Ultrastructural changes and the distribution of arabinogalactan proteins during somatic embryogenesis of banana (Musa spp. AAA cv. 'Yueyoukang 1').

Science.gov (United States)

Pan, Xiao; Yang, Xiao; Lin, Guimei; Zou, Ru; Chen, Houbin; Samaj, Jozef; Xu, Chunxiang

2011-08-01

A better understanding of somatic embryogenesis in banana (Musa spp.) may provide a practical way to improve regeneration of banana plants. In this study, we applied scanning electron microscopy (SEM) and transmission electron microscopy (TEM) to visualize the ultrastructural changes during somatic embryogenesis of banana (Musa AAA cv. 'Yueyoukang 1'). We also used histological and immunohistochemical techniques with 16 monoclonal antibodies to study the spatial distribution and cellular/subcellular localization of different arabinogalactan protein (AGP) components of the cell wall during somatic embryogenesis. Histological study with periodic acid-Schiff staining documented diverse embryogenic stages from embryogenic cells (ECs) to the late embryos. SEM revealed a mesh-like structure on the surface of proembryos which represented an early structural marker of somatic embryogenesis. TEM showed that ECs were rich in juvenile mitochondria, endoplasmic reticulum and Golgi stacks. Cells in proembryos and early globular embryos resembled ECs, but they were more vacuolated, showed more regular nuclei and slightly more developed organelles. Immunocytochemical study revealed that the signal of most AGP epitopes was stronger in starch-rich cells when compared with typical ECs. The main AGP component in the extracellular matrix surface network of banana proembryos was the MAC204 epitope. Later, AGP immunolabelling patterns varied with the developmental stages of the embryos. These results about developmental regulation of AGP epitopes along with developmental changes in the ultrastructure of cells are providing new insights into the somatic embryogenesis of banana. Copyright © Physiologia Plantarum 2011.

Distribution of some pectic and arabinogalactan protein epitopes during Solanum lycopersicum (L.) adventitious root development.

Science.gov (United States)

Sala, Katarzyna; Malarz, Katarzyna; Barlow, Peter W; Kurczyńska, Ewa U

2017-01-25

The adventitious roots (AR) of plants share the same function as primary and lateral roots (LR), although their development is mainly an adaptive reaction to stress conditions. Regeneration of grafted plants is often accompanied by AR formation thus making the grafting technique a good model for studying AR initiation and development and their means of emergence. Pectins and arabinogalactan proteins (AGP) are helpful markers of particular cellular events, such as programmed cell death (PCD), elongation, proliferation or other differentiation events that accompany AR development. However, little is known about the distribution of pectins and AGPs during AR ontogeny, either in the primordium or stem tissues from which AR arise or their correspondence with these events during LR formation. AR were developed from different stem tissues such as parenchyma, xylem rays and the cambium, depending on the stem age and treatment (grafting versus cutting) of the parental tissue. Immunochemical analysis of the presence of pectic (LM8, LM19, LM20) and AGP (JIM8, JIM13, JIM16) epitopes in AR and AR-associated tissues showed differential, tissue-specific distributions of these epitopes. Two pectic epitopes (LM19, LM20) were developmentally regulated and the occurrence of the LM8 xylogalacturonan epitope in the root cap of the AR differed from other species described so far. AGP epitopes were abundantly present in the cytoplasmic compartments (mainly the tonoplast) and were correlated with the degree of cell vacuolisation. JIM8 and JIM13 epitopes were detected in the more advanced stages of primordium development, whereas the JIM16 epitope was present from the earliest division events of the initial AR cells. The comparison between AR and LR showed quantitative (AGP,) and qualitative (pectins) differences. The chemical compositions of adventitious and lateral root cells show differences that correlate with the different origins of these cells. In AR, developmental changes in the

Behavior of Triticum durum Desf. arabinoxylans and arabinogalactan peptides during industrial pasta processing.

Science.gov (United States)

Ingelbrecht, J A; Verwimp, T; Grobet, P J; Delcour, J A

2001-04-01

Three industrial pasta processing lines for different products (macaroni, capellini and instant noodles) were sampled at three subsequent stages (semolina, extruded, and dried end products) in the process. Arabinoxylans (AX) and arabinogalactan peptides (AGP) were analyzed. Although very low endoxylanase activities were measured, the level of water-extractable AX (WE-AX) increased, probably because of mechanical forces. No change was observed in the level and structural characteristics of AGP. The WE-AX molecular weight (MW) profiles showed a very small shift toward lower MW profiles; those of AGP revealed no changes as a result of the production process. After separation of WE-AX and AGP, (1)H NMR analysis and gas chromatography of the alditol acetates obtained following hydrolysis, reduction, and acetylation revealed no changes in the arabinose substitution profile of the WE-AX samples during pasta processing. At optimal cooking times, WE-AX losses in the cooking water are small (maximally 5.9%). However, the loss of AGP is more pronounced (maximally 25.0%). Overcooking led to more losses of both components.

Effect of arabinogalactan proteins from the root caps of pea and Brassica napus on Aphanomyces euteiches zoospore chemotaxis and germination.

Science.gov (United States)

Cannesan, Marc Antoine; Durand, Caroline; Burel, Carole; Gangneux, Christophe; Lerouge, Patrice; Ishii, Tadashi; Laval, Karine; Follet-Gueye, Marie-Laure; Driouich, Azeddine; Vicré-Gibouin, Maïté

2012-08-01

Root tips of many plant species release a number of border, or border-like, cells that are thought to play a major role in the protection of root meristem. However, little is currently known on the structure and function of the cell wall components of such root cells. Here, we investigate the sugar composition of the cell wall of the root cap in two species: pea (Pisum sativum), which makes border cells, and Brassica napus, which makes border-like cells. We find that the cell walls are highly enriched in arabinose and galactose, two major residues of arabinogalactan proteins. We confirm the presence of arabinogalactan protein epitopes on root cap cell walls using immunofluorescence microscopy. We then focused on these proteoglycans by analyzing their carbohydrate moieties, linkages, and electrophoretic characteristics. The data reveal (1) significant structural differences between B. napus and pea root cap arabinogalactan proteins and (2) a cross-link between these proteoglycans and pectic polysaccharides. Finally, we assessed the impact of root cap arabinogalactan proteins on the behavior of zoospores of Aphanomyces euteiches, an oomycetous pathogen of pea roots. We find that although the arabinogalactan proteins of both species induce encystment and prevent germination, the effects of both species are similar. However, the arabinogalactan protein fraction from pea attracts zoospores far more effectively than that from B. napus. This suggests that root arabinogalactan proteins are involved in the control of early infection of roots and highlights a novel role for these proteoglycans in root-microbe interactions.

