealed a trend of increasing western immunoblotting band densities after hyaluronic acid injections. Transthyretin revealed significant increases in protein band densities in both the high and low molecular weight hyaluronic acid injection groups. This study may provide the rationale for targeting several biomarkers associated with lipid transport, inflammation, and anti-aging as possible disease modifying therapies for the treatment of supra-patellar bursitis and even degenerative joint disorders. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Closure Report for Corrective Action Unit 408: Bomblet Target Area Tonopah Test Range (TTR), Nevada, Revision 0

Energy Technology Data Exchange (ETDEWEB)

Mark Krauss

2010-09-01

This Closure Report (CR) presents information supporting the closure of Corrective Action Unit (CAU) 408: Bomblet Target Area (TTR), Tonopah Test Range, Nevada. This CR complies with the requirements of the Federal Facility Agreement and Consent Order that was agreed to by the State of Nevada; U.S. Department of Energy (DOE), Environmental Management; U.S. Department of Defense; and DOE, Legacy Management. Corrective Action Unit 408 is located at the Tonopah Test Range, Nevada, and consists of Corrective Action Site (CAS) TA-55-002-TAB2, Bomblet Target Areas. This CAS includes the following seven target areas: • Mid Target • Flightline Bomblet Location • Strategic Air Command (SAC) Target Location 1 • SAC Target Location 2 • South Antelope Lake • Tomahawk Location 1 • Tomahawk Location 2 The purpose of this CR is to provide documentation supporting the completed corrective actions and data confirming that the closure objectives for the CAS within CAU 408 were met. To achieve this, the following actions were performed: • Review the current site conditions, including the concentration and extent of contamination. • Implement any corrective actions necessary to protect human health and the environment. • Properly dispose of corrective action and investigation wastes. • Document Notice of Completion and closure of CAU 408 issued by the Nevada Division of Environmental Protection. From July 2009 through August 2010, closure activities were performed as set forth in the Streamlined Approach for Environmental Restoration Plan for CAU 408: Bomblet Target Area, Tonopah Test Range (TTR), Nevada. The purposes of the activities as defined during the data quality objectives process were as follows: • Identify and remove munitions of explosive concern (MEC) associated with DOE activities. • Investigate potential disposal pit locations. • Remove depleted uranium-contaminated fragments and soil. • Determine whether contaminants of concern (COCs) are

Differential proteomics study of platelets in asymptomatic constitutional macrothrombocytopenia: altered levels of cytoskeletal proteins.

Science.gov (United States)

Karmakar, Shilpita; Saha, Sutapa; Banerjee, Debasis; Chakrabarti, Abhijit

2015-01-01

Harris platelet syndrome (HPS), also known as asymptomatic constitutional macrothrombocytopenia (ACMT), is an autosomal dominant platelet disorder characterized by mild-to-severe thrombocytopenia and giant platelets with normal platelet aggregation and absence of bleeding symptoms. We have attempted a comparative proteomics study for profiling of platelet proteins in healthy vs. pathological states to discover characteristic protein expression changes in macrothrombocytes and decipher the factors responsible for the functionally active yet morphologically distinct platelets. We have used 2-D gel-based protein separation techniques coupled with MALDI-ToF/ToF-based mass spectrometric identification and characterization of the proteins to investigate the differential proteome profiling of platelet proteins isolated from the peripheral blood samples of patients and normal volunteers. Our study revealed altered levels of actin-binding proteins such as myosin light chain, coactosin-like protein, actin-related protein 2/3 complex, and transgelin2 that hint toward the cytoskeletal changes necessary to maintain the structural and functional integrity of macrothrombocytes. We have also observed over expressed levels of peroxiredoxin2 that signifies the prevailing oxidative stress in these cells. Additionally, altered levels of protein disulfide isomerase and transthyretin provide insights into the measures adapted by the macrothrombocytes to maintain their normal functional activity. This first proteomics study of platelets from ACMT may provide an understanding of the structural stability and normal functioning of these platelets in spite of their large size. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Aberrant proteins featured in the saliva of habitual betel quid chewers: an indication of early oral premalignancy?

Science.gov (United States)

Jessie, Kala; Jayapalan, Jaime Jacqueline; Rahim, Zubaidah Haji Abdul; Hashim, Onn Haji

2014-12-01

Prolonged chewing of betel quid is known to cause oral diseases, including cancer. The present study was performed to screen for aberrant proteins in the saliva of habitual betel quid chewers compared to nonchewers. Saliva of female subjects (n = 10) who had been chewing betel quid for more than 20 years and nonbetel quid chewers (n = 10) of the same gender and range of age was analyzed by gel-based proteomics. Increased structural microheterogeneity of saliva haptoglobin beta chains indicated by shifts of focused spots similar to that earlier reported in patients with oral squamous cell carcinoma, and their relatively higher abundance compared to nonbetel quid chewers, were detected in saliva protein profiles of all chewers. In addition, the majority of the betel quid chewers also showed significant higher abundance of hemopexin, alpha-1B glycoprotein, alpha1-antitrypsin, complement C3, and transthyretin. These proteins had previously been associated with several different cancers. Our data demonstrated different forms of protein aberration in the saliva of betel quid chewers, which may be indicative of early oral precancerous conditions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Monocrotophos pesticide decreases the plasma levels of total 3,3',5-triiodo-l-thyronine and alters the expression of genes associated with the thyroidal axis in female goldfish (Carassius auratus.

Directory of Open Access Journals (Sweden)

Xiaona Zhang

Full Text Available Our recent study showed that monocrotophos (MCP pesticide disrupted the hypothalamic-pituitary-thyroid (HPT axis in male goldfish (Carassius auratus; however, the effects of MCP on the thyroid system in female goldfish are remain unclear. In the present study, plasma thyroid hormone (TH and thyroid-stimulating hormone (TSH levels were evaluated in female goldfish exposed to 0.01, 0.10, and 1.00 mg/L of 40% MCP-based pesticide for 21 days in a semi-static exposure system. Expression profiles of HPT axis-responsive genes, including transthyretin (ttr, deiodinases (d1, d2, and d3, tshβ, thyrotropin-releasing hormone (trh, and corticotrophin-releasing hormone (crh, were determined. The results indicated that MCP decreased the plasma levels of total 3,3',5-triiodo-l-thyronine (TT3 and the ratio of TT3 to total 3,3',5,5'-l-thyroxine (TT4, and induced alternative expression of TH-related genes. Exposure to 0.01 and 0.10 mg/L MCP pesticide resulted in the up-regulation of ttr mRNA. The reduction of plasma TT3 levels was partly attributed to an increase in the metabolism of T3 in the liver, as revealed by the highly elevated hepatic d1 and d3 mRNA levels in the MCP treatment groups, and the expression of hepatic d3 showed a negative correlation with the plasma TT3/TT4 levels in females. Moreover, the plasma TSH levels were lower in females exposed to 0.01 and 0.10 mg/L MCP pesticide, whereas the up-regulation of tshβ mRNA levels was compensated by the decreased plasma TT3 levels. These results indicated that MCP had the potential to influence several pathways of HPT axis homeostasis in female goldfish.

Post-Closure Inspection Report for the Tonopah Test Range, Nevada, For Calendar Year 2008

International Nuclear Information System (INIS)

2009-01-01

This report provides the results of the annual post-closure inspections conducted at the closed Corrective Action Unit (CAU) sites located on the Tonopah Test Range (TTR), Nevada. This report covers calendar year 2008 and includes inspection and repair activities completed at the following ten CAUs: CAU 400: Bomblet Pit and Five Points Landfill (TTR) CAU 404: Roller Coaster Lagoons and Trench (TTR) CAU 407: Roller Coaster RadSafe Area (TTR) CAU 423: Area 3 Underground Discharge Point, Building 0360 (TTR) CAU 424: Area 3 Landfill Complexes (TTR) CAU 426: Cactus Spring Waste Trenches (TTR) CAU 427: Area 3 Septic Waste Systems 2, 6 (TTR) CAU 453: Area 9 UXO Landfill (TTR) CAU 484: Surface Debris, Waste Sites, and Burn Area (TTR) CAU 487: Thunderwell Site (TTR)

Post-Closure Inspection Report for the Tonopah Test Range, Nevada, For Calendar Year 2008

Energy Technology Data Exchange (ETDEWEB)

NSTec Environmental Restoration

2009-03-19

This report provides the results of the annual post-closure inspections conducted at the closed Corrective Action Unit (CAU) sites located on the Tonopah Test Range (TTR), Nevada. This report covers calendar year 2008 and includes inspection and repair activities completed at the following ten CAUs: CAU 400: Bomblet Pit and Five Points Landfill (TTR) CAU 404: Roller Coaster Lagoons and Trench (TTR) CAU 407: Roller Coaster RadSafe Area (TTR) CAU 423: Area 3 Underground Discharge Point, Building 0360 (TTR) CAU 424: Area 3 Landfill Complexes (TTR) CAU 426: Cactus Spring Waste Trenches (TTR) CAU 427: Area 3 Septic Waste Systems 2, 6 (TTR) CAU 453: Area 9 UXO Landfill (TTR) CAU 484: Surface Debris, Waste Sites, and Burn Area (TTR) CAU 487: Thunderwell Site (TTR)

Thyroid endocrine system disruption by pentachlorophenol: an in vitro and in vivo assay.

Science.gov (United States)

Guo, Yongyong; Zhou, Bingsheng

2013-10-15

The present study aimed to evaluate the disruption caused to the thyroid endocrine system by pentachlorophenol (PCP) using in vitro and in vivo assays. In the in vitro assay, rat pituitary GH3 cells were exposed to 0, 0.1, 0.3, and 1.0 μM PCP. PCP exposure significantly downregulated basal and triiodothyronine (T3)-induced Dio 1 transcription, indicating the antagonistic activity of PCP in vitro. In the in vivo assay, zebrafish embryos were exposed to 0, 1, 3, and 10 μg/L of PCP until 14 days post-fertilization. PCP exposure resulted in decreased thyroxine (T4) levels, but elevated contents of whole-body T3. PCP exposure significantly upregulated the mRNA expression of genes along hypothalamic-pituitary-thyroid (HPT) axis, including those encoding thyroid-stimulating hormone, sodium/iodide symporter, thyroglobulin, Dio 1 and Dio 2, alpha and beta thyroid hormone receptor, and uridinediphosphate-glucuronosyl-transferase. PCP exposure did not influence the transcription of the transthyretin (TTR) gene. The results indicate that PCP potentially disrupts the thyroid endocrine system both in vitro and in vivo. Copyright © 2013 Elsevier B.V. All rights reserved.

A novel proteomic biomarker panel as a diagnostic tool for patients with ovarian cancer

DEFF Research Database (Denmark)

Høgdall, Claus; Fung, Eric T; Christensen, Ib J

2011-01-01

Previous reports have shown that the proteomic markers apolipoprotein A1, hepcidin, transferrin, inter-alpha trypsin IV internal fragment, transthyretin, connective-tissue activating protein 3 and beta-2 microglobulin may discriminate between a benign pelvic mass and ovarian cancer (OC). The aim...

Validation of a prefractionation method followed by two-dimensional electrophoresis – Applied to cerebrospinal fluid proteins from frontotemporal dementia patients

Directory of Open Access Journals (Sweden)

Sjögren Magnus

2004-11-01

Full Text Available Abstract Background The aim of this study was firstly, to improve and validate a cerebrospinal fluid (CSF prefractionation method followed by two-dimensional electrophoresis (2-DE and secondly, using this strategy to investigate differences between the CSF proteome of frontotemporal dementia (FTD patients and controls. From each subject three ml of CSF was prefractionated using liquid phase isoelectric focusing prior to 2-DE. Results With respect to protein recovery and purification potential, ethanol precipitation of the prefractionated CSF sample was found superior, after testing several sample preparation methods. The reproducibility of prefractionated CSF analyzed on 2-D gels was comparable to direct 2-DE analysis of CSF. The protein spots on the prefractionated 2-D gels had an increased intensity, indicating a higher protein concentration, compared to direct 2-D gels. Prefractionated 2-DE analysis of FTD and control CSF showed that 26 protein spots were changed at least two fold. Using mass spectrometry, 13 of these protein spots were identified, including retinol-binding protein, Zn-α-2-glycoprotein, proapolipoproteinA1, β-2-microglobulin, transthyretin, albumin and alloalbumin. Conclusion The results suggest that the prefractionated 2-DE method can be useful for enrichment of CSF proteins and may provide a new tool to investigate the pathology of neurodegenerative diseases. This study confirmed reduced levels of retinol-binding protein and revealed some new biomarker candidates for FTD.

Non-invasive detection of candidate pregnancy protein biomarkers in the feces of captive polar bears (Ursus maritimus).

Science.gov (United States)

Curry, E; Stoops, M A; Roth, T L

2012-07-15

Currently, there is no method of accurately and non-invasively diagnosing pregnancy in polar bears. Specific proteins may exhibit altered profiles in the feces of pregnant bears, but predicting appropriate candidate proteins to investigate is speculative at best. The objective of this study was to identify potential pregnancy biomarker proteins based on their increased abundance in the feces of pregnant polar bears compared to pseudopregnant females (controls) using two-dimensional in-gel electrophoresis (2D-DIGE) and mass spectrometry (MS). Three 2D-DIGE gels were performed to evaluate fecal protein profiles from controls (n=3) and pregnant polar bears (n=3). There were 2224.67±52.39 (mean±SEM) spots resolved per gel. Of these, only five proteins were elevated in the pregnant group (P99.9% confidence interval. The 11 spots represented seven distinct proteins, five of which were significantly more abundant in the pregnant group: IgGFc-binding protein, filamin-C, carboxypeptidase B, transthyretin, and immunoglobulin heavy chain variable region. To our knowledge, this was the first study that employed 2D-DIGE to identify differentially expressed proteins in fecal samples to characterize a physiological condition other than those related to gastrointestinal disorders. These promising results provided a strong foundation for ensuing efforts to develop a non-invasive pregnancy assay for use in both captive and wild polar bears. Copyright © 2012 Elsevier Inc. All rights reserved.

Post-Closure Inspection Report for the Tonopah Test Range, Nevada, For Calendar Year 2010

International Nuclear Information System (INIS)

2011-01-01

This report provides the results of the annual post-closure inspections conducted at the closed Corrective Action Units (CAUs) located on the Tonopah Test Range (TTR), Nevada. This report covers calendar year 2010 and includes inspection and repair activities completed at the following seven CAUs: (1) CAU 400: Bomblet Pit and Five Points Landfill (TTR); (2) CAU 407: Roller Coaster RadSafe Area (TTR); (3) CAU 424: Area 3 Landfill Complexes (TTR); (4) CAU 426: Cactus Spring Waste Trenches (TTR); (5) CAU 453: Area 9 UXO Landfill (TTR); (6) CAU 484: Surface Debris, Waste Sites, and Burn Area (TTR); and (7) CAU 487: Thunderwell Site (TTR).

Thyroid endocrine disruption in zebrafish larvae after exposure to mono-(2-ethylhexyl phthalate (MEHP.

Directory of Open Access Journals (Sweden)

Wenhui Zhai

Full Text Available Phthalates are extensively used as plasticizers in a variety of daily-life products, resulting in widespread distribution in aquatic environments. However, limited information is available on the endocrine disrupting effects of phthalates in aquatic organisms. The aim of the present study was to examine whether exposure to mono-(2-ethylhexyl phthalate (MEHP, the hydrolytic metabolite of di-(2-ethylhexyl phthalate (DEHP disrupts thyroid endocrine system in fish. In this study, zebrafish (Danio rerio embryos were exposed to different concentrations of MEHP (1.6, 8, 40, and 200 μg/L from 2 h post-fertilization (hpf to 168 hpf. The whole-body content of thyroid hormone and transcription of genes involved in the hypothalamic-pituitary-thyroid (HPT axis were examined. Treatment with MEHP significantly decreased whole-body T4 contents and increased whole-body T3 contents, indicating thyroid endocrine disruption. The upregulation of genes related to thyroid hormone metabolism (Dio2 and UGT1ab might be responsible for decreased T4 contents. Elevated gene transcription of Dio1 was also observed in this study, which might assist to degrade increased T3 contents. Exposure to MEHP also significantly induced transcription of genes involved in thyroid development (Nkx2.1 and Pax8 and thyroid hormone synthesis (TSHβ, NIS and TG. However, the genes encoding proteins involved in TH transport (transthyretin, TTR was transcriptionally significantly down-regulated after exposure to MEHP. Overall, these results demonstrate that acute exposure to MEHP alters whole-body contents of thyroid hormones in zebrafish embryos/larvae and changes the transcription of genes involved in the HPT axis, thus exerting thyroid endocrine toxicity.

Design, synthesis, and evaluation of nonretinoid retinol binding protein 4 antagonists for the potential treatment of atrophic age-related macular degeneration and Stargardt disease.

Science.gov (United States)

Cioffi, Christopher L; Dobri, Nicoleta; Freeman, Emily E; Conlon, Michael P; Chen, Ping; Stafford, Douglas G; Schwarz, Daniel M C; Golden, Kathy C; Zhu, Lei; Kitchen, Douglas B; Barnes, Keith D; Racz, Boglarka; Qin, Qiong; Michelotti, Enrique; Cywin, Charles L; Martin, William H; Pearson, Paul G; Johnson, Graham; Petrukhin, Konstantin

2014-09-25

Accumulation of lipofuscin in the retina is associated with pathogenesis of atrophic age-related macular degeneration and Stargardt disease. Lipofuscin bisretinoids (exemplified by N-retinylidene-N-retinylethanolamine) seem to mediate lipofuscin toxicity. Synthesis of lipofuscin bisretinoids depends on the influx of retinol from serum to the retina. Compounds antagonizing the retinol-dependent interaction of retinol-binding protein 4 (RBP4) with transthyretin in the serum would reduce serum RBP4 and retinol and inhibit bisretinoid formation. We recently showed that A1120 (3), a potent carboxylic acid based RBP4 antagonist, can significantly reduce lipofuscin bisretinoid formation in the retinas of Abca4(-/-) mice. As part of the NIH Blueprint Neurotherapeutics Network project we undertook the in vitro exploration to identify novel conformationally flexible and constrained RBP4 antagonists with improved potency and metabolic stability. We also demonstrate that upon acute and chronic dosing in rats, 43, a potent cyclopentyl fused pyrrolidine antagonist, reduced circulating plasma RBP4 protein levels by approximately 60%.

Proteomic biomarkers for overall and progression-free survival in ovarian cancer patients

DEFF Research Database (Denmark)

Høgdall, Estrid; Fung, Eric T; Christensen, Ib Jarle

2010-01-01

To determine if the level of apolipoprotein A1, hepcidin, transferrin, inter-α trypsin IV internal fragment, transthyretin (TT), connective-tissue activating protein 3 (CTAP3), serum amyloid A1, β-2 microglobulin (B2M) might have impact on overall and progression-free survival for ovarian cancer...

Proteomic biomarkers for overall and progression-free survival in ovarian cancer patients

DEFF Research Database (Denmark)

Høgdall, Estrid; Fung, Eric T; Christensen, Ib Jarle

2010-01-01

To determine if the level of apolipoprotein A1, hepcidin, transferrin, inter-a trypsin IV internal fragment, transthyretin (TT), connective-tissue activating protein 3 (CTAP3), serum amyloid A1, ß-2 microglobulin (B2M) might have impact on overall and progression-free survival for ovarian cancer...

75 FR 31791 - Government-Owned Inventions; Availability for Licensing

Science.gov (United States)

2010-06-04

... response in many melanoma tumors so that researchers can better understand how to boost immunogenicity... phenotypic analysis of the 888-mel cell line in order to better understand the nature of tumor cells that... learning and memory. The products are a transthyretin and other blood brain barrier impermeable proteins...

Post-Closure Inspection Report for the Tonopah Test Range, Nevada, for Calendar Year 2012

Energy Technology Data Exchange (ETDEWEB)

NSTec Environmental Restoration

2013-01-28

This report provides the results of the annual post-closure inspections conducted at the closed Corrective Action Units (CAUs) located on the Tonopah Test Range (TTR), Nevada. This report covers calendar year 2012 and includes inspection and repair activities completed at the following CAUs: · CAU 400: Bomblet Pit and Five Points Landfill (TTR) · CAU 407: Roller Coaster RadSafe Area (TTR) · CAU 424: Area 3 Landfill Complexes (TTR) · CAU 453: Area 9 UXO Landfill (TTR) · CAU 487: Thunderwell Site (TTR)

Alterations of retinol-binding protein 4 species in patients with different stages of chronic kidney disease and their relation to lipid parameters

DEFF Research Database (Denmark)

Henze, Andrea; Frey, Simone K; Raila, Jens

2010-01-01

) was assessed in serum of 45 healthy controls and 52 patients with stage 2-5 of CKD using ELISA and RBP4 immunoprecipitation with subsequent MALDI-TOF-MS analysis. A reduction of glomerular filtration rate was accompanied by a gradual elevation of RBP4 serum levels and relative amounts of RBP4-LL. Correlation...... analysis revealed a strong association of the RBP4-TTR ratio with parameters of lipid metabolism and with diabetes-related factors. In conclusion, RBP4 serum concentration and the appearance of RBP4-LL seem to be influenced by kidney function. Furthermore, the RBP4-TTR ratio may provide diagnostic...

Chemical synthesis, characterisation, analytical method development and control to promote exposure assessments and toxicological testing. Highlights from COMPARE

Energy Technology Data Exchange (ETDEWEB)

Bergman, Aa.; Malmberg, T.; Weiss, J. [Stockholm Univ. (Sweden). Dept. of Environmental Chemistry

2004-09-15

The issue of endocrine disruptor effects in wildlife and humans grow increasingly important during the 1990s'. As part of the focus on endocrine disruptors new contaminants and their metabolites were put forward for studies with endpoints related to hormone disruption. One such large group of chemicals and/or metabolites of neutral semi-persistent or persistent compounds was the substituted phenols, particularly the halogenated phenolic compounds (HPCs). Polychlorobiphenylols (OHPCBs) were reported to be strongly retained in human blood plasma in 1995 and this article was the first study to point out the general retention of several OH-PCBs in the plasma. The metabolic formation of OH-PCBs was well known and the specific blood retention had been reported for at least one PCB congener, 3,3',4,4'-tetrachlorobiphenyl (CB-77) in some previous studies. The identification of OH-PCBs being retained in blood and their specific binding to transthyretin (TTR) has formed much of the basis for two EU R and D programs, first RENCO and now COMPARE. The present report is aimed to highlight some of the results obtained within the COMPARE program mainly dealing with the chemical synthesis, characterisation and analytical aspects of HPCs.

Streamlined Approach for Environmental Restoration (SAFER) Plan for Corrective Action Unit 408: Bomblet Target Area Tonopah Test Range (TTR), Nevada, Revision 1

Energy Technology Data Exchange (ETDEWEB)

Mark Krauss

2010-03-01

This Streamlined Approach for Environmental Restoration Plan addresses the actions needed to achieve closure of Corrective Action Unit (CAU) 408, Bomblet Target Area (TTR). Corrective Action Unit 408 is located at the Tonopah Test Range and is currently listed in Appendix III of the Federal Facility Agreement and Consent Order. Corrective Action Unit 408 comprises Corrective Action Site TA-55-002-TAB2, Bomblet Target Areas. Clean closure of CAU 408 will be accomplished by removal of munitions and explosives of concern within seven target areas and potential disposal pits. The target areas were used to perform submunitions related tests for the U.S. Department of Energy (DOE). The scope of CAU 408 is limited to submunitions released from DOE activities. However, it is recognized that the presence of other types of unexploded ordnance and munitions may be present within the target areas due to the activities of other government organizations. The CAU 408 closure activities consist of: • Clearing bomblet target areas within the study area. • Identifying and remediating disposal pits. • Collecting verification samples. • Performing radiological screening of soil. • Removing soil containing contaminants at concentrations above the action levels. Based on existing information, contaminants of potential concern at CAU 408 include unexploded submunitions, explosives, Resource Conservation Recovery Act metals, and depleted uranium. Contaminants are not expected to be present in the soil at concentrations above the action levels; however, this will be determined by radiological surveys and verification sample results.

Streamlined Approach for Environmental Restoration (SAFER) Plan for Corrective Action Unit 408: Bomblet Target Area Tonopah Test Range (TTR), Nevada, Revision 1

International Nuclear Information System (INIS)

Krauss, Mark

2010-01-01

This Streamlined Approach for Environmental Restoration Plan addresses the actions needed to achieve closure of Corrective Action Unit (CAU) 408, Bomblet Target Area (TTR). Corrective Action Unit 408 is located at the Tonopah Test Range and is currently listed in Appendix III of the Federal Facility Agreement and Consent Order. Corrective Action Unit 408 comprises Corrective Action Site TA-55-002-TAB2, Bomblet Target Areas. Clean closure of CAU 408 will be accomplished by removal of munitions and explosives of concern within seven target areas and potential disposal pits. The target areas were used to perform submunitions related tests for the U.S. Department of Energy (DOE). The scope of CAU 408 is limited to submunitions released from DOE activities. However, it is recognized that the presence of other types of unexploded ordnance and munitions may be present within the target areas due to the activities of other government organizations. The CAU 408 closure activities consist of: (1) Clearing bomblet target areas within the study area. (2) Identifying and remediating disposal pits. (3) Collecting verification samples. (4) Performing radiological screening of soil. (5) Removing soil containing contaminants at concentrations above the action levels. Based on existing information, contaminants of potential concern at CAU 408 include unexploded submunitions, explosives, Resource Conservation Recovery Act metals, and depleted uranium. Contaminants are not expected to be present in the soil at concentrations above the action levels; however, this will be determined by radiological surveys and verification sample results.

Vitamin A metabolism is changed in donors after living-kidney transplantation: an observational study

Directory of Open Access Journals (Sweden)

Henze Andrea

2011-12-01

Full Text Available Abstract Background The kidneys are essential for the metabolism of vitamin A (retinol and its transport proteins retinol-binding protein 4 (RBP4 and transthyretin. Little is known about changes in serum concentration after living donor kidney transplantation (LDKT as a consequence of unilateral nephrectomy; although an association of these parameters with the risk of cardiovascular diseases and insulin resistance has been suggested. Therefore we analyzed the concentration of retinol, RBP4, apoRBP4 and transthyretin in serum of 20 living-kidney donors and respective recipients at baseline as well as 6 weeks and 6 months after LDKT. Results As a consequence of LDKT, the kidney function of recipients was improved while the kidney function of donors was moderately reduced within 6 weeks after LDKT. With regard to vitamin A metabolism, the recipients revealed higher levels of retinol, RBP4, transthyretin and apoRBP4 before LDKT in comparison to donors. After LDKT, the levels of all four parameters decreased in serum of the recipients, while retinol, RBP4 as well as apoRBP4 serum levels of donors increased and remained increased during the follow-up period of 6 months. Conclusion LDKT is generally regarded as beneficial for allograft recipients and not particularly detrimental for the donors. However, it could be demonstrated in this study that a moderate reduction of kidney function by unilateral nephrectomy, resulted in an imbalance of components of vitamin A metabolism with a significant increase of retinol and RBP4 and apoRBP4 concentration in serum of donors.

Serum levels of RBP4 and adipose tissue levels of PTP1B are increased in obese men resident in northeast Scotland without associated changes in ER stress response genes

Directory of Open Access Journals (Sweden)

Hoggard N

2012-05-01

Full Text Available Nigel Hoggard1, Abdelali Agouni2, Nimesh Mody2, Mirela Delibegovic21Rowett Institute of Nutrition and Health, 2Integrative Physiology, University of Aberdeen, Aberdeen, UKBackground: Retinol-binding protein 4 (RBP4 is an adipokine identified as a marker of insulin resistance in mice and humans. Protein tyrosine phosphatase 1B (PTP1B expression levels as well as other genes involved in the endoplasmic reticulum (ER stress response are increased in adipose tissue of obese, high-fat-diet-fed mice. In this study we investigated if serum and/or adipose tissue RBP4 protein levels and expression levels of PTP1B and other ER stress-response genes are altered in obese and obese/diabetic men resident in northeast Scotland.Methods: We studied three groups of male volunteers: (1 normal/overweight (body mass index [BMI] < 30, (2 obese (BMI > 30, and (3 obese/diabetic (BMI > 30 controlling their diabetes either by diet or the antidiabetic drug metformin. We analyzed their serum and adipose tissue RBP4 protein levels as well as adipose tissue mRNA expression of PTP1B, binding immunoglobulin protein (BIP, activated transcription factor 4 (ATF4, and glucose-regulated protein 94 (GRP94 alongside other markers of adiposity (percentage body fat, leptin, cholesterol, triglycerides and insulin resistance (oral glucose tolerance tests, insulin, homeostatic model assessment–insulin resistance, C-reactive protein, and adiponectin.Results: We found that obese Scottish subjects had significantly higher serum RBP4 protein levels in comparison to the normal/overweight subjects (P < 0.01. Serum RBP4 levels were normalized in obese/diabetic subjects treated with diet or metformin (P < 0.05. Adipose tissue RBP4 protein levels were comparable between all three groups of subjects as were serum and adipose transthyretin levels. Adipose tissue PTP1B mRNA levels were increased in obese subjects in comparison to normal/overweight subjects (P < 0.05; however diet and/or metformin

Is Supramolecular Filament Chirality the Underlying Cause of Major Morphology Differences in Amyloid Fibrils?

Science.gov (United States)

2015-01-01

The unique enhanced sensitivity of vibrational circular dichroism (VCD) to the formation and development of amyloid fibrils in solution is extended to four additional fibril-forming proteins or peptides where it is shown that the sign of the fibril VCD pattern correlates with the sense of supramolecular filament chirality and, without exception, to the dominant fibril morphology as observed in AFM or SEM images. Previously for insulin, it has been demonstrated that the sign of the VCD band pattern from filament chirality can be controlled by adjusting the pH of the incubating solution, above pH 2 for “normal” left-hand-helical filaments and below pH 2 for “reversed” right-hand-helical filaments. From AFM or SEM images, left-helical filaments form multifilament braids of left-twisted fibrils while the right-helical filaments form parallel filament rows of fibrils with a flat tape-like morphology, the two major classes of fibril morphology that from deep UV resonance Raman scattering exhibit the same cross-β-core secondary structure. Here we investigate whether fibril supramolecular chirality is the underlying cause of the major morphology differences in all amyloid fibrils by showing that the morphology (twisted versus flat) of fibrils of lysozyme, apo-α-lactalbumin, HET-s (218–289) prion, and a short polypeptide fragment of transthyretin, TTR (105–115), directly correlates to their supramolecular chirality as revealed by VCD. The result is strong evidence that the chiral supramolecular organization of filaments is the principal underlying cause of the morphological heterogeneity of amyloid fibrils. Because fibril morphology is linked to cell toxicity, the chirality of amyloid aggregates should be explored in the widely used in vitro models of amyloid-associated diseases. PMID:24484302

Is supramolecular filament chirality the underlying cause of major morphology differences in amyloid fibrils?

Science.gov (United States)

Kurouski, Dmitry; Lu, Xuefang; Popova, Ludmila; Wan, William; Shanmugasundaram, Maruda; Stubbs, Gerald; Dukor, Rina K; Lednev, Igor K; Nafie, Laurence A

2014-02-12

The unique enhanced sensitivity of vibrational circular dichroism (VCD) to the formation and development of amyloid fibrils in solution is extended to four additional fibril-forming proteins or peptides where it is shown that the sign of the fibril VCD pattern correlates with the sense of supramolecular filament chirality and, without exception, to the dominant fibril morphology as observed in AFM or SEM images. Previously for insulin, it has been demonstrated that the sign of the VCD band pattern from filament chirality can be controlled by adjusting the pH of the incubating solution, above pH 2 for "normal" left-hand-helical filaments and below pH 2 for "reversed" right-hand-helical filaments. From AFM or SEM images, left-helical filaments form multifilament braids of left-twisted fibrils while the right-helical filaments form parallel filament rows of fibrils with a flat tape-like morphology, the two major classes of fibril morphology that from deep UV resonance Raman scattering exhibit the same cross-β-core secondary structure. Here we investigate whether fibril supramolecular chirality is the underlying cause of the major morphology differences in all amyloid fibrils by showing that the morphology (twisted versus flat) of fibrils of lysozyme, apo-α-lactalbumin, HET-s (218-289) prion, and a short polypeptide fragment of transthyretin, TTR (105-115), directly correlates to their supramolecular chirality as revealed by VCD. The result is strong evidence that the chiral supramolecular organization of filaments is the principal underlying cause of the morphological heterogeneity of amyloid fibrils. Because fibril morphology is linked to cell toxicity, the chirality of amyloid aggregates should be explored in the widely used in vitro models of amyloid-associated diseases.

Dicty_cDB: Contig-U01558-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available d uses therefor. 44 7.9 1 ( DD248358 ) USE OF TRANSTHYRETIN PEPTIDE/PROTEIN FUSIONS TO I... 44 7.9 1 ( DD246853 ) SELF-COAL...ESCING OR SELF-AGGREGATING CHIMERIC PROT... 44 7.9 1 ( DD246847 ) SELF-COAL...ESCING OR SELF-AGGREGATING CHIMERIC PROT... 44 7.9 1 ( DD246845 ) SELF-COALESCING OR SELF-AGGREGATI

Reduced Time in Therapeutic Range and Higher Mortality in Atrial Fibrillation Patients Taking Acenocoumarol.

Science.gov (United States)

Rivera-Caravaca, José Miguel; Roldán, Vanessa; Esteve-Pastor, María Asunción; Valdés, Mariano; Vicente, Vicente; Marín, Francisco; Lip, Gregory Y H

2018-01-01

The efficacy and tolerability of vitamin K antagonists (VKAs) depends on the quality of anticoagulant control, reflected by the mean time in therapeutic range (TTR) of international normalized ratio 2.0 to 3.0. In the present study, we aimed to investigate the association between TTR and change in TTR (ΔTTR) with the risk of mortality and clinically significant events in a consecutive cohort of atrial fibrillation (AF) patients. We included 1361 AF patients stable on VKAs (international normalized ratio 2.0-3.0) during at least the previous 6 months. After 6 months of follow-up we recalculated TTR, calculated ΔTTR (ie, the difference between baseline and 6-month TTRs) and investigated the association of both with the risk of mortality and "clinically significant events" (defined as the composite of stroke or systemic embolism, major bleeding, acute coronary syndrome, acute heart failure, and all-cause deaths). The median ΔTTR at 6 months of entry was 20% (interquartile range 0-34%), 796 (58.5%) patients had a TTR reduction of at least 20%, while 330 (24.2%) had a TTR <65%. During follow-up, 34 (2.5% [4.16% per year]) patients died and 61 (4.5% [7.47% per year]) had a clinically significant event. Median ΔTTR was significantly higher in patients who died (35.5% vs 20%; P = 0.002) or sustained clinically significant events (28% vs 20%; P = 0.022). Based on Cox regression analyses, the overall risk of mortality at 6 months for each decrease point in TTR was 1.02 (95% CI, 1.01-1.04; P = 0.003), and the risk of clinically significant events was 1.01 (95% CI, 1.00-1.03; P = 0.028). Patients with TTR <65% at 6 months had higher risk of mortality (hazard ratio = 2.96; 95% CI, 1.51-5.81; P = 0.002) and clinically significant events (hazard ratio = 1.71; 95% CI, 1.01-2.88; P = 0.046). Our findings suggest that in AF patients anticoagulated with VKAs, a change in TTR over 6 months (ie, ΔTTR) is an independent risk factor for mortality and clinically significant events

Identification of proteins in a human pleural exudate using two-dimensional preparative liquid-phase electrophoresis and matrix-assisted laser desorption/ionization mass spectrometry.

Science.gov (United States)

Nilsson, C L; Puchades, M; Westman, A; Blennow, K; Davidsson, P

1999-01-01

Pleural effusion may occur in patients suffering from physical trauma or systemic disorders such as infection, inflammation, or cancer. In order to investigate proteins in a pleural exudate from a patient with severe pneumonia, we used a strategy that combined preparative two-dimensional liquid-phase electrophoresis (2-D LPE), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and Western blotting. Preparative 2-D LPE is based on the same principles as analytical 2-D gel electrophoresis, except that the proteins remain in liquid phase during the entire procedure. In the first dimension, liquid-phase isoelectric focusing allows for the enrichment of proteins in liquid fractions. In the Rotofor cell, large volumes (up to 55 mL) and protein amounts (up to 1-2 g) can be loaded. Several low abundance proteins, cystatin C, haptoglobin, transthyretin, beta2-microglobulin, and transferrin, were detected after liquid-phase isoelectric focusing, through Western blotting analysis, in a pleural exudate (by definition, >25 g/L total protein). Direct MALDI-TOF-MS analysis of proteins in a Rotofor fraction is demonstrated as well. MALDI-TOF-MS analysis of a tryptic digest of a continuous elution sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) fraction confirmed the presence of cystatin C. By applying 2-D LPE, MALDI-TOF-MS, and Western blotting to the analysis of this pleural exudate, we were able to confirm the identity of proteins of potential diagnostic value. Our findings serve to illustrate the usefulness of this combination of methods in the analysis of pathological fluids.

Quality of warfarin control in atrial fibrillation patients in South East Queensland, Australia.

Science.gov (United States)

Bernaitis, N; Badrick, T; Davey, A K; Anoopkumar-Dukie, S

2016-08-01

Warfarin is widely prescribed to decrease the risk of stroke in atrial fibrillation (AF) patients. Due to patient variability in response, regular monitoring is required, and time in therapeutic range (TTR) used to indicate quality of warfarin control with a TTR>60% is recommended. Recently, an Australian Government review of anticoagulants identified the need to establish current warfarin control and determine the potential place of the newer oral anticoagulants. To determine warfarin control by a pathology practice in Queensland, Australia and identify factors influencing TTR. Retrospective data were collected from Sullivan Nicolaides Pathology, a major pathology practice offering a warfarin care programme in Australia. Patients enrolled in their programme as of September 2014 were included in the study. TTR was calculated using INR test results, and test dates using the Rosendaal method with mean patient TTR were used for analysis and comparison. Exclusions were target therapeutic range outside 2.0-3.0, less than two INR tests and programme treatment time of less than 30 days. The eligible 3692 AF patients had 73.6% of INR tests within the therapeutic range. The mean TTR was 81%, with 97% of patients above a TTR of 60%. TTR was not significantly influenced by age, gender or socioeconomic factors. The observed mean TTR of over 80% is superior to the minimum recommended threshold of 60%. The TTR achieved by the Queensland pathology practice demonstrates that dedicated warfarin programmes can produce high-quality warfarin care, ensuring the full benefit of warfarin for Australian patients. © 2016 Royal Australasian College of Physicians.

Demonstration of anticoagulation patient self-testing feasibility at an Indian Health Service facility: A case series analysis

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Schupbach RR

2013-03-01

Full Text Available Background: Anticoagulation patient self-testing (PST represents an alternative approach to warfarin monitoring by enabling patients to use coagulometers to test their international normalized ratio (INR values. PST offers several advantages that potentially improve warfarin management. Objective: To describe implementation and associated performance of a PST demonstration program at an Indian Health Service (IHS facility. Methods: A non-consecutive case series analysis of patients from a pharmacy-managed PST demonstration program was performed at an IHS facility in Oklahoma between July 2008 and February 2009.Results: Mean time in therapeutic range (TTR for the seven patients showed a small, absolute increase during the twelve weeks of PST compared to the twelve weeks prior to PST. Four of the seven patients had an increase in TTR during the twelve week course of PST compared to their baseline TTR. Three of four patients with increased TTR in the final eight week period of PST achieved a TTR of 100%. Of the three patients who experienced a decrease in TTR after initiating self-testing, two initially presented with a TTR of 100% prior to PST and one patient had a TTR of 100% for the final eight weeks of PST. The two patients not achieving a TTR of 100% during the twelve week PST period demonstrated an increase in TTR following the first four weeks of PST. Conclusion: Although anticoagulation guidelines now emphasize patient self-management (PSM only, optimal PST remains an integral process in PSM delivery. In the patients studied, the results of this analysis suggest that PST at the IHS facility provided a convenient, alternative method for management of chronic warfarin therapy for qualified patients. More than half of the patients demonstrated improvement in TTR. Although there is a learning curve immediately following PST initiation, the mean TTR for the entire PST period increased modestly when compared to the time period prior to PST.

Effects of perinatal exposure to environmentally persistent organic pollutants and heavy metals on neurobehavioral development in Japanese children: IV. Thyroid hormones and neonatal neurobehavioral status

Energy Technology Data Exchange (ETDEWEB)

Suzuki, K.; Nakai, K.; Oka, T.; Kurokawa, N.; Satoh, H. [Dept. of Environmental Health Sciences, Tohoku Univ. Graduate School of Medicine, Sendai (Japan); Hosokawa, T. [Dept. of Human Development, Tohoku Univ., Sendai (Japan); Okamura, K. [Dept. of Obstetrics, Tohoku Univ. Graduate School of Medicine, Sendai (Japan); Sakai, T. [Miyagi Childrens Hospital, Sendai (Japan)

2004-09-15

From several epidemiological studies, it has been reported that there are some associations between perinatal exposures to PCBs, dioxins and heavy metals, and neurobehavioral defects such as postnatal growth delay and poorer cognitive function. We have started a prospective cohort study to examine the effects of perinatal exposures to environmentally persistent organic pollutants on neurobehavioral development in Japanese children. Thyroid hormones (THs) are essential for normal brain development. A lack of THs in pregnancy can result in congenital hypothyroidism, which causes moderate to severe intellectual defects. It has been reported that perinatal exposure to PCBs adversely affects on children's intellectual functions. The chemical structures of some PCBs resembles thyroxine (T4), and therefore, it is suspected that the action mechanism of PCBs is disruption of TH function. Some PCBs and their metabolites are thought to bind with transthyretine (TTR), which is necessary for the transfer of T4 into the brain, and this may cause a shortage of T4 in the developing brain. To examine the effects of perinatal exposure to PCBs on children's development, it is essential to evaluate the functions of THs at a fundamental level. In this report, we examined the correlations of THs in maternal peripheral blood and cord blood, and the association between THs and neonatal neurobehavioral status.

Efficacy and safety of dabigatran compared with warfarin at different levels of international normalised ratio control for stroke prevention in atrial fibrillation: an analysis of the RE-LY trial.

Science.gov (United States)

Wallentin, Lars; Yusuf, Salim; Ezekowitz, Michael D; Alings, Marco; Flather, Marcus; Franzosi, Maria Grazia; Pais, Prem; Dans, Antonio; Eikelboom, John; Oldgren, Jonas; Pogue, Janice; Reilly, Paul A; Yang, Sean; Connolly, Stuart J

2010-09-18

Effectiveness and safety of warfarin is associated with the time in therapeutic range (TTR) with an international normalised ratio (INR) of 2·0-3·0. In the Randomised Evaluation of Long-term Anticoagulation Therapy (RE-LY) trial, dabigatran versus warfarin reduced both stroke and haemorrhage. We aimed to investigate the primary and secondary outcomes of the RE-LY trial in relation to each centre's mean TTR (cTTR) in the warfarin population. In the RE-LY trial, 18 113 patients at 951 sites were randomly assigned to 110 mg or 150 mg dabigatran twice daily versus warfarin dose adjusted to INR 2·0-3·0. Median follow-up was 2·0 years. For 18 024 patients at 906 sites, the cTTR was estimated by averaging TTR for individual warfarin-treated patients calculated by the Rosendaal method. We compared the outcomes of RE-LY across the three treatment groups within four groups defined by the quartiles of cTTR. RE-LY is registered with ClinicalTrials.gov, number NCT00262600. The quartiles of cTTR for patients in the warfarin group were: less than 57·1%, 57·1-65·5%, 65·5-72·6%, and greater than 72·6%. There were no significant interactions between cTTR and prevention of stroke and systemic embolism with either 110 mg dabigatran (interaction p=0·89) or 150 mg dabigatran (interaction p=0·20) versus warfarin. Neither were any significant interactions recorded with cTTR with regards to intracranial bleeding with 110 mg dabigatran (interaction p=0·71) or 150 mg dabigatran (interaction p=0·89) versus warfarin. There was a significant interaction between cTTR and major bleeding when comparing 150 mg dabigatran with warfarin (interaction p=0·03), with less bleeding events at lower cTTR but similar events at higher cTTR, whereas rates of major bleeding were lower with 110 mg dabigatran than with warfarin irrespective of cTTR. There were significant interactions between cTTR and effects of both 110 mg and 150 mg dabigatran versus warfarin on the composite of all

Post-Closure Inspection Report for the Tonopah Test Range, Nevada, For Calendar Year 2007

International Nuclear Information System (INIS)

NSTec Environmental Restoration

2008-01-01

This report provides the results of the semiannual post-closure inspections conducted at the closed Corrective Action Unit (CAU) sites located on the Tonopah Test Range (TTR), Nevada. This report covers calendar year 2007 and includes inspection and repair activities completed at the following nine CAUs: (1) CAU 400: Bomblet Pit and Five Points Landfill (TTR); (2) CAU 404: Roller Coaster Lagoons and Trench (TTR); (3) CAU 407: Roller Coaster RadSafe Area (TTR); (4) CAU 423: Area 3 Underground Discharge Point, Building 0360 (TTR); (5) CAU 424: Area 3 Landfill Complexes (TTR); (6) CAU 426: Cactus Spring Waste Trenches (TTR); (7) CAU 427: Area 3 Septic Waste Systems 2, 6 (TTR); (8) CAU 453: Area 9 UXO Landfill (TTR); and (9) CAU 487: Thunderwell Site (TTR). In a letter from the Nevada Division of Environmental Protection (NDEP) dated December 5, 2006, NDEP concurred with the request to reduce the frequency of post-closure inspections of CAUs at TTR to an annual frequency. This letter is included in Attachment B. Post-closure inspections were conducted on May 15-16, 2007. All inspections were conducted according to the post-closure plans in the approved Closure Reports. The post-closure inspection plan for each CAU is included in Attachment B, with the exception of CAU 400. CAU 400 does not require post-closure inspections, but inspections of the vegetation and fencing are conducted as a best management practice. The inspection checklists for each site inspection are included in Attachment C, the field notes are included in Attachment D, and the site photographs are included in Attachment E. Vegetation monitoring of CAU 400, CAU 404, CAU 407, and CAU 426 was performed in May 2007, and the vegetation monitoring report is included in Attachment F. Maintenance and/or repairs were performed at CAU 453. Animal burrows observed during the annual inspection at CAU 453 were backfilled on August 1, 2007. At this time, the TTR post-closure site inspections should continue as

Post-Closure Inspection Report for the Tonopah Test Range, Nevada, For Calendar Year 2007

Energy Technology Data Exchange (ETDEWEB)

NSTec Environmental Restoration

2008-06-01

This report provides the results of the semiannual post-closure inspections conducted at the closed Corrective Action Unit (CAU) sites located on the Tonopah Test Range (TTR), Nevada. This report covers calendar year 2007 and includes inspection and repair activities completed at the following nine CAUs: (1) CAU 400: Bomblet Pit and Five Points Landfill (TTR); (2) CAU 404: Roller Coaster Lagoons and Trench (TTR); (3) CAU 407: Roller Coaster RadSafe Area (TTR); (4) CAU 423: Area 3 Underground Discharge Point, Building 0360 (TTR); (5) CAU 424: Area 3 Landfill Complexes (TTR); (6) CAU 426: Cactus Spring Waste Trenches (TTR); (7) CAU 427: Area 3 Septic Waste Systems 2, 6 (TTR); (8) CAU 453: Area 9 UXO Landfill (TTR); and (9) CAU 487: Thunderwell Site (TTR). In a letter from the Nevada Division of Environmental Protection (NDEP) dated December 5, 2006, NDEP concurred with the request to reduce the frequency of post-closure inspections of CAUs at TTR to an annual frequency. This letter is included in Attachment B. Post-closure inspections were conducted on May 15-16, 2007. All inspections were conducted according to the post-closure plans in the approved Closure Reports. The post-closure inspection plan for each CAU is included in Attachment B, with the exception of CAU 400. CAU 400 does not require post-closure inspections, but inspections of the vegetation and fencing are conducted as a best management practice. The inspection checklists for each site inspection are included in Attachment C, the field notes are included in Attachment D, and the site photographs are included in Attachment E. Vegetation monitoring of CAU 400, CAU 404, CAU 407, and CAU 426 was performed in May 2007, and the vegetation monitoring report is included in Attachment F. Maintenance and/or repairs were performed at CAU 453. Animal burrows observed during the annual inspection at CAU 453 were backfilled on August 1, 2007. At this time, the TTR post-closure site inspections should continue as

Amyloidoses as seen by the Rheumatologist

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J.Ch Gerster

2011-09-01

Full Text Available Amyloidosis is due to extracellular deposition in various organs and tissues of amorphous materials made of protein fibrils, whose thickness is 10 nm. Seventeen different amyloid fibrils are known (1. Amyloidosis can be localised or systemic. There are 4 systemic amyloidoses (2: Familial amyloidosis with mutated transthyretin. Primary, paraprotein associated, amyloidosis AL. Secondary AA amyloidosis in long- standing inflammation. β2-microglobulin...