Effect of Arabinogalactan Proteins from the Root Caps of Pea and Brassica napus on Aphanomyces euteiches Zoospore Chemotaxis and Germination12[C][W

Science.gov (United States)

Cannesan, Marc Antoine; Durand, Caroline; Burel, Carole; Gangneux, Christophe; Lerouge, Patrice; Ishii, Tadashi; Laval, Karine; Follet-Gueye, Marie-Laure; Driouich, Azeddine; Vicré-Gibouin, Maïté

2012-01-01

Root tips of many plant species release a number of border, or border-like, cells that are thought to play a major role in the protection of root meristem. However, little is currently known on the structure and function of the cell wall components of such root cells. Here, we investigate the sugar composition of the cell wall of the root cap in two species: pea (Pisum sativum), which makes border cells, and Brassica napus, which makes border-like cells. We find that the cell walls are highly enriched in arabinose and galactose, two major residues of arabinogalactan proteins. We confirm the presence of arabinogalactan protein epitopes on root cap cell walls using immunofluorescence microscopy. We then focused on these proteoglycans by analyzing their carbohydrate moieties, linkages, and electrophoretic characteristics. The data reveal (1) significant structural differences between B. napus and pea root cap arabinogalactan proteins and (2) a cross-link between these proteoglycans and pectic polysaccharides. Finally, we assessed the impact of root cap arabinogalactan proteins on the behavior of zoospores of Aphanomyces euteiches, an oomycetous pathogen of pea roots. We find that although the arabinogalactan proteins of both species induce encystment and prevent germination, the effects of both species are similar. However, the arabinogalactan protein fraction from pea attracts zoospores far more effectively than that from B. napus. This suggests that root arabinogalactan proteins are involved in the control of early infection of roots and highlights a novel role for these proteoglycans in root-microbe interactions. PMID:22645070

Identification of fasciclin-like arabinogalactan proteins in textile hemp (Cannabis sativa L.): in silico analyses and gene expression patterns in different tissues.

Science.gov (United States)

Guerriero, Gea; Mangeot-Peter, Lauralie; Legay, Sylvain; Behr, Marc; Lutts, Stanley; Siddiqui, Khawar Sohail; Hausman, Jean-Francois

2017-09-20

The fasciclin-like arabinogalactan proteins (FLAs) belong to the arabinogalactan protein (AGP) superfamily and are known to play different physiological roles in plants. This class of proteins was shown to participate in plant growth, development, defense against abiotic stresses and, notably, cell wall biosynthesis. Although some studies are available on the characterization of FLA genes from different species, both woody and herbaceous, no detailed information is available on the FLA family of textile hemp (Cannabis sativa L.), an economically important fibre crop. By searching the Cannabis genome and EST databases, 23 CsaFLAs have been here identified which are divided into four phylogenetic groups. A real-time qPCR analysis performed on stem tissues (isolated bast fibres and shivs sampled at three heights), hypocotyls (6-9-12-15-17-20 days-old), whole seedlings, roots, leaves and female/male flowers of the monoecious fibre variety Santhica 27, indicates that the identified FLA genes are differentially expressed. Interestingly, some hemp FLAs are expressed during early phases of fibre growth (elongation), while others are more expressed in the middle and base of the stem and thus potentially involved in secondary cell wall formation (fibre thickening). The bioinformatic analysis of the promoter regions shows that the FLAs upregulated in the younger regions of the stem share a conserved motif related to flowering control and regulation of photoperiod perception. The promoters of the FLA genes expressed at higher levels in the older stem regions, instead, share a motif putatively recognized by MYB3, a transcriptional repressor belonging to the MYB family subgroup S4. These results point to the existence of a transcriptional network fine-tuning the expression of FLA genes in the older and younger regions of the stem, as well as in the bast fibres/shivs of textile hemp. In summary, our study paves the way for future analyses on the biological functions of FLAs in

The role of wine polysaccharides on salivary protein-tannin interaction: A molecular approach.

Science.gov (United States)

Brandão, Elsa; Silva, Mafalda Santos; García-Estévez, Ignacio; Williams, Pascale; Mateus, Nuno; Doco, Thierry; de Freitas, Victor; Soares, Susana

2017-12-01

Polysaccharides are described to inhibit aggregation between food polyphenols and salivary proteins (SP) and may hence lead to astringency modulation. In this work, the effect of two wine polysaccharides (arabinogalactan proteins-AGPs and rhamnogalacturonan II- RGII) on SP-polyphenol interaction was evaluated. In general, both polysaccharides were effective to inhibit or reduce SP-polyphenol interaction and aggregation. They can act by two different mechanisms (ternary or competitive) depending on the SP-tannin pair. In the case of salivary P-B peptide, AGPs and RGII seem to act by a ternary mechanism, in which they surround this complex, enhancing its solubility. Concerning acidic proline-rich proteins (aPRPs), it was possible to observe both mechanisms, depending on the tannin and the polysaccharide involved. Overall, this work point out for a specific property of wine polysaccharides important to modulate this and other beverages and food astringency perception. Copyright © 2017 Elsevier Ltd. All rights reserved.

Interaction with bovine serum albumin of an anti-oxidative pectic arabinogalactan from Andrographis paniculata.

Science.gov (United States)

Chatterjee, Udipta R; Ray, Sayani; Micard, Valérie; Ghosh, Debjani; Ghosh, Kanika; Bandyopadhyay, Shruti S; Ray, Bimalendu

2014-01-30

A pectic arabinogalactan was obtained from the leaves of Andrographis paniculata by aqueous extraction followed by α-amylase treatment, deproteination, and anion exchange chromatography. Methylation analysis, Smith degradation, and NMR spectroscopy indicated that it was a highly branched arabinogalactan containing a (1→3)-linked β-d-Galp main chain, substituted at O-6 by (1→6)-linked β-d-Galp side chains. The latter residues were substituted at O-3 by (1→5)- and (1→3)-linked α-l-Araf chains, and non reducing end-units of α-l-Araf and β-d-Galp. This homogeneous arabinogalactan (36 kDa), which contained phenolic acids, showed dose-dependent anti-oxidative properties. The phenolic acid moieties might be the functional sites. This arabinogalactan can form a complex with bovine serum albumin having binding constant K=6.48 × 10(6)/M. Thus, this study is an important step forward to investigate the involvement of arabinogalactan in processes including interaction with biologically important transport proteins. Copyright © 2013 Elsevier Ltd. All rights reserved.

Characterization of Carbohydrate Active Enzymes Involved in Arabinogalactan Protein Metabolism

DEFF Research Database (Denmark)

Knoch, Eva

and tissues, their functions and synthesis are still poorly understood. The aim of the research presented in the thesis was to characterize carbohydrate active enzymes involved in AGP biosynthesis and modification to gain insights into the biosynthesis of the glycoproteins in plants. Candidate...... glycosyltransferases and glycoside hydrolases were selected based on co-expression profiles from a transcriptomics analysis. Reverse genetics approach on a novel glucuronosyltransferase involved in AGP biosynthesis has revealed that the enzyme activity is required for normal cell elongation in etiolated seedlings....... The enzymatic activity of a hydrolase from GH family 17 was investigated, without successful determination of the activity. Members of hydrolase family 43 appeared to be localized in the Golgi-apparatus, which is also the compartment for glycan biosynthesis. The localization of these glycoside hydrolases...

Agp2, a Member of the Yeast Amino Acid Permease Family, Positively Regulates Polyamine Transport at the Transcriptional Level

KAUST Repository

Aouida, Mustapha

2013-06-03

Agp2 is a plasma membrane protein of the Saccharomyces cerevisiae amino acid transporter family, involved in high-affinity uptake of various substrates including L-carnitine and polyamines. The discovery of two high affinity polyamine permeases, Dur3 and Sam3, prompted us to investigate whether Agp2 directly transports polyamines or acts instead as a regulator. Herein, we show that neither dur3? nor sam3? single mutant is defective in polyamine transport, while the dur3? sam3? double mutant exhibits a sharp decrease in polyamine uptake and an increased resistance to polyamine toxicity similar to the agp2? mutant. Studies of Agp2 localization indicate that in the double mutant dur3? sam3?, Agp2-GFP remains plasma membrane-localized, even though transport of polyamines is strongly reduced. We further demonstrate that Agp2 controls the expression of several transporter genes including DUR3 and SAM3, the carnitine transporter HNM1 and several hexose, nucleoside and vitamin permease genes, in addition to SKY1 encoding a SR kinase that positively regulates low-affinity polyamine uptake. Furthermore, gene expression analysis clearly suggests that Agp2 is a strong positive regulator of additional biological processes. Collectively, our data suggest that Agp2 might respond to environmental cues and thus regulate the expression of several genes including those involved in polyamine transport. © 2013 Aouida et al.

Agp2, a Member of the Yeast Amino Acid Permease Family, Positively Regulates Polyamine Transport at the Transcriptional Level

KAUST Repository

Aouida, Mustapha; Texeira, Marta Rubio; Thevelein, Johan M.; Poulin, Richard; Ramotar, Dindial

2013-01-01

Agp2 is a plasma membrane protein of the Saccharomyces cerevisiae amino acid transporter family, involved in high-affinity uptake of various substrates including L-carnitine and polyamines. The discovery of two high affinity polyamine permeases, Dur3 and Sam3, prompted us to investigate whether Agp2 directly transports polyamines or acts instead as a regulator. Herein, we show that neither dur3? nor sam3? single mutant is defective in polyamine transport, while the dur3? sam3? double mutant exhibits a sharp decrease in polyamine uptake and an increased resistance to polyamine toxicity similar to the agp2? mutant. Studies of Agp2 localization indicate that in the double mutant dur3? sam3?, Agp2-GFP remains plasma membrane-localized, even though transport of polyamines is strongly reduced. We further demonstrate that Agp2 controls the expression of several transporter genes including DUR3 and SAM3, the carnitine transporter HNM1 and several hexose, nucleoside and vitamin permease genes, in addition to SKY1 encoding a SR kinase that positively regulates low-affinity polyamine uptake. Furthermore, gene expression analysis clearly suggests that Agp2 is a strong positive regulator of additional biological processes. Collectively, our data suggest that Agp2 might respond to environmental cues and thus regulate the expression of several genes including those involved in polyamine transport. © 2013 Aouida et al.

Back to the future with the AGP–Ca2+ flux capacitor

Science.gov (United States)

Lamport, Derek T. A.; Varnai, Peter; Seal, Charlotte E.

2014-01-01

Background Arabinogalactan proteins (AGPs) are ubiquitous in green plants. AGPs comprise a widely varied group of hydroxyproline (Hyp)-rich cell surface glycoproteins (HRGPs). However, the more narrowly defined classical AGPs massively predominate and cover the plasma membrane. Extensive glycosylation by pendant polysaccharides O-linked to numerous Hyp residues like beads of a necklace creates a unique ionic compartment essential to a wide range of physiological processes including germination, cell extension and fertilization. The vital clue to a precise molecular function remained elusive until the recent isolation of small Hyp–arabinogalactan polysaccharide subunits; their structural elucidation by nuclear magentic resonance imaging, molecular simulations and direct experiment identified a 15-residue consensus subunit as a β-1,3-linked galactose trisaccharide with two short branched sidechains each with a single glucuronic acid residue that binds Ca2+ when paired with its adjacent sidechain. Scope AGPs bind Ca2+ (Kd ∼ 6 μm) at the plasma membrane (PM) at pH ∼5·5 but release it when auxin-dependent PM H+-ATPase generates a low periplasmic pH that dissociates AGP–Ca2+ carboxylates (pka ∼3); the consequential large increase in free Ca2+ drives entry into the cytosol via Ca2+ channels that may be voltage gated. AGPs are thus arguably the primary source of cytosolic oscillatory Ca2+ waves. This differs markedly from animals, in which cytosolic Ca2+ originates mostly from internal stores such as the sarcoplasmic reticulum. In contrast, we propose that external dynamic Ca2+ storage by a periplasmic AGP capacitor co-ordinates plant growth, typically involving exocytosis of AGPs and recycled Ca2+, hence an AGP–Ca2+ oscillator. Conclusions The novel concept of dynamic Ca2+ recycling by an AGP–Ca2+ oscillator solves the long-standing problem of a molecular-level function for classical AGPs and thus integrates three fields: AGPs, Ca2+ signalling and auxin