Modeling Travel Time Reliability of Road Network Considering Connected Vehicle Guidance Characteristics Indexes

Directory of Open Access Journals (Sweden)

Jiangfeng Wang

2017-01-01

Full Text Available Travel time reliability (TTR is one of the important indexes for effectively evaluating the performance of road network, and TTR can effectively be improved using the real-time traffic guidance information. Compared with traditional traffic guidance, connected vehicle (CV guidance can provide travelers with more timely and accurate travel information, which can further improve the travel efficiency of road network. Five CV characteristics indexes are selected as explanatory variables including the Congestion Level (CL, Penetration Rate (PR, Compliance Rate (CR, release Delay Time (DT, and Following Rate (FR. Based on the five explanatory variables, a TTR model is proposed using the multilogistic regression method, and the prediction accuracy and the impact of characteristics indexes on TTR are analyzed using a CV guidance scenario. The simulation results indicate that 80% of the RMSE is concentrated within the interval of 0 to 0.0412. The correlation analysis of characteristics indexes shows that the influence of CL, PR, CR, and DT on the TTR is significant. PR and CR have a positive effect on TTR, and the average improvement rate is about 77.03% and 73.20% with the increase of PR and CR, respectively, while CL and DT have a negative effect on TTR, and TTR decreases by 31.21% with the increase of DT from 0 to 180 s.

Sensitive targeted multiple protein quantification based on elemental detection of Quantum Dots

Energy Technology Data Exchange (ETDEWEB)

Montoro Bustos, Antonio R.; Garcia-Cortes, Marta [Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, Oviedo 33006 (Spain); González-Iglesias, Hector [Fundación de Investigación Oftalmológica, Instituto Oftalmológico Fernandez-Vega, Avenida Doctores Fernández-Vega, 34, Oviedo 33012 (Spain); Ruiz Encinar, Jorge, E-mail: ruizjorge@uniovi.es [Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, Oviedo 33006 (Spain); Costa-Fernández, José M. [Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, Oviedo 33006 (Spain); Coca-Prados, Miguel [Fundación de Investigación Oftalmológica, Instituto Oftalmológico Fernandez-Vega, Avenida Doctores Fernández-Vega, 34, Oviedo 33012 (Spain); Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT 06510 (United States); Sanz-Medel, Alfredo, E-mail: asm@uniovi.es [Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, Oviedo 33006 (Spain)

2015-06-16

Highlights: • Novel generic platform for multiparametric quantification of proteins. • QDs labeling and ICP-MS detection allow significant analytical signal amplification. • ICP-MS mass balances information provided an internal validation of the immunoassay. • Multiparametric determination of 5 proteins in human serum samples. • ICP-MS reduced matrix effects as compared to other conventional detection techniques. - Abstract: A generic strategy based on the use of CdSe/ZnS Quantum Dots (QDs) as elemental labels for protein quantification, using immunoassays with elemental mass spectrometry (ICP-MS), detection is presented. In this strategy, streptavidin modified QDs (QDs-SA) are bioconjugated to a biotinylated secondary antibody (b-Ab{sub 2}). After a multi-technique characterization of the synthesized generic platform (QDs-SA-b-Ab{sub 2}) it was applied to the sequential quantification of five proteins (transferrin, complement C3, apolipoprotein A1, transthyretin and apolipoprotein A4) at different concentration levels in human serum samples. It is shown how this generic strategy does only require the appropriate unlabeled primary antibody for each protein to be detected. Therefore, it introduces a way out to the need for the cumbersome and specific bioconjugation of the QDs to the corresponding specific recognition antibody for every target analyte (protein). Results obtained were validated with those obtained using UV–vis spectrophotometry and commercial ELISA Kits. As expected, ICP-MS offered one order of magnitude lower DL (0.23 fmol absolute for transferrin) than the classical spectrophotometric detection (3.2 fmol absolute). ICP-MS precision and detection limits, however turned out to be compromised by procedural blanks. The full analytical performance of the ICP-MS-based immunoassay proposed was assessed for detection of transferrin (Tf), present at the low ng mL{sup −1} range in a complex “model” synthetic matrix, where the total protein

Patients' time in therapeutic range on warfarin among US patients with atrial fibrillation: Results from ORBIT-AF registry.

Science.gov (United States)

Pokorney, Sean D; Simon, DaJuanicia N; Thomas, Laine; Fonarow, Gregg C; Kowey, Peter R; Chang, Paul; Singer, Daniel E; Ansell, Jack; Blanco, Rosalia G; Gersh, Bernard; Mahaffey, Kenneth W; Hylek, Elaine M; Go, Alan S; Piccini, Jonathan P; Peterson, Eric D

2015-07-01

Time in therapeutic range (TTR) of international normalized ratio (INR) of 2.0 to 3.0 is important for the safety and effectiveness of warfarin anticoagulation. There are few data on TTR among patients with atrial fibrillation (AF) in community-based clinical practice. Using the US Outcomes Registry for Better Informed Treatment of Atrial Fibrillation (ORBIT-AF), we examined TTR (using a modified Rosendaal method) among 5,210 patients with AF on warfarin and treated at 155 sites. Patients were grouped into quartiles based on TTR data. Multivariable logistic regression modeling with generalized estimating equations was used to determine patient and provider factors associated with the lowest (worst) TTR. Overall, 59% of the measured INR values were between 2.0 and 3.0, with an overall mean and median TTR of 65% ± 20% and 68% (interquartile range [IQR] 53%-79%). The median times below and above the therapeutic range were 17% (IQR 8%-29%) and 10% (IQR 3%-19%), respectively. Patients with renal dysfunction, advanced heart failure, frailty, prior valve surgery, and higher risk for bleeding (ATRIA score) or stroke (CHA2DS2-VASc score) had significantly lower TTR (P range. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

The effect of the amiodarone-warfarin interaction on anticoagulation quality in a single, high-quality anticoagulation center.

Science.gov (United States)

White, Ryan D; Riggs, Kyle W; Ege, Ed J; Petroski, Gregory F; Koerber, Scott M; Flaker, Greg

2016-03-01

Clinical trials have reported a low time in therapeutic range (TTR) in patients with atrial fibrillation treated with both warfarin andamiodarone. These trials included centers and countries with both high and low TTRs. What is the impact of amiodarone on the TTR in a single, high-quality anticoagulation clinic? TTR was assessed in amiodarone and nonamiodarone-treated patients from a University anticoagulation clinic. Baseline characteristics between patients ever-taking or never-taking amiodarone were similar, except more amiodarone patients were smokers (19.5 vs. 6.1%, P = 0.0031). The TTR calculated from 8901international normalized ratios (INRs) in 249 nonamiodarone patients with a mean follow-up of 34 ± 20 months (mean INR 36 ± 18) was 66 ± 16.6% compared with 61.3 ± 16.2% (P = 0.111) from 1455 INRs in 41 amiodarone-treated patients with a mean follow-up of 28 ± 20 months (mean INR 35 ± 22). Factors associated with a low TTR were male sex (P = 0.0013), smoker (P = 0.0048), and amiodarone use (P = 0.0374). A second on-treatment analysis, in which the TTR was calculated only during amiodarone therapy, resulted in similar findings; however, amiodarone did not emerge as a predictor of a low TTR. In 11 patients, the TTR prior to amiodarone (54.5 ± 22.2%) was not significantly different in the first 3 months (54.6 ± 33.4%) or after 3 months (67.2 ± 33.7%) of amiodarone. In a single high-quality anticoagulation center, anticoagulation quality, as measured by the TTR, can be comparable in amiodarone and nonamiodarone-treated patients.

Impact of co-morbidities and patient characteristics on international normalized ratio control over time in patients with nonvalvular atrial fibrillation.

Science.gov (United States)

Nelson, Winnie W; Choi, Jiyoon C; Vanderpoel, Julie; Damaraju, Chandrasekharra V; Wildgoose, Peter; Fields, Larry E; Schein, Jeffrey R

2013-08-15

This study determined the association between co-morbidities, including heart failure (HF) and time in therapeutic range (TTR), in patients with nonvalvular atrial fibrillation. Longitudinal patient-level anticoagulation management records collected from 2006 to 2010 were analyzed. Adult patients with nonvalvular atrial fibrillation who used warfarin for a 12-month period with no gap of >60 days between visits were identified. TTR <55% was defined as "lower" TTR. CHADS₂ score of ≥2 was defined as "higher" CHADS₂. Logistic regression analyses were conducted to determine the association between co-morbidities and TTR. A total of 23,425 patients met the study criteria. The mean age ± SD was 74.8 ± 9.7 years, with 84.8% aged ≥65 years. The most common co-morbidities were hypertension (41.7%), diabetes (24.1%), HF (11.7%), and previous stroke (11.1%). The mean TTR ± SD was 67.3 ± 14.4%, with 18.6% of patients in the lower TTR range. In multivariate analyses using age, gender, hypertension, diabetes, stroke, and region as covariates, HF (adjusted odds ratio [OR] 1.41, 95% confidence interval [CI] 1.28 to 1.56; p <0.001), diabetes (OR 1.28, 95% CI 1.19 to 1.38; p <0.001), and previous stroke (OR 1.15, 95% CI 1.04 to 1.27; p <0.001) were associated with lower TTR. In a second set of multivariate analyses using gender and region as covariates, a higher CHADS₂ score was associated with lower TTR (OR 1.11, 95% CI 1.04 to 1.18; p <0.001). In conclusion, HF was associated with the greatest likelihood of a lower TTR, followed by diabetes, then stroke. Anticoagulation control may be more challenging for patients with these conditions. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Post-Closure Inspection Report for the Tonopah Test Range, Nevada

International Nuclear Information System (INIS)

NSTec Environmental Restoration

2007-01-01

This report provides the results of the semiannual post-closure inspections conducted at the closed Corrective Action Unit (CAU) sites located on the Tonopah Test Range (TTR), Nevada. This report covers calendar year 2006 and includes inspection and repair activities completed at the following nine CAUs: CAU 400: Bomblet Pit and Five Points Landfill (TTR); CAU 404: Roller Coaster Lagoons and Trench (TTR); CAU 407: Roller Coaster RadSafe Area (TTR); CAU 423: Area 3 Underground Discharge Point, Building 0360 (TTR); CAU 424: Area 3 Landfill Complexes (TTR); CAU 426: Cactus Spring Waste Trenches (TTR); CAU 427: Area 3 Septic Waste Systems 2, 6 (TTR); CAU 453: Area 9 UXO Landfill (TTR); and CAU 487: Thunderwell Site (TTR). Post-closure inspections were conducted on May 9, 2006, May 31, 2006, and November 15, 2006. All inspections were conducted according to the post-closure plans in the approved Closure Reports. The post-closure inspection plan for each CAU is included in Attachment B, with the exception of CAU 400. CAU 400 does not require post-closure inspections, but inspections of the vegetation and fencing are conducted as a best management practice. The inspection checklists for each site inspection are included in Attachment C, the field notes are included in Attachment D, and the site photographs are included in Attachment E. Vegetation monitoring of CAU 400, CAU 404, CAU 407, and CAU 426 was performed in June 2006, and the vegetation monitoring report is included in Attachment F. Maintenance and/or repairs were performed at CAU 400, CAU 407, CAU 426, CAU 453, and CAU 487 in 2006. During the May inspection of CAU 400, it was identified that the east and west sections of chickenwire fencing beyond the standard fencing were damaged; they were repaired in June 2006. Also in June 2006, the southeast corner fence post and one warning sign at CAU 407 were reinforced and reattached, the perimeter fencing adjacent to the gate at CAU 426 was tightened, and large animal

Post-Closure Inspection Report for the Tonopah Test Range, Nevada

Energy Technology Data Exchange (ETDEWEB)

NSTec Environmental Restoration

2007-06-01

This report provides the results of the semiannual post-closure inspections conducted at the closed Corrective Action Unit (CAU) sites located on the Tonopah Test Range (TTR), Nevada. This report covers calendar year 2006 and includes inspection and repair activities completed at the following nine CAUs: CAU 400: Bomblet Pit and Five Points Landfill (TTR); CAU 404: Roller Coaster Lagoons and Trench (TTR); CAU 407: Roller Coaster RadSafe Area (TTR); CAU 423: Area 3 Underground Discharge Point, Building 0360 (TTR); CAU 424: Area 3 Landfill Complexes (TTR); CAU 426: Cactus Spring Waste Trenches (TTR); CAU 427: Area 3 Septic Waste Systems 2, 6 (TTR); CAU 453: Area 9 UXO Landfill (TTR); and CAU 487: Thunderwell Site (TTR). Post-closure inspections were conducted on May 9, 2006, May 31, 2006, and November 15, 2006. All inspections were conducted according to the post-closure plans in the approved Closure Reports. The post-closure inspection plan for each CAU is included in Attachment B, with the exception of CAU 400. CAU 400 does not require post-closure inspections, but inspections of the vegetation and fencing are conducted as a best management practice. The inspection checklists for each site inspection are included in Attachment C, the field notes are included in Attachment D, and the site photographs are included in Attachment E. Vegetation monitoring of CAU 400, CAU 404, CAU 407, and CAU 426 was performed in June 2006, and the vegetation monitoring report is included in Attachment F. Maintenance and/or repairs were performed at CAU 400, CAU 407, CAU 426, CAU 453, and CAU 487 in 2006. During the May inspection of CAU 400, it was identified that the east and west sections of chickenwire fencing beyond the standard fencing were damaged; they were repaired in June 2006. Also in June 2006, the southeast corner fence post and one warning sign at CAU 407 were reinforced and reattached, the perimeter fencing adjacent to the gate at CAU 426 was tightened, and large animal

A novel proteomic biomarker panel as a diagnostic tool for patients with ovarian cancer

DEFF Research Database (Denmark)

Høgdall, Claus; Fung, Eric T; Christensen, Ib J

2011-01-01

Previous reports have shown that the proteomic markers apolipoprotein A1, hepcidin, transferrin, inter-alpha trypsin IV internal fragment, transthyretin, connective-tissue activating protein 3 and beta-2 microglobulin may discriminate between a benign pelvic mass and ovarian cancer (OC). The aim...... was to determine if these serum proteomic biomarkers alone as well as in combination with age and serum CA125, could be helpful in triage of women with a pelvic mass....

Non-vitamin K antagonist oral anticoagulants compared with warfarin at different levels of INR control in atrial fibrillation: A meta-analysis of randomized trials.

Science.gov (United States)

Carmo, João; Ferreira, Jorge; Costa, Francisco; Carmo, Pedro; Cavaco, Diogo; Carvalho, Salomé; Morgado, Francisco; Adragão, Pedro; Mendes, Miguel

2017-10-01

The efficacy and safety of warfarin for stroke prevention in atrial fibrillation (AF) depend on the time in the therapeutic range (TTR) with an international normalised ratio (INR) of 2.0-3.0. This meta-analysis focused the relative efficacy and safety of non-VKA oral anticoagulants (NOAC) compared with warfarin at different thresholds of centre's TTR (cTTR). We searched PubMed, Embase, CENTRAL and websites of regulatory agencies, limiting searches to randomized phase 3 trials. Primary outcomes were stroke or systemic embolism (SSE) and major or non-major clinically relevant (NMCR) bleeding. We used a random-effects model to pool effect on outcomes according to different thresholds of cTTR. Four TTR sub-studies with a total of 71,222 patients were included. The benefit of NOAC in reducing SSE compared with warfarin was significantly higher in patients at cTTRwarfarin in patients at all sub-groups (0.67, 0.54-0.83 for patients at cTTRwarfarin for stroke prevention is lost above a cTTR threshold of approximately 70%, but the relative safety appears to be less modified by the centre-based quality of INR control. Copyright © 2017 Elsevier B.V. All rights reserved.

Post-Closure Inspection Report for the Tonopah Test Range, Nevada, for Calendar Year 2014

Energy Technology Data Exchange (ETDEWEB)

Silvas, A. J. [National Security Technologies, LLC, Las Vegas, NV (United States). Nevada Test Site; Lantow, Tiffany A. [National Security Technologies, LLC, Las Vegas, NV (United States). Nevada Test Site

2015-03-25

This report provides the results of the annual post-closure inspections conducted at the closed Corrective Action Units (CAUs) located on the Tonopah Test Range (TTR), Nevada. This report covers calendar year 2014 and includes inspection and repair activities completed at the following CAUs; CAU 400: Bomblet Pit and Five Points Landfill (TTR); CAU 407: Roller Coaster RadSafe Area (TTR); CAU 424: Area 3 Landfill Complexes (TTR); CAU 453: Area 9 UXO Landfill (TTR); and CAU 487: Thunderwell Site (TTR) Inspections were conducted according to the post-closure plans in the approved Closure Reports and subsequent correspondence with the Nevada Division of Environmental Protection. The post-closure inspection plans and subsequent correspondence modifying the requirements for each CAU are included in Appendix B. The inspection checklists are included in Appendix C. Photographs taken during inspections are included in Appendix D. The annual post-closure inspections were conducted on May 28, 2014. Maintenance was required at CAU 407. Animal burrows were backfilled and erosion repairs were performed. Vegetation monitoring was performed at CAU 407 in June 2014. The vegetation monitoring report is included in Appendix E.

Assessment of the Quality of Chronic Anticoagulation Control With Time in Therapeutic Range in Atrial Fibrillation Patients Treated With Vitamin K Antagonists by Hemostasis Specialists: The TERRA Registry: Tiempo en rango en la República Argentina.

Science.gov (United States)

Tajer, Carlos; Ceresetto, José; Bottaro, Federico Jorge; Martí, Alejandra; Casey, Marcelo

2017-07-01

Oral anticoagulation therapy with vitamin K antagonists (VKA) such as warfarin and acenocoumarol is recommended in patients with atrial fibrillation (AF) and risk factors for embolism. The quality of anticoagulation control with VKA may be assessed by the time in therapeutic range (TTR). In our country, there are no data available about the quality of anticoagulation in patients with AF. The primary goal of our study was to assess the level of effective anticoagulation in a multicenter network of anticoagulation clinics in Argentina, which included patients with nonvalvular AF (NVAF) treated with VKA oral anticoagulants. The TERRA trial is a multicenter, cross-sectional study involving 14 anticoagulation clinics that were invited to participate and recruit 100 consecutive patients with NVAF treated with VKA for more than 1 year. The international normalized ratio (INR) values were retrospectively obtained from patient charts, and TTR was calculated using the Rosendaal method. A total of 1190 patients were included in the analysis. Mean age was 74.9 ± 9.9 years, and 52.5% of the patients were male. Median TTR was 67.5% (interquartile interval 54-80). During 55% of the TTR, INR was >3. Interinstitution variability was substantial, with a range of 57.7% ± 17% to 87.7% ± 17%, P < .001. The 10th percentile of TTR was 41%, the 20th percentile was 50%, the 30th was 58%, and the 35th percentile was 60%. In 40% of patients, TTR was <70%. In this multicenter study, mean TTR values in patients with AF under VKA were similar to those in international therapeutic clinical trials (55%-65%). Marked variations among institutions were observed and, although average results obtained were high, one third of the patients exhibited a TTR below 60%. This cutoff value is conservative according to current recommendations, and guidelines suggest that when management with VKA cannot be improved, patients should be switched to direct oral anticoagulants. The addition of TTR calculation to

The Comparative Power of Type/Token and Hapax legomena/Type Ratios: A Corpus-based Study of Authorial Differentiation

Directory of Open Access Journals (Sweden)

Sundus Muhsin Ali

2014-06-01

Full Text Available This paper presents an attempt to verify the comparative power of two statistical features: Type/Token, and Hapax legomena/Token ratios (henceforth TTR and HTR. A corpus of ten novels is compiled. Then sixteen samples (each is 5,000 tokens in length are taken randomly out of these novels as representative blocks. The researchers observe the way TTR and HTR behave in discriminating four novelists: Joyce, Woolf, Faulkner and Hemingway. When compared to the traditional statistical features (e.g. word length average, Sentence length average, etc., TTR and HTR are by far more competent in comparing the distinctive quantitative behavior of each novelist. It turns out that TTR and HTR contribute more or less in creating a sort of statistical identity which can be used in giving a vivid comparison and discrimination of the four novelists involved in this paper. Nevertheless, HTR sounds more viable in achieving the discriminating task than TTR.

Hepatic gene expression changes in pigs experimentally infected with the lung pathogen Actinobacillus pleuropneumoniae as analysed with an innate immunity focused microarray

DEFF Research Database (Denmark)

Skovgaard, Kerstin; Mortensen, Shila; Boye, Mette

2010-01-01

Knowledge on gene expression in the liver during respiratory infections is limited although it is well-established that this organ is an important site of synthesis of several systemic innate immune components as response to infections. In the present study, the early transcriptional hepatic...... in initiating and orchestrating the innate immune response to A. pleuropneumoniae infection. Keywords: acute phase protein, hepatic transcriptional response, innate defence, gene expression, pig...... differentially expressed. A large group of these genes encoded proteins involved in the acute phase response, including serum amyloid A, C-reactive protein, fibrinogen, haptoglobin and tumor necrosis factor-a the expression of which were all found to be up-regulated and glutathione S-transferase, transthyretin...

Factors influencing warfarin control in Australia and Singapore.

Science.gov (United States)

Bernaitis, Nijole; Ching, Chi Keong; Teo, Siew Chong; Chen, Liping; Badrick, Tony; Davey, Andrew K; Crilly, Julia; Anoopkumar-Dukie, Shailendra

2017-09-01

Warfarin is widely used for patients with non-valvular atrial fibrillation (NVAF). Variations in warfarin control, as measured by time in therapeutic range (TTR), have been reported across different regions and ethnicities, particularly between Western and Asian countries. However, there is limited data on comparative factors influencing warfarin control in Caucasian and Asian patients. Therefore, the aim of this study was to determine warfarin control and potential factors influencing this in patients with NVAF in Australia and Singapore. Retrospective data was collected for patients receiving warfarin for January to June 2014 in Australia and Singapore. TTR was calculated for individuals with mean patient TTR used for analysis. Possible influential factors on TTR were analysed including age, gender, concurrent co-morbidities, and concurrent medication. The mean TTR was significantly higher in Australia (82%) than Singapore (58%). At both sites, chronic kidney disease significantly lowered this TTR. Further factors influencing control were anaemia and ageWarfarin control was significantly higher in Australia compared to Singapore, however chronic kidney disease reduced control at both sites. The different levels of control in these two countries, together with patient factors further reducing control may impact on anticoagulant choice in these countries with better outcomes from warfarin in Australia compared to Singapore. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanism

DEFF Research Database (Denmark)

Sørensen, Jesper; Hamelberg, Donald; Schiøtt, Birgit

2007-01-01

Proteins can misfold and aggregate, which is believed to be the cause of a variety of diseases, affecting very diverse organs in the body. Many questions about the nature of aggregation and the proteins that are involved in these events are still left unanswered. One of the proteins that is known...

Effect of a combined education and eHealth programme on the control of oral anticoagulation patients (PORTALS study): a parallel cohort design in Dutch primary care.

Science.gov (United States)

Talboom-Kamp, Esther P W A; Verdijk, Noortje A; Kasteleyn, Marise J; Harmans, Lara M; Talboom, Irvin J S H; Numans, Mattijs E; Chavannes, Niels H

2017-09-27

To analyse the effect on therapeutic control and self-management skills of the implementation of self-management programmes, including eHealth by e-learning versus group training. Primary Care Thrombosis Service Center. Of the 247 oral anticoagulation therapy (OAT) patients, 63 started self-management by e-learning, 74 self-management by group training and 110 received usual care. Parallel cohort design with two randomised self-management groups (e-learning and group training) and a group receiving usual care. The effect of implementation of self-management on time in therapeutic range (TTR) was analysed with multilevel linear regression modelling. Usage of a supporting eHealth platform and the impact on self-efficacy (Generalised Self-Efficacy Scale (GSES)) and education level were analysed with linear regression analysis. After intervention, TTR was measured in three time periods of 6 months. (1) TTR, severe complications,(2) usage of an eHealth platform,(3) GSES, education level. Analysis showed no significant differences in TTR between the three time periods (p=0.520), the three groups (p=0.460) or the groups over time (p=0.263). Comparison of e-learning and group training showed no significant differences in TTR between the time periods (p=0.614), the groups (p=0.460) or the groups over time (p=0.263). No association was found between GSES and TTR (p=0.717) or education level and TTR (p=0.107). No significant difference was found between the self-management groups in usage of the platform (0-6 months p=0.571; 6-12 months p=0.866; 12-18 months p=0.260). The percentage of complications was low in all groups (3.2%; 1.4%; 0%). No differences were found between OAT patients trained by e-learning or by a group course regarding therapeutic control (TTR) and usage of a supporting eHealth platform. The TTR was similar in self-management and regular care patients. With adequate e-learning or group training, self-management seems safe and reliable for a selected

2013 Annual Site Environmental Report for Sandia National Laboratories Tonopah Test Range Nevada & Kauai Test Facility Hawaii

Energy Technology Data Exchange (ETDEWEB)

Griffith, Stacy Rene [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Agogino, Karen [National Nuclear Security Administration (NNSA), Washington, DC (United States); Li, Jun [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); White, Nancy [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Minitrez, Alexandra [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Avery, Penny [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Bailey-White, Brenda [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Bonaguidi, Joseph [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Catechis, Christopher [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); duMond, Michael [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Eckstein, Joanna [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Evelo, Stacie [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Forston, William [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Herring, III, Allen [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Lantow, Tiffany [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Martinez, Reuben [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Mauser, Joseph [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Miller, Amy [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Miller, Mark [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Payne, Jennifer [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Peek, Dennis [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Reiser, Anita [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Ricketson, Sherry [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Roma, Charles [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Salinas, Stephanie [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Ullrich, Rebecca [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

2014-08-01

Tonopah Test Range (TTR) in Nevada and Kauai Test Facility (KTF) in Hawaii are government-owned, contractor-operated facilities managed and operated by Sandia Corporation (Sandia), a wholly owned subsidiary of Lockheed Martin Corporation. The U.S. Department of Energy (DOE), National Nuclear Security Administration (NNSA), through the Sandia Field Office (SFO), in Albuquerque, New Mexico, administers the contract and oversees contractor operations at TTR and KTF. Sandia manages and conducts operations at TTR in support of the DOE/NNSA’s Weapons Ordnance Program and has operated the site since 1957. Navarro Research and Engineering subcontracts to Sandia in administering most of the environmental programs at TTR. Sandia operates KTF as a rocket preparation launching and tracking facility. This Annual Site Environmental Report summarizes data and the compliance status of the sustainability, environmental protection, and monitoring program at TTR and KTF through Calendar Year 2013. The compliance status of environmental regulations applicable at these sites include state and federal regulations governing air emissions, wastewater effluent, waste management, terrestrial surveillance, Environmental Restoration (ER) cleanup activities, and the National Environmental Policy Act. Sandia is responsible only for those environmental program activities related to its operations. The DOE/NNSA/Nevada Field Office retains responsibility for the cleanup and management of TTR ER sites. Environmental monitoring and surveillance programs are required by DOE Order 231.1B, Environment, Safety, and Health Reporting (DOE 2012).

Generic amyloidogenicity of mammalian prion proteins from species susceptible and resistant to prions.

Science.gov (United States)

Nyström, Sofie; Hammarström, Per

2015-05-11

Prion diseases are lethal, infectious diseases associated with prion protein (PrP) misfolding. A large number of mammals are susceptible to both sporadic and acquired prion diseases. Although PrP is highly conserved and ubiquitously expressed in all mammals, not all species exhibit prion disease. By employing full length recombinant PrP from five known prion susceptible species (human, cattle, cat, mouse and hamster) and two species considered to be prion resistant (pig and dog) the amyloidogenicity of these PrPs has been delineated. All the mammalian PrPs, even from resistant species, were swiftly converted from the native state to amyloid-like structure when subjected to a native condition conversion assay. The PrPs displayed amyloidotypic tinctorial and ultrastructural hallmarks. Self-seeded conversion of the PrPs displayed significantly decreased lag phases demonstrating that nucleation dependent polymerization is a dominating mechanism in the fibrillation process. Fibrils from Aβ1-40, Aβ1-42, Lysozyme, Insulin and Transthyretin did not accelerate conversion of HuPrP whereas fibrils from HuPrP90-231 and HuPrP121-231 as well as full length PrPs of all PrPs efficiently seeded conversion showing specificity of the assay requiring the C-terminal PrP sequence. Our findings have implications for PrP misfolding and could have ramifications in the context of prion resistant species and silent carriers.

Post-Closure Inspection Report for the Tonopah Test Range, Nevada, for Calendar Year 2009

International Nuclear Information System (INIS)

2010-01-01

This report provides the results of the annual post-closure inspections conducted at the closed Corrective Action Unit (CAU) sites located on the Tonopah Test Range (TTR), Nevada. This report covers calendar year 2009 and includes inspection and repair activities completed at the following seven CAUs: (1) CAU 400: Bomblet Pit and Five Points Landfill (TTR); (2) CAU 407: Roller Coaster RadSafe Area (TTR); (3) CAU 424: Area 3 Landfill Complexes (TTR); (4) CAU 426: Cactus Spring Waste Trenches (TTR); (5) CAU 453: Area 9 UXO Landfill (TTR); (6) CAU 484: Surface Debris, Waste Sites, and Burn Area (TTR); and (7) CAU 487: Thunderwell Site (TTR). The annual post-closure inspections were conducted May 5-6, 2009. All inspections were conducted according to the post-closure plans in the approved Closure Reports. The post-closure inspection plan for each CAU is included in Attachment B, with the exception of CAU 400. CAU 400 does not require post-closure inspections, but inspections of the vegetation and fencing are conducted as a best management practice. The inspection checklists for each site inspection are included in Attachment C, the field notes are included in Attachment D, and the site photographs are included in Attachment E. Vegetation monitoring of CAU 400, CAU 404, CAU 407, and CAU 426 was performed in June 2009, and the vegetation monitoring report is included in Attachment F. Maintenance was performed at CAU 453. Animal burrows observed during the annual inspection were backfilled, and a depression was restored to grade on June 25, 2009. Post-closure site inspections should continue as scheduled. Vegetation survey inspections have been conducted annually at CAUs 400, 404, 407, and 426. Discontinuation of vegetation surveys is recommended at the CAU 400 Bomblet Pit and CAU 426, which have been successfully revegetated. Discontinuation of vegetation surveys is also recommended at CAU 404, which has been changed to an administrative closure with no inspections

Post-Closure Inspection Report for the Tonopah Test Range, Nevada, for Calendar Year 2009

Energy Technology Data Exchange (ETDEWEB)

NSTec Environmental Restoration

2010-05-28

This report provides the results of the annual post-closure inspections conducted at the closed Corrective Action Unit (CAU) sites located on the Tonopah Test Range (TTR), Nevada. This report covers calendar year 2009 and includes inspection and repair activities completed at the following seven CAUs: · CAU 400: Bomblet Pit and Five Points Landfill (TTR) · CAU 407: Roller Coaster RadSafe Area (TTR) · CAU 424: Area 3 Landfill Complexes (TTR) · CAU 426: Cactus Spring Waste Trenches (TTR) · CAU 453: Area 9 UXO Landfill (TTR) · CAU 484: Surface Debris, Waste Sites, and Burn Area (TTR) · CAU 487: Thunderwell Site (TTR) The annual post-closure inspections were conducted May 5–6, 2009. All inspections were conducted according to the post-closure plans in the approved Closure Reports. The post-closure inspection plan for each CAU is included in Attachment B, with the exception of CAU 400. CAU 400 does not require post-closure inspections, but inspections of the vegetation and fencing are conducted as a best management practice. The inspection checklists for each site inspection are included in Attachment C, the field notes are included in Attachment D, and the site photographs are included in Attachment E. Vegetation monitoring of CAU 400, CAU 404, CAU 407, and CAU 426 was performed in June 2009, and the vegetation monitoring report is included in Attachment F. Maintenance was performed at CAU 453. Animal burrows observed during the annual inspection were backfilled, and a depression was restored to grade on June 25, 2009. Post-closure site inspections should continue as scheduled. Vegetation survey inspections have been conducted annually at CAUs 400, 404, 407, and 426. Discontinuation of vegetation surveys is recommended at the CAU 400 Bomblet Pit and CAU 426, which have been successfully revegetated. Discontinuation of vegetation surveys is also recommended at CAU 404, which has been changed to an administrative closure with no inspections required. Vegetation

Post-Closure Inspection Report for the Tonopah Test Range, Nevada. For Calendar Year 2015, Revision 0

International Nuclear Information System (INIS)

Matthews, Patrick; Petrello, Jaclyn

2016-01-01

This report provides the results of the annual post-closure inspections conducted at the closed corrective action units (CAUs) located on the Tonopah Test Range (TTR), Nevada. This report covers calendar year 2015 and includes inspection and repair activities completed at the following CAUs; CAU 400: Bomblet Pit and Five Points Landfill (TTR); CAU 407: Roller Coaster RadSafe Area (TTR); CAU 424: Area 3 Landfill Complexes (TTR); CAU 453: Area 9 UXO Landfill (TTR); and CAU 487: Thunderwell Site (TTR) Inspections were conducted according to the post-closure plans in the approved closure reports and subsequent correspondence with the Nevada Division of Environmental Protection. The post-closure inspection plans and subsequent correspondence modifying the requirements for each CAU are included in Appendix B. The inspection checklists are included in Appendix C. Field notes are included in Appendix D. The annual post-closure inspections were conducted on May 12, 2015. Maintenance was required at CAU 453. Cracking along the north trench was repaired. One monument is missing at CAU 424; it will be replaced in 2016. Postings at CAUs 407, 424, 453, and 487 contain contact information for TTR Security. It was noted that protocols may not be in place to ensure that the U.S. Department of Energy, National Nuclear Security Administration Nevada Field Office (NNSA/NFO) is notified if access is needed at these sites. NNSA/NFO is working with the U.S. Air Force and Sandia to determine whether more appropriate contact information or new protocols are warranted for each CAU. Based on these inspections, there has not been a significant change in vegetation, and vegetation monitoring was not recommended at CAU 400 or CAU 407 in 2015.

Quality of warfarin therapy and risk of stroke, bleeding, and mortality among patients with atrial fibrillation: results from the nationwide FinWAF Registry.

Science.gov (United States)

Lehto, Mika; Niiranen, Jussi; Korhonen, Pasi; Mehtälä, Juha; Khanfir, Houssem; Hoti, Fabian; Lassila, Riitta; Raatikainen, Pekka

2017-06-01

The most important management strategy in atrial fibrillation (AF) patients is preventing stroke with oral anticoagulants. Warfarin is still used as a first-line anticoagulant, although non-vitamin K antagonist oral anticoagulants are currently recommended to manage AF. Using a large, unselected national sample of AF patients, we evaluated the relationships between quality of warfarin therapy and the risks of thromboembolism, bleeding complications, and mortality. The nationwide FinWAF study included 54 568 AF patients taking warfarin. Time in the therapeutic range (TTR) was calculated on a continuous basis using the Rosendaal method and international normalized ratio values over the previous 60 days. Adjusted Cox proportional hazard models were prepared for different TTR levels and major clinical end points. The mean age of patients was 73.1 years (standard deviation 10.8), and 47% were female. The mean follow-up time was 3.2 ± 1.6 years (median 3.4). In the TTR groups of ≤40%, 60-70%, 70-80%, and >80%, the annual risk of stroke was 9.3%, 4.7%, 4.6%, and 3.1%; bleeding events 7.5%, 4.5%, 4.3%, and 2.6%; and overall mortality 20.9%, 8.5%, 6.4%, and 3.1%, respectively. All differences among the TTR groups were highly significant (p warfarin treatment was strongly associated with the risk of stroke and the prognosis of AF patients. Patient outcomes continued to improve with increasing TTR values up to a TTR ≥80%; therefore, the target for the TTR should exceed 80% instead of the traditional range of at least 60-70%. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Post-Closure Inspection Report for the Tonopah Test Range, Nevada. For Calendar Year 2015, Revision 0

Energy Technology Data Exchange (ETDEWEB)

Matthews, Patrick [Navarro, Las Vegas, NV (United States); Petrello, Jaclyn [Navarro, Las Vegas, NV (United States)

2016-03-01

This report provides the results of the annual post-closure inspections conducted at the closed corrective action units (CAUs) located on the Tonopah Test Range (TTR), Nevada. This report covers calendar year 2015 and includes inspection and repair activities completed at the following CAUs; CAU 400: Bomblet Pit and Five Points Landfill (TTR); CAU 407: Roller Coaster RadSafe Area (TTR); CAU 424: Area 3 Landfill Complexes (TTR); CAU 453: Area 9 UXO Landfill (TTR); and CAU 487: Thunderwell Site (TTR) Inspections were conducted according to the post-closure plans in the approved closure reports and subsequent correspondence with the Nevada Division of Environmental Protection. The post-closure inspection plans and subsequent correspondence modifying the requirements for each CAU are included in Appendix B. The inspection checklists are included in Appendix C. Field notes are included in Appendix D. The annual post-closure inspections were conducted on May 12, 2015. Maintenance was required at CAU 453. Cracking along the north trench was repaired. One monument is missing at CAU 424; it will be replaced in 2016. Postings at CAUs 407, 424, 453, and 487 contain contact information for TTR Security. It was noted that protocols may not be in place to ensure that the U.S. Department of Energy, National Nuclear Security Administration Nevada Field Office (NNSA/NFO) is notified if access is needed at these sites. NNSA/NFO is working with the U.S. Air Force and Sandia to determine whether more appropriate contact information or new protocols are warranted for each CAU. Based on these inspections, there has not been a significant change in vegetation, and vegetation monitoring was not recommended at CAU 400 or CAU 407 in 2015.

Calendar Year 2004 annual site environmental report : Tonopah Test Range, Nevada and Kauai Test Facility, Hawaii

International Nuclear Information System (INIS)

Montoya, Amber L.; Wagner, Katrina; Goering, Teresa Lynn; Koss, Susan I.; Salinas, Stephanie A.

2005-01-01

Tonopah Test Range (TTR) in Nevada and Kauai Test Facility (KTF) in Hawaii are government-owned, contractor-operated facilities operated by Sandia Corporation, a subsidiary of Lockheed Martin Corporation. The U.S. Department of Energy (DOE), National Nuclear Security Administration (NNSA), through the Sandia Site Office (SSO), in Albuquerque, NM, manages TTR and KTF's operations. Sandia Corporation conducts operations at TTR in support of DOE/NNSA's Weapons Ordnance Program and has operated the site since 1957. Westinghouse Government Services subcontracts to Sandia Corporation in administering most of the environmental programs at TTR. Sandia Corporation operates KTF as a rocket preparation launching and tracking facility. This Annual Site Environmental Report (ASER) summarizes data and the compliance status of the environmental protection and monitoring program at TTR and KTF through Calendar Year (CY) 2004. The compliance status of environmental regulations applicable at these sites include state and federal regulations governing air emissions, wastewater effluent, waste management, terrestrial surveillance, and Environmental Restoration (ER) cleanup activities. Sandia Corporation is responsible only for those environmental program activities related to its operations. The DOE/NNSA, Nevada Site Office (NSO) retains responsibility for the cleanup and management of ER TTR sites. Currently, there are no ER Sites at KTF. Environmental monitoring and surveillance programs are required by DOE Order 450.1, Environmental Protection Program (DOE 2005) and DOE Order 231.1A, Environment, Safety, and Health Reporting (DOE 2004b)

Calendar Year 2004 annual site environmental report : Tonopah Test Range, Nevada & Kauai Test Facility, Hawaii.

Energy Technology Data Exchange (ETDEWEB)

Montoya, Amber L.; Wagner, Katrina; Goering, Teresa Lynn; Koss, Susan I.; Salinas, Stephanie A.

2005-09-01

Tonopah Test Range (TTR) in Nevada and Kauai Test Facility (KTF) in Hawaii are government-owned, contractor-operated facilities operated by Sandia Corporation, a subsidiary of Lockheed Martin Corporation. The U.S. Department of Energy (DOE), National Nuclear Security Administration (NNSA), through the Sandia Site Office (SSO), in Albuquerque, NM, manages TTR and KTF's operations. Sandia Corporation conducts operations at TTR in support of DOE/NNSA's Weapons Ordnance Program and has operated the site since 1957. Westinghouse Government Services subcontracts to Sandia Corporation in administering most of the environmental programs at TTR. Sandia Corporation operates KTF as a rocket preparation launching and tracking facility. This Annual Site Environmental Report (ASER) summarizes data and the compliance status of the environmental protection and monitoring program at TTR and KTF through Calendar Year (CY) 2004. The compliance status of environmental regulations applicable at these sites include state and federal regulations governing air emissions, wastewater effluent, waste management, terrestrial surveillance, and Environmental Restoration (ER) cleanup activities. Sandia Corporation is responsible only for those environmental program activities related to its operations. The DOE/NNSA, Nevada Site Office (NSO) retains responsibility for the cleanup and management of ER TTR sites. Currently, there are no ER Sites at KTF. Environmental monitoring and surveillance programs are required by DOE Order 450.1, Environmental Protection Program (DOE 2005) and DOE Order 231.1A, Environment, Safety, and Health Reporting (DOE 2004b).

Calendar year 2007 annual site environmental report for Tonopah Test Range, Nevada and Kauai Test Facility, Hawaii,

Energy Technology Data Exchange (ETDEWEB)

Agogino, Karen [Department of Energy, Albuquerque, NM (United States). National Nuclear Security Administration (NNSA); Sanchez, Rebecca [Sandia Corp., Albuquerque, NM (United States)

2008-09-30

Tonopah Test Range (TTR) in Nevada and Kauai Test Facility (KTF) in Hawaii are government-owned, contractor-operated facilities operated by Sandia Corporation (Sandia), a wholly owned subsidiary of Lockheed Martin Corporation. The U.S. Department of Energy (DOE)/National Nuclear Security Administration (NNSA), through the Sandia Site Offi ce (SSO), in Albuquerque, NM, administers the contract and oversees contractor operations at TTR and KTF. Sandia manages and conducts operations at TTR in support of the DOE/NNSA’s Weapons Ordnance Program and has operated the site since 1957. Washington Group International subcontracts to Sandia in administering most of the environmental programs at TTR. Sandia operates KTF as a rocket preparation launching and tracking facility. This Annual Site Environmental Report (ASER) summarizes data and the compliance status of the environmental protection and monitoring program at TTR and KTF through Calendar Year (CY) 2007. The compliance status of environmental regulations applicable at these sites include state and federal regulations governing air emissions, wastewater effluent, waste management, terrestrial surveillance, and Environmental Restoration (ER) cleanup activities. Sandia is responsible only for those environmental program activities related to its operations. The DOE/NNSA/Nevada Site Offi ce (NSO) retains responsibility for the cleanup and management of ER TTR sites. Currently, there are no ER Sites at KTF. Environmental monitoring and surveillance programs are required by DOE Order 450.1, Environmental Protection Program (DOE 2007a) and DOE Manual 231.1-1A, Environment, Safety, and Health Reporting Manual (DOE 2007).

Calendar year 2002 annual site environmental report for Tonopah Test Range, Nevada and Kauai Test Facility, Hawaii.

Energy Technology Data Exchange (ETDEWEB)

Wagner, Katrina; Sanchez, Rebecca V.; Mayeux, Lucie; Koss, Susan I.; Salinas, Stephanie A.

2003-09-01

Tonopah Test Range (TTR) in Nevada and Kauai Test Facility (KTF) in Hawaii are government-owned, contractor-operated facilities operated by Sandia Corporation, a subsidiary of Lockheed Martin Corporation. The U.S. Department of Energy (DOE), National Nuclear Security Administration (NNSA), through the Sandia Site Office (SSO), in Albuquerque, NM, oversees TTR and KTF's operations. Sandia Corporation conducts operations at TTR in support of DOE/NNSA's Weapons Ordnance Program and has operated the site since 1957. Westinghouse Government Services subcontracts to Sandia Corporation in administering most of the environmental programs at TTR. Sandia Corporation operates KTF as a rocket preparation launching and tracking facility. This Annual Site Environmental Report (ASER) summarizes data and the compliance status of the environmental protection and monitoring program at TTR and KTF through Calendar Year (CY) 2002. The compliance status of environmental regulations applicable at these sites include state and federal regulations governing air emissions, wastewater effluent, waste management, terrestrial surveillance, and Environmental Restoration (ER) cleanup activities. Sandia Corporation is responsible only for those environmental program activities related to its operations. The DOE/NNSA, Nevada Site Office (NSO) retains responsibility for the cleanup and management of ER TTR sites. Currently, there are no ER Sites at KTF. Environmental monitoring and surveillance programs are required by DOE Order 5400.1, General Environmental Protection Program (DOE 1990) and DOE Order 231.1, Environment, Safety, and Health Reporting (DOE 1996).

Results from the interim salt disposition program macrobatch 10 tank ²¹H qualification samples

Energy Technology Data Exchange (ETDEWEB)

Peters, T. B. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Bannochie, C. J. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

2017-02-23

Savannah River National Laboratory (SRNL) analyzed samples from Tank 21H in support of qualification of Macrobatch (Salt Batch) 10 for the Interim Salt Disposition Program (ISDP). This document reports characterization data on the samples of Tank 21H and fulfills the requirements of Deliverable 3 of the Technical Task Request (TTR). Further work will report the results of the Extraction-Scrub-Strip (ESS) testing (Task 5 of the TTR) using the Tank 21H material. Task 4 of the TTR (MST Strike) will not be completed for Salt Batch 10.

Modeling, implementation, and validation of arterial travel time reliability : [summary].

Science.gov (United States)

2013-11-01

Travel time reliability (TTR) has been proposed as : a better measure of a facilitys performance than : a statistical measure like peak hour demand. TTR : is based on more information about average traffic : flows and longer time periods, thus inc...

Corino de Andrade disease: mechanisms and impact on reproduction

Science.gov (United States)

Lopes, Rita A; Coelho, Teresa; Barros, Alberto; Sousa, Mário

2017-01-01

Familial amyloid polyneuropathy was first described by Corino de Andrade in 1952 in Northern Portugal. It is a fatal autosomal dominant neurodegenerative disorder characterized by a progression of neurologic symptoms, beginning early in the reproductive life. The Transthyretin gene mutation originates a mutated protein that precipitates in the connective tissue as amyloid deposits. This disease is presently named Transthyretin-related hereditary amyloidosis. We performed an extensive review on this disease based on searches in Medical databases and in paper references. In this review, we briefly summarize the epidemiology and the mechanisms involved on amyloid deposition; we detailed how to evaluate the mechanisms implicated on the development of the major signs and symptoms associated with reproductive dysfunction; and we discuss the mechanisms involved in secondary sexual dysfunction after psychological treatments. Treatment of the disease is directed towards relieving specific symptoms in association with liver transplant, and molecular and genetic therapeutics. Although the current clinical trials indicate symptoms relief, no data on the reproductive function was reported. Thus, preimplantation genetic diagnosis is presently the only available technique that eradicates the disease as it avoids the birth of new patients. PMID:28609277

Sorption and biodegradation of selected benzotriazoles and hydroxybenzothiazole in activated sludge and estimation of their fate during wastewater treatment

DEFF Research Database (Denmark)

Mazioti, Aikaterini A.; Stasinakis, Athanasios S.; Gatidou, Georgia

2015-01-01

Biodegradation of benzotriazole (BTR), 5-chlorobenzotriazole (CBTR), xylytriazole (XTR), 4-methyl-1H-benzotriazole (4TTR), 5-methy-1H-lbenzotriazole (5TTR) and 2-hydroxybenzothiazole (OHBTH) was studied in activated sludge batch experiments under aerobic and anoxic conditions, presence of organic...