INFLUENCE OF THE DIHYDROQUERCETIN AND ARABINOGALACTAN COMPOSITION ON LYMPH FLOW

Directory of Open Access Journals (Sweden)

A. Yu. Shamanaev

2014-01-01

Full Text Available Purpose. To evaluate lymphokinetic activity of the dihydroquercetin and arabinogalactan composition.Material and methods. The investigation was carried out on male Wistar rats. Lymphokinetic activity was determined by the rate of lymph outflow through the puncture of cisterna chili after intragastricall administration of the dihydroquercetin and arabinogalactan composition with ratio 1 : 5 (50 mg/kg + 250 mg/kg.Results. It was established that lymphokinetic activity of the dihydroquercetin and arabinogalactan composition with ratio 1 : 5 (50 mg/kg + 250 mg/kg exceeds activity of it´s components.

Structure of the arabinogalactan from gum tragacanth (Astralagus gummifer).

Science.gov (United States)

Tischer, Cesar A; Iacomini, Marcello; Gorin, Philip A J

2002-10-08

The polysaccharide obtained by ethanol precipitation from an aqueous solution of gum tragacanth contained arabinogalactan and tragacanthic acid, as well as starch ( approximately 0.6%). GC-MS, NMR, and ESI-MS analyses showed the structure of the arabinogalactan to be even more complex than previously determined, with core structures containing Arap, beta-Araf, and alpha-Galp units, as well as known terminal, and 2-O- and 3-O-substituted alpha-Araf units. Analysis was aided by examination of free, reducing oligosaccharides present in the gum. In addition to maltose, maltotriose, maltotetraose, and maltopentaose, the following were characterized: mixed alpha-Araf (1-->2)-alpha-Araf-(1-->4)-Ara and alpha-Araf-(1-->2)-alpha-Araf-(1-->5)-Ara, which correspond to the side chains of the arabinogalactan, beta-Galp-(1-->4)-beta-Galp-(1-->4)-beta-Galp-(1-->4)-Gal; and a mixture of beta-Galp-(1-->4)-beta-Galp-(1-->4)-Gal and beta-Glcp-(1-->4)-beta-Galp-(1-->4)-beta-Galp-(1-->4)-Gal, which did not resemble side-chain structures of the arabinogalactan. The latter are suggested to be related to tragacanthic acid, which has been previously found to contain beta-Galp nonreducing end-units.

Antitussive arabinogalactan of Andrographis paniculata demonstrates synergistic effect with andrographolide.

Science.gov (United States)

Nosáľová, Gabriela; Majee, Sujay Kumar; Ghosh, Kanika; Raja, Washim; Chatterjee, Udipta Ranjan; Jureček, Ludovít; Ray, Bimalendu

2014-08-01

Traditional Indian medicines have been used in humans for thousands of years. While the link to a particular indication has been established in man, the active principle of the formulations often remains unknown. In this study, we aim to investigate the structural features and antitussive activity of fractions from Andrographis paniculata leaves. In vivo investigations of water extract (WE), and both ethanol-soluble (WES) and precipitated (WEP) fractions from WE on the citric-acid induced cough efforts and airways smooth muscle reactivity in guinea pigs were performed. Chemical, chromatographic and spectroscopic analysis revealed the existence of a highly branched pectic arabinogalactan (109kDa) in WEP and andrographolide in WES. WEP showed significant antitussive activity while the potencies of WE and WES are even higher. Neither WE nor WES significantly alter specific airway smooth muscle reactivity. Remarkably, the antitussive activity of arabinogalactan could be increased by synergistic action with andrographolide. Finally, traditional aqueous extraction method provides an arabinogalactan from A. paniculata, which stimulate biological response but without addiction. Copyright © 2014 Elsevier B.V. All rights reserved.

The AGP-Project conceptual design for a Spanish HLW final disposal facility

International Nuclear Information System (INIS)

Biurrun, E.; Engelmann, H.-J.; Huertas, F.; Ulibarri, A.

1992-01-01

Within the framework of the AGP Project a Conceptual Design for a HLW Final Disposal Facility to be eventually built in an underground salt formation in Spain has been developed. The AGP Project has the character of a system analysis. In the current project phase I several alternatives has been considered for different subsystems and/or components of the repository. The system variants, developed to such extent as to allow a comparison of their advantages and disadvantages, will allow the selection of a reference concept, which will be further developed to technical maturity in subsequent project phases. (author)

Identification of a novel group of putative Arabidopsis thaliana beta-(1,3)-galactosyltransferases

DEFF Research Database (Denmark)

Qu, Yongmei; Egelund, Jack; Gilson, Paul R

2008-01-01

To begin biochemical and molecular studies on the biosynthesis of the type II arabinogalactan chains on arabinogalactan-proteins (AGPs), we adopted a bioinformatic approach to identify and systematically characterise the putative galactosyltransferases (GalTs) responsible for synthesizing the beta......-(1,3)-Gal linkage from CAZy GT-family-31 from Arabidopsis thaliana. These analyses confirmed that 20 members of the GT-31 family contained domains/motifs typical of biochemically characterised beta-(1,3)-GTs from mammalian systems. Microarray data confirm that members of this family are expressed......,3)-GalT activity. This bioinformatic/molecular study of CAZy GT-family-31 was validated by the recent report of Strasser et al. (Plant Cell 19:2278-2292, 2007) that another member of this family (At1g26810; GALT1) encodes a beta-(1,3)-GalT involved in the biosynthesis of the Lewis a epitope of N...