Corrective action investigation plan for Corrective Action Unit Number 427: Area 3 septic waste system numbers 2 and 6, Tonopah Test Range, Nevada

International Nuclear Information System (INIS)

1997-01-01

This Corrective Action Investigation Plan (CAIP) contains the environmental sample collection objectives and the criteria for conducting site investigation activities at the Area 3 Compound, specifically Corrective Action Unit (CAU) Number 427, which is located at the Tonopah Test Range (TTR). The TTR, included in the Nellis Air Force Range, is approximately 255 kilometers (140 miles) northwest of Las Vegas, Nevada. The Corrective Action Unit Work Plan, Tonopah Test Range, Nevada divides investigative activities at TTR into Source Groups. The Septic Tanks and Lagoons Group consists of seven CAUs. Corrective Action Unit Number 427 is one of three septic waste system CAUs in TTR Area 3. Corrective Action Unit Numbers 405 and 428 will be investigated at a future data. Corrective Action Unit Number 427 is comprised of Septic Waste Systems Number 2 and 6 with respective CAS Numbers 03-05-002-SW02 and 03-05-002-SW06

Evaluation of a pharmacogenetic-based warfarin dosing algorithm in patients with low time in therapeutic range - study protocol for a randomized controlled trial.

Science.gov (United States)

Marcatto, Leiliane Rodrigues; Sacilotto, Luciana; Bueno, Carolina Tosin; Facin, Mirella; Strunz, Celia Maria Cassaro; Darrieux, Francisco Carlos Costa; Scanavacca, Maurício Ibrahim; Krieger, Jose Eduardo; Pereira, Alexandre Costa; Santos, Paulo Caleb Junior Lima

2016-11-17

Time in therapeutic range (TTR) is a measurement of quality of warfarin therapy and lower TTR values (algorithm specifically calibrated for a Brazilian patient sample. The aims of this study are: to evaluate the impact of a genetic-based algorithm, compared to traditional anticoagulation, in the time to achieve the therapeutic target and in TTR percentage; and to assess the cost-effectiveness of genotype-guided warfarin dosing in a specific cohort of patients with low TTR (algorithm will be used. At the second, third, fourth and fifth consultations (with an interval of 7 days each) INR will be measured and, if necessary, the dose will be adjusted based on guidelines. Afterwards, patients who are INR stable will begin measuring their INR in 30 day intervals; if the patient's INR is not stable, the patient will return in 7 days for a new measurement of the INR. Outcomes measures will include the time to achieve the therapeutic target and the percentage of TTR at 4 and 12 weeks. In addition, as a secondary end-point, pharmacoeconomic analysis will be carried out. Ethical approval was granted by the Ethics Committee for Medical Research on Human Beings of the Clinical Hospital of the University of São Paulo Medical School. This randomized study will include patients with low TTR and it will evaluate whether a population-specific genetic algorithm might be more effective than traditional anticoagulation for a selected group of poorly anticoagulated patients. ClinicalTrials.gov, NCT02592980 . Registered on 29 October 2015.

POST-CLOSURE INSPECTION REPORT FOR THE TONOPAH TEST RANGE, NEVADA, FOR CALENDAR YEAR 2004

Energy Technology Data Exchange (ETDEWEB)

BECHTEL NEVADA

2005-04-01

This Post-Closure Inspection Report provides an analysis and summary of the semi-annual inspections conducted at the Tonopah Test Range (TTR) during Calendar Year 2004. The report includes the inspection and/or repair activities completed at the following nine Corrective Action Units (CAUs) located at TTR, Nevada: (1) CAU 400: Bomblet Pit and Five Points Landfill (TTR); (2) CAU 404: Roller Coaster Lagoons and Trench (TTR); (3) CAU 407: Roller Coaster RadSafe Area (TTR); (4) CAU 423: Area 3 Underground Discharge Point, Building 0360 (TTR) (5) CAU 424: Area 3 Landfill Complexes (TTR); (6) CAU 426: Cactus Spring Waste Trenches (TTR); (7) CAU 427: Area 3 Septic Waste Systems 2,6 (TTR); (8) CAU 453: Area 9 UXO Landfill (TTR); and (9) CAU 487: Thunderwell Site (TTR). Site inspections were conducted on July 7,2004, and November 9-10,2004. All inspections were conducted according to the post-closure plans in the approved Closure Reports (CRs). The post-closure inspection plan for each CAU is included in Appendix B, with the exception of CAU 400 and CAU 423. CAU 400 does not require post-closure inspections, but inspections of the vegetation and fencing are conducted as a best management practice. In addition, post-closure inspections are not currently required at CAU 423; however, the CR is being revised to include inspection requirements. The inspection checklists for each site inspection are included in Appendix C, the field notes are included in Appendix D, and the site photographs are included in Appendix E. Vegetation monitoring of CAU 400, CAU 404, CAU 407, and CAU 426 was performed in June 2004, and the vegetation monitoring report is included in Appendix F. In addition, topographic survey results of two repaired landfill cells in CAU 424 are included in Appendix G. Maintenance and/or repairs were performed at the CAU 400 Five Points Landfill, CAU 407, CAU 424, CAU 427, and CAU 487. CAU 400 repairs included mending the fence, reseeding of a flood damaged area, and

The use of subcutaneous fat tissue for amyloid typing by enzyme-linked immunosorbent assay

DEFF Research Database (Denmark)

Olsen, K E; Sletten, K; Westermark, Per

1999-01-01

for typing the most common systemic amyloidoses of AL, AA, and transthyretin types by enzyme-linked immunosorbent assay (ELISA), using abdominal wall subcutaneous fat biopsy specimens. The method was tested on 21 abdominal fat biopsy specimens that were sent to the laboratory. Of these, 15 contained amyloid......The amyloidoses are biochemically heterogeneous diseases with pathophysiologic deposits of various proteins. The clinical course, prognosis, and therapy are different for each type of amyloidosis and, therefore, a type-specific diagnosis is demanded as early as possible. We describe a method...

Tonopah Test Range - Index

Science.gov (United States)

Capabilities Test Operations Center Test Director Range Control Track Control Communications Tracking Radars Photos Header Facebook Twitter YouTube Flickr RSS Tonopah Test Range Top TTR_TOC Tonopah is the testing range of choice for all national security missions. Tonopah Test Range (TTR) provides research and

Hybrid Moving Bed Biofilm Reactor for the biodegradation of benzotriazoles and hydroxy-benzothiazole in wastewater

DEFF Research Database (Denmark)

Mazioti, Aikaterini A.; Stasinakis, Athanasios S.; Psoma, Aikaterini K.

2017-01-01

and a settling tank. The average removal of target compounds ranged between 41% (4-methyl-1H-benzotriazole; 4TTR) and 88% (2-hydroxybenzothiazole; OHBTH). Except for 4TTR, degradation mainly occurred in the first bioreactor. Calculation of biodegradation constants in batch experiments and application of a model...

Post-Closure Inspection Report for the Tonopah Test Range, Nevada, for Calendar Year 2013

Energy Technology Data Exchange (ETDEWEB)

Silvas, A. J.

2014-03-03

This report provides the results of the annual post-closure inspections conducted at the closed Corrective Action Units (CAUs) located on the Tonopah Test Range (TTR), Nevada. This report covers calendar year 2013 and includes inspection and repair activities completed at the following CAUs: • CAU 400: Bomblet Pit and Five Points Landfill (TTR) • CAU 407: Roller Coaster RadSafe Area (TTR) • CAU 424: Area 3 Landfill Complexes (TTR) • CAU 453: Area 9 UXO Landfill (TTR) • CAU 487: Thunderwell Site (TTR) Inspections were conducted according to the post-closure plans in the approved Closure Reports and subsequent correspondence with the Nevada Division of Environmental Protection. The post-closure inspection plans and subsequent correspondence modifying the requirements for each CAU are included in Appendix B. The inspection checklists are included in Appendix C. Field notes are included in Appendix D. Photographs taken during inspections are included in Appendix E. The annual post-closure inspections were conducted on May 14, 2013. Maintenance was performed at CAU 400, CAU 424, and CAU 453. At CAU 400, animal burrows were backfilled. At CAU 424, erosion repairs were completed at Landfill Cell A3-3, subsidence was repaired at Landfill Cell A3-4, and additional lava rock was placed in high-traffic areas to mark the locations of the surface grade monuments at Landfill Cell A3-3 and Landfill Cell A3-8. At CAU 453, two areas of subsidence were repaired and animal burrows were backfilled. Vegetation monitoring was performed at the CAU 400 Five Points Landfill and CAU 407 in June 2013. The vegetation monitoring report is included in Appendix F.

Corrective action investigation plan for CAU Number 453: Area 9 Landfill, Tonopah Test Range

International Nuclear Information System (INIS)

1997-01-01

This Corrective Action Investigation Plan (CAIP) contains the environmental sample collection objectives and criteria for conducting site investigation activities at the Area 9 Landfill, Corrective Action Unit (CAU) 453/Corrective Action (CAS) 09-55-001-0952, which is located at the Tonopah Test Range (TTR). The TTR, included in the Nellis Air Force Range, is approximately 255 kilometers (140 miles) northwest of Las Vegas, Nevada. The Area 9 Landfill is located northwest of Area 9 on the TTR. The landfill cells associated with CAU 453 were excavated to receive waste generated from the daily operations conducted at Area 9 and from range cleanup which occurred after test activities

Development and Initial Testing of the Tiltrotor Test Rig

Science.gov (United States)

Acree, C. W., Jr.; Sheikman, A. L.

2018-01-01

The NASA Tiltrotor Test Rig (TTR) is a new, large-scale proprotor test system, developed jointly with the U.S. Army and Air Force, to develop a new, large-scale proprotor test system for the National Full-Scale Aerodynamics Complex (NFAC). The TTR is designed to test advanced proprotors up to 26 feet in diameter at speeds up to 300 knots, and even larger rotors at lower airspeeds. This combination of size and speed is unprecedented and is necessary for research into 21st-century tiltrotors and other advanced rotorcraft concepts. The TTR will provide critical data for validation of state-of-the-art design and analysis tools.

Visualization of multiple organ amyloid involvement in systemic amyloidosis using {sup 11}C-PiB PET imaging

Energy Technology Data Exchange (ETDEWEB)

Ezawa, Naoki; Katoh, Nagaaki; Yoshinaga, Tsuneaki [Shinshu University School of Medicine, Department of Medicine (Neurology and Rheumatology), Nagano (Japan); Oguchi, Kazuhiro [Jisenkai Brain Imaging Research Center, Matsumoto (Japan); Yazaki, Masahide [Shinshu University School of Health Sciences, Department of Biomedical Laboratory Sciences, Matsumoto (Japan); Shinshu University, Institute for Biomedical Sciences, Matsumoto (Japan); Sekijima, Yoshiki [Shinshu University School of Medicine, Department of Medicine (Neurology and Rheumatology), Nagano (Japan); Jisenkai Brain Imaging Research Center, Matsumoto (Japan); Shinshu University, Institute for Biomedical Sciences, Matsumoto (Japan)

2018-03-15

To investigate the utility of Pittsburgh compound B (PiB) positron emission tomography (PET) imaging for evaluating whole-body amyloid involvement in patients with systemic amyloidosis. Whole-body {sup 11}C-PiB PET was performed in seven patients with systemic immunoglobulin light-chain (AL) amyloidosis, seven patients with hereditary transthyretin (ATTRm) amyloidosis, one asymptomatic TTR mutation carrier and three healthy controls. The correlations between clinical organ involvement, radiological {sup 11}C-PiB uptake and histopathological findings were analysed for each organ. Organ involvement on {sup 11}C-PiB PET imaging showed good correlations with the clinical findings for the heart and stomach. Abnormal tracer uptake was also observed in the spleen, lachrymal gland, submandibular gland, sublingual gland, lymph node, brain, scalp, extraocular muscles, nasal mucosa, pharynx, tongue and nuchal muscles, most of which were asymptomatic. Physiological tracer uptake was universally observed in the urinary tract (kidney, renal pelvis, ureter and bladder) and enterohepatic circulatory system (liver, gallbladder, bile duct and small intestine) in all participants. Most of the patients and one healthy control subject showed asymptomatic tracer uptake in the lung and parotid gland. The peripheral nervous system did not show any tracer uptake even in patients with apparent peripheral neuropathy. Histological amyloid deposition was confirmed in biopsied myocardium and gastric mucosa where abnormal {sup 11}C-PiB retention was observed. {sup 11}C-PiB PET imaging can be used clinically in the systemic evaluation of amyloid distribution in patients with AL and ATTRm amyloidosis. Quantitative analysis of {sup 11}C-PiB PET images may be useful in therapy evaluation and will reveal whether amyloid clearance is correlated with clinical response. (orig.)

Post-Closure Inspection Report for the Tonopah Test Range, Nevada, For Calendar Year 2011

International Nuclear Information System (INIS)

2012-01-01

This report provides the results of the annual post-closure inspections conducted at the closed Corrective Action Units (CAUs) located on the Tonopah Test Range (TTR), Nevada. This report covers calendar year 2011 and includes inspection and repair activities completed at the following CAUs: (1) CAU 400: Bomblet Pit and Five Points Landfill (TTR); (2) CAU 407: Roller Coaster RadSafe Area (TTR); (3) CAU 424: Area 3 Landfill Complexes (TTR); (4) CAU 453: Area 9 UXO Landfill (TTR); and (5) CAU 487: Thunderwell Site (TTR) Inspections were conducted according to the post-closure plans in the approved Closure Reports. The post-closure inspection plan for each CAU is included in Appendix B. The inspection checklists are included in Appendix C, field notes are included in Appendix D, and photographs taken during inspections are included in Appendix E. The annual post-closure inspections were conducted May 3 and 4, 2011. Maintenance was performed at CAU 424, CAU 453, and CAU 487. At CAU 424, two surface grade monuments at Landfill Cell A3-3 could not be located during the inspection. The two monuments were located and marked with lava rock on July 13, 2011. At CAU 453, there was evidence of animal burrowing. Animal burrows were backfilled on July 13, 2011. At CAU 487, one use restriction warning sign was missing, and wording was faded on the remaining signs. A large animal burrow was also present. The signs were replaced, and the animal burrow was backfilled on July 12, 2011. As a best management practice, the use restriction warning signs at CAU 407 were replaced with standard Federal Facility Agreement and Consent Order signs on July 13, 2011. Vegetation monitoring was performed at the CAU 400 Five Points Landfill and CAU 407 in June 2011, and the vegetation monitoring report is included in Appendix F.

Multi-dose drug dispensing as a tool to improve medication adherence: A study in patients using vitamin K antagonists.

Science.gov (United States)

van Rein, Nienke; de Geus, Kristel S; Cannegieter, Suzanne C; Reitsma, Pieter H; van der Meer, Felix J M; Lijfering, Willem M

2018-01-01

Multi-dose drug dispensing (MDD) is a dosing aid that provides patients with disposable bags containing all drugs intended for 1 dosing moment. MDD is believed to increase medication adherence, but studies are based on self-reported data, and results may depend on socially desirable answers. Therefore, our purpose was to determine the effect of MDD on medication adherence in non-adherent patients taking vitamin K antagonists (VKAs), and to compare with instructing patients on medication use. We conducted a before-after study in non-adherent patients where MDD was the exposure and change in adherence after MDD initiation was the outcome (within patient comparison). Time in therapeutic range (TTR) was selected as a measure for adherence, as this reflects stability of VKA treatment. To analyze whether MDD improved adherence as compared with standard care (ie, letters or calls from nurses of the anticoagulation clinic), non-adherent patients without MDD were also followed to estimate their TTR change over time (between patient comparison). Eighty-three non-adherent VKA patients started using MDD. The median TTR was 63% before MDD and 73% 6 months after MDD. The within patient TTR increased on average by 13% (95%CI 6% to 21%) within 1 month after starting MDD and remained stable during the next 5 months. The TTR of MDD-patients increased 10% (95%CI 2% to 19%) higher as compared with non-MDD patients within 1 month but was similar after 4 months (TTR difference 3%, 95%CI -2% to 9%). Adherence improved after initiation of MDD. Compared with instructing patients, MDD was associated with better adherence within 1 month but was associated with similar improvement after 4 months. Copyright © 2017 John Wiley & Sons, Ltd.

Post-Closure Inspection Report for the Tonopah Test Range, Nevada, For Calendar Year 2011

Energy Technology Data Exchange (ETDEWEB)

NSTec Environmental Restoration

2012-02-21

This report provides the results of the annual post-closure inspections conducted at the closed Corrective Action Units (CAUs) located on the Tonopah Test Range (TTR), Nevada. This report covers calendar year 2011 and includes inspection and repair activities completed at the following CAUs: (1) CAU 400: Bomblet Pit and Five Points Landfill (TTR); (2) CAU 407: Roller Coaster RadSafe Area (TTR); (3) CAU 424: Area 3 Landfill Complexes (TTR); (4) CAU 453: Area 9 UXO Landfill (TTR); and (5) CAU 487: Thunderwell Site (TTR) Inspections were conducted according to the post-closure plans in the approved Closure Reports. The post-closure inspection plan for each CAU is included in Appendix B. The inspection checklists are included in Appendix C, field notes are included in Appendix D, and photographs taken during inspections are included in Appendix E. The annual post-closure inspections were conducted May 3 and 4, 2011. Maintenance was performed at CAU 424, CAU 453, and CAU 487. At CAU 424, two surface grade monuments at Landfill Cell A3-3 could not be located during the inspection. The two monuments were located and marked with lava rock on July 13, 2011. At CAU 453, there was evidence of animal burrowing. Animal burrows were backfilled on July 13, 2011. At CAU 487, one use restriction warning sign was missing, and wording was faded on the remaining signs. A large animal burrow was also present. The signs were replaced, and the animal burrow was backfilled on July 12, 2011. As a best management practice, the use restriction warning signs at CAU 407 were replaced with standard Federal Facility Agreement and Consent Order signs on July 13, 2011. Vegetation monitoring was performed at the CAU 400 Five Points Landfill and CAU 407 in June 2011, and the vegetation monitoring report is included in Appendix F.

Clinical Prediction Model for Time in Therapeutic Range While on Warfarin in Newly Diagnosed Atrial Fibrillation.

Science.gov (United States)

Williams, Brent A; Evans, Michael A; Honushefsky, Ashley M; Berger, Peter B

2017-10-12

Though warfarin has historically been the primary oral anticoagulant for stroke prevention in newly diagnosed atrial fibrillation (AF), several new direct oral anticoagulants may be preferred when anticoagulation control with warfarin is expected to be poor. This study developed a prediction model for time in therapeutic range (TTR) among newly diagnosed AF patients on newly initiated warfarin as a tool to assist decision making between warfarin and direct oral anticoagulants. This electronic medical record-based, retrospective study included newly diagnosed, nonvalvular AF patients with no recent warfarin exposure receiving primary care services through a large healthcare system in rural Pennsylvania. TTR was estimated as the percentage of time international normalized ratio measurements were between 2.0 and 3.0 during the first year following warfarin initiation. Candidate predictors of TTR were chosen from data elements collected during usual clinical care. A TTR prediction model was developed and temporally validated and its predictive performance was compared with the SAMe-TT 2 R 2 score (sex, age, medical history, treatment, tobacco, race) using R 2 and c-statistics. A total of 7877 newly diagnosed AF patients met study inclusion criteria. Median (interquartile range) TTR within the first year of starting warfarin was 51% (32, 67). Of 85 candidate predictors evaluated, 15 were included in the final validated model with an R 2 of 15.4%. The proposed model showed better predictive performance than the SAMe-TT 2 R 2 score ( R 2 =3.0%). The proposed prediction model may assist decision making on the proper mode of oral anticoagulant among newly diagnosed AF patients. However, predicting TTR on warfarin remains challenging. © 2017 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley.

Post-Closure Inspection Report for the Tonopah Test Range, Nevada: For Calendar Year 2017, Revision 0

Energy Technology Data Exchange (ETDEWEB)

Alvarado, Juan; Matthews, Patrick

2018-05-01

This report provides the results of the annual post-closure inspections conducted at the closed corrective action units (CAUs) located on the Tonopah Test Range (TTR) and the Nevada Test and Training Range (NTTR). This report covers calendar year 2017 and includes visual inspection and repair activities completed at the following CAUs: • CAU 400: Bomblet Pit and Five Points Landfill (TTR) • CAU 407: Roller Coaster RadSafe Area (TTR) • CAU 424: Area 3 Landfill Complexes (TTR) • CAU 453: Area 9 UXO Landfill (TTR) • CAU 487: Thunderwell Site (TTR) Visual inspections were conducted according to the post-closure plans in the approved closure reports and subsequent correspondence with the Nevada Division of Environmental Protection. The annual post-closure inspections were conducted on May 23, 2017. No maintenance or repair issues were noted at CAU 400 and CAU 487. Maintenance items and subsequent repairs include the following: • CAU 407: A large animal burrow was observed in the southeast corner of the cover during the inspection. Two additional animal burrows were discovered during repair actions. All cover defects were repaired on January 9, 2018. • CAU 424: CAS 03-08-002-A304 (Landfill Cell A3-4): A new monument was installed and the subsidence area was repaired on January 9, 2018. • CAU 424: CAS 03-08-002-A308 (Landfill Cell A3-8): Lava rock, used to mark the two eastern monument locations, was noted as missing during the inspection. The lava rock was replaced on January 9, 2018. • CAU 453: Five large animal burrows, located near the east–central portion of cover, was noted during the inspection. Eight additional animal burrows were discovered during repair actions. All cover defects were repaired on January 9, 2018.

Status of endangered and threatened plant species on Tonopah Test Range: a survey

International Nuclear Information System (INIS)

Rhoads, W.A.; Cochrane, S.A.; Williams, M.P.

1979-10-01

Six species under consideration by the US Fish and Wildlife Service (FWS) for endangered or threatened status were found on or near the Tonopah Test Range (TTR) in southern central Nevada. Based on recognized threats to these species, their overall distribution, rarity, and other factors, status recommendations were prepared for Sandia Corporation. In addition, ten species that occur in the vicinity of TTR, and which may yet be found on TTR, are discussed in brief. Each species is discussed in relation to distribution, rarity, taxonomy, habitat requirements, endangerment, assessment of status, and proposed protection and monitoring needs. Construction activities and off-road vehicle travel are the most prominent man-caused threats to species on TTR; habitat destruction by trampling and over-grazing by feral horses and non-permit cattle significantly modifies habitats of certain species. We recommend two kinds of protective measures. First is the planning of activities so that habitats, particularly the suggested protected habitats, are not disturbed. Second, and directed to the same end, off-road traffic should be curtailed in the regions of the proposed protected habitats

Quality of oral anticoagulation with phenprocoumon in regular medical care and its potential for improvement in a telemedicine-based coagulation service--results from the prospective, multi-center, observational cohort study thrombEVAL.

Science.gov (United States)

Prochaska, Jürgen H; Göbel, Sebastian; Keller, Karsten; Coldewey, Meike; Ullmann, Alexander; Lamparter, Heidrun; Jünger, Claus; Al-Bayati, Zaid; Baer, Christina; Walter, Ulrich; Bickel, Christoph; ten Cate, Hugo; Münzel, Thomas; Wild, Philipp S

2015-01-23

The majority of studies on quality of oral anticoagulation (OAC) therapy with vitamin K-antagonists are performed with short-acting warfarin. Data on long-acting phenprocoumon, which is frequently used in Europe for OAC therapy and is considered to enable more stable therapy adjustment, are scarce. In this study, we aimed to assess quality of OAC therapy with phenprocoumon in regular medical care and to evaluate its potential for optimization in a telemedicine-based coagulation service. In the prospective observational cohort study program thrombEVAL we investigated 2,011 patients from regular medical care in a multi-center cohort study and 760 patients from a telemedicine-based coagulation service in a single-center cohort study. Data were obtained from self-reported data, computer-assisted personal interviews, and laboratory measurements according to standard operating procedures with detailed quality control. Time in therapeutic range (TTR) was calculated by linear interpolation method to assess quality of OAC therapy. Study monitoring was carried out by an independent institution. Overall, 15,377 treatment years and 48,955 international normalized ratio (INR) measurements were analyzed. Quality of anticoagulation, as measured by median TTR, was 66.3% (interquartile range (IQR) 47.8/81.9) in regular medical care and 75.5% (IQR 64.2/84.4) in the coagulation service (P service with TTR at 76.2% [(IQR 65.6/84.7); P = 0.001)]. Prospective follow-up of coagulation service patients with pretreatment in regular medical care showed an improvement of the TTR from 66.2% (IQR 49.0/83.6) to 74.5% (IQR 62.9/84.2; P service. Treatment in the coagulation service contributed to an optimization of the profile of time outside therapeutic range, a 2.2-fold increase of stabile INR adjustment and a significant decrease in TTR variability by 36% (P Quality of anticoagulation with phenprocoumon was comparably high in this real-world sample of regular medical care. Treatment in a

2016 Annual Site Environmental report Sandia National Laboratories Tonopah Test Range Nevada & Kaua'i Test Facility Hawai'i.

Energy Technology Data Exchange (ETDEWEB)

Salas, Angela Maria [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Griffith, Stacy R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2017-07-01

Sandia National Laboratories (SNL) is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s (DOE’s), National Nuclear Security Administration (NNSA) under contract DE-NA0003525. The DOE/NNSA Sandia Field Office administers the contract and oversees contractor operations at the SNL, Tonopah Test Range (SNL/TTR) in Nevada and the SNL, Kaua‘i Test Facility (SNL/KTF) in Hawai‘i. SNL personnel manage and conduct operations at SNL/TTR in support of the DOE/NNSA’s Weapons Ordnance Program and have operated the site since 1957. Navarro Research and Engineering personnel perform most of the environmental programs activities at SNL/TTR. The DOE/NNSA/Nevada Field Office retains responsibility for cleanup and management of SNL/TTR Environmental Restoration sites. SNL personnel operate SNL/KTF as a rocket preparation launching and tracking facility. This Annual Site Environmental Report (ASER) summarizes data and the compliance status of sustainability, environmental protection, and monitoring programs at SNL/TTR and SNL/KTF during calendar year 2016. Major environmental programs include air quality, water quality, groundwater protection, terrestrial and biological surveillance, waste management, pollution prevention, environmental restoration, oil and chemical spill prevention, and implementation of the National Environmental Policy Act. This ASER is prepared in accordance with and as required by DOE O 231.1B, Admin Change 1, Environment, Safety, and Health Reporting.

A moderate elevation of circulating levels of IGF-I does not alter ErbB2 induced mammary tumorigenesis

International Nuclear Information System (INIS)

Dearth, Robert K; Kuiatse, Isere; Wang, Yu-Fen; Liao, Lan; Hilsenbeck, Susan G; Brown, Powel H; Xu, Jianming; Lee, Adrian V

2011-01-01

Epidemiological evidence suggests that moderately elevated levels of circulating insulin-like growth factor-I (IGF-I) are associated with increased risk of breast cancer in women. How circulating IGF-I may promote breast cancer incidence is unknown, however, increased IGF-I signaling is linked to trastuzumab resistance in ErbB2 positive breast cancer. Few models have directly examined the effect of moderately high levels of circulating IGF-I on breast cancer initiation and progression. The purpose of this study was to assess the ability of circulating IGF-I to independently initiate mammary tumorigenesis and/or accelerate the progression of ErbB2 mediated mammary tumor growth. We crossed heterozygous TTR-IGF-I mice with heterozygous MMTV-ErbB2 mice to generate 4 different genotypes: TTR-IGF-I/MMTV-ErbB2 (bigenic), TTR-IGF-I only, MMTV-ErbB2 only, and wild type (wt). Virgin females were palpated twice a week and harvested when tumors reached 1000 mm 3 . For study of normal development, blood and tissue were harvested at 4, 6 and 9 weeks of age in TTR-IGF-I and wt mice. TTR-IGF-I and TTR-IGF-I/ErbB2 bigenic mice showed a moderate 35% increase in circulating total IGF-I compared to ErbB2 and wt control mice. Elevation of circulating IGF-I had no effect upon pubertal mammary gland development. The transgenic increase in IGF-I alone wasn't sufficient to initiate mammary tumorigenesis. Elevated circulating IGF-I had no effect upon ErbB2-induced mammary tumorigenesis or metastasis, with median time to tumor formation being 30 wks and 33 wks in TTR-IGF-I/ErbB2 bigenic and ErbB2 mice respectively (p = 0.65). Levels of IGF-I in lysates from ErbB2/TTR-IGF-I tumors compared to ErbB2 was elevated in a similar manner to the circulating IGF-I, however, there was no effect on the rate of tumor growth (p = 0.23). There were no morphological differences in tumor type (solid adenocarcinomas) between bigenic and ErbB2 mammary glands. Using the first transgenic animal model to

Laser microdissection and mass spectrometry-based proteomics aids the diagnosis and typing of renal amyloidosis.

Science.gov (United States)

Sethi, Sanjeev; Vrana, Julie A; Theis, Jason D; Leung, Nelson; Sethi, Anjali; Nasr, Samih H; Fervenza, Fernando C; Cornell, Lynn D; Fidler, Mary E; Dogan, Ahmet

2012-07-01

Accurate diagnosis and typing of renal amyloidosis is critical for prognosis, genetic counseling, and treatment. Laser microdissection and mass spectrometry are emerging techniques for the analysis and diagnosis of many renal diseases. Here we present the results of laser microdissection and mass spectrometry performed on 127 cases of renal amyloidosis during 2008-2010. We found the following proteins in the amyloid deposits: immunoglobulin light and heavy chains, secondary reactive serum amyloid A protein, leukocyte cell-derived chemotaxin-2, fibrinogen-α chain, transthyretin, apolipoprotein A-I and A-IV, gelsolin, and β-2 microglobulin. Thus, laser microdissection of affected areas within the kidney followed by mass spectrometry provides a direct test of the composition of the deposit and forms a useful ancillary technique for the accurate diagnosis and typing of renal amyloidosis in a single procedure.

Nevada National Security Site Environmental Report 2010

Energy Technology Data Exchange (ETDEWEB)

C. Wills, ed.

2011-09-13

This NNSSER was prepared to satisfy DOE Order DOE O 231.1B, “Environment, Safety and Health Reporting.” Its purpose is to (1) report compliance status with environmental standards and requirements, (2) present results of environmental monitoring of radiological and nonradiological effluents, (3) report estimated radiological doses to the public from releases of radioactive material, (4) summarize environmental incidents of noncompliance and actions taken in response to them, (5) describe the NNSA/NSO Environmental Management System and characterize its performance, and (6) highlight significant environmental programs and efforts. This NNSSER summarizes data and compliance status for calendar year 2010 at the Nevada National Security Site (NNSS) (formerly the Nevada Test Site) and its two support facilities, the North Las Vegas Facility (NLVF) and the Remote Sensing Laboratory–Nellis (RSL-Nellis). It also addresses environmental restoration (ER) projects conducted at the Tonopah Test Range (TTR). Through a Memorandum of Agreement, NNSA/NSO is responsible for the oversight of TTR ER projects, and the Sandia Site Office of NNSA (NNSA/SSO) has oversight of all other TTR activities. NNSA/SSO produces the TTR annual environmental report available at http://www.sandia.gov/news/publications/environmental/index.html.

Teledermatology as a means to improve access to inpatient dermatology care.

Science.gov (United States)

Sharma, Priyank; Kovarik, Carrie L; Lipoff, Jules B

2016-07-01

Many hospitals have limited inpatient dermatology consultation access. Most dermatologists are outpatient-based and may find the distance and time to complete inpatient consultations prohibitive. Teledermatology may improve access to inpatient dermatology care by reducing barriers of distance and time. We conducted a prospective two-phase pilot study at two academic hospitals comparing time needed to complete inpatient consultations after resident dermatologists initially evaluated patients, called average handling time (AHT), and time needed to respond to the primary team, called time to response (TTR), with and without teledermatology with surveys to capture changes in dermatologist opinion on teledermatology. Teledermatology was only used in the study phase, and patients were seen in-person in both study phases. Teledermatology alone sufficiently answered consultations in 10 of 25 study consultations. The mean AHT in the study phase (sAHT) was 26.9 min compared to the baseline phase (bAHT) of 43.5 min, a 16.6 min reduction (p = 0.004). The 10 study cases where teledermatology alone was sufficient had mean study TTR (sTTR) of 273.3 min compared to a baseline TTR (bTTR) of 405.7 min, a 132.4 min reduction (p = 0.032). Teledermatology reduces the time required for an attending dermatologist to respond and the time required for a primary team to receive a response for an inpatient dermatology consultation in a subset of cases. These findings suggest teledermatology can be used as a tool to improve access to inpatient dermatology care. © The Author(s) 2015.

Long-Term Statin Administration Does Not Affect Warfarin Time in Therapeutic Range in Australia or Singapore

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Nijole Bernaitis

2018-05-01

Full Text Available Background: Warfarin requires ongoing monitoring of the International Normalised Ratio (INR. This is because numerous factors influence the response, including drug interactions with commonly-prescribed medications, such as statins. The administration of statins with warfarin may change INR; however, there is limited information regarding the effects on warfarin control as measured by time in therapeutic range (TTR. Statins may also alter bleeds with warfarin, but there are conflicting reports demonstrating both increased and decreased bleeds, and limited data on diverse ethnic populations. Therefore, the aim of this study was to determine the effect of statin administration on warfarin control and bleeds in patients in Australia and Singapore. Methods: Retrospective data were collected for patients on warfarin between January and June 2014 in Australia and Singapore. Patient data were used to calculate TTR and bleed events. Concurrent statin therapy was assessed and comparisons of TTR and bleed incidence were made across patient subgroups. Results: Warfarin control in Australia and Singapore was not significantly affected by statins, as measured by TTR (83% and 58%, respectively, frequency of testing, and warfarin doses. In Australia, statin use did not significantly affect bleeds, whilst in Singapore the bleed incidence was significantly lower for patients on statins. Conclusions: Chronic concurrent administration of statins with warfarin does not adversely affect warfarin TTR in Australia or Singapore. In Singapore, patients on statins, compared to no statins, had a lower bleed incidence and this requires further investigation, especially given the potential genetic influences of ethnicity on both statin and warfarin metabolism.

Corrective Action Decision Document/Corrective Action Plan for Corrective Action Unit 413: Clean Slate II Plutonium Dispersion (TTR) Tonopah Test Range, Nevada. Revision 0

Energy Technology Data Exchange (ETDEWEB)

Matthews, Patrick [Navarro, Las Vegas, NV (United States)

2017-05-01

This Corrective Action Decision Document/Corrective Action Plan provides the rationale and supporting information for the selection and implementation of corrective actions at Corrective Action Unit (CAU) 413, Clean Slate II Plutonium Dispersion (TTR). CAU 413 is located on the Tonopah Test Range and includes one corrective action site, TA-23-02CS. CAU 413 consists of the release of radionuclides to the surface and shallow subsurface from the Clean Slate II (CSII) storage–transportation test conducted on May 31, 1963. The CSII test was a non-nuclear detonation of a nuclear device located inside a concrete bunker covered with 2 feet of soil. To facilitate site investigation and the evaluation of data quality objectives decisions, the releases at CAU 413 were divided into seven study groups: 1 Undisturbed Areas 2 Disturbed Areas 3 Sedimentation Areas 4 Former Staging Area 5 Buried Debris 6 Potential Source Material 7 Soil Mounds Corrective action investigation (CAI) activities, as set forth in the CAU 413 Corrective Action Investigation Plan, were performed from June 2015 through May 2016. Radionuclides detected in samples collected during the CAI were used to estimate total effective dose using the Construction Worker exposure scenario. Corrective action was required for areas where total effective dose exceeded, or was assumed to exceed, the radiological final action level (FAL) of 25 millirem per year. The results of the CAI and the assumptions made in the data quality objectives resulted in the following conclusions: The FAL is exceeded in surface soil in SG1, Undisturbed Areas; The FAL is assumed to be exceeded in SG5, Buried Debris, where contaminated debris and soil were buried after the CSII test; The FAL is not exceeded at SG2, SG3, SG4, SG6, or SG7. Because the FAL is exceeded at CAU 413, corrective action is required and corrective action alternatives (CAAs) must be evaluated. For CAU 413, three CAAs were evaluated: no further action, clean closure, and

Generation of healthy mice from gene-corrected disease-specific induced pluripotent stem cells.

Directory of Open Access Journals (Sweden)

Guangming Wu

2011-07-01

Full Text Available Using the murine model of tyrosinemia type 1 (fumarylacetoacetate hydrolase [FAH] deficiency; FAH⁻/⁻ mice as a paradigm for orphan disorders, such as hereditary metabolic liver diseases, we evaluated fibroblast-derived FAH⁻/⁻-induced pluripotent stem cells (iPS cells as targets for gene correction in combination with the tetraploid embryo complementation method. First, after characterizing the FAH⁻/⁻ iPS cell lines, we aggregated FAH⁻/⁻-iPS cells with tetraploid embryos and obtained entirely FAH⁻/⁻-iPS cell-derived mice that were viable and exhibited the phenotype of the founding FAH⁻/⁻ mice. Then, we transduced FAH cDNA into the FAH⁻/⁻-iPS cells using a third-generation lentiviral vector to generate gene-corrected iPS cells. We could not detect any chromosomal alterations in these cells by high-resolution array CGH analysis, and after their aggregation with tetraploid embryos, we obtained fully iPS cell-derived healthy mice with an astonishing high efficiency for full-term development of up to 63.3%. The gene correction was validated functionally by the long-term survival and expansion of FAH-positive cells of these mice after withdrawal of the rescuing drug NTBC (2-(2-nitro-4-fluoromethylbenzoyl-1,3-cyclohexanedione. Furthermore, our results demonstrate that both a liver-specific promoter (transthyretin, TTR-driven FAH transgene and a strong viral promoter (from spleen focus-forming virus, SFFV-driven FAH transgene rescued the FAH-deficiency phenotypes in the mice derived from the respective gene-corrected iPS cells. In conclusion, our data demonstrate that a lentiviral gene repair strategy does not abrogate the full pluripotent potential of fibroblast-derived iPS cells, and genetic manipulation of iPS cells in combination with tetraploid embryo aggregation provides a practical and rapid approach to evaluate the efficacy of gene correction of human diseases in mouse models.

Fluoride caused thyroid endocrine disruption in male zebrafish (Danio rerio).

Science.gov (United States)

Jianjie, Chen; Wenjuan, Xue; Jinling, Cao; Jie, Song; Ruhui, Jia; Meiyan, Li

2016-02-01

Excessive fluoride in natural water ecosystem has the potential to detrimentally affect thyroid endocrine system, but little is known of such effects or underlying mechanisms in fish. In the present study, we evaluated the effects of fluoride on growth performance, thyroid histopathology, thyroid hormone levels, and gene expressions in the HPT axis in male zebrafish (Danio rerio) exposed to different determined concentrations of 0.1, 0.9, 2.0 and 4.1 M of fluoride to investigate the effects of fluoride on thyroid endocrine system and the potential toxic mechanisms caused by fluoride. The results indicated that the growth of the male zebrafish used in the experiments was significantly inhibited, the thyroid microtrastructure was changed, and the levels of T3 and T4 were disturbed in fluoride-exposed male fish. In addition, the expressional profiles of genes in HPT axis displayed alteration. The expressions of all studied genes were significantly increased in all fluoride-exposed male fish after exposure for 45 days. The transcriptional levels of corticotrophin-releasing hormone (CRH), thyroid-stimulating hormone (TSH), thyroglobulin (TG), sodium iodide symporter (NIS), iodothyronine I (DIO1), and thyroid hormone receptor alpha (TRα) were also elevated in all fluoride-exposed male fish after 90 days of exposure, while the inconsistent expressions were found in the mRNA of iodothyronineⅡ (DIO2), UDP glucuronosyltransferase 1 family a, b (UGT1ab), transthyretin (TTR), and thyroid hormone receptor beta (TRβ). These results demonstrated that fluoride could notably inhibit the growth of zebrafish, and significantly affect thyroid endocrine system by changing the microtrastructure of thyroid, altering thyroid hormone levels and endocrine-related gene expressions in male zebrafish. All above indicated that fluoride could pose a great threat to thyroid endocrine system, thus detrimentally affected the normal function of thyroid of male zebrafish. Copyright © 2015

Gadoxetic acid-enhanced magnetic resonance imaging characteristics of hepatocellular carcinoma occurring in liver transplants

Energy Technology Data Exchange (ETDEWEB)

Kim, Mimi [Sungkyunkwan University School of Medicine, Department of Radiology and Center for Imaging Science, Samsung Medical Center, Seoul (Korea, Republic of); Hanyang University of Hospital, Department of Radiology, Seoul (Korea, Republic of); Kang, Tae Wook; Jeong, Woo Kyoung; Kim, Young Kon; Kim, Seong Hyun [Sungkyunkwan University School of Medicine, Department of Radiology and Center for Imaging Science, Samsung Medical Center, Seoul (Korea, Republic of); Kim, Jong Man [Sungkyunkwan University School of Medicine, Department of Surgery, Samsung Medical Center, Seoul (Korea, Republic of); Sinn, Dong Hyun [Sungkyunkwan University School of Medicine, Division of hepatology, Department of Medicine, Samsung Medical Center, Seoul (Korea, Republic of); Kim, Min-Ji; Jung, Sin-ho [Samsung Medical Center, Biostatics and Clinical Epidemiology Center, Seoul (Korea, Republic of)

2017-08-15

Characteristics of hepatocellular carcinoma (HCC) on magnetic resonance (MR) images were compared in patients who did or did not undergo liver transplantation (LT), and we evaluated the relationship of these findings with overall survival (OS) and time-to-tumour recurrence (TTR) after transplantation. The enhancement pattern of gadoxetic acid-enhanced MR images of 25 patients with recurrent HCCs (LT group) and 25 surgically confirmed HCC patients in the non-transplanted (control) group were compared. Typical enhancement was defined as 1) arterial enhancement and delayed wash-out and 2) absence of typical features of cholangiocarcinoma consisting of arterial rim enhancement and target appearance on hepatobiliary phase images. OS and TTR were analyzed in the LT group according to these patterns using the log-rank test. HCCs in the LT group significantly more often had an atypical enhancement pattern (16/25, 64.0%) than those in the control group (5/25, 20.0%; p = 0.004). However, OS and TTR did not differ significantly according to these enhancement patterns of recurrent HCC (p > 0.05). Although enhancement patterns of recurrent HCC in transplanted liver did not affect OS and TTR, these HCCs that arise after LT frequently revealed atypical enhancement on gadoxetic acid-enhanced MR imaging. (orig.)

Gadoxetic acid-enhanced magnetic resonance imaging characteristics of hepatocellular carcinoma occurring in liver transplants

International Nuclear Information System (INIS)

Kim, Mimi; Kang, Tae Wook; Jeong, Woo Kyoung; Kim, Young Kon; Kim, Seong Hyun; Kim, Jong Man; Sinn, Dong Hyun; Kim, Min-Ji; Jung, Sin-ho

2017-01-01

Characteristics of hepatocellular carcinoma (HCC) on magnetic resonance (MR) images were compared in patients who did or did not undergo liver transplantation (LT), and we evaluated the relationship of these findings with overall survival (OS) and time-to-tumour recurrence (TTR) after transplantation. The enhancement pattern of gadoxetic acid-enhanced MR images of 25 patients with recurrent HCCs (LT group) and 25 surgically confirmed HCC patients in the non-transplanted (control) group were compared. Typical enhancement was defined as 1) arterial enhancement and delayed wash-out and 2) absence of typical features of cholangiocarcinoma consisting of arterial rim enhancement and target appearance on hepatobiliary phase images. OS and TTR were analyzed in the LT group according to these patterns using the log-rank test. HCCs in the LT group significantly more often had an atypical enhancement pattern (16/25, 64.0%) than those in the control group (5/25, 20.0%; p = 0.004). However, OS and TTR did not differ significantly according to these enhancement patterns of recurrent HCC (p > 0.05). Although enhancement patterns of recurrent HCC in transplanted liver did not affect OS and TTR, these HCCs that arise after LT frequently revealed atypical enhancement on gadoxetic acid-enhanced MR imaging. (orig.)

A Comparison between Three Methods of Language Sampling: Freeplay, Narrative Speech and Conversation

Directory of Open Access Journals (Sweden)

Yasser Rezapour

2011-10-01

Full Text Available Objectives: The spontaneous language sample analysis is an important part of the language assessment protocol. Language samples give us useful information about how children use language in the natural situations of daily life. The purpose of this study was to compare Conversation, Freeplay, and narrative speech in aspects of Mean Length of Utterance (MLU, Type-token ratio (TTR, and the number of utterances. Methods: By cluster sampling method, a total of 30 Semnanian five-year-old boys with normal speech and language development were selected from the active kindergartens in Semnan city. Conversation, Freeplay, and narrative speech were three applied language sample elicitation methods to obtain 15 minutes of children’s spontaneous language samples. Means for MLU, TTR, and the number of utterances are analyzed by dependent ANOVA. Results: The result showed no significant difference in number of elicited utterances among these three language sampling methods. Narrative speech elicited longer MLU than freeplay and conversation, and compared to freeplay and narrative speech, conversation elicited higher TTR. Discussion: Results suggest that in the clinical assessment of the Persian-language children, it is better to use narrative speech to elicit longer MLU and to use conversation to elicit higher TTR.

Thromboembolic and Major Bleeding Events With Rivaroxaban Versus Warfarin Use in a Real-World Setting.

Science.gov (United States)

Russo-Alvarez, Giavanna; Martinez, Kathryn A; Valente, Megan; Bena, James; Hu, Bo; Luxenburg, Jennifer; Chaitoff, Alexander; Ituarte, Catherine; Brateanu, Andrei; Rothberg, Michael B

2018-01-01

Although randomized trials demonstrate the noninferiority of rivaroxaban compared with warfarin in the context of nonvalvular atrial fibrillation (AF), little is known about how these drugs compare in practice. To assess the relative effectiveness and safety of rivaroxaban versus warfarin in a large health system and to evaluate this association by time in therapeutic range (TTR). We conducted a retrospective cohort study with propensity matching in the Cleveland Clinic Health System. The study included patients initiated on warfarin or rivaroxaban for thromboembolic prevention in nonvalvular AF between January 2012 and July 2016. The main outcomes were thromboembolic events and major bleeds. Analyses were stratified by warfarin patients' TTR. The cohort consisted of 472 propensity-matched pairs. The mean age was 73.6 years (SD = 11.7), and the mean CHADS 2 score was 1.8. The median TTR for warfarin patients was 64%. In the propensity-matched analysis, there was no significant difference in thromboembolic or major bleeding events between groups. Among warfarin patients with a TTR warfarin and rivaroxaban were associated with similar safety and effectiveness, even among those with suboptimal therapeutic control. Individualized decision making, taking into account the nontherapeutic tradeoffs associated with these medications (eg, monitoring, half-life, cost) is warranted.

An aerial radiological survey of the Tonopah Test Range including Clean Slate 1,2,3, Roller Coaster, decontamination area, Cactus Springs Ranch target areas. Central Nevada

International Nuclear Information System (INIS)

Proctor, A.E.; Hendricks, T.J.

1995-08-01

An aerial radiological survey was conducted of major sections of the Tonopah Test Range (TTR) in central Nevada from August through October 1993. The survey consisted of aerial measurements of both natural and man-made gamma radiation emanating from the terrestrial surface. The initial purpose of the survey was to locate depleted uranium (detecting 238 U) from projectiles which had impacted on the TTR. The examination of areas near Cactus Springs Ranch (located near the western boundary of the TTR) and an animal burial area near the Double Track site were secondary objectives. When more widespread than expected 241 Am contamination was found around the Clean Slates sites, the survey was expanded to cover the area surrounding the Clean Slates and also the Double Track site. Results are reported as radiation isopleths superimposed on aerial photographs of the area

Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons.