Pectic type II arabinogalactans from starfruit (Averrhoa carambola L.).

Science.gov (United States)

Leivas, Carolina Lopes; Iacomini, Marcello; Cordeiro, Lucimara M C

2016-05-15

A structural characterization of polysaccharides from edible tropical fruit named starfruit (Averrhoa carambola L.) was carried out. After the purification steps, two homogeneous fractions were obtained. Fraction 50R was composed of rhamnose, arabinose, galactose and uronic acid in 4.3:56.2:37.4:2M ratio, respectively and fraction 10R was composed of rhamnose, arabinose, galactose and uronic acid in 2.8:65.8:28.5:3M ratio, respectively. Methylation and NMR spectroscopy analyses showed that these fractions are formed by pectic arabinogalactans, which contain (1→3), (1→6) and (1→3,6)-linked Galp units. The side chains have 3-O-, 5-O- and 3,5-di-O-linked α-Araf and nonreducing end-units of α-Araf, Arap, β-Galp and α-GlcpA. These arabinogalactans were linked to type I rhamnogalacturonans. Copyright © 2015 Elsevier Ltd. All rights reserved.

Interaction of wine mannoproteins and arabinogalactans with anthocyanins.

Science.gov (United States)

Gonçalves, Fernando J; Fernandes, Pedro A R; Wessel, Dulcineia F; Cardoso, Susana M; Rocha, Silvia M; Coimbra, Manuel A

2018-03-15

Wine polymeric material (WPM), which includes polysaccharides, proteins, and polyphenolic compounds, interacts with anthocyanins. To determine the contribution of polysaccharides in these interactions, the diffusion performance of anthocyanins along a dialysis membrane was determined in the presence and absence of isolated mannoproteins (MP) and arabinogalactans (AG) from WPM. Furthermore, to estimate the extent of the interaction between WPM and polyphenolic compounds, the activation energy (E a ) required for their diffusion in the presence of WPM was determined. AG, generally more abundant than MP in wine, interact in a greater extent with anthocyanins, showing their relevant contribution for WPM/anthocyanins interactions. The E a for the diffusion of polyphenolic compounds in presence of WPM indicated the occurrence of interactions with relative weak to strong intensities (2.6-50.8kJ/mol). As not all polyphenolic compounds were able to be released from WPM, stronger interactions, possibly by covalent linkages, are involved, providing new insights on WPM/polyphenolic compounds relationships. Copyright © 2017 Elsevier Ltd. All rights reserved.

Role of proline in cell wall synthesis and plant development and its implications in plant ontogeny

Directory of Open Access Journals (Sweden)

POLAVARAPU BILHAN KAVI KISHOR

2015-07-01

Full Text Available Proline is a proteogenic amino acid and accumulates both under stress and non-stress conditions as a beneficial solute in plants. Recent discoveries point out that proline plays an important role in plant growth and differentiation across life cycle. It is a key determinant of many cell wall proteins that plays important roles in plant development. The role of extensins (EXTs, arabinogalactan proteins (AGPs and hydroxyproline- and proline-rich proteins (H/PRPs as important components of cell wall proteins that play pivotal roles in cell wall signal transduction cascades, plant development and stress tolerance is discussed in this review. Molecular insights are also provided here into the plausible roles of proline transporters modulating key events in plant development. In addition, the roles of proline during seed developmental transitions including storage protein synthesis are discussed.

Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes.

Science.gov (United States)

Johnson, Kim L; Cassin, Andrew M; Lonsdale, Andrew; Wong, Gane Ka-Shu; Soltis, Douglas E; Miles, Nicholas W; Melkonian, Michael; Melkonian, Barbara; Deyholos, Michael K; Leebens-Mack, James; Rothfels, Carl J; Stevenson, Dennis W; Graham, Sean W; Wang, Xumin; Wu, Shuangxiu; Pires, J Chris; Edger, Patrick P; Carpenter, Eric J; Bacic, Antony; Doblin, Monika S; Schultz, Carolyn J

2017-06-01

The carbohydrate-rich cell walls of land plants and algae have been the focus of much interest given the value of cell wall-based products to our current and future economies. Hydroxyproline-rich glycoproteins (HRGPs), a major group of wall glycoproteins, play important roles in plant growth and development, yet little is known about how they have evolved in parallel with the polysaccharide components of walls. We investigate the origins and evolution of the HRGP superfamily, which is commonly divided into three major multigene families: the arabinogalactan proteins (AGPs), extensins (EXTs), and proline-rich proteins. Using motif and amino acid bias, a newly developed bioinformatics pipeline, we identified HRGPs in sequences from the 1000 Plants transcriptome project (www.onekp.com). Our analyses provide new insights into the evolution of HRGPs across major evolutionary milestones, including the transition to land and the early radiation of angiosperms. Significantly, data mining reveals the origin of glycosylphosphatidylinositol (GPI)-anchored AGPs in green algae and a 3- to 4-fold increase in GPI-AGPs in liverworts and mosses. The first detection of cross-linking (CL)-EXTs is observed in bryophytes, which suggests that CL-EXTs arose though the juxtaposition of preexisting SP n EXT glycomotifs with refined Y-based motifs. We also detected the loss of CL-EXT in a few lineages, including the grass family (Poaceae), that have a cell wall composition distinct from other monocots and eudicots. A key challenge in HRGP research is tracking individual HRGPs throughout evolution. Using the 1000 Plants output, we were able to find putative orthologs of Arabidopsis pollen-specific GPI-AGPs in basal eudicots. © 2017 American Society of Plant Biologists. All Rights Reserved.

Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes1[OPEN

Science.gov (United States)

Cassin, Andrew M.; Soltis, Douglas E.; Miles, Nicholas W.; Melkonian, Michael; Melkonian, Barbara; Wu, Shuangxiu; Edger, Patrick P.; Carpenter, Eric J.