Science.gov (United States)

Popa, Vlad; Trecroce, Danielle A; McAllister, Robert G; Konermann, Lars

2016-06-16

Electrospray ionization mass spectrometry (ESI-MS) has become an indispensable technique for examining noncovalent protein complexes. Collision-induced dissociation (CID) of these multiply protonated gaseous ions usually culminates in ejection of a single subunit with a disproportionately large amount of charge. Experiments suggest that this process involves subunit unfolding prior to separation from the residual complex, as well as H(+) migration onto the unravelling chain. Molecular dynamics (MD) simulations are a promising avenue for gaining detailed insights into these CID events. Unfortunately, typical MD algorithms do not allow for mobile protons. Here we address this limitation by implementing a strategy that combines atomistic force fields (such as OPLS/AA and CHARMM36) with a proton hopping algorithm, focusing on the tetrameric complexes transthyretin and streptavidin. Protons are redistributed over all acidic and basic sites in 20 ps intervals, subject to an energy function that reflects electrostatic interactions and proton affinities. Our simulations predict that nativelike conformers at the onset of collisional heating contain multiple salt bridges. Collisional heating initially causes subtle structural changes that lead to a gradual decline of these zwitterionic patterns. Many of the MD runs show gradual unfolding of a single subunit in conjunction with H(+) migration, culminating in subunit separation from the complex. However, there are also instances where two or more chains start to unfold simultaneously, giving rise to charge competition. The scission point where the "winning" subunit separates from the complex can be attained for different degrees of unfolding, giving rise to product ions in various charge states. The simulated product ion distributions are in close agreement with experimental CID data. Proton enrichment in the departing subunit is driven by charge-charge repulsion, but the combination of salt bridge depletion, charge migration

Identification of Tetranectin as a Potential Biomarker for Metastatic Oral Cancer

Directory of Open Access Journals (Sweden)

Shen Hu

2010-09-01

Full Text Available Lymph node involvement is the most important predictor of survival rates in patients with oral squamous cell carcinoma (OSCC. A biomarker that can indicate lymph node metastasis would be valuable to classify patients with OSCC for optimal treatment. In this study, we have performed a serum proteomic analysis of OSCC using 2-D gel electrophoresis and liquid chromatography/tandem mass spectrometry. One of the down-regulated proteins in OSCC was identified as tetranectin, which is a protein encoded by the CLEC3B gene (C-type lectin domain family 3, member B. We further tested the protein level in serum and saliva from patients with lymph-node metastatic and primary OSCC. Tetranectin was found significantly under-expressed in both serum and saliva of metastatic OSCC compared to primary OSCC. Our results suggest that serum or saliva tetranectin may serve as a potential biomarker for metastatic OSCC. Other candidate serum biomarkers for OSCC included superoxide dismutase, ficolin 2, CD-5 antigen-like protein, RalA binding protein 1, plasma retinol-binding protein and transthyretin. Their clinical utility for OSCC detection remains to be further tested in cancer patients.

Disease biomarkers in cerebrospinal fluid of patients with first-onset psychosis.

Directory of Open Access Journals (Sweden)

Jeffrey T-J Huang

2006-11-01

Full Text Available BACKGROUND: Psychosis is a severe mental condition that is characterized by a loss of contact with reality and is typically associated with hallucinations and delusional beliefs. There are numerous psychiatric conditions that present with psychotic symptoms, most importantly schizophrenia, bipolar affective disorder, and some forms of severe depression referred to as psychotic depression. The pathological mechanisms resulting in psychotic symptoms are not understood, nor is it understood whether the various psychotic illnesses are the result of similar biochemical disturbances. The identification of biological markers (so-called biomarkers of psychosis is a fundamental step towards a better understanding of the pathogenesis of psychosis and holds the potential for more objective testing methods. METHODS AND FINDINGS: Surface-enhanced laser desorption ionization mass spectrometry was employed to profile proteins and peptides in a total of 179 cerebrospinal fluid samples (58 schizophrenia patients, 16 patients with depression, five patients with obsessive-compulsive disorder, ten patients with Alzheimer disease, and 90 controls. Our results show a highly significant differential distribution of samples from healthy volunteers away from drug-naïve patients with first-onset paranoid schizophrenia. The key alterations were the up-regulation of a 40-amino acid VGF-derived peptide, the down-regulation of transthyretin at approximately 4 kDa, and a peptide cluster at approximately 6,800-7,300 Da (which is likely to be influenced by the doubly charged ions of the transthyretin protein cluster. These schizophrenia-specific protein/peptide changes were replicated in an independent sample set. Both experiments achieved a specificity of 95% and a sensitivity of 80% or 88% in the initial study and in a subsequent validation study, respectively. CONCLUSIONS: Our results suggest that the application of modern proteomics techniques, particularly mass

Skjaldar þáttr Danakonungs

DEFF Research Database (Denmark)

Lavender, Philip Thomas

2016-01-01

In this article I discuss a reference in Illuga saga Gríðarfóstra to a Skjaldar þáttur ok Hermanns. Previous commentators have said that this reference is either made up or alludes to a now lost saga. I show that the reference to the saga is not a fabrication: the narrative of Skjöldr and Hermann...

INR targets and site-level anticoagulation control: results from the Veterans AffaiRs Study to Improve Anticoagulation (VARIA).

Science.gov (United States)

Rose, A J; Berlowitz, D R; Miller, D R; Hylek, E M; Ozonoff, A; Zhao, S; Reisman, J I; Ash, A S

2012-04-01

Not all clinicians target the same International Normalized Ratio (INR) for patients with a guideline-recommended target range of 2-3. A patient's mean INR value suggests the INR that was actually targeted. We hypothesized that sites would vary by mean INR, and that sites of care with mean values nearest to 2.5 would achieve better anticoagulation control, as measured by per cent time in therapeutic range (TTR). To examine variations among sites in mean INR and the relationship with anticoagulation control in an integrated system of care. We studied 103,897 patients receiving oral anticoagulation with an expected INR target between 2 and 3 at 100 Veterans Health Administration (VA) sites from 1 October 2006 to 30 September 2008. Key site-level variables were: proportion near 2.5 (that is, percentage of patients with mean INR between 2.3 and 2.7) and mean risk-adjusted TTR. Site mean INR ranged from 2.22 to 2.89; proportion near 2.5, from 30 to 64%. Sites' proportions of patients near 2.5, below 2.3 and above 2.7 were consistent from year to year. A 10 percentage point increase in the proportion near 2.5 predicted a 3.8 percentage point increase in risk-adjusted TTR (P < 0.001). Proportion of patients with mean INR near 2.5 is a site-level 'signature' of care and an implicit measure of targeted INR. This proportion varies by site and is strongly associated with site-level TTR. Our study suggests that sites wishing to improve TTR, and thereby improve patient outcomes, should avoid the explicit or implicit pursuit of non-standard INR targets. © 2012 International Society on Thrombosis and Haemostasis.

Clinical diagnosis and typing of systemic amyloidosis in subcutaneous fat aspirates by mass spectrometry-based proteomics.

Science.gov (United States)

Vrana, Julie A; Theis, Jason D; Dasari, Surendra; Mereuta, Oana M; Dispenzieri, Angela; Zeldenrust, Steven R; Gertz, Morie A; Kurtin, Paul J; Grogg, Karen L; Dogan, Ahmet

2014-07-01

Examination of abdominal subcutaneous fat aspirates is a practical, sensitive and specific method for the diagnosis of systemic amyloidosis. Here we describe the development and implementation of a clinical assay using mass spectrometry-based proteomics to type amyloidosis in subcutaneous fat aspirates. First, we validated the assay comparing amyloid-positive (n=43) and -negative (n=26) subcutaneous fat aspirates. The assay classified amyloidosis with 88% sensitivity and 96% specificity. We then implemented the assay as a clinical test, and analyzed 366 amyloid-positive subcutaneous fat aspirates in a 4-year period as part of routine clinical care. The assay had a sensitivity of 90%, and diverse amyloid types, including immunoglobulin light chain (74%), transthyretin (13%), serum amyloid A (%1), gelsolin (1%), and lysozyme (1%), were identified. Using bioinformatics, we identified a universal amyloid proteome signature, which has high sensitivity and specificity for amyloidosis similar to that of Congo red staining. We curated proteome databases which included variant proteins associated with systemic amyloidosis, and identified clonotypic immunoglobulin variable gene usage in immunoglobulin light chain amyloidosis, and the variant peptides in hereditary transthyretin amyloidosis. In conclusion, mass spectrometry-based proteomic analysis of subcutaneous fat aspirates offers a powerful tool for the diagnosis and typing of systemic amyloidosis. The assay reveals the underlying pathogenesis by identifying variable gene usage in immunoglobulin light chains and the variant peptides in hereditary amyloidosis. Copyright© Ferrata Storti Foundation.

Treatment of amyloidosis.

Science.gov (United States)

Tan, S Y; Pepys, M B; Hawkins, P N

1995-08-01

Amyloidosis is the extracellular deposition of normally soluble autologous protein in a characteristic abnormal fibrillar form. Systemic amyloidosis and some local forms are progressive, cause major morbidity, and are often fatal. No treatment specifically causes the resolution of amyloid deposits, but therapy that reduces the supply of amyloid fibril precursor proteins can improve survival and preserve organ function. Major regression of amyloid occurs in at least a proportion of such cases, suggesting that the clinical improvement reflects mobilization of amyloid. The clearest evidence for regression of amyloid has been obtained in juvenile rheumatoid arthritis patients with AA amyloidosis treated with chlorambucil. This drug suppresses the acute phase production of serum amyloid A protein, the precursor of AA amyloid fibrils, and is associated with remission of proteinuria and greatly improved survival. In many such patients, scintigraphy with serum amyloid P component shows major regression of amyloid over 12 to 36 months and frequently reveals a discrepancy between the local amyloid load and organ dysfunction. Measurement of target organ function is therefore not an adequate method for monitoring treatment aimed at promoting the resolution of amyloid. In monoclonal immunoglobulin light chain (AL) amyloidosis the aim of treatment is to suppress the underlying B-cell clone and, therefore, production of the amyloid fibril precursor protein. This can be difficult to achieve or sustain and, since the prognosis is so poor, many patients die before benefits of therapy are realized. A recent development has been the introduction of liver transplantation as treatment for familial amyloid polyneuropathy caused by transthyretin gene mutations. This leads to the disappearance of variant transthyretin from the plasma and halts progression of the neurologic disease. Features of autonomic neuropathy frequently ameliorate, and improvement in peripheral motor nerve function

Tear dynamics in healthy and dry eyes.

Science.gov (United States)

Cerretani, Colin F; Radke, C J

2014-06-01

Dry-eye disease, an increasingly prevalent ocular-surface disorder, significantly alters tear physiology. Understanding the basic physics of tear dynamics in healthy and dry eyes benefits both diagnosis and treatment of dry eye. We present a physiological-based model to describe tear dynamics during blinking. Tears are compartmentalized over the ocular surface; the blink cycle is divided into three repeating phases. Conservation laws quantify the tear volume and tear osmolarity of each compartment during each blink phase. Lacrimal-supply and tear-evaporation rates are varied to reveal the dependence of tear dynamics on dry-eye conditions, specifically tear osmolarity, tear volume, tear-turnover rate (TTR), and osmotic water flow. Predicted periodic-steady tear-meniscus osmolarity is 309 and 321 mOsM in normal and dry eyes, respectively. Tear osmolarity, volume, and TTR all match available clinical measurements. Osmotic water flow through the cornea and conjunctiva contribute 10 and 50% to the total tear supply in healthy and dry-eye conditions, respectively. TTR in aqueous-deficient dry eye (ADDE) is only half that in evaporative dry eye (EDE). The compartmental periodic-steady tear-dynamics model accurately predicts tear behavior in normal and dry eyes. Inclusion of osmotic water flow is crucial to match measured tear osmolarity. Tear-dynamics predictions corroborate the use of TTR as a clinical discriminator between ADDE and EDE. The proposed model is readily extended to predict the dynamics of aqueous solutes such as drugs or fluorescent tags.

1991 Environmental Monitoring Report Tonopah Test Range, Tonopah, Nevada

International Nuclear Information System (INIS)

Howard, D.; Culp, T.

1992-11-01

This report summarizes the environmental surveillance activities conducted by the US Environmental Protection Agency (EPA) and Reynolds Electrical and Engineering Company (REECO) for the Tonopah Test Range (TTR) operated by Sandia National Laboratories (SNL). Other environmental compliance programs such as the National Environmental Policy Act of 1969 (NEPA), environmental permits, environmental restoration, and waste management programs are also included. The 1991 SNL, TTR, operations had no discernible impact on the general public or the environment. This report 3-s prepared for the US Department of Energy (DOE) in compliance with DOE Order 5400.1

Sandia National Laboratories, Tonopah Test Range Fire Control Bunker (Building 09-51): Photographs and Written Historical and Descriptive Data

Energy Technology Data Exchange (ETDEWEB)

Ullrich, Rebecca A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Corporate Archives and History Program

2017-08-01

The Fire Control Bunker (Building 09-51) is a contributing element to the Sandia National Laboratories (SNL) Tonopah Test Range (TTR) Historic District. The SNL TTR Historic District played a significant role in U.S. Cold War history in the areas of stockpile surveillance and non-nuclear field testing of nuclear weapons design. The district covers approximately 179,200 acres and illustrates Cold War development testing of nuclear weapons components and systems. This report includes historical information, architectural information, sources of information, project information, maps, blueprints, and photographs.

Sandia National Laboratories, Tonopah Test Range Assembly Building 9B (Building 09-54): Photographs and Written Historical and Descriptive Data

Energy Technology Data Exchange (ETDEWEB)

Ullrich, Rebecca A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Corporate Archives and History Program

2017-08-01

Assembly Building 9B (Building 09-54) is a contributing element to the Sandia National Laboratories (SNL) Tonopah Test Range (TTR) Historic District. The SNL TTR Historic District played a significant role in U.S. Cold War history in the areas of stockpile surveillance and non-nuclear field testing of nuclear weapons designs. The district covers approximately 179,200 acres and illustrates Cold War development testing of nuclear weapons components and systems. This report includes historical information, architectural information, sources of information, project information, maps, blueprints, and photographs.

NESHAP Annual Report for CY 2015 Sandia National Laboratories Tonopah Test Range

Energy Technology Data Exchange (ETDEWEB)

Evelo, Stacie [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2016-05-01

This National Emission Standards for Hazardous Air Pollutants (NESHAP) Annual Report has been prepared in a format to comply with the reporting requirements of 40 CFR 61.94 and the April 5, 1995 Memorandum of Agreement (MOA) between the Department of Energy (DOE) and the Environmental Protection Agency (EPA). According to the EPA approved NESHAP Monitoring Plan for the Tonopah Test Range (TTR), 40 CFR 61, subpart H, and the MOA, no additional monitoring or measurements are required at TTR in order to demonstrate compliance with the NESHAP regulation.

U.S. Department of Energy NESHAP Annual Report for CY 2014 Sandia National Laboratories Tonopah Test Range

Energy Technology Data Exchange (ETDEWEB)

Evelo, Stacie [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Miller, Mark L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2015-05-01

This National Emission Standards for Hazardous Air Pollutants (NESHAP) Annual Report has been prepared in a format to comply with the reporting requirements of 40 CFR 61.94 and the April 5, 1995 Memorandum of Agreement (MOA) between the Department of Energy (DOE) and the Environmental Protection Agency (EPA). According to the EPA approved NESHAP Monitoring Plan for the Tonopah Test Range (TTR), 40 CFR 61, subpart H, and the MOA, no additional monitoring or measurements are required at TTR in order to demonstrate compliance with the NESHAP regulation.

The significance of PIWI family expression in human lung embryogenesis and non-small cell lung cancer.

Science.gov (United States)

Navarro, Alfons; Tejero, Rut; Viñolas, Nuria; Cordeiro, Anna; Marrades, Ramon M; Fuster, Dolors; Caritg, Oriol; Moises, Jorge; Muñoz, Carmen; Molins, Laureano; Ramirez, Josep; Monzo, Mariano

2015-10-13

The expression of Piwi-interacting RNAs, small RNAs that bind to PIWI proteins, was until recently believed to be limited to germinal stem cells. We have studied the expression of PIWI genes during human lung embryogenesis and in paired tumor and normal tissue prospectively collected from 71 resected non-small-cell lung cancer patients. The mRNA expression analysis showed that PIWIL1 was highly expressed in 7-week embryos and downregulated during the subsequent weeks of development. PIWIL1 was expressed in 11 of the tumor samples but in none of the normal tissue samples. These results were validated by immunohistochemistry, showing faint cytoplasmic reactivity in the PIWIL1-positive samples. Interestingly, the patients expressing PIWIL1 had a shorter time to relapse (TTR) (p = 0.006) and overall survival (OS) (p = 0.0076) than those without PIWIL1 expression. PIWIL2 and 4 were downregulated in tumor tissue in comparison to the normal tissue (p < 0.001) and the patients with lower levels of PIWIL4 had shorter TTR (p = 0.048) and OS (p = 0.033). In the multivariate analysis, PIWIL1 expression emerged as an independent prognostic marker. Using 5-Aza-dC treatment and bisulfite sequencing, we observed that PIWIL1 expression could be regulated in part by methylation. Finally, an in silico study identified a stem-cell expression signature associated with PIWIL1 expression.

Radiological and Environmental Monitoring at the Clean Slate I and III Sites, Tonopah Test Range, Nevada, With Emphasis on the Implications for Off-site Transport

Energy Technology Data Exchange (ETDEWEB)

Mizell, Steve A [Desert Research Inst. (DRI), Las Vegas, NV (United States); Etyemezian, Vic [Desert Research Inst. (DRI), Las Vegas, NV (United States); McCurdy, Greg [Desert Research Inst. (DRI), Las Vegas, NV (United States); Nikolich, George [Desert Research Inst. (DRI), Las Vegas, NV (United States); Shadel, Craig [Desert Research Inst. (DRI), Las Vegas, NV (United States); Miller, Julianne J [Desert Research Inst. (DRI), Las Vegas, NV (United States)

2014-09-01

In 1963, the U.S. Department of Energy (DOE) (formerly the Atomic Energy Commission [AEC]) implemented Operation Roller Coaster on the Tonopah Test Range (TTR) and an adjacent area of the Nevada Test and Training Range (NTTR) (formerly the Nellis Air Force Range [NAFR]). Operation Roller Coaster consisted of four tests in which chemical explosions were detonated in the presence of nuclear devices to assess the dispersal of radionuclides and evaluate the effectiveness of storage structures to contain the ejected radionuclides. These tests resulted in the dispersal of plutonium over the ground surface downwind of the test ground zero (GZ). Three tests—Clean Slate I, II, and III—were conducted on the TTR in Cactus Flat. The fourth, Double Tracks, was conducted in Stonewall Flat on the NTTR. The Desert Research Institute (DRI) installed two monitoring stations in 2008, Station 400 at the Sandia National Laboratories (SNL) Range Operations Center (ROC) and Station 401 at Clean Slate III. Station 402 was installed at Clean Slate I in 2011 to measure radiological, meteorological, and dust conditions. The monitoring activity was implemented to determine if radionuclide contamination in the soil at the Clean Slate sites was being transported beyond the contamination area boundaries. Some of the data collected also permits comparison of radiological exposure at the TTR monitoring stations to conditions observed at Community Environmental Monitoring Program (CEMP) stations around the NTTR. Annual average gross alpha values from the TTR monitoring stations are higher than values from the surrounding CEMP stations. Annual average gross beta values from the TTR monitoring stations are generally lower than values observed for the surrounding CEMP stations. This may be due to use of sample filters with larger pore space because when glass-fiber filters began to be used at TTR Station 400, gross beta values increased. Gamma spectroscopy typically identified only naturally

Patient-Specific Tailored Intervention Improves INR Time in Therapeutic Range and INR Variability in Heart Failure Patients.

Science.gov (United States)

Gotsman, Israel; Ezra, Orly; Hirsh Raccah, Bruria; Admon, Dan; Lotan, Chaim; Dekeyser Ganz, Freda

2017-08-01

Many patients with heart failure need anticoagulants, including warfarin. Good control is particularly challenging in heart failure patients, with range, thereby increasing the risk of complications. This study aimed to evaluate the effect of a patient-specific tailored intervention on anticoagulation control in patients with heart failure. Patients with heart failure taking warfarin therapy (n = 145) were randomized to either standard care or a 1-time intervention assessing potential risk factors for lability of INR, in which they received patient-specific instructions. Time in therapeutic range (TTR) using Rosendaal's linear model was assessed 3 months before and after the intervention. The patient-tailored intervention significantly increased anticoagulation control. The median TTR levels before intervention were suboptimal in the interventional and control groups (53% vs 45%, P = .14). After intervention the median TTR increased significantly in the interventional group compared with the control group (80% [interquartile range, 62%-93%] vs 44% [29%-61%], P <.0001). The intervention resulted in a significant improvement in the interventional group before versus after intervention (53% vs 80%, P <.0001) but not in the control group (45% vs 44%, P = .95). The percentage of patients with a TTR ≥60%, considered therapeutic, was substantially higher in the interventional group: 79% versus 25% (P <.0001). The INR variability (standard deviation of each patient's INR measurements) decreased significantly in the interventional group, from 0.53 to 0.32 (P <.0001) after intervention but not in the control group. Patient-specific tailored intervention significantly improves anticoagulation therapy in patients with heart failure. Copyright © 2017 Elsevier Inc. All rights reserved.

An evaluation of the transition temperature range of super-elastic orthodontic NiTi springs using differential scanning calorimetry.

Science.gov (United States)

Barwart, O; Rollinger, J M; Burger, A

1999-10-01

Differential scanning calorimetry (DSC) was used to determine the transition temperature ranges (TTR) of four types of super-elastic orthodontic nickel-titanium coil springs (Sentalloy). A knowledge of the TTR provides information on the temperature at which a NiTi wire or spring can assume superelastic properties and when this quality disappears. The spring types in this study can be distinguished from each other by their characteristic TTR during cooling and heating. For each tested spring type a characteristic TTR during heating (austenite transformation) and cooling (martensite transformation) was evaluated. The hysteresis of the transition temperature, found between cooling and heating, was 3.4-5.2 K. Depending on the spring type the austenite transformation started (As) at 9.7-17.1 degrees C and finished (Af) at 29.2-37 degrees C. The martensite transformation starting temperature (Ms) was evaluated at 32.6-25.4 degrees C, while Mf (martensite transformation finishing temperature) was 12.7-6.5 degrees C. The results show that the springs become super-elastic when the temperature increases and As is reached. They undergo a loss of super-elastic properties and a rapid decrease in force delivery when they are cooled to Mf. For the tested springs, Mf and As were found to be below room temperature. Thus, at room temperature and some degrees lower, all the tested springs exert super-elastic properties. For orthodontic treatment this means the maintenance of super-elastic behaviour, even when mouth temperature decreases to about room temperature as can occur, for example, during meals.

Thyroxine transport in choroid plexus

International Nuclear Information System (INIS)

Dickson, P.W.; Aldred, A.R.; Menting, J.G.; Marley, P.D.; Sawyer, W.H.; Schreiber, G.

1987-01-01

The role of the choroid plexus in thyroid hormone transport between body and brain, suggested by strong synthesis and secretion of transthyretin in this tissue, was investigated in in vitro and in vivo systems. Rat choroid plexus pieces incubated in vitro were found to accumulate thyroid hormones from surrounding medium in a non-saturable process. At equilibrium, the ratio of thyroid hormone concentration in choroid plexus pieces to that in medium decreased upon increasing the concentration of transthyretin in the medium. Fluorescence quenching of fluorophores located at different depths in liposome membranes showed maximal hormone accumulation in the middle of the phospholipid bilayer. Partition coefficients of thyroxine and triiodothyronine between lipid and aqueous phase were about 20,000. After intravenous injection of 125 I-labeled thyroid hormones, choroid plexus and parts of the brain steadily accumulated 125 I-thyroxine, but not [ 125 I]triiodothyronine, for many hours. The accumulation of 125 I-thyroxine in choroid plexus preceded that in brain. The amount of 125 I-thyroxine in non-brain tissues and the [ 125 I]triiodothyronine content of all tissues decreased steadily beginning immediately after injection. A model is proposed for thyroxine transport from the bloodstream into cerebrospinal fluid based on partitioning of thyroxine between choroid plexus and surrounding fluids and binding of thyroxine to transthyretin newly synthesized and secreted by choroid plexus

Overview of systemic and localized amyloidosis

Directory of Open Access Journals (Sweden)

Saulius Girnius

2013-10-01

Full Text Available Amyloidosis is a family of protein misfolding disorders, in which insoluble fibrillar proteins deposit extracellularly and cause end organ damage. Depending on the precursor protein, clinical manifestations in amyloidosis vary significantly. In systemic amyloidosis, the heart, kidneys, and nerves are most commonly affected, resulting in congestive heart failure, arrhythmia, nephrotic syndrome, renal failure, and peripheral and autonomic neuropathies. In localized amyloidosis, amyloid deposits at the site of production, so only one organ is disrupted. Once amyloidosis is confirmed histologically, the precursor subtype must be identified using immunohistochemistry, immunofixation, electron microscopy, or laser microdissection and mass spectrometry. Treatment should not be initiated prior to the identification of the type of amyloidosis. Currently, treatment focuses on the suppression of the precursor protein: in AL amyloidosis, chemotherapy or autologous stem cell transplants suppress production of immunoglobulin light chains; in AA amyloidosis, anti-microbial and anti-inflammatory agents suppress amyloid A production; and in AF amyloidosis, a liver transplantation removes the source of mutant transthyretin protein production. Newer drugs are being developed to target amyloidosis at an epigenetic level or stabilize folding intermediates, but there are currently in development.http://dx.doi.org/10.7175/rhc.v4i4.662

Nucleation and droplet growth from supersaturated vapor at temperatures below the triple point temperature

DEFF Research Database (Denmark)

Toxværd, Søren

2016-01-01

temperature Ttr.p. crystallizes via a liquid droplet is an example of Ostwald's step rule. The homogeneous nucleation in the supersaturated gas is not to a crystal, but to a liquid-like critical nucleus. We have for the first time performed constant energy (NVE) Molecular Dynamics (MD) of homogeneous...... nucleation without the use of a thermostat. The simulations of homogeneous nucleation in a Lennard-Jones system from supersaturated vapor at temperatures below Ttr.p. reveals that the nucleation to a liquid-like critical nucleus is initiated by a small cold cluster [S. Toxvaerd, J. Chem. Phys. \\textbf{143...

Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets

Energy Technology Data Exchange (ETDEWEB)

Hsu, Po Jen; Lai, S. K., E-mail: sklai@coll.phy.ncu.edu.tw [Complex Liquids Laboratory, Department of Physics, National Central University, Chungli 320, Taiwan and Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan (China); Rapallo, Arnaldo [Istituto per lo Studio delle Macromolecole (ISMAC) Consiglio Nazionale delle Ricerche (CNR), via E. Bassini 15, C.A.P 20133 Milano (Italy)

2014-03-14

Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit

Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets

International Nuclear Information System (INIS)

Hsu, Po Jen; Lai, S. K.; Rapallo, Arnaldo

2014-01-01

Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit

Nevada Test Site Environmental Report 2009

Energy Technology Data Exchange (ETDEWEB)

Cathy Wills, ed.

2010-09-13

The Nevada Test Site Environmental Report 2009 was prepared to meet the information needs of the public and the requirements and guidelines of the U.S. Department of Energy (DOE) for annual site environmental reports. It was prepared by National Security Technologies, LLC (NSTec), for the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office (NNSA/NSO). This and previous years’ Nevada Test Site Environmental Reports (NTSERs) are posted on the NNSA/NSO website at http://www.nv.doe.gov/library/publications/aser.aspx. This NTSER was prepared to satisfy DOE Order DOE O 231.1A, “Environment, Safety and Health Reporting.” Its purpose is to (1) report compliance status with environmental standards and requirements, (2) present results of environmental monitoring of radiological and nonradiological effluents, (3) report estimated radiological doses to the public from releases of radioactive material, (4) summarize environmental incidents of noncompliance and actions taken in response to them, (5) describe the NNSA/NSO Environmental Management System and characterize its performance, and (6) highlight significant environmental programs and efforts. This NTSER summarizes data and compliance status for calendar year 2009 at the Nevada Test Site (NTS) and its two support facilities, the North Las Vegas Facility (NLVF) and the Remote Sensing Laboratory (RSL)-Nellis. It also addresses environmental restoration (ER) projects conducted at the Tonopah Test Range (TTR). Through a Memorandum of Agreement, NNSA/NSO is responsible for the oversight of TTR ER projects, and the Sandia Site Office of NNSA (NNSA/SSO) has oversight of all other TTR activities. NNSA/SSO produces the TTR annual environmental report available at http://www.sandia.gov/news/publications/environmental/index.html.

Air Monitoring Network at Tonopah Test Range: Network Description, Capabilities, and Analytical Results

International Nuclear Information System (INIS)

Hartwell, William T.; Daniels, Jeffrey; Nikolich, George; Shadel, Craig; Giles, Ken; Karr, Lynn; Kluesner, Tammy

2012-01-01

During the period April to June 2008, at the behest of the Department of Energy (DOE), National Nuclear Security Administration, Nevada Site Office (NNSA/NSO); the Desert Research Institute (DRI) constructed and deployed two portable environmental monitoring stations at the Tonopah Test Range (TTR) as part of the Environmental Restoration Project Soils Activity. DRI has operated these stations since that time. A third station was deployed in the period May to September 2011. The TTR is located within the northwest corner of the Nevada Test and Training Range (NTTR), and covers an area of approximately 725.20 km2 (280 mi2). The primary objective of the monitoring stations is to evaluate whether and under what conditions there is wind transport of radiological contaminants from Soils Corrective Action Units (CAUs) associated with Operation Roller Coaster on TTR. Operation Roller Coaster was a series of tests, conducted in 1963, designed to examine the stability and dispersal of plutonium in storage and transportation accidents. These tests did not result in any nuclear explosive yield. However, the tests did result in the dispersal of plutonium and contamination of surface soils in the surrounding area.

Sex-dependent behavioral changes in rat offspring after in utero administration of a single low dose PBDE 47

Energy Technology Data Exchange (ETDEWEB)

Kuriyama, S.N.; Talsness, C.E.; Chahoud, I. [Charite Univ. Medical School Berlin (Germany). Inst. of Clinical Pharmacology and Toxicology, Dept. Toxicology, Campus Benjamin Franklin

2004-09-15

Increasing levels of polybrominated diphenyl ethers (PBDEs) in environmental and human samples has resulted in intensive discussion regarding possible hazard identification and risk assessment in the last years. In rodents, exposure to PBDE mixtures or single congeners has resulted in a mixed induction of CYP450- dependent enzymes, showing increased activity of hepatic EROD and PROD. In addition, genotoxicity has been observed in recombination assays, and neurotoxicity has been reported in mice exposed during development. Acute and sub-chronic exposures of mice and rats to a PBDE mixture (DE-71) cause dose-dependent reductions in serum concentrations of thyroxin (T4), and stressinduced elevations in plasma corticosterone. Further, some hydroxylated metabolites of PBDE congeners exhibit a higher potency in vivo than T4 in competitive binding to human transthyretin (TTR), the transport protein mediating transfer of thyroid hormones across the placenta and into the brain. The available information in the literature clearly indicates that PBDEs are potent neurotoxicants, causing effects at doses lower than that able to disrupt thyroid hormone profiles and change CYP 450 activities. Neurobehavior effects, which includes defects in learning and memory, and changes in nicotinic receptors were found at doses starting at 0.45 ppm in mouse (9). The congeners, PBDE 47 and PBDE 99, have also been shown to cause permanent aberrations in spontaneous behavior in mice which was more pronounced with increasing age. PBDE 47 is the most predominant congener found in environmental and human samples, including human breast milk. Its presence in breast milk highlights the importance of evaluating possible effects following early developmental exposure and because this period represents a critical time which an organism is extremely susceptible to minor changes in hormonal milieu. Variances in terms of time point and concentration of exposure to steroids can lead to an organizational

Intradialytic parenteral nutrition in maintenance hemodialysis patients suffering from protein-energy wasting. Results of a multicenter, open, prospective, randomized trial.

Science.gov (United States)

Marsen, Tobias A; Beer, Justinus; Mann, Helmut

2017-02-01

Protein-energy wasting (PEW) is increasingly becoming a clinical problem in maintenance hemodialysis patients and guidelines call for nutritional interventions. Serum prealbumin (transthyretin) represents a critical nutritional marker positively correlated with patient survival and negatively correlated with morbidity. Nutritional counseling, oral supplementation as well as intradialytic parenteral nutrition (IDPN) are recommended to fight PEW, however clinical trials on their use are scarce. We conducted a prospective, multicenter, randomized, open-label, controlled, parallel-group Phase IV clinical trial in 107 maintenance hemodialysis patients suffering from PEW to assess the impact of IDPN on prealbumin and other biochemical and clinical parameters reflecting nutritional status. Patients randomized to the intervention group received standardized nutritional counseling plus IDPN three times weekly over 16 weeks followed by a treatment-free period of 12 weeks. The control group received standardized nutritional counseling only. Main trial inclusion criteria included moderate to severe malnutrition (SGA score B or C), maintenance hemodialysis therapy (3 times per week) for more than six months, and presence of two out of the following three criteria: albumin 30 mg/L at week 16 (48.7% vs. 31.8%). Prealbumin response to IDPN therapy was more prominent in patients suffering from moderate malnutrition (SGA score B) compared to patients with severe malnutrition (SGA score C). The results of this trial demonstrate for the first time that IDPN therapy, given three times weekly in a 16-week short-term intervention, results in a statistically significant and clinically relevant increase in mean serum prealbumin, a surrogate marker for outcome and survival in hemodialysis patients suffering from PEW, and is superior to nutritional counseling. Clinical trial registry:www.clinicaltrials.gov (NCT00501956). Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights

Optimal identification of semi-rigid domains in macromolecules from molecular dynamics simulation.

Directory of Open Access Journals (Sweden)

Stefan Bernhard

Full Text Available Biological function relies on the fact that biomolecules can switch between different conformations and aggregation states. Such transitions involve a rearrangement of parts of the biomolecules involved that act as dynamic domains. The reliable identification of such domains is thus a key problem in biophysics. In this work we present a method to identify semi-rigid domains based on dynamical data that can be obtained from molecular dynamics simulations or experiments. To this end the average inter-atomic distance-deviations are computed. The resulting matrix is then clustered by a constrained quadratic optimization problem. The reliability and performance of the method are demonstrated for two artificial peptides. Furthermore we correlate the mechanical properties with biological malfunction in three variants of amyloidogenic transthyretin protein, where the method reveals that a pathological mutation destabilizes the natural dimer structure of the protein. Finally the method is used to identify functional domains of the GroEL-GroES chaperone, thus illustrating the efficiency of the method for large biomolecular machines.

Nevada National Security Site Environmental Report 2011

International Nuclear Information System (INIS)

Wills, Cathy

2012-01-01

This report was prepared to meet the information needs of the public and the requirements and guidelines of the U.S. Department of Energy (DOE) for annual site environmental reports. It was prepared by National Security Technologies, LLC (NSTec), for the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office (NNSA/NSO). This and previous years reports, called Annual Site Environmental Reports (ASERs), Nevada Test Site Environmental Reports (NTSERs), and, beginning in 2010, Nevada National Security Site Environmental Reports (NNSSERs), are posted on the NNSA/NSO website at http://www.nv.energy.gov/library/publications/aser.aspx. This NNSSER was prepared to satisfy DOE Order DOE O 231.1B, 'Environment, Safety and Health Reporting.' Its purpose is to (1) report compliance status with environmental standards and requirements, (2) present results of environmental monitoring of radiological and nonradiological effluents, (3) report estimated radiological doses to the public from releases of radioactive material, (4) summarize environmental incidents of noncompliance and actions taken in response to them, (5) describe the NNSA/NSO Environmental Management System and characterize its performance, and (6) highlight significant environmental programs and efforts. This NNSSER summarizes data and compliance status for calendar year 2011 at the Nevada National Security Site (NNSS) (formerly the Nevada Test Site) and its two support facilities, the North Las Vegas Facility (NLVF) and the Remote Sensing Laboratory-Nellis (RSL-Nellis). It also addresses environmental restoration (ER) projects conducted at the Tonopah Test Range (TTR). Through a Memorandum of Agreement, NNSA/NSO is responsible for the oversight of TTR ER projects, and the Sandia Site Office of NNSA (NNSA/SSO) has oversight of all other TTR activities. NNSA/SSO produces the TTR annual environmental report available at http://www.sandia.gov/news/publications/environmental/index.html.

Cohort study of Anticoagulation Self-Monitoring (CASM): a prospective study of its effectiveness in the community.

Science.gov (United States)

Ward, Alison; Tompson, Alice; Fitzmaurice, David; Sutton, Stephen; Perera, Rafael; Heneghan, Carl

2015-07-01

Trials show that oral anticoagulation therapy (OAT) substantially reduces thromboembolic events without an increase in major haemorrhagic events, but it is not known whether these results translate into routine practice. To estimate the current levels of control and adverse events in patients self-monitoring OAT, explore the factors that predict success, and determine whether the level of side effects reported from randomised controlled trials are translated to a non-selected population. Prospective cohort study in the UK. Participants were aged ≥18 years and registered with a GP. Main outcomes were the proportion of participants, over 12 months, who were still self-monitoring, had not experienced adverse events, and had achieved >80% of time in therapeutic range (TTR). In total, 296 participants were recruited; their median age was 61 years and 55.1% were male. Participants were predominately professional or held a university qualification (82.7%). At 12 months, 267 (90.2%) were still self-monitoring. Mean TTR was 75.3% (standard deviation 16.9).Six serious and two minor adverse events were reported by GPs. Only 45.9% of participants received any in-person training at the outset. Increased age (P = 0.027), general wellbeing (EQ-5D visual score, P = 0.020), and lower target international normalised range (INR, P = 0.032) were all associated with high (>80% TTR) levels of control. The findings show that, even with little training, people on OAT can successfully self-monitor, and even self-manage, their INR. TTR was shown to improve with age. However, widespread use of self-monitoring of INR may be limited by the initial costs, as well as a lack of training and support at the outset. © British Journal of General Practice 2015.

Nevada National Security Site Environmental Report 2011

Energy Technology Data Exchange (ETDEWEB)

Cathy Wills, ed

2012-09-12

This report was prepared to meet the information needs of the public and the requirements and guidelines of the U.S. Department of Energy (DOE) for annual site environmental reports. It was prepared by National Security Technologies, LLC (NSTec), for the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office (NNSA/NSO). This and previous years reports, called Annual Site Environmental Reports (ASERs), Nevada Test Site Environmental Reports (NTSERs), and, beginning in 2010, Nevada National Security Site Environmental Reports (NNSSERs), are posted on the NNSA/NSO website at http://www.nv.energy.gov/library/publications/aser.aspx. This NNSSER was prepared to satisfy DOE Order DOE O 231.1B, 'Environment, Safety and Health Reporting.' Its purpose is to (1) report compliance status with environmental standards and requirements, (2) present results of environmental monitoring of radiological and nonradiological effluents, (3) report estimated radiological doses to the public from releases of radioactive material, (4) summarize environmental incidents of noncompliance and actions taken in response to them, (5) describe the NNSA/NSO Environmental Management System and characterize its performance, and (6) highlight significant environmental programs and efforts. This NNSSER summarizes data and compliance status for calendar year 2011 at the Nevada National Security Site (NNSS) (formerly the Nevada Test Site) and its two support facilities, the North Las Vegas Facility (NLVF) and the Remote Sensing Laboratory-Nellis (RSL-Nellis). It also addresses environmental restoration (ER) projects conducted at the Tonopah Test Range (TTR). Through a Memorandum of Agreement, NNSA/NSO is responsible for the oversight of TTR ER projects, and the Sandia Site Office of NNSA (NNSA/SSO) has oversight of all other TTR activities. NNSA/SSO produces the TTR annual environmental report available at http://www.sandia.gov/news/publications/environmental/index.html.

Uso de testes complementares para avaliação do congelamento do sêmen de bodes submetidos ao manejo de fotoperíodo artificial Use of complementary tests to evaluate the freezing ability of semen from goats under artificial photoperiod exposure

Directory of Open Access Journals (Sweden)

Anselmo Domingos Ferreira Santos

2006-10-01

Full Text Available O congelamento do sêmen de bodes das raças Alpina e Saanen submetidos ao manejo de fotoperíodo artificial foi avaliado por meio dos testes de termorresistência (TTR, hiposmótico (HOST e de integridade do acrossoma. Foram utilizados oito machos caprinos (quatro da raça Alpina e quatro da raça Saanen de duas idades diferentes (jovens e adultos. A qualidade do sêmen durante as etapas do congelamento foi superior em bodes jovens de ambas as raças. Avaliada pelo TTR, a motilidade do sêmen fresco apresentou longevidade pós-descongelamento. Os resultados de motilidade espermática, obtidos imediatamente após o descongelamento, tiveram reflexos positivos sobre o TTR, indicando que os sêmens que apresentaram maior motilidade pós-coleta (86,2% vs 79,3% e pós-descongelamento (37,7% vs 32,0% tiveram maior longevidade seminal. Os resultados do HOST, tanto para o sêmen fresco quanto para o congelado, não diferiram entre raças e idades. Houve redução na porcentagem de espermatozóides íntegros após o congelamento e descongelamento do sêmen dos animais da raça Alpina e dos adultos Saanen. Houve redução superior a 14% nos valores do HOST para o sêmen congelado em relação aos valores observados para o sêmen fresco (38,0 vs 52,0%, respectivamente. A motilidade espermática progressiva mostrou maior sensibilidade à criopreservação que a integridade da membrana espermática, indicando que a motilidade espermática é mais afetada pelo processo de congelamento que a membrana plasmática. A integridade do acrossoma não foi influenciada pelo descongelamento. Os índices de danos acrossomais (edema, desprendimento parcial e até perda total de acrossoma mostraram-se dentro do padrão aceitável (44,5%, tanto no pós-descongelamento como após o término do TTR.The freezing ability of semen from Alpine and Saanen goats submitted to an artificial photoperiod exposure were evaluated by the thermo-resistance (TTR and hypoosmotic (HOST tests

A cytogenetic model predicts relapse risk and survival in patients with acute myeloid leukemia undergoing hematopoietic stem cell transplantation in morphologic complete remission.

Science.gov (United States)

Rashidi, Armin; Cashen, Amanda F

2015-01-01

Up to 30% of patients with acute myeloid leukemia (AML) and abnormal cytogenetics have persistent cytogenetic abnormalities (pCytAbnl) at morphologic complete remission (mCR). We hypothesized that the prognostic significance of pCytAbnl in patients undergoing allogeneic hematopoietic stem cell transplantation (HSCT) in mCR varies with cytogenetic risk group. We analyzed the data on 118 patients with AML and abnormal cytogenetics who underwent HSCT in mCR, and developed a risk stratification model based on pCytAbnl and cytogenetic risk group. The model distinguished three groups of patients (Pcytogenetics (n=25) had the shortest median time to relapse (TTR; 5 months), relapse-free survival (RFS; 3 months), and overall survival (OS; 7 months). The group with favorable/intermediate risk cytogenetics and without pCytAbnl (n=43) had the longest median TTR (not reached), RFS (57 months), and OS (57 months). The group with pCytAbnl and favorable/intermediate risk cytogenetics, or, without pCytAbnl but with unfavorable risk cytogenetics (n=50) experienced intermediate TTR (18 months), RFS (9 months), and OS (18 months). In conclusion, a cytogenetic risk model identifies patients with AML in mCR with distinct rates of relapse and survival following HSCT. Copyright © 2014 Elsevier Ltd. All rights reserved.

SAMe-TT2R2 Score in the Outpatient Anticoagulation Clinic to Predict Time in Therapeutic Range and Adverse Events.

Science.gov (United States)

Pivatto Junior, Fernando; Scheffel, Rafael Selbach; Ries, Lucas; Wolkind, Ricardo Roitman; Marobin, Roberta; Barkan, Sabrina Sigal; Amon, Luís Carlos; Biolo, Andréia

2017-04-01

The SAMe-TT2R2 score was developed to predict which patients on oral anticoagulation with vitamin K antagonists (VKAs) will reach an adequate time in therapeutic range (TTR) (> 65%-70%). Studies have reported a relationship between this score and the occurrence of adverse events. To describe the TTR according to the score, in addition to relating the score obtained with the occurrence of adverse events in patients with nonvalvular atrial fibrillation (AF) on oral anticoagulation with VKAs. Retrospective cohort study including patients with nonvalvular AF attending an outpatient anticoagulation clinic of a tertiary hospital. Visits to the outpatient clinic and emergency, as well as hospital admissions to the institution, during 2014 were evaluated. The TTR was calculated through the Rosendaal´s method. We analyzed 263 patients (median TTR, 62.5%). The low-risk group (score 0-1) had a better median TTR as compared with the high-risk group (score ≥ 2): 69.2% vs. 56.3%, p = 0.002. Similarly, the percentage of patients with TTR ≥ 60%, 65% or 70% was higher in the low-risk group (p vitamina K (AVKs) atingirão um tempo na faixa terapêutica (TFT) adequado (> 65%-70%) no seguimento. Estudos também o relacionaram com a ocorrência de eventos adversos. Descrever o TFT de acordo com o escore, além de relacionar a pontuação obtida com a ocorrência de eventos adversos adversos em pacientes com fibrilação atrial (FA) não valvar em anticoagulação oral com AVKs. Estudo de coorte retrospectivo incluindo pacientes com FA não valvar em acompanhamento em ambulatório de anticoagulação de um hospital terciário. Foi realizada uma avaliação retrospectiva de consultas ambulatoriais, visitas a emergência e internações hospitalares na instituição no período de janeiro-dezembro/2014. O TFT foi calculado aplicando-se o método de Rosendaal. Foram analisados 263 pacientes com TFT mediano de 62,5%. O grupo de baixo risco (0-1 ponto) obteve um TFT mediano maior em

Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.

Science.gov (United States)

Gaines, J C; Acebes, S; Virrueta, A; Butler, M; Regan, L; O'Hern, C S

2018-05-01

We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins. © 2018 Wiley Periodicals, Inc.

The roles of the trading time risks on stock investment return and risks in stock price crashes

Science.gov (United States)

Li, Jiang-Cheng; Dong, Zhi-Wei; Yang, Guo-Hui; Long, Chao

2017-03-01

The roles of the trading time risks (TTRs) on stock investment return and risks are investigated in the condition of stock price crashes with Hushen300 data (CSI300) and Dow Jones Industrial Average (ˆDJI), respectively. In order to describe the TTR, we employ the escape time that the stock price drops from the maximum to minimum value in a data window length (DWL). After theoretical and empirical research on probability density function of return, the results in both ˆDJI and CSI300 indicate that: (i) As increasing DWL, the expectation of returns and its stability are weakened. (ii) An optimal TTR is related to a maximum return and minimum risk of stock investment in stock price crashes.