2017-01-01

The carbohydrate-rich cell walls of land plants and algae have been the focus of much interest given the value of cell wall-based products to our current and future economies. Hydroxyproline-rich glycoproteins (HRGPs), a major group of wall glycoproteins, play important roles in plant growth and development, yet little is known about how they have evolved in parallel with the polysaccharide components of walls. We investigate the origins and evolution of the HRGP superfamily, which is commonly divided into three major multigene families: the arabinogalactan proteins (AGPs), extensins (EXTs), and proline-rich proteins. Using motif and amino acid bias, a newly developed bioinformatics pipeline, we identified HRGPs in sequences from the 1000 Plants transcriptome project (www.onekp.com). Our analyses provide new insights into the evolution of HRGPs across major evolutionary milestones, including the transition to land and the early radiation of angiosperms. Significantly, data mining reveals the origin of glycosylphosphatidylinositol (GPI)-anchored AGPs in green algae and a 3- to 4-fold increase in GPI-AGPs in liverworts and mosses. The first detection of cross-linking (CL)-EXTs is observed in bryophytes, which suggests that CL-EXTs arose though the juxtaposition of preexisting SPn EXT glycomotifs with refined Y-based motifs. We also detected the loss of CL-EXT in a few lineages, including the grass family (Poaceae), that have a cell wall composition distinct from other monocots and eudicots. A key challenge in HRGP research is tracking individual HRGPs throughout evolution. Using the 1000 Plants output, we were able to find putative orthologs of Arabidopsis pollen-specific GPI-AGPs in basal eudicots. PMID:28446636

Proprietary arabinogalactan extract increases antibody response to the pneumonia vaccine: a randomized, double-blind, placebo-controlled, pilot study in healthy volunteers

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Udani Jay K

2010-08-01

Full Text Available Abstract Background Arabinogalactan from Larch tree (Larix spp. bark has previously demonstrated immunostimulatory activity. The purpose of this study was to test the hypothesis that ingestion of a proprietary arabinogalactan extract, ResistAid™, would selectively enhance the antibody response to the pneumococcal (pneumonia vaccine in healthy adults. Methods This randomized, double-blind, placebo-controlled, parallel group pilot study included 45 healthy adults who had not previously been vaccinated against Streptococcus pneumoniae. The volunteers began taking the study product or placebo (daily dosage 4.5 g at the screening visit (V1-Day 0 and continued over the entire 72 day study period. After 30 days the subjects received the 23-valent pneumococcal vaccine (V2. They were monitored the following day (V3-Day 31, as well as 21 days (V4-Day 51 and 42 days (V5-Day 72 after vaccination. Responses by the adaptive immune system (antigen specific were measured via pneumococcal IgG antibodies (subtypes 4, 6B, 9V, 14, 18C, 19F, and 23F and salivary IgA levels. Responses by the innate immune system (non-specific were measured via white blood cell counts, inflammatory cytokines and the complement system. Results Vaccination significantly increased pneumococcal IgG levels as expected. The arabinogalactan group demonstrated a statistically significant greater IgG antibody response than the placebo group in two antibodies subtypes (18C and 23F at both Day 51 (p = 0.006 and p = 0.002 and at Day 72 (p = 0.008 and p = 0.041. These same subtypes (18C and 23F also demonstrated change scores from baseline which were significant, in favor of the arabinogalactan group, at Day 51 (p = 0.033 and 0.001 and at Day 72 (p = 0.012 and p = 0.003. Change scores from baseline and mean values were greater in the arabinogalactan group than placebo for most time points in antibody subtypes 4, 6B, 9V, and 19F, but these differences did not reach statistical significance. There

Proprietary arabinogalactan extract increases antibody response to the pneumonia vaccine: a randomized, double-blind, placebo-controlled, pilot study in healthy volunteers.

Science.gov (United States)

Udani, Jay K; Singh, Betsy B; Barrett, Marilyn L; Singh, Vijay J

2010-08-26

Arabinogalactan from Larch tree (Larix spp.) bark has previously demonstrated immunostimulatory activity. The purpose of this study was to test the hypothesis that ingestion of a proprietary arabinogalactan extract, ResistAid™, would selectively enhance the antibody response to the pneumococcal (pneumonia) vaccine in healthy adults. This randomized, double-blind, placebo-controlled, parallel group pilot study included 45 healthy adults who had not previously been vaccinated against Streptococcus pneumoniae. The volunteers began taking the study product or placebo (daily dosage 4.5 g) at the screening visit (V1-Day 0) and continued over the entire 72 day study period. After 30 days the subjects received the 23-valent pneumococcal vaccine (V2). They were monitored the following day (V3-Day 31), as well as 21 days (V4-Day 51) and 42 days (V5-Day 72) after vaccination. Responses by the adaptive immune system (antigen specific) were measured via pneumococcal IgG antibodies (subtypes 4, 6B, 9V, 14, 18C, 19F, and 23F) and salivary IgA levels. Responses by the innate immune system (non-specific) were measured via white blood cell counts, inflammatory cytokines and the complement system. Vaccination significantly increased pneumococcal IgG levels as expected. The arabinogalactan group demonstrated a statistically significant greater IgG antibody response than the placebo group in two antibodies subtypes (18C and 23F) at both Day 51 (p = 0.006 and p = 0.002) and at Day 72 (p = 0.008 and p = 0.041). These same subtypes (18C and 23F) also demonstrated change scores from baseline which were significant, in favor of the arabinogalactan group, at Day 51 (p = 0.033 and 0.001) and at Day 72 (p = 0.012 and p = 0.003). Change scores from baseline and mean values were greater in the arabinogalactan group than placebo for most time points in antibody subtypes 4, 6B, 9V, and 19F, but these differences did not reach statistical significance. There was no effect from the vaccine or

Entrapment of alpha1-acid glycoprotein in high-performance affinity columns for drug-protein binding studies.