Acute exposure to synthetic pyrethroids causes bioconcentration and disruption of the hypothalamus–pituitary–thyroid axis in zebrafish embryos

International Nuclear Information System (INIS)

Tu, Wenqing; Xu, Chao; Lu, Bin; Lin, Chunmian; Wu, Yongming; Liu, Weiping

2016-01-01

Synthetic pyrethroids (SPs) have the potential to disrupt the thyroid endocrine system in mammals; however, little is known of the effects of SPs and underlying mechanisms in fish. In the current study, embryonic zebrafish were exposed to various concentrations (1, 3 and 10 μg/L) of bifenthrin (BF) or λ-cyhalothrin (λ-CH) until 72 h post fertilization, and body condition, bioaccumulation, thyroid hormone levels and transcription of related genes along the hypothalamus–pituitary–thyroid (HPT) axis examined. Body weight was significantly decreased in the λ-CH exposure groups, but not the BF exposure groups. BF and λ-CH markedly accumulated in the larvae, with concentrations ranging from 90.7 to 596.8 ng/g. In both exposure groups, alterations were observed in thyroxine (T 4 ) and triiodothyronine (T 3 ) levels. In addition, the majority of the HPT axis-related genes examined, including CRH, TSHβ, TTR, UGT1ab, Pax8, Dio2 and TRα, were significantly upregulated in the presence of BF. Compared to BF, λ-CH induced different transcriptional regulation patterns of the tested genes, in particular, significant stimulation of TTR, Pax8, Dio2 and TRα levels along with concomitant downregulation of Dio1. Molecular docking analyses revealed that at the atomic level, BF binds to thyroid hormone receptor (TRα) protein more potently than λ-CH, consequently affecting HPT axis signal transduction. In vitro and in silico experiments disclosed that during the early stages of zebrafish development, BF and λ-CH have the potential to disrupt thyroid endocrine system. - Highlights: • Following respective exposure of embryos to BF and λ-CH, thyroid endocrine disruption was investigated in zebrafish embryos. • Thyroid hormones (T3 and T4 levels) were significantly altered after being exposed to BF and λ-CH. • Gene transcription modulation in the HPT axis was examined. • BF and λ-CH bioconcentration in zebrafish larvae were evident. • BF binds to thyroid hormone

Acute exposure to synthetic pyrethroids causes bioconcentration and disruption of the hypothalamus–pituitary–thyroid axis in zebrafish embryos

Energy Technology Data Exchange (ETDEWEB)

Tu, Wenqing [Research Institute of Poyang Lake, Jiangxi Academy of Sciences, Nanchang 330029 (China); Institute of Environmental Science, College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032 (China); Xu, Chao, E-mail: chaoxu@zjut.edu.cn [Institute of Environmental Science, College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032 (China); Lu, Bin; Lin, Chunmian [Institute of Environmental Science, College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032 (China); Wu, Yongming [Research Institute of Poyang Lake, Jiangxi Academy of Sciences, Nanchang 330029 (China); Liu, Weiping [Institute of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058 (China)

2016-01-15

Synthetic pyrethroids (SPs) have the potential to disrupt the thyroid endocrine system in mammals; however, little is known of the effects of SPs and underlying mechanisms in fish. In the current study, embryonic zebrafish were exposed to various concentrations (1, 3 and 10 μg/L) of bifenthrin (BF) or λ-cyhalothrin (λ-CH) until 72 h post fertilization, and body condition, bioaccumulation, thyroid hormone levels and transcription of related genes along the hypothalamus–pituitary–thyroid (HPT) axis examined. Body weight was significantly decreased in the λ-CH exposure groups, but not the BF exposure groups. BF and λ-CH markedly accumulated in the larvae, with concentrations ranging from 90.7 to 596.8 ng/g. In both exposure groups, alterations were observed in thyroxine (T{sub 4}) and triiodothyronine (T{sub 3}) levels. In addition, the majority of the HPT axis-related genes examined, including CRH, TSHβ, TTR, UGT1ab, Pax8, Dio2 and TRα, were significantly upregulated in the presence of BF. Compared to BF, λ-CH induced different transcriptional regulation patterns of the tested genes, in particular, significant stimulation of TTR, Pax8, Dio2 and TRα levels along with concomitant downregulation of Dio1. Molecular docking analyses revealed that at the atomic level, BF binds to thyroid hormone receptor (TRα) protein more potently than λ-CH, consequently affecting HPT axis signal transduction. In vitro and in silico experiments disclosed that during the early stages of zebrafish development, BF and λ-CH have the potential to disrupt thyroid endocrine system. - Highlights: • Following respective exposure of embryos to BF and λ-CH, thyroid endocrine disruption was investigated in zebrafish embryos. • Thyroid hormones (T3 and T4 levels) were significantly altered after being exposed to BF and λ-CH. • Gene transcription modulation in the HPT axis was examined. • BF and λ-CH bioconcentration in zebrafish larvae were evident. • BF binds to thyroid

Protein docking prediction using predicted protein-protein interface

Directory of Open Access Journals (Sweden)

Li Bin

2012-01-01

Full Text Available Abstract Background Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. Results We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm, is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. Conclusion We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

Protein docking prediction using predicted protein-protein interface.

Science.gov (United States)

Li, Bin; Kihara, Daisuke

2012-01-10

Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm), is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks

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Peng Liu

2015-01-01

Full Text Available A method for predicting protein-protein interactions based on detected protein complexes is proposed to repair deficient interactions derived from high-throughput biological experiments. Protein complexes are pruned and decomposed into small parts based on the adaptive k-cores method to predict protein-protein interactions associated with the complexes. The proposed method is adaptive to protein complexes with different structure, number, and size of nodes in a protein-protein interaction network. Based on different complex sets detected by various algorithms, we can obtain different prediction sets of protein-protein interactions. The reliability of the predicted interaction sets is proved by using estimations with statistical tests and direct confirmation of the biological data. In comparison with the approaches which predict the interactions based on the cliques, the overlap of the predictions is small. Similarly, the overlaps among the predicted sets of interactions derived from various complex sets are also small. Thus, every predicted set of interactions may complement and improve the quality of the original network data. Meanwhile, the predictions from the proposed method replenish protein-protein interactions associated with protein complexes using only the network topology.

Gaps in monitoring during oral anticoagulation: insights into care transitions, monitoring barriers, and medication nonadherence.

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Rose, Adam J; Miller, Donald R; Ozonoff, Al; Berlowitz, Dan R; Ash, Arlene S; Zhao, Shibei; Reisman, Joel I; Hylek, Elaine M

2013-03-01

Among patients receiving oral anticoagulation, a gap of > 56 days between international normalized ratio tests suggests loss to follow-up that could lead to poor anticoagulation control and serious adverse events. We studied long-term oral anticoagulation care for 56,490 patients aged 65 years and older at 100 sites of care in the Veterans Health Administration. We used the rate of gaps in monitoring per patient-year to predict percentage time in therapeutic range (TTR) at the 100 sites. Many patients (45%) had at least one gap in monitoring during an average of 1.6 years of observation; 5% had two or more gaps per year. The median gap duration was 74 days (interquartile range, 62-107). The average TTR for patients with two or more gaps per year was 10 percentage points lower than for patients without gaps (P < .001). Patient-level predictors of gaps included nonwhite race, area poverty, greater distance from care, dementia, and major depression. Site-level gaps per patient-year varied from 0.19 to 1.78; each one-unit increase was associated with a 9.2 percentage point decrease in site-level TTR (P < .001). Site-level gap rates varied widely within an integrated care system. Sites with more gaps per patient-year had worse anticoagulation control. Strategies to address and reduce gaps in monitoring may improve anticoagulation control.

Does phosphorylation of cofilin affect the progression of human bladder cancer?

International Nuclear Information System (INIS)

Chung, Hong; Kim, Hong Sup; Kim, Bokyung; Jung, Seung-Hyo; Won, Kyung-Jong; Jiang, Xiaowen; Lee, Chang-Kwon; Lim, So Dug; Yang, Sang-Kuk; Song, Ki Hak

2013-01-01

We determined the differently expressed protein profiles and their functions in bladder cancer tissues with the aim of identifying possible target proteins and underlying molecular mechanisms for taking part in their progression. We examined the expression of proteins by proteomic analysis and western blot in normal urothelium, non-muscle-invasive bladder cancers (NMIBCs), and muscle-invasive bladder cancers (MIBCs). The function of cofilin was analyzed using T24 human bladder cancer cells. The expression levels of 12 proteins were altered between bladder cancers and normal bladder tissues. Of these proteins, 14-3-3σ was upregulated in both NMIBCs and MIBCs compared with controls. On the other hand, myosin regulatory light chain 2, galectin-1, lipid-binding AI, annexin V, transthyretin, CARD-inhibitor of NF-κB-activating ligand, and actin prepeptide were downregulated in cancer samples. Cofilin, an actin-depolymerizing factor, was prominent in both NMIBCs and MIBCs compared with normal bladder tissues. Furthermore, we confirmed that cofilin phosphorylation was more prominent in MIBCs than in NMIBCs using immunoblotting and immunohistochemcal analyses. Epidermal growth factor (EGF) increased the phosphorylation of cofilin and elevated the migration in T24 cells. Knockdown of cofilin expression with small interfering RNA attenuated the T24 cell migration in response to EGF. These results demonstrate that the increased expression and phosphorylation of cofilin might play a role in the occurrence and invasiveness of bladder cancer. We suspected that changes in cofilin expression may participate in the progression of the bladder cancer

Tonopah Test Range Environmental Restoration Corrective Action Sites

International Nuclear Information System (INIS)

Ronald B. Jackson

2007-01-01

Corrective Action Sites (CASs) and Corrective Action Units (CAUs) at the Tonopah Test Range (TTR) may be placed into three categories: Clean Closure/No Further Action, Closure in Place, or Closure in Progress

Quality of management of oral anticoagulation as assessed by time in therapeutic INR range in elderly and younger patients with low mean years of formal education: a prospective cohort study.

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Costa, Gustavo Lamego de Barros; Ferreira, Diana Carvalho; Valacio, Reginaldo Aparecido; Vieira Moreira, Maria da Consolação

2011-05-01

despite the overwhelming evidence of its effectiveness, oral anticoagulation continues to be underused in the elderly, presumably due to physicians' misconceptions when estimating bleeding risk and ability to comply with treatment. to investigate the quality of anticoagulation control among deprived elderly and younger patients. prospective observational study. a public anticoagulation clinic in a developing country. all adult patients on intended long-term (>90 days) oral anticoagulation. We studied 171 patients (79 elderly and 92 non-elderly) with a mean follow-up of 273 ± 84.9 days. the main outcome measure was the quality of anticoagulation management as measured by the time in therapeutic (TTR) international normalised ratio (INR) range. Elderly patients (≥60 years) were compared with younger patients with respect to the educational level and co-morbidities. the mean number of years of formal education was 4.37 ± 3.2 years. The mean TTR was 62.50 ± 17.9% in non-elderly and 62.10 ± 16.6% in elderly (P = 0.862) subjects, despite the higher prevalence of co-morbidities in the latter group: heart failure (46.3 versus 28.6%, P = 0.042), diabetes mellitus (22.8 versus 8.7%, P = 0.011), renal failure (estimated glomerular filtration rate educational levels (3.42 ± 2.5 versus 5.55 ± 3.4 years of formal education, P < 0.001) and higher rates of cognitive impairment (34.0 versus 13.1%, P = 0.004), but a similar mean TTR (62.46 ± 16.1 versus 63.02 ± 17.8%, P = 0.856). The oldest (≥75 years) patients did as well as those aged ≤50 years (mean TTR: 62.54 ± 16.0 versus 62.23 ± 16.4%, respectively, P = 0.98). good-quality management of oral anticoagulation is achievable in deprived populations attending an anticoagulation clinic. Elderly patients may experience similar quality of anticoagulation despite having higher levels of co-morbidities and polypharmacy. These results add evidence to the safety of such therapeutic interventions in the elderly.

Associations between cigarette smoking status and colon cancer prognosis among participants in North Central Cancer Treatment Group Phase III Trial N0147.

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Phipps, Amanda I; Shi, Qian; Newcomb, Polly A; Nelson, Garth D; Sargent, Daniel J; Alberts, Steven R; Limburg, Paul J

2013-06-01

By using data from North Central Cancer Treatment Group Phase III Trial N0147, a randomized adjuvant trial of patients with stage III colon cancer, we assessed the relationship between smoking and cancer outcomes, disease-free survival (DFS), and time to recurrence (TTR), accounting for heterogeneity by patient and tumor characteristics. PATIENTS AND METHODS Before random assignment to infusional fluorouracil, leucovorin, and oxaliplatin (FOLFOX) or FOLFOX plus cetuximab, 1,968 participants completed a questionnaire on smoking history and other risk factors. Cox models assessed the association between smoking history and the primary trial outcome of DFS (ie, time to recurrence or death), as well as TTR, adjusting for other clinical and patient factors. The median follow-up was 3.5 years among patients who did not experience events. Compared with never-smokers, ever smokers experienced significantly shorter DFS (3-year DFS proportion: 70% v 74%; hazard ratio [HR], 1.21; 95% CI, 1.02 to 1.42). This association persisted after multivariate adjustment (HR, 1.23; 95% CI, 1.02 to 1.49). There was significant interaction in this association by BRAF mutation status (P = .03): smoking was associated with shorter DFS in patients with BRAF wild-type (HR, 1.36; 95% CI, 1.11 to 1.66) but not BRAF mutated (HR, 0.80; 95% CI, 0.50 to 1.29) colon cancer. Smoking was more strongly associated with poorer DFS in those with KRAS mutated versus KRAS wild-type colon cancer (HR, 1.50 [95% CI, 1.12 to 2.00] v HR, 1.09 [95% CI, 0.85 to 1.39]), although interaction by KRAS mutation status was not statistically significant (P = .07). Associations were comparable in analyses of TTR. Overall, smoking was significantly associated with shorter DFS and TTR in patients with colon cancer. These adverse relationships were most evident in patients with BRAF wild-type or KRAS mutated colon cancer.

Tonopah Test Range Air Monitoring: CY2016 Meteorological, Radiological, and Wind Transported Particulate Observations

Energy Technology Data Exchange (ETDEWEB)

Chapman, Jenny [Desert Research Inst. (DRI), Las Vegas, NV (United States); Nikolich, George [Desert Research Inst. (DRI), Las Vegas, NV (United States); Shadel, Craig [Desert Research Inst. (DRI), Las Vegas, NV (United States); McCurdy, Greg [Desert Research Inst. (DRI), Las Vegas, NV (United States); Etyemezian, Vicken [Desert Research Inst. (DRI), Las Vegas, NV (United States); Miller, Julianne J [Desert Research Inst. (DRI), Las Vegas, NV (United States); Mizell, Steve [Desert Research Inst. (DRI), Las Vegas, NV (United States)

2017-10-01

In 1963, the U.S. Department of Energy (DOE) (formerly the Atomic Energy Commission [AEC]), implemented Operation Roller Coaster on the Tonopah Test Range (TTR) and an adjacent area of the Nevada Test and Training Range (NTTR) (formerly the Nellis Air Force Range). This operation resulted in radionuclide-contaminated soils at the Clean Slate I, II, and III sites. This report documents observations made during ongoing monitoring of radiological, meteorological, and dust conditions at stations installed adjacent to Clean Slate I and Clean Slate III, and at the TTR Sandia National Laboratories (SNL) Range Operations Control (ROC) center. The primary objective of the monitoring effort is to determine if wind blowing across the Clean Slate sites is transporting particles of radionuclide-contaminated soil beyond the physical and administrative boundaries of the sites.

Exome analysis identified a novel mutation in the RBP4 gene in a consanguineous pedigree with retinal dystrophy and developmental abnormalities.

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Catherine Cukras

Full Text Available Retinitis Pigmentosa (RP is a common form of retinal degeneration characterized by photoreceptor degeneration and retinal pigment epithelium (RPE atrophy causing loss of visual field and acuities. Exome sequencing identified a novel homozygous splice site variant (c.111+1G>A in the gene encoding retinol binding protein 4 (RBP4. This change segregated with early onset, progressive, and severe autosomal recessive retinitis pigmentosa (arRP in an eight member consanguineous pedigree of European ancestry. Additionally, one patient exhibited developmental abnormalities including patent ductus arteriosus and chorioretinal and iris colobomas. The second patient developed acne from young age and extending into the 5(th decade. Both patients had undetectable levels of RBP4 in the serum suggesting that this mutation led to either mRNA or protein instability resulting in a null phenotype. In addition, the patients exhibited severe vitamin A deficiency, and diminished serum retinol levels. Circulating transthyretin levels were normal. This study identifies the RBP4 splice site change as the cause of RP in this pedigree. The presence of developmental abnormalities and severe acne in patients with retinal degeneration may indicate the involvement of genes that regulate vitamin A absorption, transport and metabolism.

Exome analysis identified a novel mutation in the RBP4 gene in a consanguineous pedigree with retinal dystrophy and developmental abnormalities.

Science.gov (United States)

Cukras, Catherine; Gaasterland, Terry; Lee, Pauline; Gudiseva, Harini V; Chavali, Venkata R M; Pullakhandam, Raghu; Maranhao, Bruno; Edsall, Lee; Soares, Sandra; Reddy, G Bhanuprakash; Sieving, Paul A; Ayyagari, Radha

2012-01-01

Retinitis Pigmentosa (RP) is a common form of retinal degeneration characterized by photoreceptor degeneration and retinal pigment epithelium (RPE) atrophy causing loss of visual field and acuities. Exome sequencing identified a novel homozygous splice site variant (c.111+1G>A) in the gene encoding retinol binding protein 4 (RBP4). This change segregated with early onset, progressive, and severe autosomal recessive retinitis pigmentosa (arRP) in an eight member consanguineous pedigree of European ancestry. Additionally, one patient exhibited developmental abnormalities including patent ductus arteriosus and chorioretinal and iris colobomas. The second patient developed acne from young age and extending into the 5(th) decade. Both patients had undetectable levels of RBP4 in the serum suggesting that this mutation led to either mRNA or protein instability resulting in a null phenotype. In addition, the patients exhibited severe vitamin A deficiency, and diminished serum retinol levels. Circulating transthyretin levels were normal. This study identifies the RBP4 splice site change as the cause of RP in this pedigree. The presence of developmental abnormalities and severe acne in patients with retinal degeneration may indicate the involvement of genes that regulate vitamin A absorption, transport and metabolism.

Fulltext PDF

Indian Academy of Sciences (India)

2013-12-06

Dec 6, 2013 ... allows for appropriate diagnosis, management and treatment of a variety ... test turn-around time with wasted costs, as tests are repeated .... Pathogenic alteration in TTR gene accounting for observed structural change. 59%.

Influence of Coding Variability in APP-Aβ Metabolism Genes in Sporadic Alzheimer's Disease.

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Celeste Sassi

Full Text Available The cerebral deposition of Aβ42, a neurotoxic proteolytic derivate of amyloid precursor protein (APP, is a central event in Alzheimer's disease (AD(Amyloid hypothesis. Given the key role of APP-Aβ metabolism in AD pathogenesis, we selected 29 genes involved in APP processing, Aβ degradation and clearance. We then used exome and genome sequencing to investigate the single independent (single-variant association test and cumulative (gene-based association test effect of coding variants in these genes as potential susceptibility factors for AD, in a cohort composed of 332 sporadic and mainly late-onset AD cases and 676 elderly controls from North America and the UK. Our study shows that common coding variability in these genes does not play a major role for the disease development. In the single-variant association analysis, the main hits, none of which statistically significant after multiple testing correction (1.9e-4TTR, ACE, clearance (LRP1 and APP trafficking and recycling (SORL1. These results were partially replicated in the gene-based analysis (c-alpha and SKAT tests, that reports ECE1, LYZ and TTR as nominally associated to AD (1.7e-3

Proteomic analysis of cerebrospinal fluid in canine cervical spondylomyelopathy.

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Martin-Vaquero, Paula; da Costa, Ronaldo C; Allen, Matthew J; Moore, Sarah A; Keirsey, Jeremy K; Green, Kari B

2015-05-01

Prospective study. To identify proteins with differential expression in the cerebrospinal fluid (CSF) from 15 clinically normal (control) dogs and 15 dogs with cervical spondylomyelopathy (CSM). Canine CSM is a spontaneous, chronic, compressive cervical myelopathy similar to human cervical spondylotic myelopathy. There is a limited knowledge of the molecular mechanisms underlying these conditions. Differentially expressed CSF proteins may contribute with novel information about the disease pathogenesis in both dogs and humans. Protein separation was performed with 2-dimensional electrophoresis. A Student t test was used to detect significant differences between groups (P liquid chromatography tandem mass spectrometry. A total of 96 spots had a significant average change of at least 1.25-fold in 1 of the 3 comparisons. Compared with the CSF of control dogs, CSM-affected dogs demonstrated increased CSF expression of 8 proteins including vitamin D-binding protein, gelsolin, creatine kinase B-type, angiotensinogen, α-2-HS-glycoprotein, SPARC (secreted protein, acidic, rich in cysteine), calsyntenin-1, and complement C3, and decreased expression of pigment epithelium-derived factor, prostaglandin-H2 D-isomerase, apolipoprotein E, and clusterin. In the CSF of CSM-affected dogs, corticosteroid treatment increased the expression of haptoglobin, transthyretin isoform 2, cystatin C-like, apolipoprotein E, and clusterin, and decreased the expression of angiotensinogen, α-2-HS-glycoprotein, and gelsolin. Many of the differentially expressed proteins are associated with damaged neural tissue, bone turnover, and/or compromised blood-spinal cord barrier. The knowledge of the protein changes that occur in CSM and upon corticosteroid treatment of CSM-affected patients will aid in further understanding the pathomechanisms underlying this disease. N/A.

Oligomeric protein structure networks: insights into protein-protein interactions

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Brinda KV

2005-12-01

Full Text Available Abstract Background Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In this study, oligomeric protein structures are viewed from a network perspective to obtain new insights into protein association. Structure graphs of proteins have been constructed from a non-redundant set of protein oligomer crystal structures by considering amino acid residues as nodes and the edges are based on the strength of the non-covalent interactions between the residues. The analysis of such networks has been carried out in terms of amino acid clusters and hubs (highly connected residues with special emphasis to protein interfaces. Results A variety of interactions such as hydrogen bond, salt bridges, aromatic and hydrophobic interactions, which occur at the interfaces are identified in a consolidated manner as amino acid clusters at the interface, from this study. Moreover, the characterization of the highly connected hub-forming residues at the interfaces and their comparison with the hubs from the non-interface regions and the non-hubs in the interface regions show that there is a predominance of charged interactions at the interfaces. Further, strong and weak interfaces are identified on the basis of the interaction strength between amino acid residues and the sizes of the interface clusters, which also show that many protein interfaces are stronger than their monomeric protein cores. The interface strengths evaluated based on the interface clusters and hubs also correlate well with experimentally determined dissociation constants for known complexes. Finally, the interface hubs identified using the present method correlate very well with experimentally determined hotspots in the interfaces of protein complexes obtained from the Alanine Scanning Energetics database (ASEdb. A few predictions of interface hot

Protein nanoparticles for therapeutic protein delivery.

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Herrera Estrada, L P; Champion, J A

2015-06-01

Therapeutic proteins can face substantial challenges to their activity, requiring protein modification or use of a delivery vehicle. Nanoparticles can significantly enhance delivery of encapsulated cargo, but traditional small molecule carriers have some limitations in their use for protein delivery. Nanoparticles made from protein have been proposed as alternative carriers and have benefits specific to therapeutic protein delivery. This review describes protein nanoparticles made by self-assembly, including protein cages, protein polymers, and charged or amphipathic peptides, and by desolvation. It presents particle fabrication and delivery characterization for a variety of therapeutic and model proteins, as well as comparison of the features of different protein nanoparticles.

Protein-protein interactions: an application of Tus-Ter mediated protein microarray system.

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Sitaraman, Kalavathy; Chatterjee, Deb K

2011-01-01

In this chapter, we present a novel, cost-effective microarray strategy that utilizes expression-ready plasmid DNAs to generate protein arrays on-demand and its use to validate protein-protein interactions. These expression plasmids were constructed in such a way so as to serve a dual purpose of synthesizing the protein of interest as well as capturing the synthesized protein. The microarray system is based on the high affinity binding of Escherichia coli "Tus" protein to "Ter," a 20 bp DNA sequence involved in the regulation of DNA replication. The protein expression is carried out in a cell-free protein synthesis system, with rabbit reticulocyte lysates, and the target proteins are detected either by labeled incorporated tag specific or by gene-specific antibodies. This microarray system has been successfully used for the detection of protein-protein interaction because both the target protein and the query protein can be transcribed and translated simultaneously in the microarray slides. The utility of this system for detecting protein-protein interaction is demonstrated by a few well-known examples: Jun/Fos, FRB/FKBP12, p53/MDM2, and CDK4/p16. In all these cases, the presence of protein complexes resulted in the localization of fluorophores at the specific sites of the immobilized target plasmids. Interestingly, during our interactions studies we also detected a previously unknown interaction between CDK2 and p16. Thus, this Tus-Ter based system of protein microarray can be used for the validation of known protein interactions as well as for identifying new protein-protein interactions. In addition, it can be used to examine and identify targets of nucleic acid-protein, ligand-receptor, enzyme-substrate, and drug-protein interactions.

Truly Absorbed Microbial Protein Synthesis, Rumen Bypass Protein, Endogenous Protein, and Total Metabolizable Protein from Starchy and Protein-Rich Raw Materials

NARCIS (Netherlands)

Parand, Ehsan; Vakili, Alireza; Mesgaran, Mohsen Danesh; Duinkerken, Van Gert; Yu, Peiqiang

2015-01-01

This study was carried out to measure truly absorbed microbial protein synthesis, rumen bypass protein, and endogenous protein loss, as well as total metabolizable protein, from starchy and protein-rich raw feed materials with model comparisons. Predictions by the DVE2010 system as a more

The future distribution of the savannah biome: model-based and biogeographic contingency.

Science.gov (United States)

Moncrieff, Glenn R; Scheiter, Simon; Langan, Liam; Trabucco, Antonio; Higgins, Steven I

2016-09-19

The extent of the savannah biome is expected to be profoundly altered by climatic change and increasing atmospheric CO2 concentrations. Contrasting projections are given when using different modelling approaches to estimate future distributions. Furthermore, biogeographic variation within savannahs in plant function and structure is expected to lead to divergent responses to global change. Hence the use of a single model with a single savannah tree type will likely lead to biased projections. Here we compare and contrast projections of South American, African and Australian savannah distributions from the physiologically based Thornley transport resistance statistical distribution model (TTR-SDM)-and three versions of a dynamic vegetation model (DVM) designed and parametrized separately for specific continents. We show that attempting to extrapolate any continent-specific model globally biases projections. By 2070, all DVMs generally project a decrease in the extent of savannahs at their boundary with forests, whereas the TTR-SDM projects a decrease in savannahs at their boundary with aridlands and grasslands. This difference is driven by forest and woodland expansion in response to rising atmospheric CO2 concentrations in DVMs, unaccounted for by the TTR-SDM. We suggest that the most suitable models of the savannah biome for future development are individual-based dynamic vegetation models designed for specific biogeographic regions.This article is part of the themed issue 'Tropical grassy biomes: linking ecology, human use and conservation'. © 2016 The Author(s).

MODELING CST ION EXCHANGE FOR CESIUM REMOVAL FROM SCIX BATCHES 1 - 4

Energy Technology Data Exchange (ETDEWEB)

Smith, F.

2011-04-25

The objective of this work is, through modeling, to predict the performance of Crystalline Silicotitinate (CST) for the removal of cesium from Small Column Ion Exchange (SCIX) Batches 1-4 (as proposed in Revision 16 of the Liquid Waste System Plan). The scope of this task is specified in Technical Task Request (TTR) 'SCIX Feed Modeling', HLE-TTR-2011-003, which specified using the Zheng, Anthony, Miller (ZAM) code to predict CST isotherms for six given SCIX feed compositions and the VErsatile Reaction and SEparation simulator for Liquid Chromatography (VERSE-LC) code to predict ion-exchange column behavior. The six SCIX feed compositions provided in the TTR represent SCIX Batches 1-4 and Batches 1 and 2 without caustic addition. The study also investigated the sensitivity in column performance to: (1) Flow rates of 5, 10, and 20 gpm with 10 gpm as the nominal flow; and (2) Temperatures of 25, 35, and 45 C with 35 C as the nominal temperature. The isotherms and column predictions presented in this report reflect the expected performance of engineered CST IE-911. This form of CST was used in experiments conducted at the Savannah River National Laboratory (SRNL) that formed the basis for estimating model parameters (Hamm et al., 2002). As has been done previously, the engineered resin capacity is estimated to be 68% of the capacity of particulate CST without binder.

Environmental Issues in Thyroid Diseases.

Science.gov (United States)

Ferrari, Silvia Martina; Fallahi, Poupak; Antonelli, Alessandro; Benvenga, Salvatore

2017-01-01

Environmental factors are determinant for the appearance of autoimmune thyroid diseases (AITD) in susceptible subjects. Increased iodine intake, selenium, and vitamin D deficiency, exposure to radiation, from nuclear fallout or due to medical radiation, are environmental factors increasing AITD. Cigarette smoking is associated with Graves' disease and Graves' ophthalmopathy, while it decreases the risk of hypothyroidism and thyroid autoimmunity. Viral infections are important environmental factors in the pathogenesis of AITD, too, particularly human parvovirus B19 (EVB19) and hepatitis C virus. Among the many chemical contaminants, halogenated organochlorines and pesticides variably disrupt thyroid function. Polychlorinated biphenyls and their metabolites and polybrominated diethyl ethers bind to thyroid transport proteins, such as transthyretin, displace thyroxine, and disrupt thyroid function. Among drugs, interferon- and iodine-containing drugs have been associated with AITD. Moreover intestinal dysbiosis causes autoimmune thyroiditis. To reduce the risk to populations and also in each patient, it is necessary to comprehend the association between environmental agents and thyroid dysfunction.

Mass spectral analysis of urine proteomic profiles of dairy cows suffering from clinical ketosis.

Science.gov (United States)

Xu, Chuang; Shu, Shi; Xia, Cheng; Wang, Pengxian; Sun, Yuhang; Xu, Chuchu; Li, Changsheng

2015-01-01

Ketosis is an important metabolic disorder in dairy cows during the transition period. The urine proteomics of ketosis has not been investigated using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS). The aim is to determine differences between urine proteomic profiles of healthy cows and those with clinical ketosis, and facilitate studies of the underlying physiological and biochemical mechanisms that lead to liver pathology in ketosis. We analyzed the urine samples of 20 cows with clinical ketosis (group 1) and 20 control cows (group 2) using SELDI-TOF-MS. Thirty-nine peptide peaks differed between both groups. Polypeptides corresponding to 26 of these differential peptide peaks were identified using the SWISS-PROT protein database. We found that the peaks of 11 distinct polypeptides from the urine samples of the ketosis group were significantly reduced, compared with those of the control group as based on the Wilcoxon rank sum test. Among these were VGF (non-acronymic) protein, amyloid precursor protein, serum amyloid A (SAA), fibrinogen, C1INH, apolipoprotein C-III, cystatin C, transthyretin, hepcidin, human neutrophil peptides, and osteopontin. These proteins may represent novel biomarkers of the metabolic changes that occur in dairy cows with ketosis. Our results will help to better understand the physiological changes and pathogenesis observed in cows with ketosis. The SELDI-TOF-MS can be used to understand the physiological and biochemical mechanisms of ketosis and identify biomarkers of the disease.

Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces.

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Ruzianisra Mohamed

Full Text Available Protein-protein interactions (PPIs play a major role in many biological processes and they represent an important class of targets for therapeutic intervention. However, targeting PPIs is challenging because often no convenient natural substrates are available as starting point for small-molecule design. Here, we explored the characteristics of protein interfaces in five non-redundant datasets of 174 protein-protein (PP complexes, and 161 protein-ligand (PL complexes from the ABC database, 436 PP complexes, and 196 PL complexes from the PIBASE database and a dataset of 89 PL complexes from the Timbal database. In all cases, the small molecule ligands must bind at the respective PP interface. We observed similar amino acid frequencies in all three datasets. Remarkably, also the characteristics of PP contacts and overlapping PL contacts are highly similar.

Protein- protein interaction detection system using fluorescent protein microdomains

Science.gov (United States)

Waldo, Geoffrey S.; Cabantous, Stephanie

2010-02-23

The invention provides a protein labeling and interaction detection system based on engineered fragments of fluorescent and chromophoric proteins that require fused interacting polypeptides to drive the association of the fragments, and further are soluble and stable, and do not change the solubility of polypeptides to which they are fused. In one embodiment, a test protein X is fused to a sixteen amino acid fragment of GFP (.beta.-strand 10, amino acids 198-214), engineered to not perturb fusion protein solubility. A second test protein Y is fused to a sixteen amino acid fragment of GFP (.beta.-strand 11, amino acids 215-230), engineered to not perturb fusion protein solubility. When X and Y interact, they bring the GFP strands into proximity, and are detected by complementation with a third GFP fragment consisting of GFP amino acids 1-198 (strands 1-9). When GFP strands 10 and 11 are held together by interaction of protein X and Y, they spontaneous association with GFP strands 1-9, resulting in structural complementation, folding, and concomitant GFP fluorescence.

Identification of Protein-Protein Interactions with Glutathione-S-Transferase (GST) Fusion Proteins.

Science.gov (United States)

Einarson, Margret B; Pugacheva, Elena N; Orlinick, Jason R

2007-08-01

INTRODUCTIONGlutathione-S-transferase (GST) fusion proteins have had a wide range of applications since their introduction as tools for synthesis of recombinant proteins in bacteria. GST was originally selected as a fusion moiety because of several desirable properties. First and foremost, when expressed in bacteria alone, or as a fusion, GST is not sequestered in inclusion bodies (in contrast to previous fusion protein systems). Second, GST can be affinity-purified without denaturation because it binds to immobilized glutathione, which provides the basis for simple purification. Consequently, GST fusion proteins are routinely used for antibody generation and purification, protein-protein interaction studies, and biochemical analysis. This article describes the use of GST fusion proteins as probes for the identification of protein-protein interactions.

Protein-protein interaction network-based detection of functionally similar proteins within species.

Science.gov (United States)

Song, Baoxing; Wang, Fen; Guo, Yang; Sang, Qing; Liu, Min; Li, Dengyun; Fang, Wei; Zhang, Deli

2012-07-01

Although functionally similar proteins across species have been widely studied, functionally similar proteins within species showing low sequence similarity have not been examined in detail. Identification of these proteins is of significant importance for understanding biological functions, evolution of protein families, progression of co-evolution, and convergent evolution and others which cannot be obtained by detection of functionally similar proteins across species. Here, we explored a method of detecting functionally similar proteins within species based on graph theory. After denoting protein-protein interaction networks using graphs, we split the graphs into subgraphs using the 1-hop method. Proteins with functional similarities in a species were detected using a method of modified shortest path to compare these subgraphs and to find the eligible optimal results. Using seven protein-protein interaction networks and this method, some functionally similar proteins with low sequence similarity that cannot detected by sequence alignment were identified. By analyzing the results, we found that, sometimes, it is difficult to separate homologous from convergent evolution. Evaluation of the performance of our method by gene ontology term overlap showed that the precision of our method was excellent. Copyright © 2012 Wiley Periodicals, Inc.

Protein-Protein Docking in Drug Design and Discovery.

Science.gov (United States)

Kaczor, Agnieszka A; Bartuzi, Damian; Stępniewski, Tomasz Maciej; Matosiuk, Dariusz; Selent, Jana

2018-01-01

Protein-protein interactions (PPIs) are responsible for a number of key physiological processes in the living cells and underlie the pathomechanism of many diseases. Nowadays, along with the concept of so-called "hot spots" in protein-protein interactions, which are well-defined interface regions responsible for most of the binding energy, these interfaces can be targeted with modulators. In order to apply structure-based design techniques to design PPIs modulators, a three-dimensional structure of protein complex has to be available. In this context in silico approaches, in particular protein-protein docking, are a valuable complement to experimental methods for elucidating 3D structure of protein complexes. Protein-protein docking is easy to use and does not require significant computer resources and time (in contrast to molecular dynamics) and it results in 3D structure of a protein complex (in contrast to sequence-based methods of predicting binding interfaces). However, protein-protein docking cannot address all the aspects of protein dynamics, in particular the global conformational changes during protein complex formation. In spite of this fact, protein-protein docking is widely used to model complexes of water-soluble proteins and less commonly to predict structures of transmembrane protein assemblies, including dimers and oligomers of G protein-coupled receptors (GPCRs). In this chapter we review the principles of protein-protein docking, available algorithms and software and discuss the recent examples, benefits, and drawbacks of protein-protein docking application to water-soluble proteins, membrane anchoring and transmembrane proteins, including GPCRs.

Evolution of protein-protein interactions

Indian Academy of Sciences (India)

Evolution of protein-protein interactions · Our interests in protein-protein interactions · Slide 3 · Slide 4 · Slide 5 · Slide 6 · Slide 7 · Slide 8 · Slide 9 · Slide 10 · Slide 11 · Slide 12 · Slide 13 · Slide 14 · Slide 15 · Slide 16 · Slide 17 · Slide 18 · Slide 19 · Slide 20.

Protein function prediction using neighbor relativity in protein-protein interaction network.

Science.gov (United States)

Moosavi, Sobhan; Rahgozar, Masoud; Rahimi, Amir

2013-04-01

There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interaction information to predict function for un-annotated proteins. In this paper, we propose a novel approach called "Neighbor Relativity Coefficient" (NRC) based on interaction network topology which estimates the functional similarity between two proteins. NRC is calculated for each pair of proteins based on their graph-based features including distance, common neighbors and the number of paths between them. In order to ascribe function to an un-annotated protein, NRC estimates a weight for each neighbor to transfer its annotation to the unknown protein. Finally, the unknown protein will be annotated by the top score transferred functions. We also investigate the effect of using different coefficients for various types of functions. The proposed method has been evaluated on Saccharomyces cerevisiae and Homo sapiens interaction networks. The performance analysis demonstrates that NRC yields better results in comparison with previous protein function prediction approaches that utilize interaction network. Copyright © 2012 Elsevier Ltd. All rights reserved.

Protein Structure Prediction by Protein Threading

Science.gov (United States)

Xu, Ying; Liu, Zhijie; Cai, Liming; Xu, Dong

The seminal work of Bowie, Lüthy, and Eisenberg (Bowie et al., 1991) on "the inverse protein folding problem" laid the foundation of protein structure prediction by protein threading. By using simple measures for fitness of different amino acid types to local structural environments defined in terms of solvent accessibility and protein secondary structure, the authors derived a simple and yet profoundly novel approach to assessing if a protein sequence fits well with a given protein structural fold. Their follow-up work (Elofsson et al., 1996; Fischer and Eisenberg, 1996; Fischer et al., 1996a,b) and the work by Jones, Taylor, and Thornton (Jones et al., 1992) on protein fold recognition led to the development of a new brand of powerful tools for protein structure prediction, which we now term "protein threading." These computational tools have played a key role in extending the utility of all the experimentally solved structures by X-ray crystallography and nuclear magnetic resonance (NMR), providing structural models and functional predictions for many of the proteins encoded in the hundreds of genomes that have been sequenced up to now.

Specificity and affinity quantification of protein-protein interactions.

Science.gov (United States)

Yan, Zhiqiang; Guo, Liyong; Hu, Liang; Wang, Jin

2013-05-01

Most biological processes are mediated by the protein-protein interactions. Determination of the protein-protein structures and insight into their interactions are vital to understand the mechanisms of protein functions. Currently, compared with the isolated protein structures, only a small fraction of protein-protein structures are experimentally solved. Therefore, the computational docking methods play an increasing role in predicting the structures and interactions of protein-protein complexes. The scoring function of protein-protein interactions is the key responsible for the accuracy of the computational docking. Previous scoring functions were mostly developed by optimizing the binding affinity which determines the stability of the protein-protein complex, but they are often lack of the consideration of specificity which determines the discrimination of native protein-protein complex against competitive ones. We developed a scoring function (named as SPA-PP, specificity and affinity of the protein-protein interactions) by incorporating both the specificity and affinity into the optimization strategy. The testing results and comparisons with other scoring functions show that SPA-PP performs remarkably on both predictions of binding pose and binding affinity. Thus, SPA-PP is a promising quantification of protein-protein interactions, which can be implemented into the protein docking tools and applied for the predictions of protein-protein structure and affinity. The algorithm is implemented in C language, and the code can be downloaded from http://dl.dropbox.com/u/1865642/Optimization.cpp.

[Prevalence of oral anticoagulation and quality of its management in primary healthcare: A study by the Health Sentinel Network of the Region of Valencia (Spain)].

Science.gov (United States)

Boned-Ombuena, Ana; Pérez-Panadés, Jordi; López-Maside, Aurora; Miralles-Espí, Maite; Guardiola Vilarroig, Sandra; Adam Ruiz, Desamparados; Zurriaga, Oscar

2017-11-01

To estimate the prevalence of patients with oral anticoagulant therapy (OAT) in the Region of Valencia and to evaluate the quality of management of OAT with vitaminK antagonists (VKA) carried out in primary healthcare. Observational cross-sectional study conducted through the Health Sentinel Network of the Region of Valencia, which includes a survey and the retrospective analysis of OAT monitoring. Primary healthcare, Region of Valencia, Spain. All patients aged 18years or older on OAT who consulted during the year 2014. The population covered by the 59 doctors of the Health Sentinel Network constitutes 2.2% of the adult population of the Region of Valencia, and it is representative of it. Demographic, socioeconomic and health data as well as information concerning OAT. Quality of OAT management with VKA was assessed by means of the percentage of time in therapeutic range (TTR), computed using the Rosendaal method. A total of 1,144 patients were recorded (mean age 74.5±11 years; 49.7% women). Prevalence of OAT in the Region of Valencia is 1.3 cases per 100 population. The characteristic profile of these patients is an old person, with several comorbidities and a low level of education, who lives accompanied. Atrial fibrillation is the most common indication. 82.8% of patients on OAT with VKA were monitored in primary healthcare. The average TTR was 65.0%, and 53.9% of patients had a TTR ≥65%. Among inadequately controlled patients, 74.4% were perceived as well-controlled by their primary care doctor. Prevalence of OAT is high, and it is expected to increase. The degree of control achieved meets the generally accepted quality standard (mean TTR ≥65%), and it is comparable to that observed in other national and international studies. However, there is wide scope for improvement. It is crucial to optimize the management of this therapy in the most effective and cost-effective way. Among other measures, access of physicians to their patients' clinical information

Investigation of the interaction between separate calcium feeding and phytase supplementation on growth performance, calcium intake, nutrient digestibility and energy utilisation in broiler starters

NARCIS (Netherlands)

Abdollahi, M.R.; Duangnumsawang, Y.; Kwakkel, R.P.; Steenfeldt, S.; Bootwalla, S.M.; Ravindran, V.

2016-01-01

The interaction between separate calcium (Ca) feeding and phytase supplementation on performance, coefficient of apparent ileal digestibility (CAID) of nitrogen (N), starch, fat and phosphorus (P), total tract retention (TTR) of Ca and P, and apparent metabolisable energy (AME) in broiler

Detection of protein complex from protein-protein interaction network using Markov clustering

International Nuclear Information System (INIS)

Ochieng, P J; Kusuma, W A; Haryanto, T

2017-01-01

Detection of complexes, or groups of functionally related proteins, is an important challenge while analysing biological networks. However, existing algorithms to identify protein complexes are insufficient when applied to dense networks of experimentally derived interaction data. Therefore, we introduced a graph clustering method based on Markov clustering algorithm to identify protein complex within highly interconnected protein-protein interaction networks. Protein-protein interaction network was first constructed to develop geometrical network, the network was then partitioned using Markov clustering to detect protein complexes. The interest of the proposed method was illustrated by its application to Human Proteins associated to type II diabetes mellitus. Flow simulation of MCL algorithm was initially performed and topological properties of the resultant network were analysed for detection of the protein complex. The results indicated the proposed method successfully detect an overall of 34 complexes with 11 complexes consisting of overlapping modules and 20 non-overlapping modules. The major complex consisted of 102 proteins and 521 interactions with cluster modularity and density of 0.745 and 0.101 respectively. The comparison analysis revealed MCL out perform AP, MCODE and SCPS algorithms with high clustering coefficient (0.751) network density and modularity index (0.630). This demonstrated MCL was the most reliable and efficient graph clustering algorithm for detection of protein complexes from PPI networks. (paper)

Coarse-grain modelling of protein-protein interactions

NARCIS (Netherlands)

Baaden, Marc; Marrink, Siewert J.

2013-01-01

Here, we review recent advances towards the modelling of protein-protein interactions (PPI) at the coarse-grained (CG) level, a technique that is now widely used to understand protein affinity, aggregation and self-assembly behaviour. PPI models of soluble proteins and membrane proteins are

Use of vitamin K antagonist therapy in geriatrics: a French national survey from the French Society of Geriatrics and Gerontology (SFGG).

Science.gov (United States)

Plichart, Matthieu; Berrut, Gilles; Maubourguet, Nathalie; Jeandel, Claude; Emeriau, Jean-Paul; Ankri, Joël; Bouvier, Hélène; Ruault, Geneviève; Hanon, Olivier

2013-12-01

We aimed to evaluate the quality and determinants of vitamin K antagonists (VKA) control among very elderly patients in geriatric settings. A national cross-sectional survey was conducted among patients aged ≥80 years who were hospitalized in rehabilitation care or institutionalized in a nursing home and who were treated by VKA. Time in therapeutic range (TTR) was computed according to Rosendaal's method. A total of 2,633 patients were included. Mean [± standard deviation (SD)] age was 87.2 ± 4.4 years and 72.9 % were women. The main indication for VKA therapy was atrial fibrillation (AF; 71.4 %). Mean (±SD) TTR was 57.9 ± 40.4 %. After backward logistic regression, poorer VKA control (TTR 12 months) = 1.70; 95 % CI 1.08-2.67), the type of VKA (OR(fluindione vs. warfarin) = 1.22; 95 % CI 1.00-1.49), a history of international normalized ratio >4.5 (OR = 1.50; 95 % CI 1.21-1.84), a history of major bleeding (OR = 1.88; 95 % CI 1.00-3.53), antibiotic use (OR = 1.83; 95 % CI 1.24-2.70), and falls (OR(≥2 falls during the past year vs. <2) = 1.26; 95 % CI 1.01-1.56). Overall, VKA control remains insufficient in very old patients. Poorer VKA control was associated with taking VKA for a prosthetic heart valve, a recent VKA prescription, the use of other VKAs than warfarin, a history of overcoagulation and major bleeding, antibiotic use, and falls.

Contemporary Patterns of Multiple Organ Dysfunction in Trauma.

Science.gov (United States)

Shepherd, Joanna M; Cole, Elaine; Brohi, Karim

2017-04-01

Multiple organ dysfunction syndrome (MODS) is associated with poor outcomes for trauma patients. Different forms of MODS may exist and have different consequences. The ability to distinguish them clinically may have implications for prognosis and treatment. We wished to study whether prolonged MODS (PRMODS) could be observed as a distinct clinical entity to early resolving MODS (ERMODS) in critically injured patients. Adult major trauma patients recruited to a prospective observational study at a single major trauma center were eligible for inclusion. MODS was defined as Sequential Organ Failure Assessment (SOFA) score >5; and PRMODS as lasting >7 days. Time to recovery (TTR) was calculated as the number of days before the SOFA fell below the MODS threshold (≤5). Five hundred ninety-five patients were enrolled of whom 285 developed ERMODS (48%) and 184 (31%) PRMODS. Organ dysfunction was more severe and protracted in PRMODS, especially in patients without brain injury (mean SOFA 11 vs. 6, Day 2, P < 0.001; TTR 17 vs. 3 days, P < 0.001). PRMODS exhibited higher rates of hepatic and renal dysfunction (84% vs. 56%; and 78% vs. 47%, P≤0.001). Patterns of recovery were distinct in hepatic, renal, and neurological systems (TTR 15 vs. 4; 20 vs. 3; and 28 vs. 7 days, P < 0.01). PRMODS was associated with higher infection and mortality rates (91% vs. 41%; and 22% vs. 7%, P < 0.001). PRMODS appears common, a distinct clinical entity, and associated with worse patient outcomes. PRMODS may represent an important endpoint for studies evaluating outcomes following trauma.

Detection of protein-protein interactions by ribosome display and protein in situ immobilisation.

Science.gov (United States)

He, Mingyue; Liu, Hong; Turner, Martin; Taussig, Michael J

2009-12-31

We describe a method for identification of protein-protein interactions by combining two cell-free protein technologies, namely ribosome display and protein in situ immobilisation. The method requires only PCR fragments as the starting material, the target proteins being made through cell-free protein synthesis, either associated with their encoding mRNA as ribosome complexes or immobilised on a solid surface. The use of ribosome complexes allows identification of interacting protein partners from their attached coding mRNA. To demonstrate the procedures, we have employed the lymphocyte signalling proteins Vav1 and Grb2 and confirmed the interaction between Grb2 and the N-terminal SH3 domain of Vav1. The method has promise for library screening of pairwise protein interactions, down to the analytical level of individual domain or motif mapping.

Coevolution study of mitochondria respiratory chain proteins: toward the understanding of protein--protein interaction.