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Bi, Cong; Jackson, Abby; Vargas-Badilla, John; Li, Rong; Rada, Giana; Anguizola, Jeanethe; Pfaunmiller, Erika; Hage, David S

2016-05-15

A slurry-based method was developed for the entrapment of alpha1-acid glycoprotein (AGP) for use in high-performance affinity chromatography to study drug interactions with this serum protein. Entrapment was achieved based on the physical containment of AGP in hydrazide-activated porous silica supports and by using mildly oxidized glycogen as a capping agent. The conditions needed for this process were examined and optimized. When this type of AGP column was used in binding studies, the association equilibrium constant (Ka) measured by frontal analysis at pH 7.4 and 37°C for carbamazepine with AGP was found to be 1.0 (±0.5)×10(5)M(-1), which agreed with a previously reported value of 1.0 (±0.1)×10(5)M(-1). Binding studies based on zonal elution were conducted for several other drugs with such columns, giving equilibrium constants that were consistent with literature values. An entrapped AGP column was also used in combination with a column containing entrapped HSA in a screening assay format to compare the binding of various drugs to AGP and HSA. These results also agreed with previous data that have been reported in literature for both of these proteins. The same entrapment method could be extended to other proteins and to the investigation of additional types of drug-protein interactions. Potential applications include the rapid quantitative analysis of biological interactions and the high-throughput screening of drug candidates for their binding to a given protein. Copyright © 2015 Elsevier B.V. All rights reserved.

An update on post-translational modifications of hydroxyproline-rich glycoproteins: Towards a model highlighting their contribution to plant cell wall architecture

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May eHijazi

2014-08-01

Full Text Available Plant cell walls are composite structures mainly composed of polysaccharides, also containing a large set of proteins involved in diverse functions such as growth, environmental sensing, signaling, and defense. Research on cell wall proteins (CWPs is a challenging field since present knowledge of their role into the structure and function of cell walls is very incomplete. Among CWPs, hydroxyproline (Hyp-rich O-glycoproteins (HRGPs were classified into three categories: (i moderately glycosylated extensins (EXTs able to form covalent scaffolds; (ii hyperglycosylated arabinogalactan proteins (AGPs; and (iii Hyp/proline (Pro-Rich proteins (H/PRPs that may be non-, weakly- or highly-glycosylated. In this review, we provide a description of the main features of their post-translational modifications (PTMs, biosynthesis, structure and function. We propose a new model integrating HRGPs and their partners in cell walls. Altogether, they could form a continuous glyco-network with non-cellulosic polysaccharides via covalent bonds or non-covalent interactions, thus strongly contributing to cell wall architecture.

Solvable model with an extreme AGP ground state: relationships among fermion pairs, pairons, and natural spin geminals

International Nuclear Information System (INIS)

Larson, E.G.

1986-01-01

A model many-fermion Hamiltonian is presented for which the ground state is asymptotically an Antisymmetrized Geminal Powers (AGP) wave function with largest possible greatest eigenvalue for its two-particle reduced density matrix. Closed analytical expressions and plane-wave expansions are presented for the generating geminal of the AGP ground state and for its one-particle reduced density matrix. The natural orbitals for this generating geminal are plane waves. The generating geminal shows intensely local character in its intracule and corresponds to the formation of a quasi-boson from two fermions. One may appropriately modify this generating geminal to introduce zero occupation numbers of its one-particle reduced density matrix and to make all the nonzero occupation numbers of its one-particle reduced density matrix equal, thus making this geminal a generator of an extreme AGP wave function, with an extreme large eigenvalue for its two-particle reduced density matrix. Closed analytical expressions are also given for this modified geminal and for its one-particle reduced density matrix. The similarities and differences of the features of this model and the accepted models of the superconducting ground state of electrons in metals, and the superfluid ground state of liquid He 4 are mentioned

Increased systemic elastase and C-reactive protein in aggressive periodontitis (CLOI-D-00160R2).

Science.gov (United States)

Wohlfeil, Martin; Scharf, Susanne; Siegelin, Yasemin; Schacher, Beate; Oremek, Gerhard M; Sauer-Eppel, Hildegund; Schubert, Ralf; Eickholz, Peter

2012-08-01

The inflammatory mediators, serum elastase and C-reactive protein (CRP), are associated with an increased risk for coronary heart disease. Thus, the aim of this study is to compare systemic inflammatory mediators in periodontally healthy controls (C), patients with untreated aggressive (AgP) and chronic (ChP) periodontitis. C [periodontal pocket probing depth (PPD)  30% of sites; age >35 years), and AgP (clinically healthy; PDD ≥ 3.6 mm at >30% of sites, bone loss ≥50% at ≥2 teeth; age ≤35 years) were examined clinically, and the body mass index was assessed. Blood was sampled for assessment of serum levels of elastase, CRP, lipopolysaccharide binding protein (LBP), interleukin (IL) 6, 8, and leukocyte counts. Thirty C, 31 ChP, and 29 AgP were analyzed. Elastase, CRP, LBP, and IL-6 levels were elevated in AgP compared to C (p C. AgP patients exhibit a stronger systemic inflammatory burden than C patients.

Process Optimization of Ultrasonic-Assisted Extraction of Arabinogalactan from Dihydroquercetin Extracted Residues by Response Surface Methodology and Evaluation of Its Antioxidant Activity

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Zaizhi Liu

2013-01-01

Full Text Available Ultrasound was used for the extraction of larch arabinogalactan from Larix gmelinii. The optimal conditions for ultrasound extraction were determined by response surface methodology. Specifically, the Box-Behnken design was employed to evaluate the effects of three independent variables: ultrasound time, temperature, and liquid-solid ratio. The highest arabinogalactan yield (11.18% was obtained under the optimal extraction condition (extraction temperature 41.5°C, extraction time 24.3 min, and liquid-solid ratio 40 mL/g. In addition, the antioxidant activity of arabinogalactan that was extracted from dihydroquercetin extraction residues exhibited a moderate and concentration-dependent hydroxyl radical-scavenging capacity, ferric-reducing power, and reducing power. The wood material was characterized before and after processing by scanning electron microscopy and Fourier-transform infrared spectroscopy.