Science.gov (United States)

Yang, Ming; Ge, Yan; Wu, Jiayan; Xiao, Jingfa; Yu, Jun

2011-05-20

Coevolution can be seen as the interdependency between evolutionary histories. In the context of protein evolution, functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity. As to complex system, there are two forms of protein--protein interactions in vivo, which refer to inter-complex interaction and intra-complex interaction. In this paper, we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using "Mirror tree" method on the respiratory chain (RC) proteins. We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein--protein interaction in intra-complex and the binary protein--protein interaction in inter-complex, respectively. A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions (Wilcoxon test, p-value = 4.4 × 10(-6)). Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein--protein interaction. Furthermore, the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane. More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study. Copyright © 2011. Published by Elsevier Ltd.

A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction

Directory of Open Access Journals (Sweden)

Meijing Li

2015-01-01

Full Text Available Many researchers focus on developing protein-named entity recognition (Protein-NER or PPI extraction systems. However, the studies about these two topics cannot be merged well; then existing PPI extraction systems’ Protein-NER still needs to improve. In this paper, we developed the protein-protein interaction extraction system named PPIMiner based on Support Vector Machine (SVM and parsing tree. PPIMiner consists of three main models: natural language processing (NLP model, Protein-NER model, and PPI discovery model. The Protein-NER model, which is named ProNER, identifies the protein names based on two methods: dictionary-based method and machine learning-based method. ProNER is capable of identifying more proteins than dictionary-based Protein-NER model in other existing systems. The final discovered PPIs extracted via PPI discovery model are represented in detail because we showed the protein interaction types and the occurrence frequency through two different methods. In the experiments, the result shows that the performances achieved by our ProNER and PPI discovery model are better than other existing tools. PPIMiner applied this protein-named entity recognition approach and parsing tree based PPI extraction method to improve the performance of PPI extraction. We also provide an easy-to-use interface to access PPIs database and an online system for PPIs extraction and Protein-NER.

Protein complex prediction in large ontology attributed protein-protein interaction networks.

Science.gov (United States)

Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian; Li, Yanpeng; Xu, Bo

2013-01-01

Protein complexes are important for unraveling the secrets of cellular organization and function. Many computational approaches have been developed to predict protein complexes in protein-protein interaction (PPI) networks. However, most existing approaches focus mainly on the topological structure of PPI networks, and largely ignore the gene ontology (GO) annotation information. In this paper, we constructed ontology attributed PPI networks with PPI data and GO resource. After constructing ontology attributed networks, we proposed a novel approach called CSO (clustering based on network structure and ontology attribute similarity). Structural information and GO attribute information are complementary in ontology attributed networks. CSO can effectively take advantage of the correlation between frequent GO annotation sets and the dense subgraph for protein complex prediction. Our proposed CSO approach was applied to four different yeast PPI data sets and predicted many well-known protein complexes. The experimental results showed that CSO was valuable in predicting protein complexes and achieved state-of-the-art performance.

Protein surface shielding agents in protein crystallization

International Nuclear Information System (INIS)

Hašek, J.

2011-01-01

The crystallization process can be controlled by protein surface shielding agents blocking undesirable competitive adhesion modes during non-equilibrium processes of deposition of protein molecules on the surface of growing crystalline blocks. The hypothesis is based on a number of experimental proofs from diffraction experiments and also retrieved from the Protein Data Bank. The molecules adhering temporarily on the surface of protein molecules change the propensity of protein molecules to deposit on the crystal surface in a definite position and orientation. The concepts of competitive adhesion modes and protein surface shielding agents acting on the surface of molecules in a non-equilibrium process of protein crystallization provide a useful platform for the control of crystallization. The desirable goal, i.e. a transient preference of a single dominating adhesion mode between protein molecules during crystallization, leads to uniform deposition of proteins in a crystal. This condition is the most important factor for diffraction quality and thus also for the accuracy of protein structure determination. The presented hypothesis is a generalization of the experimentally well proven behaviour of hydrophilic polymers on the surface of protein molecules of other compounds

The Development of Protein Microarrays and Their Applications in DNA-Protein and Protein-Protein Interaction Analyses of Arabidopsis Transcription Factors

Science.gov (United States)

Gong, Wei; He, Kun; Covington, Mike; Dinesh-Kumar, S. P.; Snyder, Michael; Harmer, Stacey L.; Zhu, Yu-Xian; Deng, Xing Wang

2009-01-01

We used our collection of Arabidopsis transcription factor (TF) ORFeome clones to construct protein microarrays containing as many as 802 TF proteins. These protein microarrays were used for both protein-DNA and protein-protein interaction analyses. For protein-DNA interaction studies, we examined AP2/ERF family TFs and their cognate cis-elements. By careful comparison of the DNA-binding specificity of 13 TFs on the protein microarray with previous non-microarray data, we showed that protein microarrays provide an efficient and high throughput tool for genome-wide analysis of TF-DNA interactions. This microarray protein-DNA interaction analysis allowed us to derive a comprehensive view of DNA-binding profiles of AP2/ERF family proteins in Arabidopsis. It also revealed four TFs that bound the EE (evening element) and had the expected phased gene expression under clock-regulation, thus providing a basis for further functional analysis of their roles in clock regulation of gene expression. We also developed procedures for detecting protein interactions using this TF protein microarray and discovered four novel partners that interact with HY5, which can be validated by yeast two-hybrid assays. Thus, plant TF protein microarrays offer an attractive high-throughput alternative to traditional techniques for TF functional characterization on a global scale. PMID:19802365

Led induced chlorophyll fluorescence transient imager for measurements of health and stress status of whole plants

NARCIS (Netherlands)

Jalink, H.; Schoor, van der R.

2011-01-01

We have developed LED (light emitting diode) induced fluorescence transient imaging instrumentation to image the plant health/stress status by calculation of two images: Fv/Fm (variable fluorescence over saturation level of fluorescence) and the time response, tTR, of the fluorescence time curve.

Protein sequence comparison and protein evolution

Energy Technology Data Exchange (ETDEWEB)

Pearson, W.R. [Univ. of Virginia, Charlottesville, VA (United States). Dept. of Biochemistry

1995-12-31

This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. This tutorial examines how the information conserved during the evolution of a protein molecule can be used to infer reliably homology, and thus a shared proteinfold and possibly a shared active site or function. The authors start by reviewing a geological/evolutionary time scale. Next they look at the evolution of several protein families. During the tutorial, these families will be used to demonstrate that homologous protein ancestry can be inferred with confidence. They also examine different modes of protein evolution and consider some hypotheses that have been presented to explain the very earliest events in protein evolution. The next part of the tutorial will examine the technical aspects of protein sequence comparison. Both optimal and heuristic algorithms and their associated parameters that are used to characterize protein sequence similarities are discussed. Perhaps more importantly, they survey the statistics of local similarity scores, and how these statistics can both be used to improve the selectivity of a search and to evaluate the significance of a match. They them examine distantly related members of three protein families, the serine proteases, the glutathione transferases, and the G-protein-coupled receptors (GCRs). Finally, the discuss how sequence similarity can be used to examine internal repeated or mosaic structures in proteins.

On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking

DEFF Research Database (Denmark)

Feliu, Elisenda; Aloy, Patrick; Oliva, Baldo

2011-01-01

Development of effective methods to screen binary interactions obtained by rigid-body protein-protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein-protein binding. We have derived empirical knowledge-based potential functions for s...... and with independence of the partner. This information is encoded at the residue level and could be easily incorporated in the initial grid scoring for Fast Fourier Transform rigid-body docking methods.......Development of effective methods to screen binary interactions obtained by rigid-body protein-protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein-protein binding. We have derived empirical knowledge-based potential functions...... for selecting rigid-body docking poses. These potentials include the energetic component that provides the residues with a particular secondary structure and surface accessibility. These scoring functions have been tested on a state-of-art benchmark dataset and on a decoy dataset of permanent interactions. Our...

Proteins interacting with cloning scars: a source of false positive protein-protein interactions.

Science.gov (United States)

Banks, Charles A S; Boanca, Gina; Lee, Zachary T; Florens, Laurence; Washburn, Michael P

2015-02-23

A common approach for exploring the interactome, the network of protein-protein interactions in cells, uses a commercially available ORF library to express affinity tagged bait proteins; these can be expressed in cells and endogenous cellular proteins that copurify with the bait can be identified as putative interacting proteins using mass spectrometry. Control experiments can be used to limit false-positive results, but in many cases, there are still a surprising number of prey proteins that appear to copurify specifically with the bait. Here, we have identified one source of false-positive interactions in such studies. We have found that a combination of: 1) the variable sequence of the C-terminus of the bait with 2) a C-terminal valine "cloning scar" present in a commercially available ORF library, can in some cases create a peptide motif that results in the aberrant co-purification of endogenous cellular proteins. Control experiments may not identify false positives resulting from such artificial motifs, as aberrant binding depends on sequences that vary from one bait to another. It is possible that such cryptic protein binding might occur in other systems using affinity tagged proteins; this study highlights the importance of conducting careful follow-up studies where novel protein-protein interactions are suspected.

The effect of protein-protein and protein-membrane interactions on membrane fouling in ultrafiltration

NARCIS (Netherlands)

Huisman, I.H.; Prádanos, P.; Hernández, A.

2000-01-01

It was studied how protein-protein and protein-membrane interactions influence the filtration performance during the ultrafiltration of protein solutions over polymeric membranes. This was done by measuring flux, streaming potential, and protein transmission during filtration of bovine serum albumin

Fluorogen-activating proteins: beyond classical fluorescent proteins

Directory of Open Access Journals (Sweden)

Shengnan Xu

2018-05-01

Full Text Available Fluorescence imaging is a powerful technique for the real-time noninvasive monitoring of protein dynamics. Recently, fluorogen activating proteins (FAPs/fluorogen probes for protein imaging were developed. Unlike the traditional fluorescent proteins (FPs, FAPs do not fluoresce unless bound to their specific small-molecule fluorogens. When using FAPs/fluorogen probes, a washing step is not required for the removal of free probes from the cells, thus allowing rapid and specific detection of proteins in living cells with high signal-to-noise ratio. Furthermore, with different fluorogens, living cell multi-color proteins labeling system was developed. In this review, we describe about the discovery of FAPs, the design strategy of FAP fluorogens, the application of the FAP technology and the advances of FAP technology in protein labeling systems. KEY WORDS: Fluorogen activating proteins, Fluorogens, Genetically encoded sensors, Fluorescence imaging, Molecular imaging

Inhibition of apoptic cell death induced by Pseudomonas syringae pv. Tabaci and mycotoxin fumonisin B1

NARCIS (Netherlands)

Iakimova, E.T.; Batchvorova, R.; Kapchina, V.; Popov, T.; Atanassov, A.; Woltering, E.J.

2004-01-01

The impact of programmed cell death (PCD) inhibitors on lesion formation and biochemical events in transgenic (ttr line) and non-transgenic (Nevrokop 1164) tobacco infected with Pseudomonas syringae pv. tabaci was tested. Programmed cell death in tomato cell culture was induced by Fumonisin B1 (FUM)

Protein immobilization strategies for protein biochips

NARCIS (Netherlands)

Rusmini, F.; Rusmini, Federica; Zhong, Zhiyuan; Feijen, Jan

2007-01-01

In the past few years, protein biochips have emerged as promising proteomic and diagnostic tools for obtaining information about protein functions and interactions. Important technological innovations have been made. However, considerable development is still required, especially regarding protein

Corrective action investigation plan for Corrective Action Unit Number 423: Building 03-60 Underground Discharge Point, Tonopah Test Range, Nevada

International Nuclear Information System (INIS)

1997-01-01

This Corrective Action Investigation Plan (CAIP) contains the environmental sample collection objectives and the criteria for conducting site investigation activities at Corrective Action Unit (CAU) Number 423, the Building 03-60 Underground Discharge Point (UDP), which is located in Area 3 at the Tonopah Test Range (TTR). The TTR, part of the Nellis Air Force Range, is approximately 225 kilometers (140 miles) northwest of Las Vegas, Nevada. CAU Number 423 is comprised of only one Corrective Action Site (CAS) which includes the Building 03-60 UDP and an associated discharge line extending from Building 03-60 to a point approximately 73 meters (240 feet) northwest. The UDP was used between approximately 1965 and 1990 to dispose of waste fluids from the Building 03-60 automotive maintenance shop. It is likely that soils surrounding the UDP have been impacted by oil, grease, cleaning supplies and solvents as well as waste motor oil and other automotive fluids released from the UDP

Biosensor-based microRNA detection: techniques, design, performance, and challenges.

Science.gov (United States)

Johnson, Blake N; Mutharasan, Raj

2014-04-07

The current state of biosensor-based techniques for amplification-free microRNA (miRNA) detection is critically reviewed. Comparison with non-sensor and amplification-based molecular techniques (MTs), such as polymerase-based methods, is made in terms of transduction mechanism, associated protocol, and sensitivity. Challenges associated with miRNA hybridization thermodynamics which affect assay selectivity and amplification bias are briefly discussed. Electrochemical, electromechanical, and optical classes of miRNA biosensors are reviewed in terms of transduction mechanism, limit of detection (LOD), time-to-results (TTR), multiplexing potential, and measurement robustness. Current trends suggest that biosensor-based techniques (BTs) for miRNA assay will complement MTs due to the advantages of amplification-free detection, LOD being femtomolar (fM)-attomolar (aM), short TTR, multiplexing capability, and minimal sample preparation requirement. Areas of future importance in miRNA BT development are presented which include focus on achieving high measurement confidence and multiplexing capabilities.

Corrective action investigation plan for Corrective Action Unit Number 423: Building 03-60 Underground Discharge Point, Tonopah Test Range, Nevada

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-10-27

This Corrective Action Investigation Plan (CAIP) contains the environmental sample collection objectives and the criteria for conducting site investigation activities at Corrective Action Unit (CAU) Number 423, the Building 03-60 Underground Discharge Point (UDP), which is located in Area 3 at the Tonopah Test Range (TTR). The TTR, part of the Nellis Air Force Range, is approximately 225 kilometers (140 miles) northwest of Las Vegas, Nevada. CAU Number 423 is comprised of only one Corrective Action Site (CAS) which includes the Building 03-60 UDP and an associated discharge line extending from Building 03-60 to a point approximately 73 meters (240 feet) northwest. The UDP was used between approximately 1965 and 1990 to dispose of waste fluids from the Building 03-60 automotive maintenance shop. It is likely that soils surrounding the UDP have been impacted by oil, grease, cleaning supplies and solvents as well as waste motor oil and other automotive fluids released from the UDP.

Corrective action investigation plan for CAU No. 424: Area 3 Landfill Complex, Tonopah Test Range, Nevada

International Nuclear Information System (INIS)

1997-04-01

This Correction Action Investigation Plan contains the environmental sample collection objectives and the criteria for conducting site investigation activities at the Area 3 Landfill Complex, CAU No. 424, which is located at the Tonopah Test Range (TTR). The TTR, included in the Nellis Air Force Range, is approximately 255 kilometers (140 miles) northwest of Las Vegas, nevada. The CAU 424 is comprised of eight individual landfill sites that are located around and within the perimeter of the Area 3 Compound. Due to the unregulated disposal activities commonly associated with early landfill operations, an investigation will be conducted at each CAS to complete the following tasks: identify the presence and nature of possible contaminant migration from the landfills; determine the vertical and lateral extent of possible contaminant migration; ascertain the potential impact to human health and the environment; and provide sufficient information and data to develop and evaluate appropriate corrective action strategies for each CAS

Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

International Nuclear Information System (INIS)

Yu, P.

2007-01-01

The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

Early Ankle Mobilization Promotes Healing in a Rabbit Model of Achilles Tendon Rupture.

Science.gov (United States)

Jielile, Jiasharete; Asilehan, Batiza; Wupuer, Aikeremu; Qianman, Bayixiati; Jialihasi, Ayidaer; Tangkejie, Wulanbai; Maimaitiaili, Abudouheilil; Shawutali, Nuerai; Badelhan, Aynaz; Niyazebieke, Hadelebieke; Aizezi, Adili; Aisaiding, Amuding; Bakyt, Yerzat; Aibek, Rakimbaiev; Wuerliebieke, Jianati

2016-01-01

The use of early mobilization of the ankle joint without orthosis in the treatment of Achilles tendon rupture has been advocated as the optimal management. The goal of this study was to compare outcomes in a postoperative rabbit model of Achilles tendon rupture between early mobilization and immobilized animals using a differential proteomics approach. In total, 135 rabbits were randomized into the control group (n=15), the postoperative cast immobilization (PCI) group (n=60), and the early mobilization (EM) group (n=60). A rupture of the Achilles tendon was created in each animal model and repaired microsurgically, and tendon samples were removed at 3, 7, 14, and 21 days postoperatively. Proteins were separated using 2-dimensional polyacrylamide gel electrophoresis and identified using peptide mass fingerprinting, tandem mass spectrometry, NCBI database searches, and bioinformatics analyses. A series of differentially expressed proteins were identified between groups, some of which may play an important role in Achilles tendon healing. Notable candidate proteins that were upregulated in the EM group were identified, such as CRMP-2, galactokinase 1, tropomyosin-4, and transthyretin. The healing of ruptured Achilles tendons appears to be affected at the level of protein expression with the use of early mobilization. The classic postoperative treatment of Achilles tendon rupture with an orthosis ignored the self-protecting instinct of humans. With a novel operative technique, the repaired tendon can persist the load that comes from traction in knee and ankle joint functional movement. In addition, kinesitherapy provided an excellent experimental outcome via a mechanobiological mechanism. Copyright 2016, SLACK Incorporated.

Proteomic analysis in type 2 diabetes patients before and after a very low calorie diet reveals potential disease state and intervention specific biomarkers.

Directory of Open Access Journals (Sweden)

Maria A Sleddering

Full Text Available Very low calorie diets (VLCD with and without exercise programs lead to major metabolic improvements in obese type 2 diabetes patients. The mechanisms underlying these improvements have so far not been elucidated fully. To further investigate the mechanisms of a VLCD with or without exercise and to uncover possible biomarkers associated with these interventions, blood samples were collected from 27 obese type 2 diabetes patients before and after a 16-week VLCD (Modifast ∼ 450 kcal/day. Thirteen of these patients followed an exercise program in addition to the VCLD. Plasma was obtained from 27 lean and 27 obese controls as well. Proteomic analysis was performed using mass spectrometry (MS and targeted multiple reaction monitoring (MRM and a large scale isobaric tags for relative and absolute quantitation (iTRAQ approach. After the 16-week VLCD, there was a significant decrease in body weight and HbA1c in all patients, without differences between the two intervention groups. Targeted MRM analysis revealed differences in several proteins, which could be divided in diabetes-associated (fibrinogen, transthyretin, obesity-associated (complement C3, and diet-associated markers (apolipoproteins, especially apolipoprotein A-IV. To further investigate the effects of exercise, large scale iTRAQ analysis was performed. However, no proteins were found showing an exercise effect. Thus, in this study, specific proteins were found to be differentially expressed in type 2 diabetes patients versus controls and before and after a VLCD. These proteins are potential disease state and intervention specific biomarkers.Controlled-Trials.com ISRCTN76920690.

Urinary proteomic profiling reveals diclofenac-induced renal injury and hepatic regeneration in mice

Energy Technology Data Exchange (ETDEWEB)

Swelm, Rachel P.L. van [Department of Pharmacology and Toxicology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen (Netherlands); Laarakkers, Coby M.M. [Department of Laboratory Medicine, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen (Netherlands); Pertijs, Jeanne C.L.M.; Verweij, Vivienne; Masereeuw, Rosalinde [Department of Pharmacology and Toxicology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen (Netherlands); Russel, Frans G.M., E-mail: F.Russel@pharmtox.umcn.nl [Department of Pharmacology and Toxicology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen (Netherlands)

2013-06-01

Diclofenac (DF) is a widely used non-steroidal anti-inflammatory drug for the treatment of rheumatic disorders, but is often associated with liver injury. We applied urinary proteomic profiling using MALDI-TOF MS to identify biomarkers for DF-induced hepatotoxicity in mice. Female CH3/HeOUJIco mice were treated with 75 mg/kg bw DF by oral gavage and 24 h urine was collected. Proteins identified in urine of DF-treated mice included epidermal growth factor, transthyretin, kallikrein, clusterin, fatty acid binding protein 1 and urokinase, which are related to liver regeneration but also to kidney injury. Both organs showed enhanced levels of oxidative stress (TBARS, p < 0.01). Kidney injury was confirmed by histology and increased Kim1 and Il-6 mRNA expression levels (p < 0.001 and p < 0.01). Liver histology and plasma ALT levels in DF-treated mice were not different from control, but mRNA expression of Stat3 (p < 0.001) and protein expression of PCNA (p < 0.05) were increased, indicating liver regeneration. In conclusion, urinary proteome analysis revealed that DF treatment in mice induced kidney and liver injury. Within 24 h, however, the liver was able to recover by activating tissue regeneration processes. Hence, the proteins found in urine of DF-treated mice represent kidney damage rather than hepatic injury. - Highlights: • The urinary proteome shows biological processes involved in adverse drug reactions. • Urine proteins of DF-treated mice relate to kidney injury rather than liver injury. • Liver regeneration, not liver injury, is apparent 24h after oral DF administration. • Pretreatment with LPS does not enhance DF-induced liver injury in mice.

Information assessment on predicting protein-protein interactions

Directory of Open Access Journals (Sweden)

Gerstein Mark

2004-10-01

Full Text Available Abstract Background Identifying protein-protein interactions is fundamental for understanding the molecular machinery of the cell. Proteome-wide studies of protein-protein interactions are of significant value, but the high-throughput experimental technologies suffer from high rates of both false positive and false negative predictions. In addition to high-throughput experimental data, many diverse types of genomic data can help predict protein-protein interactions, such as mRNA expression, localization, essentiality, and functional annotation. Evaluations of the information contributions from different evidences help to establish more parsimonious models with comparable or better prediction accuracy, and to obtain biological insights of the relationships between protein-protein interactions and other genomic information. Results Our assessment is based on the genomic features used in a Bayesian network approach to predict protein-protein interactions genome-wide in yeast. In the special case, when one does not have any missing information about any of the features, our analysis shows that there is a larger information contribution from the functional-classification than from expression correlations or essentiality. We also show that in this case alternative models, such as logistic regression and random forest, may be more effective than Bayesian networks for predicting interactions. Conclusions In the restricted problem posed by the complete-information subset, we identified that the MIPS and Gene Ontology (GO functional similarity datasets as the dominating information contributors for predicting the protein-protein interactions under the framework proposed by Jansen et al. Random forests based on the MIPS and GO information alone can give highly accurate classifications. In this particular subset of complete information, adding other genomic data does little for improving predictions. We also found that the data discretizations used in the

Mapping Protein-Protein Interactions by Quantitative Proteomics

DEFF Research Database (Denmark)

Dengjel, Joern; Kratchmarova, Irina; Blagoev, Blagoy

2010-01-01

spectrometry (MS)-based proteomics in combination with affinity purification protocols has become the method of choice to map and track the dynamic changes in protein-protein interactions, including the ones occurring during cellular signaling events. Different quantitative MS strategies have been used...... to characterize protein interaction networks. In this chapter we describe in detail the use of stable isotope labeling by amino acids in cell culture (SILAC) for the quantitative analysis of stimulus-dependent dynamic protein interactions.......Proteins exert their function inside a cell generally in multiprotein complexes. These complexes are highly dynamic structures changing their composition over time and cell state. The same protein may thereby fulfill different functions depending on its binding partners. Quantitative mass...

ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval.

Science.gov (United States)

Wang, Jingyan; Gao, Xin; Wang, Quanquan; Li, Yongping

2012-05-08

The need to retrieve or classify protein molecules using structure or sequence-based similarity measures underlies a wide range of biomedical applications. Traditional protein search methods rely on a pairwise dissimilarity/similarity measure for comparing a pair of proteins. This kind of pairwise measures suffer from the limitation of neglecting the distribution of other proteins and thus cannot satisfy the need for high accuracy of the retrieval systems. Recent work in the machine learning community has shown that exploiting the global structure of the database and learning the contextual dissimilarity/similarity measures can improve the retrieval performance significantly. However, most existing contextual dissimilarity/similarity learning algorithms work in an unsupervised manner, which does not utilize the information of the known class labels of proteins in the database. In this paper, we propose a novel protein-protein dissimilarity learning algorithm, ProDis-ContSHC. ProDis-ContSHC regularizes an existing dissimilarity measure dij by considering the contextual information of the proteins. The context of a protein is defined by its neighboring proteins. The basic idea is, for a pair of proteins (i, j), if their context N(i) and N(j) is similar to each other, the two proteins should also have a high similarity. We implement this idea by regularizing dij by a factor learned from the context N(i) and N(j).Moreover, we divide the context to hierarchial sub-context and get the contextual dissimilarity vector for each protein pair. Using the class label information of the proteins, we select the relevant (a pair of proteins that has the same class labels) and irrelevant (with different labels) protein pairs, and train an SVM model to distinguish between their contextual dissimilarity vectors. The SVM model is further used to learn a supervised regularizing factor. Finally, with the new Supervised learned Dissimilarity measure, we update the Protein Hierarchial

Preliminary evaluation of Am/Cm melter feed preparation process upset recovery flowsheets

International Nuclear Information System (INIS)

Stone, M.E.

2000-01-01

This document summarizes the results from the development of flowsheets to recover from credible processing errors specified in TTR 99-MNSS/SE-006. The proposed flowsheets were developed in laboratory scale equipment and will be utilized with minor modifications for full scale demonstrations in the Am/Cm Pilot Facility

Biophysics of protein evolution and evolutionary protein biophysics

Science.gov (United States)

Sikosek, Tobias; Chan, Hue Sun

2014-01-01

The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence–structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by ‘hidden’ conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution. PMID:25165599

High quality protein microarray using in situ protein purification

Directory of Open Access Journals (Sweden)

Fleischmann Robert D

2009-08-01

Full Text Available Abstract Background In the postgenomic era, high throughput protein expression and protein microarray technologies have progressed markedly permitting screening of therapeutic reagents and discovery of novel protein functions. Hexa-histidine is one of the most commonly used fusion tags for protein expression due to its small size and convenient purification via immobilized metal ion affinity chromatography (IMAC. This purification process has been adapted to the protein microarray format, but the quality of in situ His-tagged protein purification on slides has not been systematically evaluated. We established methods to determine the level of purification of such proteins on metal chelate-modified slide surfaces. Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays. Results Two slide surfaces were examined, chelated Cu2+ slides suspended on a polyethylene glycol (PEG coating and chelated Ni2+ slides immobilized on a support without PEG coating. Using PEG-coated chelated Cu2+ slides, consistently higher purities of recombinant proteins were measured. An optimized wash buffer (PBST composed of 10 mM phosphate buffer, 2.7 mM KCl, 140 mM NaCl and 0.05% Tween 20, pH 7.4, further improved protein purity levels. Using Escherichia coli cell lysates expressing 90 recombinant Streptococcus pneumoniae proteins, 73 proteins were successfully immobilized, and 66 proteins were in situ purified with greater than 90% purity. We identified several antigens among the in situ-purified proteins via assays with anti-S. pneumoniae rabbit antibodies and a human patient antiserum, as a demonstration project of large scale microarray-based immunoproteomics profiling. The methodology is compatible with higher throughput formats of in vivo protein expression, eliminates the need for resin-based purification and circumvents

Cost effectiveness of novel oral anticoagulants for stroke prevention in atrial fibrillation depending on the quality of warfarin anticoagulation control.

Science.gov (United States)

Janzic, Andrej; Kos, Mitja

2015-04-01

Vitamin K antagonists, such as warfarin, are standard treatments for stroke prophylaxis in patients with atrial fibrillation. Patient outcomes depend on quality of warfarin management, which includes regular monitoring and dose adjustments. Recently, novel oral anticoagulants (NOACs) that do not require regular monitoring offer an alternative to warfarin. The aim of this study was to evaluate whether cost effectiveness of NOACs for stroke prevention in atrial fibrillation depends on the quality of warfarin control. We developed a Markov decision model to simulate warfarin treatment outcomes in relation to the quality of anticoagulation control, expressed as percentage of time in the therapeutic range (TTR). Standard treatment with adjusted-dose warfarin and improved anticoagulation control by genotype-guided dosing were compared with dabigatran, rivaroxaban, apixaban and edoxaban. The analysis was performed from the Slovenian healthcare payer perspective using 2014 costs. In the base case, the incremental cost-effectiveness ratio for apixaban, dabigatran and edoxaban was below the threshold of €25,000 per quality-adjusted life-years compared with adjusted-dose warfarin with a TTR of 60%. The probability that warfarin was a cost-effective option was around 1%. This percentage rises as the quality of anticoagulation control improves. At a TTR of 70%, warfarin was the preferred treatment in half the iterations. The cost effectiveness of NOACs for stroke prevention in patients with nonvalvular atrial fibrillation who are at increased risk for stroke is highly sensitive to warfarin anticoagulation control. NOACs are more likely to be cost-effective options in settings with poor warfarin management than in settings with better anticoagulation control, where they may not represent good value for money.

Can infrared spectroscopy provide information on protein-protein interactions?

Science.gov (United States)

Haris, Parvez I

2010-08-01

For most biophysical techniques, characterization of protein-protein interactions is challenging; this is especially true with methods that rely on a physical phenomenon that is common to both of the interacting proteins. Thus, for example, in IR spectroscopy, the carbonyl vibration (1600-1700 cm(-1)) associated with the amide bonds from both of the interacting proteins will overlap extensively, making the interpretation of spectral changes very complicated. Isotope-edited infrared spectroscopy, where one of the interacting proteins is uniformly labelled with (13)C or (13)C,(15)N has been introduced as a solution to this problem, enabling the study of protein-protein interactions using IR spectroscopy. The large shift of the amide I band (approx. 45 cm(-1) towards lower frequency) upon (13)C labelling of one of the proteins reveals the amide I band of the unlabelled protein, enabling it to be used as a probe for monitoring conformational changes. With site-specific isotopic labelling, structural resolution at the level of individual amino acid residues can be achieved. Furthermore, the ability to record IR spectra of proteins in diverse environments means that isotope-edited IR spectroscopy can be used to structurally characterize difficult systems such as protein-protein complexes bound to membranes or large insoluble peptide/protein aggregates. In the present article, examples of application of isotope-edited IR spectroscopy for studying protein-protein interactions are provided.

Protein and protein hydrolysates in sports nutrition.

Science.gov (United States)

van Loon, Luc J C; Kies, Arie K; Saris, Wim H M

2007-08-01

With the increasing knowledge about the role of nutrition in increasing exercise performance, it has become clear over the last 2 decades that amino acids, protein, and protein hydrolysates can play an important role. Most of the attention has been focused on their effects at a muscular level. As these nutrients are ingested, however, it also means that gastrointestinal digestibility and absorption can modulate their efficacy significantly. Therefore, discussing the role of amino acids, protein, and protein hydrolysates in sports nutrition entails holding a discussion on all levels of the metabolic route. On May 28-29, 2007, a small group of researchers active in the field of exercise science and protein metabolism presented an overview of the different aspects of the application of protein and protein hydrolysates in sports nutrition. In addition, they were asked to share their opinions on the future progress in their fields of research. In this overview, an introduction to the workshop and a short summary of its outcome is provided.

ProDis-ContSHC: Learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval

KAUST Repository

Wang, Jim Jing-Yan

2012-05-08

Background: The need to retrieve or classify protein molecules using structure or sequence-based similarity measures underlies a wide range of biomedical applications. Traditional protein search methods rely on a pairwise dissimilarity/similarity measure for comparing a pair of proteins. This kind of pairwise measures suffer from the limitation of neglecting the distribution of other proteins and thus cannot satisfy the need for high accuracy of the retrieval systems. Recent work in the machine learning community has shown that exploiting the global structure of the database and learning the contextual dissimilarity/similarity measures can improve the retrieval performance significantly. However, most existing contextual dissimilarity/similarity learning algorithms work in an unsupervised manner, which does not utilize the information of the known class labels of proteins in the database.Results: In this paper, we propose a novel protein-protein dissimilarity learning algorithm, ProDis-ContSHC. ProDis-ContSHC regularizes an existing dissimilarity measure dij by considering the contextual information of the proteins. The context of a protein is defined by its neighboring proteins. The basic idea is, for a pair of proteins (i, j), if their context N (i) and N (j) is similar to each other, the two proteins should also have a high similarity. We implement this idea by regularizing dij by a factor learned from the context N (i) and N (j). Moreover, we divide the context to hierarchial sub-context and get the contextual dissimilarity vector for each protein pair. Using the class label information of the proteins, we select the relevant (a pair of proteins that has the same class labels) and irrelevant (with different labels) protein pairs, and train an SVM model to distinguish between their contextual dissimilarity vectors. The SVM model is further used to learn a supervised regularizing factor. Finally, with the new Supervised learned Dissimilarity measure, we update

Targeting protein-protein interaction between MLL1 and reciprocal proteins for leukemia therapy.

Science.gov (United States)

Wang, Zhi-Hui; Li, Dong-Dong; Chen, Wei-Lin; You, Qi-Dong; Guo, Xiao-Ke

2018-01-15

The mixed lineage leukemia protein-1 (MLL1), as a lysine methyltransferase, predominantly regulates the methylation of histone H3 lysine 4 (H3K4) and functions in hematopoietic stem cell (HSC) self-renewal. MLL1 gene fuses with partner genes that results in the generation of MLL1 fusion proteins (MLL1-FPs), which are frequently detected in acute leukemia. In the progress of leukemogenesis, a great deal of proteins cooperate with MLL1 to form multiprotein complexes serving for the dysregulation of H3K4 methylation, the overexpression of homeobox (HOX) cluster genes, and the consequent generation of leukemia. Hence, disrupting the interactions between MLL1 and the reciprocal proteins has been considered to be a new treatment strategy for leukemia. Here, we reviewed potential protein-protein interactions (PPIs) between MLL1 and its reciprocal proteins, and summarized the inhibitors to target MLL1 PPIs. The druggability of MLL1 PPIs for leukemia were also discussed. Copyright © 2017. Published by Elsevier Ltd.

Protein kinase substrate identification on functional protein arrays

Directory of Open Access Journals (Sweden)

Zhou Fang

2008-02-01

Full Text Available Abstract Background Over the last decade, kinases have emerged as attractive therapeutic targets for a number of different diseases, and numerous high throughput screening efforts in the pharmaceutical community are directed towards discovery of compounds that regulate kinase function. The emerging utility of systems biology approaches has necessitated the development of multiplex tools suitable for proteomic-scale experiments to replace lower throughput technologies such as mass spectroscopy for the study of protein phosphorylation. Recently, a new approach for identifying substrates of protein kinases has applied the miniaturized format of functional protein arrays to characterize phosphorylation for thousands of candidate protein substrates in a single experiment. This method involves the addition of protein kinases in solution to arrays of immobilized proteins to identify substrates using highly sensitive radioactive detection and hit identification algorithms. Results To date, the factors required for optimal performance of protein array-based kinase substrate identification have not been described. In the current study, we have carried out a detailed characterization of the protein array-based method for kinase substrate identification, including an examination of the effects of time, buffer compositions, and protein concentration on the results. The protein array approach was compared to standard solution-based assays for assessing substrate phosphorylation, and a correlation of greater than 80% was observed. The results presented here demonstrate how novel substrates for protein kinases can be quickly identified from arrays containing thousands of human proteins to provide new clues to protein kinase function. In addition, a pooling-deconvolution strategy was developed and applied that enhances characterization of specific kinase-substrate relationships and decreases reagent consumption. Conclusion Functional protein microarrays are an

Protein kinesis: The dynamics of protein trafficking and stability

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-12-31

The purpose of this conference is to provide a multidisciplinary forum for exchange of state-of-the-art information on protein kinesis. This volume contains abstracts of papers in the following areas: protein folding and modification in the endoplasmic reticulum; protein trafficking; protein translocation and folding; protein degradation; polarity; nuclear trafficking; membrane dynamics; and protein import into organelles.

HKC: An Algorithm to Predict Protein Complexes in Protein-Protein Interaction Networks

Directory of Open Access Journals (Sweden)

Xiaomin Wang

2011-01-01

Full Text Available With the availability of more and more genome-scale protein-protein interaction (PPI networks, research interests gradually shift to Systematic Analysis on these large data sets. A key topic is to predict protein complexes in PPI networks by identifying clusters that are densely connected within themselves but sparsely connected with the rest of the network. In this paper, we present a new topology-based algorithm, HKC, to detect protein complexes in genome-scale PPI networks. HKC mainly uses the concepts of highest k-core and cohesion to predict protein complexes by identifying overlapping clusters. The experiments on two data sets and two benchmarks show that our algorithm has relatively high F-measure and exhibits better performance compared with some other methods.

75 FR 6635 - Foreign-Trade Zone 33-Pittsburgh, Pennsylvania, Expansion of Manufacturing Authority, Subzone 33E...

Science.gov (United States)

2010-02-10

...-81u), and the regulations of the Board (15 CFR part 400). It was formally filed on February 4, 2010. Subzone 33E (123 employees, 360 million square meters coating capacity) currently has authority for the... the production of monochrome TTR printer rolls (some 336 million square meters capacity), using...

Molecular tweezers modulate 14-3-3 protein-protein interactions

Science.gov (United States)

Bier, David; Rose, Rolf; Bravo-Rodriguez, Kenny; Bartel, Maria; Ramirez-Anguita, Juan Manuel; Dutt, Som; Wilch, Constanze; Klärner, Frank-Gerrit; Sanchez-Garcia, Elsa; Schrader, Thomas; Ottmann, Christian

2013-03-01

Supramolecular chemistry has recently emerged as a promising way to modulate protein functions, but devising molecules that will interact with a protein in the desired manner is difficult as many competing interactions exist in a biological environment (with solvents, salts or different sites for the target biomolecule). We now show that lysine-specific molecular tweezers bind to a 14-3-3 adapter protein and modulate its interaction with partner proteins. The tweezers inhibit binding between the 14-3-3 protein and two partner proteins—a phosphorylated (C-Raf) protein and an unphosphorylated one (ExoS)—in a concentration-dependent manner. Protein crystallography shows that this effect arises from the binding of the tweezers to a single surface-exposed lysine (Lys214) of the 14-3-3 protein in the proximity of its central channel, which normally binds the partner proteins. A combination of structural analysis and computer simulations provides rules for the tweezers' binding preferences, thus allowing us to predict their influence on this type of protein-protein interactions.

Changes in protein composition and protein phosphorylation during ...

African Journals Online (AJOL)

Changes in protein profiles and protein phosphorylation were studied in various stages of germinating somatic and zygotic embryos. Many proteins, which were expressed in cotyledonary stage somatic embryos, were also present in the zygotic embryos obtained from mature dry seed. The intensity of 22 kDa protein was ...

An ontology-based search engine for protein-protein interactions.

Science.gov (United States)

Park, Byungkyu; Han, Kyungsook

2010-01-18

Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database. We have developed a new method for representing protein-protein interactions and the Gene Ontology (GO) using modified Gödel numbers. This representation is hidden from users but enables a search engine using the representation to efficiently search protein-protein interactions in a biologically meaningful way. Given a query protein with optional search conditions expressed in one or more GO terms, the search engine finds all the interaction partners of the query protein by unique prime factorization of the modified Gödel numbers representing the query protein and the search conditions. Representing the biological relations of proteins and their GO annotations by modified Gödel numbers makes a search engine efficiently find all protein-protein interactions by prime factorization of the numbers. Keyword matching or ID matching search methods often miss the interactions involving a protein that has no explicit annotations matching the search condition, but our search engine retrieves such interactions as well if they satisfy the search condition with a more specific term in the ontology.

Water-Protein Interactions: The Secret of Protein Dynamics

Directory of Open Access Journals (Sweden)

Silvia Martini

2013-01-01

Full Text Available Water-protein interactions help to maintain flexible conformation conditions which are required for multifunctional protein recognition processes. The intimate relationship between the protein surface and hydration water can be analyzed by studying experimental water properties measured in protein systems in solution. In particular, proteins in solution modify the structure and the dynamics of the bulk water at the solute-solvent interface. The ordering effects of proteins on hydration water are extended for several angstroms. In this paper we propose a method for analyzing the dynamical properties of the water molecules present in the hydration shells of proteins. The approach is based on the analysis of the effects of protein-solvent interactions on water protons NMR relaxation parameters. NMR relaxation parameters, especially the nonselective (R1NS and selective (R1SE spin-lattice relaxation rates of water protons, are useful for investigating the solvent dynamics at the macromolecule-solvent interfaces as well as the perturbation effects caused by the water-macromolecule interactions on the solvent dynamical properties. In this paper we demonstrate that Nuclear Magnetic Resonance Spectroscopy can be used to determine the dynamical contributions of proteins to the water molecules belonging to their hydration shells.

Two Chimeric Regulators of G-protein Signaling (RGS) Proteins Differentially Modulate Soybean Heterotrimeric G-protein Cycle*

Science.gov (United States)

Roy Choudhury, Swarup; Westfall, Corey S.; Laborde, John P.; Bisht, Naveen C.; Jez, Joseph M.; Pandey, Sona

2012-01-01

Heterotrimeric G-proteins and the regulator of G-protein signaling (RGS) proteins, which accelerate the inherent GTPase activity of Gα proteins, are common in animals and encoded by large gene families; however, in plants G-protein signaling is thought to be more limited in scope. For example, Arabidopsis thaliana contains one Gα, one Gβ, three Gγ, and one RGS protein. Recent examination of the Glycine max (soybean) genome reveals a larger set of G-protein-related genes and raises the possibility of more intricate G-protein networks than previously observed in plants. Stopped-flow analysis of GTP-binding and GDP/GTP exchange for the four soybean Gα proteins (GmGα1–4) reveals differences in their kinetic properties. The soybean genome encodes two chimeric RGS proteins with an N-terminal seven transmembrane domain and a C-terminal RGS box. Both GmRGS interact with each of the four GmGα and regulate their GTPase activity. The GTPase-accelerating activities of GmRGS1 and -2 differ for each GmGα, suggesting more than one possible rate of the G-protein cycle initiated by each of the Gα proteins. The differential effects of GmRGS1 and GmRGS2 on GmGα1–4 result from a single valine versus alanine difference. The emerging picture suggests complex regulation of the G-protein cycle in soybean and in other plants with expanded G-protein networks. PMID:22474294

Alignment of non-covalent interactions at protein-protein interfaces.

Directory of Open Access Journals (Sweden)

Hongbo Zhu

Full Text Available BACKGROUND: The study and comparison of protein-protein interfaces is essential for the understanding of the mechanisms of interaction between proteins. While there are many methods for comparing protein structures and protein binding sites, so far no methods have been reported for comparing the geometry of non-covalent interactions occurring at protein-protein interfaces. METHODOLOGY/PRINCIPAL FINDINGS: Here we present a method for aligning non-covalent interactions between different protein-protein interfaces. The method aligns the vector representations of van der Waals interactions and hydrogen bonds based on their geometry. The method has been applied to a dataset which comprises a variety of protein-protein interfaces. The alignments are consistent to a large extent with the results obtained using two other complementary approaches. In addition, we apply the method to three examples of protein mimicry. The method successfully aligns respective interfaces and allows for recognizing conserved interface regions. CONCLUSIONS/SIGNIFICANCE: The Galinter method has been validated in the comparison of interfaces in which homologous subunits are involved, including cases of mimicry. The method is also applicable to comparing interfaces involving non-peptidic compounds. Galinter assists users in identifying local interface regions with similar patterns of non-covalent interactions. This is particularly relevant to the investigation of the molecular basis of interaction mimicry.

The Ser/Thr Protein Kinase Protein-Protein Interaction Map of M. tuberculosis.

Science.gov (United States)

Wu, Fan-Lin; Liu, Yin; Jiang, He-Wei; Luan, Yi-Zhao; Zhang, Hai-Nan; He, Xiang; Xu, Zhao-Wei; Hou, Jing-Li; Ji, Li-Yun; Xie, Zhi; Czajkowsky, Daniel M; Yan, Wei; Deng, Jiao-Yu; Bi, Li-Jun; Zhang, Xian-En; Tao, Sheng-Ce

2017-08-01

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, the leading cause of death among all infectious diseases. There are 11 eukaryotic-like serine/threonine protein kinases (STPKs) in Mtb, which are thought to play pivotal roles in cell growth, signal transduction and pathogenesis. However, their underlying mechanisms of action remain largely uncharacterized. In this study, using a Mtb proteome microarray, we have globally identified the binding proteins in Mtb for all of the STPKs, and constructed the first STPK protein interaction (KPI) map that includes 492 binding proteins and 1,027 interactions. Bioinformatics analysis showed that the interacting proteins reflect diverse functions, including roles in two-component system, transcription, protein degradation, and cell wall integrity. Functional investigations confirmed that PknG regulates cell wall integrity through key components of peptidoglycan (PG) biosynthesis, e.g. MurC. The global STPK-KPIs network constructed here is expected to serve as a rich resource for understanding the key signaling pathways in Mtb, thus facilitating drug development and effective control of Mtb. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces.

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Ching-Tai Chen

Full Text Available Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins and were tested on an independent dataset (consisting of 142 proteins. The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted

Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces

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Chen, Ching-Tai; Peng, Hung-Pin; Jian, Jhih-Wei; Tsai, Keng-Chang; Chang, Jeng-Yih; Yang, Ei-Wen; Chen, Jun-Bo; Ho, Shinn-Ying; Hsu, Wen-Lian; Yang, An-Suei

2012-01-01

Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with

Bioinformatic Prediction of WSSV-Host Protein-Protein Interaction

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Zheng Sun

2014-01-01

Full Text Available WSSV is one of the most dangerous pathogens in shrimp aquaculture. However, the molecular mechanism of how WSSV interacts with shrimp is still not very clear. In the present study, bioinformatic approaches were used to predict interactions between proteins from WSSV and shrimp. The genome data of WSSV (NC_003225.1 and the constructed transcriptome data of F. chinensis were used to screen potentially interacting proteins by searching in protein interaction databases, including STRING, Reactome, and DIP. Forty-four pairs of proteins were suggested to have interactions between WSSV and the shrimp. Gene ontology analysis revealed that 6 pairs of these interacting proteins were classified into “extracellular region” or “receptor complex” GO-terms. KEGG pathway analysis showed that they were involved in the “ECM-receptor interaction pathway.” In the 6 pairs of interacting proteins, an envelope protein called “collagen-like protein” (WSSV-CLP encoded by an early virus gene “wsv001” in WSSV interacted with 6 deduced proteins from the shrimp, including three integrin alpha (ITGA, two integrin beta (ITGB, and one syndecan (SDC. Sequence analysis on WSSV-CLP, ITGA, ITGB, and SDC revealed that they possessed the sequence features for protein-protein interactions. This study might provide new insights into the interaction mechanisms between WSSV and shrimp.

Protein subcellular localization assays using split fluorescent proteins

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Waldo, Geoffrey S [Santa Fe, NM; Cabantous, Stephanie [Los Alamos, NM

2009-09-08

The invention provides protein subcellular localization assays using split fluorescent protein systems. The assays are conducted in living cells, do not require fixation and washing steps inherent in existing immunostaining and related techniques, and permit rapid, non-invasive, direct visualization of protein localization in living cells. The split fluorescent protein systems used in the practice of the invention generally comprise two or more self-complementing fragments of a fluorescent protein, such as GFP, wherein one or more of the fragments correspond to one or more beta-strand microdomains and are used to "tag" proteins of interest, and a complementary "assay" fragment of the fluorescent protein. Either or both of the fragments may be functionalized with a subcellular targeting sequence enabling it to be expressed in or directed to a particular subcellular compartment (i.e., the nucleus).

Human cancer protein-protein interaction network: a structural perspective.

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Gozde Kar

2009-12-01

Full Text Available Protein-protein interaction networks provide a global picture of cellular function and biological processes. Some proteins act as hub proteins, highly connected to others, whereas some others have few interactions. The dysfunction of some interactions causes many diseases, including cancer. Proteins interact through their interfaces. Therefore, studying the interface properties of cancer-related proteins will help explain their role in the interaction networks. Similar or overlapping binding sites should be used repeatedly in single interface hub proteins, making them promiscuous. Alternatively, multi-interface hub proteins make use of several distinct binding sites to bind to different partners. We propose a methodology to integrate protein interfaces into cancer interaction networks (ciSPIN, cancer structural protein interface network. The interactions in the human protein interaction network are replaced by interfaces, coming from either known or predicted complexes. We provide a detailed analysis of cancer related human protein-protein interfaces and the topological properties of the cancer network. The results reveal that cancer-related proteins have smaller, more planar, more charged and less hydrophobic binding sites than non-cancer proteins, which may indicate low affinity and high specificity of the cancer-related interactions. We also classified the genes in ciSPIN according to phenotypes. Within phenotypes, for breast cancer, colorectal cancer and leukemia, interface properties were found to be discriminating from non-cancer interfaces with an accuracy of 71%, 67%, 61%, respectively. In addition, cancer-related proteins tend to interact with their partners through distinct interfaces, corresponding mostly to multi-interface hubs, which comprise 56% of cancer-related proteins, and constituting the nodes with higher essentiality in the network (76%. We illustrate the interface related affinity properties of two cancer-related hub

Hot-spot analysis for drug discovery targeting protein-protein interactions.

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Rosell, Mireia; Fernández-Recio, Juan

2018-04-01

Protein-protein interactions are important for biological processes and pathological situations, and are attractive targets for drug discovery. However, rational drug design targeting protein-protein interactions is still highly challenging. Hot-spot residues are seen as the best option to target such interactions, but their identification requires detailed structural and energetic characterization, which is only available for a tiny fraction of protein interactions. Areas covered: In this review, the authors cover a variety of computational methods that have been reported for the energetic analysis of protein-protein interfaces in search of hot-spots, and the structural modeling of protein-protein complexes by docking. This can help to rationalize the discovery of small-molecule inhibitors of protein-protein interfaces of therapeutic interest. Computational analysis and docking can help to locate the interface, molecular dynamics can be used to find suitable cavities, and hot-spot predictions can focus the search for inhibitors of protein-protein interactions. Expert opinion: A major difficulty for applying rational drug design methods to protein-protein interactions is that in the majority of cases the complex structure is not available. Fortunately, computational docking can complement experimental data. An interesting aspect to explore in the future is the integration of these strategies for targeting PPIs with large-scale mutational analysis.

Interaction between plate make and protein in protein crystallisation screening.

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Gordon J King

Full Text Available BACKGROUND: Protein crystallisation screening involves the parallel testing of large numbers of candidate conditions with the aim of identifying conditions suitable as a starting point for the production of diffraction quality crystals. Generally, condition screening is performed in 96-well plates. While previous studies have examined the effects of protein construct, protein purity, or crystallisation condition ingredients on protein crystallisation, few have examined the effect of the crystallisation plate. METHODOLOGY/PRINCIPAL FINDINGS: We performed a statistically rigorous examination of protein crystallisation, and evaluated interactions between crystallisation success and plate row/column, different plates of same make, different plate makes and different proteins. From our analysis of protein crystallisation, we found a significant interaction between plate make and the specific protein being crystallised. CONCLUSIONS/SIGNIFICANCE: Protein crystal structure determination is the principal method for determining protein structure but is limited by the need to produce crystals of the protein under study. Many important proteins are difficult to crystallize, so that identification of factors that assist crystallisation could open up the structure determination of these more challenging targets. Our findings suggest that protein crystallisation success may be improved by matching a protein with its optimal plate make.

Protein Charge and Mass Contribute to the Spatio-temporal Dynamics of Protein-Protein Interactions in a Minimal Proteome

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Xu, Yu; Wang, Hong; Nussinov, Ruth; Ma, Buyong

2013-01-01

We constructed and simulated a ‘minimal proteome’ model using Langevin dynamics. It contains 206 essential protein types which were compiled from the literature. For comparison, we generated six proteomes with randomized concentrations. We found that the net charges and molecular weights of the proteins in the minimal genome are not random. The net charge of a protein decreases linearly with molecular weight, with small proteins being mostly positively charged and large proteins negatively charged. The protein copy numbers in the minimal genome have the tendency to maximize the number of protein-protein interactions in the network. Negatively charged proteins which tend to have larger sizes can provide large collision cross-section allowing them to interact with other proteins; on the other hand, the smaller positively charged proteins could have higher diffusion speed and are more likely to collide with other proteins. Proteomes with random charge/mass populations form less stable clusters than those with experimental protein copy numbers. Our study suggests that ‘proper’ populations of negatively and positively charged proteins are important for maintaining a protein-protein interaction network in a proteome. It is interesting to note that the minimal genome model based on the charge and mass of E. Coli may have a larger protein-protein interaction network than that based on the lower organism M. pneumoniae. PMID:23420643

Prediction of heterodimeric protein complexes from weighted protein-protein interaction networks using novel features and kernel functions.

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Peiying Ruan

Full Text Available Since many proteins express their functional activity by interacting with other proteins and forming protein complexes, it is very useful to identify sets of proteins that form complexes. For that purpose, many prediction methods for protein complexes from protein-protein interactions have been developed such as MCL, MCODE, RNSC, PCP, RRW, and NWE. These methods have dealt with only complexes with size of more than three because the methods often are based on some density of subgraphs. However, heterodimeric protein complexes that consist of two distinct proteins occupy a large part according to several comprehensive databases of known complexes. In this paper, we propose several feature space mappings from protein-protein interaction data, in which each interaction is weighted based on reliability. Furthermore, we make use of prior knowledge on protein domains to develop feature space mappings, domain composition kernel and its combination kernel with our proposed features. We perform ten-fold cross-validation computational experiments. These results suggest that our proposed kernel considerably outperforms the naive Bayes-based method, which is the best existing method for predicting heterodimeric protein complexes.

NMR Studies of Protein Hydration and Protein-Ligand Interactions

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Chong, Yuan

Water on the surface of a protein is called hydration water. Hydration water is known to play a crucial role in a variety of biological processes including protein folding, enzymatic activation, and drug binding. Although the significance of hydration water has been recognized, the underlying mechanism remains far from being understood. This dissertation employs a unique in-situ nuclear magnetic resonance (NMR) technique to study the mechanism of protein hydration and the role of hydration in alcohol-protein interactions. Water isotherms in proteins are measured at different temperatures via the in-situ NMR technique. Water is found to interact differently with hydrophilic and hydrophobic groups on the protein. Water adsorption on hydrophilic groups is hardly affected by the temperature, while water adsorption on hydrophobic groups strongly depends on the temperature around 10 C, below which the adsorption is substantially reduced. This effect is induced by the dramatic decrease in the protein flexibility below 10 C. Furthermore, nanosecond to microsecond protein dynamics and the free energy, enthalpy, and entropy of protein hydration are studied as a function of hydration level and temperature. A crossover at 10 C in protein dynamics and thermodynamics is revealed. The effect of water at hydrophilic groups on protein dynamics and thermodynamics shows little temperature dependence, whereas water at hydrophobic groups has stronger effect above 10 C. In addition, I investigate the role of water in alcohol binding to the protein using the in-situ NMR detection. The isotherms of alcohols are first measured on dry proteins, then on proteins with a series of controlled hydration levels. The free energy, enthalpy, and entropy of alcohol binding are also determined. Two distinct types of alcohol binding are identified. On the one hand, alcohols can directly bind to a few specific sites on the protein. This type of binding is independent of temperature and can be

Mapping monomeric threading to protein-protein structure prediction.

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Guerler, Aysam; Govindarajoo, Brandon; Zhang, Yang

2013-03-25

The key step of template-based protein-protein structure prediction is the recognition of complexes from experimental structure libraries that have similar quaternary fold. Maintaining two monomer and dimer structure libraries is however laborious, and inappropriate library construction can degrade template recognition coverage. We propose a novel strategy SPRING to identify complexes by mapping monomeric threading alignments to protein-protein interactions based on the original oligomer entries in the PDB, which does not rely on library construction and increases the efficiency and quality of complex template recognitions. SPRING is tested on 1838 nonhomologous protein complexes which can recognize correct quaternary template structures with a TM score >0.5 in 1115 cases after excluding homologous proteins. The average TM score of the first model is 60% and 17% higher than that by HHsearch and COTH, respectively, while the number of targets with an interface RMSD benchmark proteins. Although the relative performance of SPRING and ZDOCK depends on the level of homology filters, a combination of the two methods can result in a significantly higher model quality than ZDOCK at all homology thresholds. These data demonstrate a new efficient approach to quaternary structure recognition that is ready to use for genome-scale modeling of protein-protein interactions due to the high speed and accuracy.

DiffSLC: A graph centrality method to detect essential proteins of a protein-protein interaction network.

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Mistry, Divya; Wise, Roger P; Dickerson, Julie A

2017-01-01

Identification of central genes and proteins in biomolecular networks provides credible candidates for pathway analysis, functional analysis, and essentiality prediction. The DiffSLC centrality measure predicts central and essential genes and proteins using a protein-protein interaction network. Network centrality measures prioritize nodes and edges based on their importance to the network topology. These measures helped identify critical genes and proteins in biomolecular networks. The proposed centrality measure, DiffSLC, combines the number of interactions of a protein and the gene coexpression values of genes from which those proteins were translated, as a weighting factor to bias the identification of essential proteins in a protein interaction network. Potentially essential proteins with low node degree are promoted through eigenvector centrality. Thus, the gene coexpression values are used in conjunction with the eigenvector of the network's adjacency matrix and edge clustering coefficient to improve essentiality prediction. The outcome of this prediction is shown using three variations: (1) inclusion or exclusion of gene co-expression data, (2) impact of different coexpression measures, and (3) impact of different gene expression data sets. For a total of seven networks, DiffSLC is compared to other centrality measures using Saccharomyces cerevisiae protein interaction networks and gene expression data. Comparisons are also performed for the top ranked proteins against the known essential genes from the Saccharomyces Gene Deletion Project, which show that DiffSLC detects more essential proteins and has a higher area under the ROC curve than other compared methods. This makes DiffSLC a stronger alternative to other centrality methods for detecting essential genes using a protein-protein interaction network that obeys centrality-lethality principle. DiffSLC is implemented using the igraph package in R, and networkx package in Python. The python package can be

U.S. Naval Sea Cadet Corps 2009 Annual Report

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2009-01-01

for the Naval Sea Cadet Corps. I salute your service to our Nation in developing future leaders. Bravo Zulu and keep charging! ttr’"-- U.S...Minutemen, NLCC, sponsored by Channel Isles Council, NLUS, CA. The NSCC Hall of Fame Award: Awarded to a founder or volunteer U.S. Naval Sea Cadet

A credit-card library approach for disrupting protein-protein interactions.

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Xu, Yang; Shi, Jin; Yamamoto, Noboru; Moss, Jason A; Vogt, Peter K; Janda, Kim D

2006-04-15

Protein-protein interfaces are prominent in many therapeutically important targets. Using small organic molecules to disrupt protein-protein interactions is a current challenge in chemical biology. An important example of protein-protein interactions is provided by the Myc protein, which is frequently deregulated in human cancers. Myc belongs to the family of basic helix-loop-helix leucine zipper (bHLH-ZIP) transcription factors. It is biologically active only as heterodimer with the bHLH-ZIP protein Max. Herein, we report a new strategy for the disruption of protein-protein interactions that has been corroborated through the design and synthesis of a small parallel library composed of 'credit-card' compounds. These compounds are derived from a planar, aromatic scaffold and functionalized with four points of diversity. From a 285 membered library, several hits were obtained that disrupted the c-Myc-Max interaction and cellular functions of c-Myc. The IC50 values determined for this small focused library for the disruption of Myc-Max dimerization are quite potent, especially since small molecule antagonists of protein-protein interactions are notoriously difficult to find. Furthermore, several of the compounds were active at the cellular level as shown by their biological effects on Myc action in chicken embryo fibroblast assays. In light of our findings, this approach is considered a valuable addition to the armamentarium of new molecules being developed to interact with protein-protein interfaces. Finally, this strategy for disrupting protein-protein interactions should prove applicable to other families of proteins.

Protein Correlation Profiles Identify Lipid Droplet Proteins with High Confidence*

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Krahmer, Natalie; Hilger, Maximiliane; Kory, Nora; Wilfling, Florian; Stoehr, Gabriele; Mann, Matthias; Farese, Robert V.; Walther, Tobias C.

2013-01-01

Lipid droplets (LDs) are important organelles in energy metabolism and lipid storage. Their cores are composed of neutral lipids that form a hydrophobic phase and are surrounded by a phospholipid monolayer that harbors specific proteins. Most well-established LD proteins perform important functions, particularly in cellular lipid metabolism. Morphological studies show LDs in close proximity to and interacting with membrane-bound cellular organelles, including the endoplasmic reticulum, mitochondria, peroxisomes, and endosomes. Because of these close associations, it is difficult to purify LDs to homogeneity. Consequently, the confident identification of bona fide LD proteins via proteomics has been challenging. Here, we report a methodology for LD protein identification based on mass spectrometry and protein correlation profiles. Using LD purification and quantitative, high-resolution mass spectrometry, we identified LD proteins by correlating their purification profiles to those of known LD proteins. Application of the protein correlation profile strategy to LDs isolated from Drosophila S2 cells led to the identification of 111 LD proteins in a cellular LD fraction in which 1481 proteins were detected. LD localization was confirmed in a subset of identified proteins via microscopy of the expressed proteins, thereby validating the approach. Among the identified LD proteins were both well-characterized LD proteins and proteins not previously known to be localized to LDs. Our method provides a high-confidence LD proteome of Drosophila cells and a novel approach that can be applied to identify LD proteins of other cell types and tissues. PMID:23319140

ProteinShop: A tool for interactive protein manipulation and steering

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Crivelli, Silvia; Kreylos, Oliver; Max, Nelson; Hamann, Bernd; Bethel, Wes

2004-05-25

We describe ProteinShop, a new visualization tool that streamlines and simplifies the process of determining optimal protein folds. ProteinShop may be used at different stages of a protein structure prediction process. First, it can create protein configurations containing secondary structures specified by the user. Second, it can interactively manipulate protein fragments to achieve desired folds by adjusting the dihedral angles of selected coil regions using an Inverse Kinematics method. Last, it serves as a visual framework to monitor and steer a protein structure prediction process that may be running on a remote machine. ProteinShop was used to create initial configurations for a protein structure prediction method developed by a team that competed in CASP5. ProteinShop's use accelerated the process of generating initial configurations, reducing the time required from days to hours. This paper describes the structure of ProteinShop and discusses its main features.

Prioritizing disease candidate proteins in cardiomyopathy-specific protein-protein interaction networks based on "guilt by association" analysis.

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Wan Li

Full Text Available The cardiomyopathies are a group of heart muscle diseases which can be inherited (familial. Identifying potential disease-related proteins is important to understand mechanisms of cardiomyopathies. Experimental identification of cardiomyophthies is costly and labour-intensive. In contrast, bioinformatics approach has a competitive advantage over experimental method. Based on "guilt by association" analysis, we prioritized candidate proteins involving in human cardiomyopathies. We first built weighted human cardiomyopathy-specific protein-protein interaction networks for three subtypes of cardiomyopathies using the known disease proteins from Online Mendelian Inheritance in Man as seeds. We then developed a method in prioritizing disease candidate proteins to rank candidate proteins in the network based on "guilt by association" analysis. It was found that most candidate proteins with high scores shared disease-related pathways with disease seed proteins. These top ranked candidate proteins were related with the corresponding disease subtypes, and were potential disease-related proteins. Cross-validation and comparison with other methods indicated that our approach could be used for the identification of potentially novel disease proteins, which may provide insights into cardiomyopathy-related mechanisms in a more comprehensive and integrated way.

Modular protein switches derived from antibody mimetic proteins.

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Nicholes, N; Date, A; Beaujean, P; Hauk, P; Kanwar, M; Ostermeier, M

2016-02-01

Protein switches have potential applications as biosensors and selective protein therapeutics. Protein switches built by fusion of proteins with the prerequisite input and output functions are currently developed using an ad hoc process. A modular switch platform in which existing switches could be readily adapted to respond to any ligand would be advantageous. We investigated the feasibility of a modular protein switch platform based on fusions of the enzyme TEM-1 β-lactamase (BLA) with two different antibody mimetic proteins: designed ankyrin repeat proteins (DARPins) and monobodies. We created libraries of random insertions of the gene encoding BLA into genes encoding a DARPin or a monobody designed to bind maltose-binding protein (MBP). From these libraries, we used a genetic selection system for β-lactamase activity to identify genes that conferred MBP-dependent ampicillin resistance to Escherichia coli. Some of these selected genes encoded switch proteins whose enzymatic activity increased up to 14-fold in the presence of MBP. We next introduced mutations into the antibody mimetic domain of these switches that were known to cause binding to different ligands. To different degrees, introduction of the mutations resulted in switches with the desired specificity, illustrating the potential modularity of these platforms. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Protein-protein interactions and cancer: targeting the central dogma.

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Garner, Amanda L; Janda, Kim D

2011-01-01

Between 40,000 and 200,000 protein-protein interactions have been predicted to exist within the human interactome. As these interactions are of a critical nature in many important cellular functions and their dysregulation is causal of disease, the modulation of these binding events has emerged as a leading, yet difficult therapeutic arena. In particular, the targeting of protein-protein interactions relevant to cancer is of fundamental importance as the tumor-promoting function of several aberrantly expressed proteins in the cancerous state is directly resultant of its ability to interact with a protein-binding partner. Of significance, these protein complexes play a crucial role in each of the steps of the central dogma of molecular biology, the fundamental processes of genetic transmission. With the many important discoveries being made regarding the mechanisms of these genetic process, the identification of new chemical probes are needed to better understand and validate the druggability of protein-protein interactions related to the central dogma. In this review, we provide an overview of current small molecule-based protein-protein interaction inhibitors for each stage of the central dogma: transcription, mRNA splicing and translation. Importantly, through our analysis we have uncovered a lack of necessary probes targeting mRNA splicing and translation, thus, opening up the possibility for expansion of these fields.

Targeting protein-protein interactions for parasite control.

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Christina M Taylor

2011-04-01

Full Text Available Finding new drug targets for pathogenic infections would be of great utility for humanity, as there is a large need to develop new drugs to fight infections due to the developing resistance and side effects of current treatments. Current drug targets for pathogen infections involve only a single protein. However, proteins rarely act in isolation, and the majority of biological processes occur via interactions with other proteins, so protein-protein interactions (PPIs offer a realm of unexplored potential drug targets and are thought to be the next-generation of drug targets. Parasitic worms were chosen for this study because they have deleterious effects on human health, livestock, and plants, costing society billions of dollars annually and many sequenced genomes are available. In this study, we present a computational approach that utilizes whole genomes of 6 parasitic and 1 free-living worm species and 2 hosts. The species were placed in orthologous groups, then binned in species-specific orthologous groups. Proteins that are essential and conserved among species that span a phyla are of greatest value, as they provide foundations for developing broad-control strategies. Two PPI databases were used to find PPIs within the species specific bins. PPIs with unique helminth proteins and helminth proteins with unique features relative to the host, such as indels, were prioritized as drug targets. The PPIs were scored based on RNAi phenotype and homology to the PDB (Protein DataBank. EST data for the various life stages, GO annotation, and druggability were also taken into consideration. Several PPIs emerged from this study as potential drug targets. A few interactions were supported by co-localization of expression in M. incognita (plant parasite and B. malayi (H. sapiens parasite, which have extremely different modes of parasitism. As more genomes of pathogens are sequenced and PPI databases expanded, this methodology will become increasingly

ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.

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John A Capra

Full Text Available The evolutionary history of a protein reflects the functional history of its ancestors. Recent phylogenetic studies identified distinct evolutionary signatures that characterize proteins involved in cancer, Mendelian disease, and different ontogenic stages. Despite the potential to yield insight into the cellular functions and interactions of proteins, such comparative phylogenetic analyses are rarely performed, because they require custom algorithms. We developed ProteinHistorian to make tools for performing analyses of protein origins widely available. Given a list of proteins of interest, ProteinHistorian estimates the phylogenetic age of each protein, quantifies enrichment for proteins of specific ages, and compares variation in protein age with other protein attributes. ProteinHistorian allows flexibility in the definition of protein age by including several algorithms for estimating ages from different databases of evolutionary relationships. We illustrate the use of ProteinHistorian with three example analyses. First, we demonstrate that proteins with high expression in human, compared to chimpanzee and rhesus macaque, are significantly younger than those with human-specific low expression. Next, we show that human proteins with annotated regulatory functions are significantly younger than proteins with catalytic functions. Finally, we compare protein length and age in many eukaryotic species and, as expected from previous studies, find a positive, though often weak, correlation between protein age and length. ProteinHistorian is available through a web server with an intuitive interface and as a set of command line tools; this allows biologists and bioinformaticians alike to integrate these approaches into their analysis pipelines. ProteinHistorian's modular, extensible design facilitates the integration of new datasets and algorithms. The ProteinHistorian web server, source code, and pre-computed ages for 32 eukaryotic genomes are

Mitochondrial nucleoid interacting proteins support mitochondrial protein synthesis.

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He, J; Cooper, H M; Reyes, A; Di Re, M; Sembongi, H; Litwin, T R; Gao, J; Neuman, K C; Fearnley, I M; Spinazzola, A; Walker, J E; Holt, I J

2012-07-01

Mitochondrial ribosomes and translation factors co-purify with mitochondrial nucleoids of human cells, based on affinity protein purification of tagged mitochondrial DNA binding proteins. Among the most frequently identified proteins were ATAD3 and prohibitin, which have been identified previously as nucleoid components, using a variety of methods. Both proteins are demonstrated to be required for mitochondrial protein synthesis in human cultured cells, and the major binding partner of ATAD3 is the mitochondrial ribosome. Altered ATAD3 expression also perturbs mtDNA maintenance and replication. These findings suggest an intimate association between nucleoids and the machinery of protein synthesis in mitochondria. ATAD3 and prohibitin are tightly associated with the mitochondrial membranes and so we propose that they support nucleic acid complexes at the inner membrane of the mitochondrion.

Annotating the protein-RNA interaction sites in proteins using evolutionary information and protein backbone structure.

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Li, Tao; Li, Qian-Zhong

2012-11-07

RNA-protein interactions play important roles in various biological processes. The precise detection of RNA-protein interaction sites is very important for understanding essential biological processes and annotating the function of the proteins. In this study, based on various features from amino acid sequence and structure, including evolutionary information, solvent accessible surface area and torsion angles (φ, ψ) in the backbone structure of the polypeptide chain, a computational method for predicting RNA-binding sites in proteins is proposed. When the method is applied to predict RNA-binding sites in three datasets: RBP86 containing 86 protein chains, RBP107 containing 107 proteins chains and RBP109 containing 109 proteins chains, better sensitivities and specificities are obtained compared to previously published methods in five-fold cross-validation tests. In order to make further examination for the efficiency of our method, the RBP107 dataset is used as training set, RBP86 and RBP109 datasets are used as the independent test sets. In addition, as examples of our prediction, RNA-binding sites in a few proteins are presented. The annotated results are consistent with the PDB annotation. These results show that our method is useful for annotating RNA binding sites of novel proteins.

Evolutionary diversification of protein-protein interactions by interface add-ons.

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Plach, Maximilian G; Semmelmann, Florian; Busch, Florian; Busch, Markus; Heizinger, Leonhard; Wysocki, Vicki H; Merkl, Rainer; Sterner, Reinhard

2017-10-03

Cells contain a multitude of protein complexes whose subunits interact with high specificity. However, the number of different protein folds and interface geometries found in nature is limited. This raises the question of how protein-protein interaction specificity is achieved on the structural level and how the formation of nonphysiological complexes is avoided. Here, we describe structural elements called interface add-ons that fulfill this function and elucidate their role for the diversification of protein-protein interactions during evolution. We identified interface add-ons in 10% of a representative set of bacterial, heteromeric protein complexes. The importance of interface add-ons for protein-protein interaction specificity is demonstrated by an exemplary experimental characterization of over 30 cognate and hybrid glutamine amidotransferase complexes in combination with comprehensive genetic profiling and protein design. Moreover, growth experiments showed that the lack of interface add-ons can lead to physiologically harmful cross-talk between essential biosynthetic pathways. In sum, our complementary in silico, in vitro, and in vivo analysis argues that interface add-ons are a practical and widespread evolutionary strategy to prevent the formation of nonphysiological complexes by specializing protein-protein interactions.

The interface of protein structure, protein biophysics, and molecular evolution

Science.gov (United States)

Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

2012-01-01

Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

Racemic & quasi-racemic protein crystallography enabled by chemical protein synthesis.

Science.gov (United States)

Kent, Stephen Bh

2018-04-04

A racemic protein mixture can be used to form centrosymmetric crystals for structure determination by X-ray diffraction. Both the unnatural d-protein and the corresponding natural l-protein are made by total chemical synthesis based on native chemical ligation-chemoselective condensation of unprotected synthetic peptide segments. Racemic protein crystallography is important for structure determination of the many natural protein molecules that are refractory to crystallization. Racemic mixtures facilitate the crystallization of recalcitrant proteins, and give diffraction-quality crystals. Quasi-racemic crystallization, using a single d-protein molecule, can facilitate the determination of the structures of a series of l-protein analog molecules. Copyright © 2018 Elsevier Ltd. All rights reserved.

General protein-protein cross-linking.

Science.gov (United States)

Alegria-Schaffer, Alice

2014-01-01

This protocol describes a general protein-to-protein cross-linking procedure using the water-soluble amine-reactive homobifunctional BS(3) (bis[sulfosuccinimidyl] suberate); however, the protocol can be easily adapted using other cross-linkers of similar properties. BS(3) is composed of two sulfo-NHS ester groups and an 11.4 Å linker. Sulfo-NHS ester groups react with primary amines in slightly alkaline conditions (pH 7.2-8.5) and yield stable amide bonds. The reaction releases N-hydroxysuccinimide (see an application of NHS esters on Labeling a protein with fluorophores using NHS ester derivitization). © 2014 Elsevier Inc. All rights reserved.

Quality control methodology for high-throughput protein-protein interaction screening.

Science.gov (United States)

Vazquez, Alexei; Rual, Jean-François; Venkatesan, Kavitha

2011-01-01

Protein-protein interactions are key to many aspects of the cell, including its cytoskeletal structure, the signaling processes in which it is involved, or its metabolism. Failure to form protein complexes or signaling cascades may sometimes translate into pathologic conditions such as cancer or neurodegenerative diseases. The set of all protein interactions between the proteins encoded by an organism constitutes its protein interaction network, representing a scaffold for biological function. Knowing the protein interaction network of an organism, combined with other sources of biological information, can unravel fundamental biological circuits and may help better understand the molecular basics of human diseases. The protein interaction network of an organism can be mapped by combining data obtained from both low-throughput screens, i.e., "one gene at a time" experiments and high-throughput screens, i.e., screens designed to interrogate large sets of proteins at once. In either case, quality controls are required to deal with the inherent imperfect nature of experimental assays. In this chapter, we discuss experimental and statistical methodologies to quantify error rates in high-throughput protein-protein interactions screens.

3-D thermal stress analysis of hot spots in reactor piping using BEM

International Nuclear Information System (INIS)

Bains, R.S.; Sugimoto, Jun

1994-08-01

A three-dimensional steady state thermoelastic analysis has been conducted on the hot leg of a pressurized water reactor(PWR) containing localized hot spots resulting from fission product aerosol deposition occurring during a hypothetical severe accident. The boundary element method (BEM) of numerical solution was successfully employed to investigate the structural response of the hot leg. Convergence of solution can be realized provided sufficiently large number of elements are employed and correct modelling of the temperature transition region (TTR) adjacent to the hot spot on the inner surface is conducted. The only correct temperature field across the TTR is that which can be represented by the interpolation functions employed in the BEM code. Further, incorrect solutions can also be generated if the TTR is too thin. The nature of the deformation at the hot spot location depends on whether the thermal boundary condition on the outer surface of the hot leg is one of constant temperature or adiabatic. The analysis shows that at the location of the hot spot on the inner surface large compressive stresses can be established. On the outer surface at the same location, large tensile stresses can be established. The presence of these large stress elevations in the vicinity of the hot spot could be detrimental to the integrity of the hot leg. The tensile stresses are extremely important since they can act as sites of crack initiation and subsequent propagation. Once a crack propagates through the thickness, leak worthiness of the hot leg comes into question. Consequently, additional analysis incorporating the effects of plasticity and temperature dependence of the material properties must be conducted to ascertain the integrity of the hot leg. (J.P.N.)

Corrective action decision document, Second Gas Station, Tonopah test range, Nevada (Corrective Action Unit No. 403)

International Nuclear Information System (INIS)

1997-11-01

This Corrective Action Decision Document (CADD) for Second Gas Station (Corrective Action Unit [CAU] No. 403) has been developed for the U.S. Department of Energy's (DOE) Nevada Environmental Restoration Project to meet the requirements of the Federal Facility Agreement and Consent Order (FFACO) of 1996 as stated in Appendix VI, open-quotes Corrective Action Strategyclose quotes (FFACO, 1996). The Second Gas Station Corrective Action Site (CAS) No. 03-02-004-0360 is the only CAS in CAU No. 403. The Second Gas Station CAS is located within Area 3 of the Tonopah Test Range (TTR), west of the Main Road at the location of former Underground Storage Tanks (USTs) and their associated fuel dispensary stations. The TTR is approximately 225 kilometers (km) (140 miles [mi]) northwest of Las Vegas, Nevada, by air and approximately 56 km (35 mi) southeast of Tonopah, Nevada, by road. The TTR is bordered on the south, east, and west by the Nellis Air Force Range and on the north by sparsely populated public land administered by the Bureau of Land Management and the U.S. Forest Service. The Second Gas Station CAS was formerly known as the Underground Diesel Tank Site, Sandia Environmental Restoration Site Number 118. The gas station was in use from approximately 1965 to 1980. The USTs were originally thought to be located 11 meters (m) (36 feet [ft]) east of the Old Light Duty Shop, Building 0360, and consisted of one gasoline UST (southern tank) and one diesel UST (northern tank) (DOE/NV, 1996a). The two associated fuel dispensary stations were located northeast (diesel) and southeast (gasoline) of Building 0360 (CAU 423). Presently the site is used as a parking lot, Building 0360 is used for mechanical repairs of vehicles

Suboptimal Anticoagulant Management in Japanese Patients with Nonvalvular Atrial Fibrillation Receiving Warfarin for Stroke Prevention.

Science.gov (United States)

Hirano, Teruyuki; Kaneko, Hirokazu; Mishina, Sari; Wang, Feng; Morita, Satoshi

2017-10-01

Atrial fibrillation (AF) is the most common cardiac arrhythmia, with increasing prevalence in Japan. Although prothrombin time-international normalized ratio (PT-INR) targets for monitoring warfarin therapy in patients with nonvalvular AF (NVAF) are well defined, real-world patient characteristics and PT-INR levels remain unknown among Japanese patients with NVAF who initiate and continue warfarin (warfarin maintainers) versus those who switch from warfarin to direct oral anticoagulants (DOACs; warfarin switchers). Patients with NVAF receiving oral anticoagulants between February 2013 and June 2015 were identified using a nationwide electronic medical record (EMR) database from 69 hospitals in Japan. Demographics and characteristics of patients, PT-INR, time in therapeutic range (TTR), and frequency in range (FIR) of PT-INR between warfarin maintainers and warfarin switchers were assessed. A total of 1705 patients met inclusion criteria and were examined (1501 warfarin maintainers versus 204 warfarin switchers). CHADS 2 , CHA 2 DS 2 -VASc, and HAS-BLED scores were comparable between groups. However, these scores were significantly higher among warfarin switchers at the time of switching than at the time of warfarin initiation. Furthermore, TTR and FIR of PT-INR were lower in warfarin switchers than in maintainers. Nevertheless, TTR and FIR were below 50% (PT-INR, 1.6-2.6) in both patient groups. In this EMR-based clinical study, patients who switched to DOACs had both poor or inadequate PT-INR control and higher risk factors of stroke. Many patients receiving warfarin did not achieve sufficient PT-INR therapeutic range. DOACs could be recommended in Japanese patients with NVAF with inadequate PT-INR control and increased risk of stroke. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Quantifying the molecular origins of opposite solvent effects on protein-protein interactions.

Directory of Open Access Journals (Sweden)

Vincent Vagenende

Full Text Available Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens protein-protein interactions for others. This is exemplified by the puzzling observation that addition of glycerol oppositely affects the association constants of two antibodies, D1.3 and D44.1, with lysozyme. To resolve this conundrum, we develop a methodology based on the thermodynamic principles of preferential interaction theory and the quantitative characterization of local protein solvation from molecular dynamics simulations. We find that changes of preferential solvent interactions at the protein-protein interface quantitatively account for the opposite effects of glycerol on the antibody-antigen association constants. Detailed characterization of local protein solvation in the free and associated protein states reveals how opposite solvent effects on protein-protein interactions depend on the extent of dewetting of the protein-protein contact region and on structural changes that alter cooperative solvent-protein interactions at the periphery of the protein-protein interface. These results demonstrate the direct relationship between macroscopic solvent effects on protein-protein interactions and atom-scale solvent-protein interactions, and establish a general methodology for predicting and understanding solvent effects on protein-protein interactions in diverse biological environments.

Our interests in protein-protein interactions

Indian Academy of Sciences (India)

protein interactions. Evolution of P-P partnerships. Evolution of P-P structures. Evolutionary dynamics of P-P interactions. Dynamics of P-P interaction network. Host-pathogen interactions. CryoEM mapping of gigantic protein assemblies.

A Library of Plasmodium vivax Recombinant Merozoite Proteins Reveals New Vaccine Candidates and Protein-Protein Interactions

Science.gov (United States)

Hostetler, Jessica B.; Sharma, Sumana; Bartholdson, S. Josefin; Wright, Gavin J.; Fairhurst, Rick M.; Rayner, Julian C.

2015-01-01

Background A vaccine targeting Plasmodium vivax will be an essential component of any comprehensive malaria elimination program, but major gaps in our understanding of P. vivax biology, including the protein-protein interactions that mediate merozoite invasion of reticulocytes, hinder the search for candidate antigens. Only one ligand-receptor interaction has been identified, that between P. vivax Duffy Binding Protein (PvDBP) and the erythrocyte Duffy Antigen Receptor for Chemokines (DARC), and strain-specific immune responses to PvDBP make it a complex vaccine target. To broaden the repertoire of potential P. vivax merozoite-stage vaccine targets, we exploited a recent breakthrough in expressing full-length ectodomains of Plasmodium proteins in a functionally-active form in mammalian cells and initiated a large-scale study of P. vivax merozoite proteins that are potentially involved in reticulocyte binding and invasion. Methodology/Principal Findings We selected 39 P. vivax proteins that are predicted to localize to the merozoite surface or invasive secretory organelles, some of which show homology to P. falciparum vaccine candidates. Of these, we were able to express 37 full-length protein ectodomains in a mammalian expression system, which has been previously used to express P. falciparum invasion ligands such as PfRH5. To establish whether the expressed proteins were correctly folded, we assessed whether they were recognized by antibodies from Cambodian patients with acute vivax malaria. IgG from these samples showed at least a two-fold change in reactivity over naïve controls in 27 of 34 antigens tested, and the majority showed heat-labile IgG immunoreactivity, suggesting the presence of conformation-sensitive epitopes and native tertiary protein structures. Using a method specifically designed to detect low-affinity, extracellular protein-protein interactions, we confirmed a predicted interaction between P. vivax 6-cysteine proteins P12 and P41, further

Results from the Interim Salt Disposition Program Macrobatch 11 Tank 21H Acceptance Samples

Energy Technology Data Exchange (ETDEWEB)

Peters, T. B. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Bannochie, C. J. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

2017-11-13

Savannah River National Laboratory (SRNL) analyzed samples from Tank 21H in support of verification of Macrobatch (Salt Batch) 11 for the Interim Salt Disposition Program (ISDP) for processing. This document reports characterization data on the samples of Tank 21H and fulfills the requirements of Deliverable 3 of the Technical Task Request (TTR).

[Detection of protein-protein interactions by FRET and BRET methods].

Science.gov (United States)

Matoulková, E; Vojtěšek, B

2014-01-01

Nowadays, in vivo protein-protein interaction studies have become preferable detecting meth-ods that enable to show or specify (already known) protein interactions and discover their inhibitors. They also facilitate detection of protein conformational changes and discovery or specification of signaling pathways in living cells. One group of in vivo methods enabling these findings is based on fluorescent resonance energy transfer (FRET) and its bio-luminescent modification (BRET). They are based on visualization of protein-protein interactions via light or enzymatic excitation of fluorescent or bio-luminescent proteins. These methods allow not only protein localization within the cell or its organelles (or small animals) but they also allow us to quantify fluorescent signals and to discover weak or strong interaction partners. In this review, we explain the principles of FRET and BRET, their applications in the characterization of protein-protein interactions and we describe several findings using these two methods that clarify molecular and cellular mechanisms and signals related to cancer biology.

Protein degradation and protein synthesis in long-term memory formation

Directory of Open Access Journals (Sweden)

Timothy J Jarome

2014-06-01

Full Text Available Long-term memory (LTM formation requires transient changes in the activity of intracellular signaling cascades that are thought to regulate new gene transcription and de novo protein synthesis in the brain. Consistent with this, protein synthesis inhibitors impair LTM for a variety of behavioral tasks when infused into the brain around the time of training or following memory retrieval, suggesting that protein synthesis is a critical step in LTM storage in the brain. However, evidence suggests that protein degradation mediated by the ubiquitin-proteasome system may also be a critical regulator of LTM formation and stability following retrieval. This requirement for increased protein degradation has been shown in the same brain regions in which protein synthesis is required for LTM storage. Additionally, increases in the phosphorylation of proteins involved in translational control parallel increases in protein polyubiquitination and the increased demand for protein degradation is regulated by intracellular signaling molecules thought to regulate protein synthesis during LTM formation. In some cases inhibiting proteasome activity can rescue memory impairments that result from pharmacological blockade of protein synthesis, suggesting that protein degradation may control the requirement for protein synthesis during the memory storage process. Results such as these suggest that protein degradation and synthesis are both critical for LTM formation and may interact to properly consolidate and store memories in the brain. Here, we review the evidence implicating protein synthesis and degradation in LTM storage and highlight the areas of overlap between these two opposing processes. We also discuss evidence suggesting these two processes may interact to properly form and store memories. LTM storage likely requires a coordinated regulation between protein degradation and synthesis at multiple sites in the mammalian brain.

Evolutionary reprograming of protein-protein interaction specificity.

Science.gov (United States)

Akiva, Eyal; Babbitt, Patricia C

2015-10-22

Using mutation libraries and deep sequencing, Aakre et al. study the evolution of protein-protein interactions using a toxin-antitoxin model. The results indicate probable trajectories via "intermediate" proteins that are promiscuous, thus avoiding transitions via non-interactions. These results extend observations about other biological interactions and enzyme evolution, suggesting broadly general principles. Copyright © 2015 Elsevier Inc. All rights reserved.

Protein Annotation from Protein Interaction Networks and Gene Ontology

OpenAIRE

Nguyen, Cao D.; Gardiner, Katheleen J.; Cios, Krzysztof J.

2011-01-01

We introduce a novel method for annotating protein function that combines Naïve Bayes and association rules, and takes advantage of the underlying topology in protein interaction networks and the structure of graphs in the Gene Ontology. We apply our method to proteins from the Human Protein Reference Database (HPRD) and show that, in comparison with other approaches, it predicts protein functions with significantly higher recall with no loss of precision. Specifically, it achieves 51% precis...

Nickel-titanium alloys: a systematic review

Directory of Open Access Journals (Sweden)

Marcelo do Amaral Ferreira

2012-06-01

Full Text Available OBJECTIVE: A systematic review on nickel-titanium wires was performed. The strategy was focused on Entrez-PubMed-OLDMEDLINE, Scopus and BioMed Central from 1963 to 2008. METHODS: Papers in English and French describing the behavior of these wires and laboratorial methods to identify crystalline transformation were considered. A total of 29 papers were selected. RESULTS: Nickel-titanium wires show exceptional features in terms of elasticity and shape memory effects. However, clinical applications request a deeper knowledge of these properties in order to allow the professional to use them in a rational manner. In addition, the necessary information regarding each alloy often does not correspond to the information given by the manufacturer. Many alloys called "superelastic" do not present this effect; they just behave as less stiff alloys, with a larger springback if compared to the stainless steel wires. CONCLUSIONS: Laboratory tests are the only means to observe the real behavior of these materials, including temperature transition range (TTR and applied tensions. However, it is also possible to determine in which TTR these alloys change the crystalline structure.

CARACTERÍSTICAS DO SÊMEN CAPRINO DESCONGELADO APÓS A ADIÇÃO DE RINGER LACTATO, CITRATO DE SÓDIO E SOLUÇÃO TRIS

Directory of Open Access Journals (Sweden)

Júlio Cesar Oliveira Dias

2015-04-01

Full Text Available Cryopreservation of semen is of great importance for various reproductive biotechnologies such as artificial insemination (IA, In Vitro Embryo Production (PIV and Intracytoplasmic Sperm Injection (ICSI. The objective of this work was to evaluate the stability and persistence of motility and strength of sperm, as well as changes in the plasma membrane after the addition of Ringer Lactate, sodium citrate 2.92% or TRIS solution in thawed goat semen. Semen was collected from two Alpine Brown goats, and standard procedures for cryopreservation and seminal analysis were performed. After thawing the semen, the extenders Ringer Lactate, sodium citrate 2.92% and TRIS solution were added and Thermoresistance (TTR, Supravital and Morphology Tests were carried out. In TTR, only the group received TRIS solution presented motility and strength for a longer period (90 minutes; P 0.05. We concluded that the addition of the solutions does not allow a large persistence of motility and strength of thawed sperm, but TRIS solution could be used for expansion of seminal doses used in vitro reproductive biotechnology.

Protein supplementation with sports protein bars in renal patients.

Science.gov (United States)

Meade, Anthony

2007-05-01

Malnutrition prevalence in patients on dialysis is well established. The protein requirements for both hemodialysis and peritoneal dialysis have been documented elsewhere, including the Kidney Disease Outcomes Quality Initiative Clinical Practice Guidelines for Nutrition in Chronic Renal Failure. The clinical challenge is to assist patients in meeting these targets, especially in those with anorexia. Traditional supplements have included fluid, which is an issue for patients who are fluid restricted. The study objectives were to (1) investigate the range of sports protein supplements that may be suitable for patients on hemodialysis to use and (2) trial nonfluid protein supplements in patients on hemodialysis. Known manufacturers of sports protein bars and other sports supplements available in Australia were contacted for the nutrient breakdown of high-protein products, specifically potassium, protein, and phosphorus contents. As a result, selected high-protein sports bars (Protein FX, Aussie Bodies, Port Melbourne, Victoria, Australia) were used as an alternative to the more commonly used renal-specific fluid supplements (Nepro, Abbott Laboratories, Abbott Park, IL; Novasource Renal, Novartis Nutrition Corporation, Fremont, MI; and Renilon, Nutricia, Wiltshire, UK) in patients with poor nutritional status requiring supplementation. Patient satisfaction and clinical nutrition markers were investigated. The study took place at inpatient, in-center, and satellite hemodialysis settings in Adelaide, South Australia. A total of 32 patients (16 females and 16 males) with an average age of 62.9 years (range 32-86 years) undergoing hemodialysis (acute and maintenance) were included. Subjects were selected by the author as part of routine clinical nutrition care. Patients trialed sports protein bars as a protein supplement alone or in conjunction with other supplementary products. All patients were in favor of the trial, with 22 of 32 patients continuing with the protein

Protein enriched pasta: structure and digestibility of its protein network.

Science.gov (United States)

Laleg, Karima; Barron, Cécile; Santé-Lhoutellier, Véronique; Walrand, Stéphane; Micard, Valérie

2016-02-01

Wheat (W) pasta was enriched in 6% gluten (G), 35% faba (F) or 5% egg (E) to increase its protein content (13% to 17%). The impact of the enrichment on the multiscale structure of the pasta and on in vitro protein digestibility was studied. Increasing the protein content (W- vs. G-pasta) strengthened pasta structure at molecular and macroscopic scales but reduced its protein digestibility by 3% by forming a higher covalently linked protein network. Greater changes in the macroscopic and molecular structure of the pasta were obtained by varying the nature of protein used for enrichment. Proteins in G- and E-pasta were highly covalently linked (28-32%) resulting in a strong pasta structure. Conversely, F-protein (98% SDS-soluble) altered the pasta structure by diluting gluten and formed a weak protein network (18% covalent link). As a result, protein digestibility in F-pasta was significantly higher (46%) than in E- (44%) and G-pasta (39%). The effect of low (55 °C, LT) vs. very high temperature (90 °C, VHT) drying on the protein network structure and digestibility was shown to cause greater molecular changes than pasta formulation. Whatever the pasta, a general strengthening of its structure, a 33% to 47% increase in covalently linked proteins and a higher β-sheet structure were observed. However, these structural differences were evened out after the pasta was cooked, resulting in identical protein digestibility in LT and VHT pasta. Even after VHT drying, F-pasta had the best amino acid profile with the highest protein digestibility, proof of its nutritional interest.

HIV protein sequence hotspots for crosstalk with host hub proteins.

Directory of Open Access Journals (Sweden)

Mahdi Sarmady

Full Text Available HIV proteins target host hub proteins for transient binding interactions. The presence of viral proteins in the infected cell results in out-competition of host proteins in their interaction with hub proteins, drastically affecting cell physiology. Functional genomics and interactome datasets can be used to quantify the sequence hotspots on the HIV proteome mediating interactions with host hub proteins. In this study, we used the HIV and human interactome databases to identify HIV targeted host hub proteins and their host binding partners (H2. We developed a high throughput computational procedure utilizing motif discovery algorithms on sets of protein sequences, including sequences of HIV and H2 proteins. We identified as HIV sequence hotspots those linear motifs that are highly conserved on HIV sequences and at the same time have a statistically enriched presence on the sequences of H2 proteins. The HIV protein motifs discovered in this study are expressed by subsets of H2 host proteins potentially outcompeted by HIV proteins. A large subset of these motifs is involved in cleavage, nuclear localization, phosphorylation, and transcription factor binding events. Many such motifs are clustered on an HIV sequence in the form of hotspots. The sequential positions of these hotspots are consistent with the curated literature on phenotype altering residue mutations, as well as with existing binding site data. The hotspot map produced in this study is the first global portrayal of HIV motifs involved in altering the host protein network at highly connected hub nodes.

Different protein-protein interface patterns predicted by different machine learning methods.

Science.gov (United States)

Wang, Wei; Yang, Yongxiao; Yin, Jianxin; Gong, Xinqi

2017-11-22

Different types of protein-protein interactions make different protein-protein interface patterns. Different machine learning methods are suitable to deal with different types of data. Then, is it the same situation that different interface patterns are preferred for prediction by different machine learning methods? Here, four different machine learning methods were employed to predict protein-protein interface residue pairs on different interface patterns. The performances of the methods for different types of proteins are different, which suggest that different machine learning methods tend to predict different protein-protein interface patterns. We made use of ANOVA and variable selection to prove our result. Our proposed methods taking advantages of different single methods also got a good prediction result compared to single methods. In addition to the prediction of protein-protein interactions, this idea can be extended to other research areas such as protein structure prediction and design.

Molecular simulations of lipid-mediated protein-protein interactions

NARCIS (Netherlands)

de Meyer, F.J.M.; Venturoli, M.; Smit, B.

2008-01-01

Recent experimental results revealed that lipid-mediated interactions due to hydrophobic forces may be important in determining the protein topology after insertion in the membrane, in regulating the protein activity, in protein aggregation and in signal transduction. To gain insight into the

Detecting protein-protein interactions in living cells

DEFF Research Database (Denmark)

Gottschalk, Marie; Bach, Anders; Hansen, Jakob Lerche

2009-01-01

to the endogenous C-terminal peptide of the NMDA receptor, as evaluated by a cell-free protein-protein interaction assay. However, it is important to address both membrane permeability and effect in living cells. Therefore a bioluminescence resonance energy transfer (BRET) assay was established, where the C......-terminal of the NMDA receptor and PDZ2 of PSD-95 were fused to green fluorescent protein (GFP) and Renilla luciferase (Rluc) and expressed in COS7 cells. A robust and specific BRET signal was obtained by expression of the appropriate partner proteins and subsequently, the assay was used to evaluate a Tat......The PDZ domain mediated interaction between the NMDA receptor and its intracellular scaffolding protein, PSD-95, is a potential target for treatment of ischemic brain diseases. We have recently developed a number of peptide analogues with improved affinity for the PDZ domains of PSD-95 compared...

Personalizing Protein Nourishment

Science.gov (United States)

DALLAS, DAVID C.; SANCTUARY, MEGAN R.; QU, YUNYAO; KHAJAVI, SHABNAM HAGHIGHAT; VAN ZANDT, ALEXANDRIA E.; DYANDRA, MELISSA; FRESE, STEVEN A.; BARILE, DANIELA; GERMAN, J. BRUCE

2016-01-01

Proteins are not equally digestible—their proteolytic susceptibility varies by their source and processing method. Incomplete digestion increases colonic microbial protein fermentation (putrefaction), which produces toxic metabolites that can induce inflammation in vitro and have been associated with inflammation in vivo. Individual humans differ in protein digestive capacity based on phenotypes, particularly disease states. To avoid putrefaction-induced intestinal inflammation, protein sources and processing methods must be tailored to the consumer’s digestive capacity. This review explores how food processing techniques alter protein digestibility and examines how physiological conditions alter digestive capacity. Possible solutions to improving digestive function or matching low digestive capacity with more digestible protein sources are explored. Beyond the ileal digestibility measurements of protein digestibility, less invasive, quicker and cheaper techniques for monitoring the extent of protein digestion and fermentation are needed to personalize protein nourishment. Biomarkers of protein digestive capacity and efficiency can be identified with the toolsets of peptidomics, metabolomics, microbial sequencing and multiplexed protein analysis of fecal and urine samples. By monitoring individual protein digestive function, the protein component of diets can be tailored via protein source and processing selection to match individual needs to minimize colonic putrefaction and, thus, optimize gut health. PMID:26713355

A scored human protein-protein interaction network to catalyze genomic interpretation

DEFF Research Database (Denmark)

Li, Taibo; Wernersson, Rasmus; Hansen, Rasmus B

2017-01-01

Genome-scale human protein-protein interaction networks are critical to understanding cell biology and interpreting genomic data, but challenging to produce experimentally. Through data integration and quality control, we provide a scored human protein-protein interaction network (InWeb_InBioMap,......Genome-scale human protein-protein interaction networks are critical to understanding cell biology and interpreting genomic data, but challenging to produce experimentally. Through data integration and quality control, we provide a scored human protein-protein interaction network (In...

Transduction proteins of olfactory receptor cells: identification of guanine nucleotide binding proteins and protein kinase C

International Nuclear Information System (INIS)

Anholt, R.R.H.; Mumby, S.M.; Stoffers, D.A.; Girard, P.R.; Kuo, J.F.; Snyder, S.H.

1987-01-01

The authors have analyzed guanine nucleotide binding proteins (G-proteins) in the olfactory epithelium of Rana catesbeiana using subunit-specific antisera. The olfactory epithelium contained the α subunits of three G-proteins, migrating on polyacrylamide gels in SDS with apparent molecular weights of 45,000, 42,000, and 40,000, corresponding to G/sub s/, G/sub i/, and G/sub o/, respectively. A single β subunit with an apparent molecular weight of 36,000 was detected. An antiserum against the α subunit of retinal transducin failed to detect immunoreactive proteins in olfactory cilia detached from the epithelium. The olfactory cilia appeared to be enriched in immunoreactive G/sub sα/ relative to G/sub ichemical bond/ and G/sub ochemical bond/ when compared to membranes prepared from the olfactory epithelium after detachment of the cilia. Bound antibody was detected by autoradiography after incubation with [ 125 I]protein. Immunohistochemical studies using an antiserum against the β subunit of G-proteins revealed intense staining of the ciliary surface of the olfactory epithelium and of the axon bundles in the lamina propria. In contrast, an antiserum against a common sequence of the α subunits preferentially stained the cell membranes of the olfactory receptor cells and the acinar cells of Bowman's glands and the deep submucosal glands. In addition to G-proteins, they have identified protein kinase C in olfactory cilia via a protein kinase C specific antiserum and via phorbol ester binding. However, in contrast to the G-proteins, protein kinase C occurred also in cilia isolated from respiratory epithelium

Diffusion of Integral Membrane Proteins in Protein-Rich Membranes

DEFF Research Database (Denmark)

Javanainen, Matti; Martinez-Seara, Hector; Metzler, Ralf

2017-01-01

of being protein-poor, native cell membranes are extremely crowded with proteins. On the basis of extensive molecular simulations, we here demonstrate that protein crowding of the membrane at physiological levels leads to deviations from the SD relation and to the emergence of a stronger Stokes......-like dependence D ∝ 1/R. We propose that this 1/R law mainly arises due to geometrical factors: smaller proteins are able to avoid confinement effects much better than their larger counterparts. The results highlight that the lateral dynamics in the crowded setting found in native membranes is radically different......The lateral diffusion of embedded proteins along lipid membranes in protein-poor conditions has been successfully described in terms of the Saffman-Delbrück (SD) model, which predicts that the protein diffusion coefficient D is weakly dependent on its radius R as D ∝ ln(1/R). However, instead...

Competitive Protein Adsorption - Multilayer Adsorption and Surface Induced Protein Aggregation

DEFF Research Database (Denmark)

Holmberg, Maria; Hou, Xiaolin

2009-01-01

In this study, competitive adsorption of albumin and IgG (immunoglobulin G) from human serum solutions and protein mixtures onto polymer surfaces is studied by means of radioactive labeling. By using two different radiolabels (125I and 131I), albumin and IgG adsorption to polymer surfaces...... is monitored simultaneously and the influence from the presence of other human serum proteins on albumin and IgG adsorption, as well as their mutual influence during adsorption processes, is investigated. Exploring protein adsorption by combining analysis of competitive adsorption from complex solutions...... of high concentration with investigation of single protein adsorption and interdependent adsorption between two specific proteins enables us to map protein adsorption sequences during competitive protein adsorption. Our study shows that proteins can adsorb in a multilayer fashion onto the polymer surfaces...

Protein leverage effects of beef protein on energy intake in humans.

Science.gov (United States)

Martens, Eveline A; Tan, Sze-Yen; Dunlop, Mandy V; Mattes, Richard D; Westerterp-Plantenga, Margriet S

2014-06-01

The protein leverage hypothesis requires specific evidence that protein intake is regulated more strongly than energy intake. The objective was to determine ad libitum energy intake, body weight changes, appetite profile, and nitrogen balance in response to 3 diets with different protein-to-carbohydrate + fat ratios over 12 consecutive days, with beef as a source of protein. A 3-arm, 12-d randomized crossover study was performed in 30 men and 28 women [mean ± SD age: 33 ± 16 y; body mass index (in kg/m²): 24.4 ± 4.0] with the use of diets containing 5%, 15%, and 30% of energy (En%) from protein, predominantly from beef. Energy intake was significantly lower in the 30En%-protein condition (8.73 ± 1.93 MJ/d) than in the 5En%-protein (9.48 ± 1.67 MJ/d) and 15En%-protein (9.30 ± 1.62 MJ/d) conditions (P = 0.001), stemming largely from lower energy intake during meals (P = 0.001). Hunger (P = 0.001) and desire to eat (P = 0.001) ratings were higher and fullness ratings were lower (P = 0.001) in the 5En%-protein condition than in the 15En%-protein and 30En%-protein conditions. Nitrogen excretion was lower in the 5En%-protein condition (4.7 ± 1.5 g/24 h; P = 0.001) and was higher in the 30En%-protein condition (15.3 ± 8.7 g/24 h; P = 0.001) compared with the 15En%-protein condition (10.0 ± 5.2 g/24 h). Nitrogen balance was maintained in the 5En%-protein condition and was positive in the 15En%- and 30En%-protein conditions (P = 0.001). Complete protein leverage did not occur because subjects did not consume to a common protein amount at the expense of energy balance. Individuals did underconsume relative to energy requirements from high-protein diets. The lack of support for protein leverage effects on a low-protein diet may stem from the fact that protein intake was sufficient to maintain nitrogen balance over the 12-d trial. © 2014 American Society for Nutrition.

The clinical expression of hereditary protein C and protein S deficiency: : a relation to clinical thrombotic risk-factors and to levels of protein C and protein S

NARCIS (Netherlands)

Henkens, C. M. A.; van der Meer, J.; Hillege, J. L.; Bom, V. J. J.; Halie, M. R.; van der Schaaf, W.

We investigated 103 first-degree relatives of 13 unrelated protein C or protein S deficient patients to assess the role of additional thrombotic risk factors and of protein C and protein S levels in the clinical expression of hereditary protein C and protein S deficiency. Fifty-seven relatives were

PDZ Protein Regulation of G Protein-Coupled Receptor Trafficking and Signaling Pathways.

Science.gov (United States)

Dunn, Henry A; Ferguson, Stephen S G

2015-10-01

G protein-coupled receptors (GPCRs) contribute to the regulation of every aspect of human physiology and are therapeutic targets for the treatment of numerous diseases. As a consequence, understanding the myriad of mechanisms controlling GPCR signaling and trafficking is essential for the development of new pharmacological strategies for the treatment of human pathologies. Of the many GPCR-interacting proteins, postsynaptic density protein of 95 kilodaltons, disc large, zona occludens-1 (PDZ) domain-containing proteins appear most abundant and have similarly been implicated in disease mechanisms. PDZ proteins play an important role in regulating receptor and channel protein localization within synapses and tight junctions and function to scaffold intracellular signaling protein complexes. In the current study, we review the known functional interactions between PDZ domain-containing proteins and GPCRs and provide insight into the potential mechanisms of action. These PDZ domain-containing proteins include the membrane-associated guanylate-like kinases [postsynaptic density protein of 95 kilodaltons; synapse-associated protein of 97 kilodaltons; postsynaptic density protein of 93 kilodaltons; synapse-associated protein of 102 kilodaltons; discs, large homolog 5; caspase activation and recruitment domain and membrane-associated guanylate-like kinase domain-containing protein 3; membrane protein, palmitoylated 3; calcium/calmodulin-dependent serine protein kinase; membrane-associated guanylate kinase protein (MAGI)-1, MAGI-2, and MAGI-3], Na(+)/H(+) exchanger regulatory factor proteins (NHERFs) (NHERF1, NHERF2, PDZ domain-containing kidney protein 1, and PDZ domain-containing kidney protein 2), Golgi-associated PDZ proteins (Gα-binding protein interacting protein, C-terminus and CFTR-associated ligand), PDZ domain-containing guanine nucleotide exchange factors (GEFs) 1 and 2, regulator of G protein signaling (RGS)-homology-RhoGEFs (PDZ domain-containing RhoGEF and

Environmental Effects on Materials for Space Applications.

Science.gov (United States)

1983-03-01

o;t tnut wthicni was 6.own fby the elet -nlt,ttr t- I -w~v tool I!.- for .hoolt a f :rther 2 ritt:s,:t. Pihtogtaphs taker-. fo-r erosof 3d seontis...Luigi BALIS CREMA. Renato BARBONI, Antonio CASTELI.ANI Istituto di Tecnologia Aerospaziale Via ’udossiana, 16 -- 00184 Roma - Italy SUMMARY A. series of

Sodium Tetraphenylborate Catalyst Identification: Preliminary Studies Set 2

International Nuclear Information System (INIS)

Barnes, M.J.

1997-05-01

This document details the results of these tests and represents the second report of the task designed to identify soluble NaTPB decomposition catalysts. This task, performed as part of the DNFSB Recommendation 96-1 Implementation Plan, partially fulfills the request by High Level Waste Engineering and the ITP Flow Sheet Team in task Technical Request HLW-TTR-97008

Measuring protein breakdown rate in individual proteins in vivo

DEFF Research Database (Denmark)

Holm, Lars; Kjaer, Michael

2010-01-01

To outline different approaches of how protein breakdown can be quantified and to present a new approach to determine the fractional breakdown rate of individual slow turnover proteins in vivo.......To outline different approaches of how protein breakdown can be quantified and to present a new approach to determine the fractional breakdown rate of individual slow turnover proteins in vivo....

Novel Technology for Protein-Protein Interaction-based Targeted Drug Discovery

Directory of Open Access Journals (Sweden)

Jung Me Hwang

2011-12-01

Full Text Available We have developed a simple but highly efficient in-cell protein-protein interaction (PPI discovery system based on the translocation properties of protein kinase C- and its C1a domain in live cells. This system allows the visual detection of trimeric and dimeric protein interactions including cytosolic, nuclear, and/or membrane proteins with their cognate ligands. In addition, this system can be used to identify pharmacological small compounds that inhibit specific PPIs. These properties make this PPI system an attractive tool for screening drug candidates and mapping the protein interactome.

A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data

Directory of Open Access Journals (Sweden)

Li Min

2012-03-01

Full Text Available Abstract Background Identification of essential proteins is always a challenging task since it requires experimental approaches that are time-consuming and laborious. With the advances in high throughput technologies, a large number of protein-protein interactions are available, which have produced unprecedented opportunities for detecting proteins' essentialities from the network level. There have been a series of computational approaches proposed for predicting essential proteins based on network topologies. However, the network topology-based centrality measures are very sensitive to the robustness of network. Therefore, a new robust essential protein discovery method would be of great value. Results In this paper, we propose a new centrality measure, named PeC, based on the integration of protein-protein interaction and gene expression data. The performance of PeC is validated based on the protein-protein interaction network of Saccharomyces cerevisiae. The experimental results show that the predicted precision of PeC clearly exceeds that of the other fifteen previously proposed centrality measures: Degree Centrality (DC, Betweenness Centrality (BC, Closeness Centrality (CC, Subgraph Centrality (SC, Eigenvector Centrality (EC, Information Centrality (IC, Bottle Neck (BN, Density of Maximum Neighborhood Component (DMNC, Local Average Connectivity-based method (LAC, Sum of ECC (SoECC, Range-Limited Centrality (RL, L-index (LI, Leader Rank (LR, Normalized α-Centrality (NC, and Moduland-Centrality (MC. Especially, the improvement of PeC over the classic centrality measures (BC, CC, SC, EC, and BN is more than 50% when predicting no more than 500 proteins. Conclusions We demonstrate that the integration of protein-protein interaction network and gene expression data can help improve the precision of predicting essential proteins. The new centrality measure, PeC, is an effective essential protein discovery method.

Rapid identification of capybara (Hydrochaeris hydrochaeris through allele-specific PCR

Directory of Open Access Journals (Sweden)

Flávio Henrique-Silva

2005-07-01

Full Text Available The capybara is the largest rodent in the world and is widely distributed throughout Central and South America.  It is an animal of economic interest due to the pleasant flavor of its meat and higher protein content in comparison  to beef and pork meat.  The hide, hair and fat also have economic advantages. Thus,  as an animal with such high economic potential, it is the target of hunters, even though  hunting capybara is prohibited by law in Brazil.   Due to their  similarities,  capybara meat  is easily confused with  pork  meat.   This  occurs  upon  the apprehension of the  meat  from hunters, as well as in some restaurants that serve capybara meat that was slaughtered clandestinely. In both cases, when the meat is confiscated, those responsible for the crimes claim it is pork meat,  hindering  the enforcement of the law. A practical  course was ministered  to undergraduate biology students enrolled in the elective course Introduction to Genetic  Engineering  at Federal  University  of Sao Carlos (UFSCar, Sao Paulo  State, Brazil.  The  objective  of the  course was to establish  and  apply  a Polymerase  Chain  Reaction  (PCR assay to identify capybara meat and discriminate it in relation  to other types of meat,  including pork. Primers  were designed based  on 12S rRNA,  transthyretin and  growth  hormone  receptor  genes.  The primers generated  capybara specific fragments  of approximately 220, 290 and 330 bp for transthyretin,12S rRNA  and  growth  hormone  receptor,  respectively.   The  duplexes  developed  in the  present work can be used effectively to discriminate capybara meat  from other  animals,  contributing to combating predatory capybara hunting. The results were extensively discussed and the students have contributed to written a paper  to be submitted to a publication.

The Proteins API: accessing key integrated protein and genome information.

Science.gov (United States)

Nightingale, Andrew; Antunes, Ricardo; Alpi, Emanuele; Bursteinas, Borisas; Gonzales, Leonardo; Liu, Wudong; Luo, Jie; Qi, Guoying; Turner, Edd; Martin, Maria

2017-07-03

The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics data from large scale data sources (LSS). Using the coordinates service, researchers are able to retrieve the genomic sequence coordinates for proteins in UniProtKB. This, the LSS genomics and proteomics data for UniProt proteins is programmatically only available through this service. A Swagger UI has been implemented to provide documentation, an interface for users, with little or no programming experience, to 'talk' to the services to quickly and easily formulate queries with the services and obtain dynamically generated source code for popular programming languages, such as Java, Perl, Python and Ruby. Search results are returned as standard JSON, XML or GFF data objects. The Proteins API is a scalable, reliable, fast, easy to use RESTful services that provides a broad protein information resource for users to ask questions based upon their field of expertise and allowing them to gain an integrated overview of protein annotations available to aid their knowledge gain on proteins in biological processes. The Proteins API is available at (http://www.ebi.ac.uk/proteins/api/doc). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Multiple protonation equilibria in electrostatics of protein-protein binding.

Science.gov (United States)

Piłat, Zofia; Antosiewicz, Jan M

2008-11-27

All proteins contain groups capable of exchanging protons with their environment. We present here an approach, based on a rigorous thermodynamic cycle and the partition functions for energy levels characterizing protonation states of the associating proteins and their complex, to compute the electrostatic pH-dependent contribution to the free energy of protein-protein binding. The computed electrostatic binding free energies include the pH of the solution as the variable of state, mutual "polarization" of associating proteins reflected as changes in the distribution of their protonation states upon binding and fluctuations between available protonation states. The only fixed property of both proteins is the conformation; the structure of the monomers is kept in the same conformation as they have in the complex structure. As a reference, we use the electrostatic binding free energies obtained from the traditional Poisson-Boltzmann model, computed for a single macromolecular conformation fixed in a given protonation state, appropriate for given solution conditions. The new approach was tested for 12 protein-protein complexes. It is shown that explicit inclusion of protonation degrees of freedom might lead to a substantially different estimation of the electrostatic contribution to the binding free energy than that based on the traditional Poisson-Boltzmann model. This has important implications for the balancing of different contributions to the energetics of protein-protein binding and other related problems, for example, the choice of protein models for Brownian dynamics simulations of their association. Our procedure can be generalized to include conformational degrees of freedom by combining it with molecular dynamics simulations at constant pH. Unfortunately, in practice, a prohibitive factor is an enormous requirement for computer time and power. However, there may be some hope for solving this problem by combining existing constant pH molecular dynamics

Texturized dairy proteins.

Science.gov (United States)

Onwulata, Charles I; Phillips, John G; Tunick, Michael H; Qi, Phoebi X; Cooke, Peter H

2010-03-01

Dairy proteins are amenable to structural modifications induced by high temperature, shear, and moisture; in particular, whey proteins can change conformation to new unfolded states. The change in protein state is a basis for creating new foods. The dairy products, nonfat dried milk (NDM), whey protein concentrate (WPC), and whey protein isolate (WPI) were modified using a twin-screw extruder at melt temperatures of 50, 75, and 100 degrees C, and moistures ranging from 20 to 70 wt%. Viscoelasticity and solubility measurements showed that extrusion temperature was a more significant (P extruded dairy protein ranged from rigid (2500 N) to soft (2.7 N). Extruding at or above 75 degrees C resulted in increased peak force for WPC (138 to 2500 N) and WPI (2.7 to 147.1 N). NDM was marginally texturized; the presence of lactose interfered with its texturization. WPI products extruded at 50 degrees C were not texturized; their solubility values ranged from 71.8% to 92.6%. A wide possibility exists for creating new foods with texturized dairy proteins due to the extensive range of states achievable. Dairy proteins can be used to boost the protein content in puffed snacks made from corn meal, but unmodified, they bind water and form doughy pastes with starch. To minimize the water binding property of dairy proteins, WPI, or WPC, or NDM were modified by extrusion processing. Extrusion temperature conditions were adjusted to 50, 75, or 100 degrees C, sufficient to change the structure of the dairy proteins, but not destroy them. Extrusion modified the structures of these dairy proteins for ease of use in starchy foods to boost nutrient levels. Dairy proteins can be used to boost the protein content in puffed snacks made from corn meal, but unmodified, they bind water and form doughy pastes with starch. To minimize the water binding property of dairy proteins, whey protein isolate, whey protein concentrate, or nonfat dried milk were modified by extrusion processing. Extrusion

Protein annotation from protein interaction networks and Gene Ontology.

Science.gov (United States)

Nguyen, Cao D; Gardiner, Katheleen J; Cios, Krzysztof J

2011-10-01

We introduce a novel method for annotating protein function that combines Naïve Bayes and association rules, and takes advantage of the underlying topology in protein interaction networks and the structure of graphs in the Gene Ontology. We apply our method to proteins from the Human Protein Reference Database (HPRD) and show that, in comparison with other approaches, it predicts protein functions with significantly higher recall with no loss of precision. Specifically, it achieves 51% precision and 60% recall versus 45% and 26% for Majority and 24% and 61% for χ²-statistics, respectively. Copyright © 2011 Elsevier Inc. All rights reserved.

Dietary Protein Intake in Dutch Elderly People: A Focus on Protein Sources

Directory of Open Access Journals (Sweden)

Michael Tieland

2015-11-01

Full Text Available Introduction: Sufficient high quality dietary protein intake is required to prevent or treat sarcopenia in elderly people. Therefore, the intake of specific protein sources as well as their timing of intake are important to improve dietary protein intake in elderly people. Objectives: to assess the consumption of protein sources as well as the distribution of protein sources over the day in community-dwelling, frail and institutionalized elderly people. Methods: Habitual dietary intake was evaluated using 2- and 3-day food records collected from various studies involving 739 community-dwelling, 321 frail and 219 institutionalized elderly people. Results: Daily protein intake averaged 71 ± 18 g/day in community-dwelling, 71 ± 20 g/day in frail and 58 ± 16 g/day in institutionalized elderly people and accounted for 16% ± 3%, 16% ± 3% and 17% ± 3% of their energy intake, respectively. Dietary protein intake ranged from 10 to 12 g at breakfast, 15 to 23 g at lunch and 24 to 31 g at dinner contributing together over 80% of daily protein intake. The majority of dietary protein consumed originated from animal sources (≥60% with meat and dairy as dominant sources. Thus, 40% of the protein intake in community-dwelling, 37% in frail and 29% in institutionalized elderly originated from plant based protein sources with bread as the principle source. Plant based proteins contributed for >50% of protein intake at breakfast and between 34% and 37% at lunch, with bread as the main source. During dinner, >70% of the protein intake originated from animal protein, with meat as the dominant source. Conclusion: Daily protein intake in these older populations is mainly (>80% provided by the three main meals, with most protein consumed during dinner. More than 60% of daily protein intake consumed is of animal origin, with plant based protein sources representing nearly 40% of total protein consumed. During dinner, >70% of the protein intake originated from

Introduction to current and future protein therapeutics: a protein engineering perspective.

Science.gov (United States)

Carter, Paul J

2011-05-15

Protein therapeutics and its enabling sister discipline, protein engineering, have emerged since the early 1980s. The first protein therapeutics were recombinant versions of natural proteins. Proteins purposefully modified to increase their clinical potential soon followed with enhancements derived from protein or glycoengineering, Fc fusion or conjugation to polyethylene glycol. Antibody-based drugs subsequently arose as the largest and fastest growing class of protein therapeutics. The rationale for developing better protein therapeutics with enhanced efficacy, greater safety, reduced immunogenicity or improved delivery comes from the convergence of clinical, scientific, technological and commercial drivers that have identified unmet needs and provided strategies to address them. Future protein drugs seem likely to be more extensively engineered to improve their performance, e.g., antibodies and Fc fusion proteins with enhanced effector functions or extended half-life. Two old concepts for improving antibodies, namely antibody-drug conjugates and bispecific antibodies, have advanced to the cusp of clinical success. As for newer protein therapeutic platform technologies, several engineered protein scaffolds are in early clinical development and offer differences and some potential advantages over antibodies. Copyright © 2011 Elsevier Inc. All rights reserved.

Exploration of the dynamic properties of protein complexes predicted from spatially constrained protein-protein interaction networks.

Directory of Open Access Journals (Sweden)

Eric A Yen

2014-05-01

Full Text Available Protein complexes are not static, but rather highly dynamic with subunits that undergo 1-dimensional diffusion with respect to each other. Interactions within protein complexes are modulated through regulatory inputs that alter interactions and introduce new components and deplete existing components through exchange. While it is clear that the structure and function of any given protein complex is coupled to its dynamical properties, it remains a challenge to predict the possible conformations that complexes can adopt. Protein-fragment Complementation Assays detect physical interactions between protein pairs constrained to ≤8 nm from each other in living cells. This method has been used to build networks composed of 1000s of pair-wise interactions. Significantly, these networks contain a wealth of dynamic information, as the assay is fully reversible and the proteins are expressed in their natural context. In this study, we describe a method that extracts this valuable information in the form of predicted conformations, allowing the user to explore the conformational landscape, to search for structures that correlate with an activity state, and estimate the abundance of conformations in the living cell. The generator is based on a Markov Chain Monte Carlo simulation that uses the interaction dataset as input and is constrained by the physical resolution of the assay. We applied this method to an 18-member protein complex composed of the seven core proteins of the budding yeast Arp2/3 complex and 11 associated regulators and effector proteins. We generated 20,480 output structures and identified conformational states using principle component analysis. We interrogated the conformation landscape and found evidence of symmetry breaking, a mixture of likely active and inactive conformational states and dynamic exchange of the core protein Arc15 between core and regulatory components. Our method provides a novel tool for prediction and

BLAST-based structural annotation of protein residues using Protein Data Bank.

Science.gov (United States)

Singh, Harinder; Raghava, Gajendra P S

2016-01-25

In the era of next-generation sequencing where thousands of genomes have been already sequenced; size of protein databases is growing with exponential rate. Structural annotation of these proteins is one of the biggest challenges for the computational biologist. Although, it is easy to perform BLAST search against Protein Data Bank (PDB) but it is difficult for a biologist to annotate protein residues from BLAST search. A web-server StarPDB has been developed for structural annotation of a protein based on its similarity with known protein structures. It uses standard BLAST software for performing similarity search of a query protein against protein structures in PDB. This server integrates wide range modules for assigning different types of annotation that includes, Secondary-structure, Accessible surface area, Tight-turns, DNA-RNA and Ligand modules. Secondary structure module allows users to predict regular secondary structure states to each residue in a protein. Accessible surface area predict the exposed or buried residues in a protein. Tight-turns module is designed to predict tight turns like beta-turns in a protein. DNA-RNA module developed for predicting DNA and RNA interacting residues in a protein. Similarly, Ligand module of server allows one to predicted ligands, metal and nucleotides ligand interacting residues in a protein. In summary, this manuscript presents a web server for comprehensive annotation of a protein based on similarity search. It integrates number of visualization tools that facilitate users to understand structure and function of protein residues. This web server is available freely for scientific community from URL http://crdd.osdd.net/raghava/starpdb .

Integral UBL domain proteins: a family of proteasome interacting proteins

DEFF Research Database (Denmark)

Hartmann-Petersen, Rasmus; Gordon, Colin

2004-01-01

The family of ubiquitin-like (UBL) domain proteins (UDPs) comprises a conserved group of proteins involved in a multitude of different cellular activities. However, recent studies on UBL-domain proteins indicate that these proteins appear to share a common property in their ability to interact...

Modulation of mitogen-activated protein kinase-activated protein kinase 3 by hepatitis C virus core protein

DEFF Research Database (Denmark)

Ngo, HT; Pham, Long; Kim, JW

2013-01-01

Hepatitis C virus (HCV) is highly dependent on cellular proteins for its own propagation. In order to identify the cellular factors involved in HCV propagation, we performed protein microarray assays using the HCV core protein as a probe. Of ~9,000 host proteins immobilized in a microarray...... inducers. Binding of HCV core to MAPKAPK3 was confirmed by in vitro pulldown assay and further verified by coimmunoprecipitation assay. HCV core protein interacted with MAPKAPK3 through amino acid residues 41 to 75 of core and the N-terminal half of kinase domain of MAPKAPK3. In addition, both RNA...... increased HCV IRES-mediated translation and MAPKAPK3-dependent HCV IRES activity was further increased by core protein. These data suggest that HCV core may modulate MAPKAPK3 to facilitate its own propagation....

Genome-wide analysis of protein-protein interactions and involvement of viral proteins in SARS-CoV replication.

Directory of Open Access Journals (Sweden)

Ji'an Pan

Full Text Available Analyses of viral protein-protein interactions are an important step to understand viral protein functions and their underlying molecular mechanisms. In this study, we adopted a mammalian two-hybrid system to screen the genome-wide intraviral protein-protein interactions of SARS coronavirus (SARS-CoV and therefrom revealed a number of novel interactions which could be partly confirmed by in vitro biochemical assays. Three pairs of the interactions identified were detected in both directions: non-structural protein (nsp 10 and nsp14, nsp10 and nsp16, and nsp7 and nsp8. The interactions between the multifunctional nsp10 and nsp14 or nsp16, which are the unique proteins found in the members of Nidovirales with large RNA genomes including coronaviruses and toroviruses, may have important implication for the mechanisms of replication/transcription complex assembly and functions of these viruses. Using a SARS-CoV replicon expressing a luciferase reporter under the control of a transcription regulating sequence, it has been shown that several viral proteins (N, X and SUD domains of nsp3, and nsp12 provided in trans stimulated the replicon reporter activity, indicating that these proteins may regulate coronavirus replication and transcription. Collectively, our findings provide a basis and platform for further characterization of the functions and mechanisms of coronavirus proteins.

Protein engineering techniques gateways to synthetic protein universe

CERN Document Server

Poluri, Krishna Mohan

2017-01-01

This brief provides a broad overview of protein-engineering research, offering a glimpse of the most common experimental methods. It also presents various computational programs with applications that are widely used in directed evolution, computational and de novo protein design. Further, it sheds light on the advantages and pitfalls of existing methodologies and future perspectives of protein engineering techniques.

Topology-function conservation in protein-protein interaction networks.

Science.gov (United States)

Davis, Darren; Yaveroğlu, Ömer Nebil; Malod-Dognin, Noël; Stojmirovic, Aleksandar; Pržulj, Nataša

2015-05-15

Proteins underlay the functioning of a cell and the wiring of proteins in protein-protein interaction network (PIN) relates to their biological functions. Proteins with similar wiring in the PIN (topology around them) have been shown to have similar functions. This property has been successfully exploited for predicting protein functions. Topological similarity is also used to guide network alignment algorithms that find similarly wired proteins between PINs of different species; these similarities are used to transfer annotation across PINs, e.g. from model organisms to human. To refine these functional predictions and annotation transfers, we need to gain insight into the variability of the topology-function relationships. For example, a function may be significantly associated with specific topologies, while another function may be weakly associated with several different topologies. Also, the topology-function relationships may differ between different species. To improve our understanding of topology-function relationships and of their conservation among species, we develop a statistical framework that is built upon canonical correlation analysis. Using the graphlet degrees to represent the wiring around proteins in PINs and gene ontology (GO) annotations to describe their functions, our framework: (i) characterizes statistically significant topology-function relationships in a given species, and (ii) uncovers the functions that have conserved topology in PINs of different species, which we term topologically orthologous functions. We apply our framework to PINs of yeast and human, identifying seven biological process and two cellular component GO terms to be topologically orthologous for the two organisms. © The Author 2015. Published by Oxford University Press.

Protein space: a natural method for realizing the nature of protein universe.

Science.gov (United States)

Yu, Chenglong; Deng, Mo; Cheng, Shiu-Yuen; Yau, Shek-Chung; He, Rong L; Yau, Stephen S-T

2013-02-07

Current methods cannot tell us what the nature of the protein universe is concretely. They are based on different models of amino acid substitution and multiple sequence alignment which is an NP-hard problem and requires manual intervention. Protein structural analysis also gives a direction for mapping the protein universe. Unfortunately, now only a minuscule fraction of proteins' 3-dimensional structures are known. Furthermore, the phylogenetic tree representations are not unique for any existing tree construction methods. Here we develop a novel method to realize the nature of protein universe. We show the protein universe can be realized as a protein space in 60-dimensional Euclidean space using a distance based on a normalized distribution of amino acids. Every protein is in one-to-one correspondence with a point in protein space, where proteins with similar properties stay close together. Thus the distance between two points in protein space represents the biological distance of the corresponding two proteins. We also propose a natural graphical representation for inferring phylogenies. The representation is natural and unique based on the biological distances of proteins in protein space. This will solve the fundamental question of how proteins are distributed in the protein universe. Copyright © 2012 Elsevier Ltd. All rights reserved.

Protein intake does not increase vastus lateralis muscle protein synthesis during cycling

DEFF Research Database (Denmark)

Hulston, CJ; Wolsk, Emil; Grøndahl, Thomas Sahl

2011-01-01

PURPOSE: This study aimed to investigate the effect of protein ingestion on leg protein turnover and vastus lateralis muscle protein synthesis during bicycle exercise and recovery. METHODS: Eight healthy males participated in two experiments in which they ingested either a carbohydrate solution...... sampling, and blood flow measurements. Muscle protein synthesis was calculated from the incorporation of l-[ring-C6]phenylalanine into protein. RESULTS: Consuming protein during exercise increased leg protein synthesis and decreased net leg protein breakdown; however, protein ingestion did not increase...... protein synthesis within the highly active vastus lateralis muscle (0.029%·h(-1), ± 0.004%·h(-1), and 0.030%·h(-1), ± 0.003%·h(-1), in CHO and CHO + P, respectively; P = 0.88). In contrast, consuming protein, during exercise and recovery, increased postexercise vastus lateralis muscle protein synthesis...

Mitochondrial protein acetylation mediates nutrient sensing of mitochondrial protein synthesis and mitonuclear protein balance.

Science.gov (United States)

Di Domenico, Antonella; Hofer, Annette; Tundo, Federica; Wenz, Tina

2014-11-01

Changes in nutrient supply require global metabolic reprogramming to optimize the utilization of the nutrients. Mitochondria as a central component of the cellular metabolism play a key role in this adaptive process. Since mitochondria harbor their own genome, which encodes essential enzymes, mitochondrial protein synthesis is a determinant of metabolic adaptation. While regulation of cytoplasmic protein synthesis in response to metabolic challenges has been studied in great detail, mechanisms which adapt mitochondrial translation in response to metabolic challenges remain elusive. Our results suggest that the mitochondrial acetylation status controlled by Sirt3 and its proposed opponent GCN5L1 is an important regulator of the metabolic adaptation of mitochondrial translation. Moreover, both proteins modulate regulators of cytoplasmic protein synthesis as well as the mitonuclear protein balance making Sirt3 and GCN5L1 key players in synchronizing mitochondrial and cytoplasmic translation. Our results thereby highlight regulation of mitochondrial translation as a novel component in the cellular nutrient sensing scheme and identify mitochondrial acetylation as a new regulatory principle for the metabolic competence of mitochondrial protein synthesis. © 2014 International Union of Biochemistry and Molecular Biology.

Understanding Protein-Protein Interactions Using Local Structural Features

DEFF Research Database (Denmark)

Planas-Iglesias, Joan; Bonet, Jaume; García-García, Javier

2013-01-01

Protein-protein interactions (PPIs) play a relevant role among the different functions of a cell. Identifying the PPI network of a given organism (interactome) is useful to shed light on the key molecular mechanisms within a biological system. In this work, we show the role of structural features...... interacting and non-interacting protein pairs to classify the structural features that sustain the binding (or non-binding) behavior. Our study indicates that not only the interacting region but also the rest of the protein surface are important for the interaction fate. The interpretation...... to score the likelihood of the interaction between two proteins and to develop a method for the prediction of PPIs. We have tested our method on several sets with unbalanced ratios of interactions and non-interactions to simulate real conditions, obtaining accuracies higher than 25% in the most unfavorable...

MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping.

Science.gov (United States)

Zhang, Chengxin; Zheng, Wei; Freddolino, Peter L; Zhang, Yang

2018-03-10

Homology-based transferal remains the major approach to computational protein function annotations, but it becomes increasingly unreliable when the sequence identity between query and template decreases below 30%. We propose a novel pipeline, MetaGO, to deduce Gene Ontology attributes of proteins by combining sequence homology-based annotation with low-resolution structure prediction and comparison, and partner's homology-based protein-protein network mapping. The pipeline was tested on a large-scale set of 1000 non-redundant proteins from the CAFA3 experiment. Under the stringent benchmark conditions where templates with >30% sequence identity to the query are excluded, MetaGO achieves average F-measures of 0.487, 0.408, and 0.598, for Molecular Function, Biological Process, and Cellular Component, respectively, which are significantly higher than those achieved by other state-of-the-art function annotations methods. Detailed data analysis shows that the major advantage of the MetaGO lies in the new functional homolog detections from partner's homology-based network mapping and structure-based local and global structure alignments, the confidence scores of which can be optimally combined through logistic regression. These data demonstrate the power of using a hybrid model incorporating protein structure and interaction networks to deduce new functional insights beyond traditional sequence homology-based referrals, especially for proteins that lack homologous function templates. The MetaGO pipeline is available at http://zhanglab.ccmb.med.umich.edu/MetaGO/. Copyright © 2018. Published by Elsevier Ltd.

A Mesoscopic Model for Protein-Protein Interactions in Solution

OpenAIRE

Lund, Mikael; Jönsson, Bo

2003-01-01

Protein self-association may be detrimental in biological systems, but can be utilized in a controlled fashion for protein crystallization. It is hence of considerable interest to understand how factors like solution conditions prevent or promote aggregation. Here we present a computational model describing interactions between protein molecules in solution. The calculations are based on a molecular description capturing the detailed structure of the protein molecule using x-ray or nuclear ma...

A PQL (protein quantity loci) analysis of mature pea seed proteins identifies loci determining seed protein composition.

Science.gov (United States)

Bourgeois, Michael; Jacquin, Françoise; Cassecuelle, Florence; Savois, Vincent; Belghazi, Maya; Aubert, Grégoire; Quillien, Laurence; Huart, Myriam; Marget, Pascal; Burstin, Judith

2011-05-01

Legume seeds are a major source of dietary proteins for humans and animals. Deciphering the genetic control of their accumulation is thus of primary significance towards their improvement. At first, we analysed the genetic variability of the pea seed proteome of three genotypes over 3 years of cultivation. This revealed that seed protein composition variability was under predominant genetic control, with as much as 60% of the spots varying quantitatively among the three genotypes. Then, by combining proteomic and quantitative trait loci (QTL) mapping approaches, we uncovered the genetic architecture of seed proteome variability. Protein quantity loci (PQL) were searched for 525 spots detected on 2-D gels obtained for 157 recombinant inbred lines. Most protein quantity loci mapped in clusters, suggesting that the accumulation of the major storage protein families was under the control of a limited number of loci. While convicilin accumulation was mainly under the control of cis-regulatory regions, vicilins and legumins were controlled by both cis- and trans-regulatory regions. Some loci controlled both seed protein composition and protein content and a locus on LGIIa appears to be a major regulator of protein composition and of protein in vitro digestibility. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Using modified soy protein to enhance foaming of egg white protein.

Science.gov (United States)

Wang, Guang; Troendle, Molly; Reitmeier, Cheryll A; Wang, Tong

2012-08-15

It is well known that the foaming properties of egg white protein are significantly reduced when a small amount of yolk is mixed in the white. To improve foaming properties of yolk-contaminated egg white protein, soy protein isolate (SPI) and egg proteins were modified to make basic proteins, and effects of these modified proteins on egg white foaming were evaluated in a model and an angel cake system. SPI and egg yolk proteins were modified to have an isoelectric point of 10, and sonication was used to increase protein dispersibility after the ethyl esterification reaction. However, only the addition of sonicated and modified SPI (SMSPI) showed improvement of foaming in the 5% egg protein model system with 0.4% yolk addition. SMSPI was then used in making angel food cake to examine whether the cake performance reduction due to yolk contamination of the white would be restored by such alkaline protein. Cake performance was improved when cream of tartar was used together with SMSPI. Basic soy protein can be made and used to improve egg white foaming properties and cake performance. Copyright © 2012 Society of Chemical Industry.

Yeast ribosomal proteins

International Nuclear Information System (INIS)

Otaka, E.; Kobata, K.

1978-01-01

The cytoplasmic 80s ribosomal proteins from the cells of yeast Saccharomyces cerevisiae were analyzed by SDS two-dimensional polyacrylamide gel electrophoresis. Seventyfour proteins were identified and consecutively numbered from 1 to 74. Upon oxidation of the 80s proteins with performic acid, ten proteins (no. 15, 20, 35, 40, 44, 46, 49, 51, 54 and 55) were dislocated on the gel without change of the total number of protein spots. Five proteins (no. 8, 14, 16, 36 and 74) were phosphorylated in vivo as seen in 32 P-labelling experiments. The large and small subunits separated in low magnesium medium were analyzed by the above gel electrophoresis. At least forty-five and twenty-eight proteins were assumed to be in the large and small subunits, respectively. All proteins found in the 80s ribosomes, except for no. 3, were detected in either subunit without appearance of new spots. The acidic protein no. 3 seems to be lost during subunit dissociation. (orig.) [de

Specificity of molecular interactions in transient protein-protein interaction interfaces.

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Cho, Kyu-il; Lee, KiYoung; Lee, Kwang H; Kim, Dongsup; Lee, Doheon

2006-11-15

In this study, we investigate what types of interactions are specific to their biological function, and what types of interactions are persistent regardless of their functional category in transient protein-protein heterocomplexes. This is the first approach to analyze protein-protein interfaces systematically at the molecular interaction level in the context of protein functions. We perform systematic analysis at the molecular interaction level using classification and feature subset selection technique prevalent in the field of pattern recognition. To represent the physicochemical properties of protein-protein interfaces, we design 18 molecular interaction types using canonical and noncanonical interactions. Then, we construct input vector using the frequency of each interaction type in protein-protein interface. We analyze the 131 interfaces of transient protein-protein heterocomplexes in PDB: 33 protease-inhibitors, 52 antibody-antigens, 46 signaling proteins including 4 cyclin dependent kinase and 26 G-protein. Using kNN classification and feature subset selection technique, we show that there are specific interaction types based on their functional category, and such interaction types are conserved through the common binding mechanism, rather than through the sequence or structure conservation. The extracted interaction types are C(alpha)-- H...O==C interaction, cation...anion interaction, amine...amine interaction, and amine...cation interaction. With these four interaction types, we achieve the classification success rate up to 83.2% with leave-one-out cross-validation at k = 15. Of these four interaction types, C(alpha)--H...O==C shows binding specificity for protease-inhibitor complexes, while cation-anion interaction is predominant in signaling complexes. The amine ... amine and amine...cation interaction give a minor contribution to the classification accuracy. When combined with these two interactions, they increase the accuracy by 3.8%. In the case of

Protein-protein interactions in the regulation of WRKY transcription factors.

Science.gov (United States)

Chi, Yingjun; Yang, Yan; Zhou, Yuan; Zhou, Jie; Fan, Baofang; Yu, Jing-Quan; Chen, Zhixiang

2013-03-01

It has been almost 20 years since the first report of a WRKY transcription factor, SPF1, from sweet potato. Great progress has been made since then in establishing the diverse biological roles of WRKY transcription factors in plant growth, development, and responses to biotic and abiotic stress. Despite the functional diversity, almost all analyzed WRKY proteins recognize the TTGACC/T W-box sequences and, therefore, mechanisms other than mere recognition of the core W-box promoter elements are necessary to achieve the regulatory specificity of WRKY transcription factors. Research over the past several years has revealed that WRKY transcription factors physically interact with a wide range of proteins with roles in signaling, transcription, and chromatin remodeling. Studies of WRKY-interacting proteins have provided important insights into the regulation and mode of action of members of the important family of transcription factors. It has also emerged that the slightly varied WRKY domains and other protein motifs conserved within each of the seven WRKY subfamilies participate in protein-protein interactions and mediate complex functional interactions between WRKY proteins and between WRKY and other regulatory proteins in the modulation of important biological processes. In this review, we summarize studies of protein-protein interactions for WRKY transcription factors and discuss how the interacting partners contribute, at different levels, to the establishment of the complex regulatory and functional network of WRKY transcription factors.

Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures.

Science.gov (United States)

Kinjo, Akira R; Nakamura, Haruki

2013-01-01

Protein functions are mediated by interactions between proteins and other molecules. One useful approach to analyze protein functions is to compare and classify the structures of interaction interfaces of proteins. Here, we describe the procedures for compiling a database of interface structures and efficiently comparing the interface structures. To do so requires a good understanding of the data structures of the Protein Data Bank (PDB). Therefore, we also provide a detailed account of the PDB exchange dictionary necessary for extracting data that are relevant for analyzing interaction interfaces and secondary structures. We identify recurring structural motifs by classifying similar interface structures, and we define a coarse-grained representation of supersecondary structures (SSS) which represents a sequence of two or three secondary structure elements including their relative orientations as a string of four to seven letters. By examining the correspondence between structural motifs and SSS strings, we show that no SSS string has particularly high propensity to be found interaction interfaces in general, indicating any SSS can be used as a binding interface. When individual structural motifs are examined, there are some SSS strings that have high propensity for particular groups of structural motifs. In addition, it is shown that while the SSS strings found in particular structural motifs for nonpolymer and protein interfaces are as abundant as in other structural motifs that belong to the same subunit, structural motifs for nucleic acid interfaces exhibit somewhat stronger preference for SSS strings. In regard to protein folds, many motif-specific SSS strings were found across many folds, suggesting that SSS may be a useful description to investigate the universality of ligand binding modes.

Prediction of protein–protein interactions: unifying evolution and structure at protein interfaces

International Nuclear Information System (INIS)

Tuncbag, Nurcan; Gursoy, Attila; Keskin, Ozlem

2011-01-01

The vast majority of the chores in the living cell involve protein–protein interactions. Providing details of protein interactions at the residue level and incorporating them into protein interaction networks are crucial toward the elucidation of a dynamic picture of cells. Despite the rapid increase in the number of structurally known protein complexes, we are still far away from a complete network. Given experimental limitations, computational modeling of protein interactions is a prerequisite to proceed on the way to complete structural networks. In this work, we focus on the question 'how do proteins interact?' rather than 'which proteins interact?' and we review structure-based protein–protein interaction prediction approaches. As a sample approach for modeling protein interactions, PRISM is detailed which combines structural similarity and evolutionary conservation in protein interfaces to infer structures of complexes in the protein interaction network. This will ultimately help us to understand the role of protein interfaces in predicting bound conformations

Shotgun protein sequencing.

Energy Technology Data Exchange (ETDEWEB)

Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

2009-06-01

A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

Protein-protein interactions within late pre-40S ribosomes.

Directory of Open Access Journals (Sweden)

Melody G Campbell

2011-01-01

Full Text Available Ribosome assembly in eukaryotic organisms requires more than 200 assembly factors to facilitate and coordinate rRNA transcription, processing, and folding with the binding of the ribosomal proteins. Many of these assembly factors bind and dissociate at defined times giving rise to discrete assembly intermediates, some of which have been partially characterized with regards to their protein and RNA composition. Here, we have analyzed the protein-protein interactions between the seven assembly factors bound to late cytoplasmic pre-40S ribosomes using recombinant proteins in binding assays. Our data show that these factors form two modules: one comprising Enp1 and the export adaptor Ltv1 near the beak structure, and the second comprising the kinase Rio2, the nuclease Nob1, and a regulatory RNA binding protein Dim2/Pno1 on the front of the head. The GTPase-like Tsr1 and the universally conserved methylase Dim1 are also peripherally connected to this second module. Additionally, in an effort to further define the locations for these essential proteins, we have analyzed the interactions between these assembly factors and six ribosomal proteins: Rps0, Rps3, Rps5, Rps14, Rps15 and Rps29. Together, these results and previous RNA-protein crosslinking data allow us to propose a model for the binding sites of these seven assembly factors. Furthermore, our data show that the essential kinase Rio2 is located at the center of the pre-ribosomal particle and interacts, directly or indirectly, with every other assembly factor, as well as three ribosomal proteins required for cytoplasmic 40S maturation. These data suggest that Rio2 could play a central role in regulating cytoplasmic maturation steps.