Arabinogalactan glycosyltransferases target to a unique subcellular compartment that may function in unconventional secretion in plants

DEFF Research Database (Denmark)

Poulsen, Christian Peter; Dilokpimol, Adiphol; Mouille, Grégory

2014-01-01

-glycosylation enzymes rarely colocalized (3-18%), implicating a role of the small compartments in a part of arabinogalactan (O-glycan) biosynthesis rather than N-glycan processing. The dual localization of AtGALT31A was also observed for fluorescently tagged AtGALT31A stably expressed in an Arabidopsis atgalt31a mutant...... colocalized with neither SYP61 (syntaxin of plants 61), a marker for trans-Golgi network (TGN), nor FM4-64-stained endosomes. However, 41% colocalized with EXO70E2 (Arabidopsis thaliana exocyst protein Exo70 homolog 2), a marker for exocyst-positive organelles, and least affected by Brefeldin A and Wortmannin....... Taken together, AtGALT31A localized to small compartments that are distinct from the Golgi apparatus, the SYP61-localized TGN, FM4-64-stained endosomes and Wortmannin-vacuolated prevacuolar compartments, but may be part of an unconventional protein secretory pathway represented by EXO70E2 in plants....

A novel emulsion-forming arabinogalactan gum from the stems of Frost grape (Vitis riparia Michx.)

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A novel arabinogalactan polysaccharide (FGP) is described that is produced in large quantities from the cut stems of Frost grape (Vitis riparia Michx.). The sugar composition consists of L-arabinofuranose (L-Araf, 55.2 %) and D-galactopyranose (D-Galp 30.1%), with smaller components of D-xylose (11....

Frost Grape Polysaccharide (FGP), an Emulsion-Forming Arabinogalactan Gum from the Stems of Native North American Grape Species Vitis riparia Michx.

Science.gov (United States)

Price, Neil P J; Vermillion, Karl E; Eller, Fred J; Vaughn, Steven F

2015-08-19

A new arabinogalactan is described that is produced in large quantity from the cut stems of the North American grape species Vitis riparia (Frost grape). The sugar composition consists of l-arabinofuranose (l-Araf, 55.2%) and d-galactopyranose (d-Galp 30.1%), with smaller components of d-xylose (11.2%), d-mannose (3.5%), and glucuronic acid (GlcA, ∼2%), the latter linked via a galactosyl residue. Permethylation identified 3-linked Galp residues, some substituted at the 2-position with Galp or Manp, terminal Araf and Xylp, and an internal 3-substituted Araf. NMR (HSQC, TOCSY, HMBC, DOSY) identified βGalp and three αAraf spin systems, in an Araf-α1,3-Araf-α1,2-Araf-α1,2-Galp structural motif. Diffusion-ordered NMR showed that the FGP has a molecular weight of 1-10 MDa. Unlike gum arabic, the FGP does not contain a hydroxyproline-rich protein (HPRP). FGP forms stable gels at >15% w/v and at 1-12% solutions are viscous and are excellent emulsifiers of flavoring oils (grapefruit, clove, and lemongrass), giving stable emulsions for ≥72 h. Lower concentrations (0.1% w/v) were less viscous, yet still gave stable grapefruit oil/water emulsions. Hence, FGP is a β1,3-linked arabinogalactan with potential as a gum arabic replacement in the food and beverage industries.

Quantitative and qualitative characteristics of cell wall components and prenyl lipids in the leaves of Tilia x euchlora trees growing under salt stress.

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Milewska-Hendel, Anna; Baczewska, Aneta H; Sala, Katarzyna; Dmuchowski, Wojciech; Brągoszewska, Paulina; Gozdowski, Dariusz; Jozwiak, Adam; Chojnacki, Tadeusz; Swiezewska, Ewa; Kurczynska, Ewa

2017-01-01

The study was focused on assessing the presence of arabinogalactan proteins (AGPs) and pectins within the cell walls as well as prenyl lipids, sodium and chlorine content in leaves of Tilia x euchlora trees. The leaves that were analyzed were collected from trees with and without signs of damage that were all growing in the same salt stress conditions. The reason for undertaking these investigations was the observations over many years that indicated that there are trees that present a healthy appearance and trees that have visible symptoms of decay in the same habitat. Leaf samples were collected from trees growing in the median strip between roadways that have been intensively salted during the winter season for many years. The sodium content was determined using atomic spectrophotometry, chloride using potentiometric titration and poly-isoprenoids using HPLC/UV. AGPs and pectins were determined using immunohistochemistry methods. The immunohistochemical analysis showed that rhamnogalacturonans I (RG-I) and homogalacturonans were differentially distributed in leaves from healthy trees in contrast to leaves from injured trees. In the case of AGPs, the most visible difference was the presence of the JIM16 epitope. Chemical analyses of sodium and chloride showed that in the leaves from injured trees, the level of these ions was higher than in the leaves from healthy trees. Based on chromatographic analysis, four poly-isoprenoid alcohols were identified in the leaves of T. x euchlora. The levels of these lipids were higher in the leaves from healthy trees. The results suggest that the differences that were detected in the apoplast and symplasm may be part of the defensive strategy of T. x euchlora trees to salt stress, which rely on changes in the chemical composition of the cell wall with respect to the pectic and AGP epitopes and an increased synthesis of prenyl lipids.

Isolation and characterization of gene sequences expressed in cotton fiber

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Taciana de Carvalho Coutinho

2016-06-01

Full Text Available ABSTRACT Cotton fiber are tubular cells which develop from the differentiation of ovule epidermis. In addition to being one of the most important natural fiber of the textile group, cotton fiber afford an excellent experimental system for studying the cell wall. The aim of this work was to isolate and characterise the genes expressed in cotton fiber (Gossypium hirsutum L. to be used in future work in cotton breeding. Fiber of the cotton cultivar CNPA ITA 90 II were used to extract RNA for the subsequent generation of a cDNA library. Seventeen sequences were obtained, of which 14 were already described in the NCBI database (National Centre for Biotechnology Information, such as those encoding the lipid transfer proteins (LTPs and arabinogalactans (AGP. However, other cDNAs such as the B05 clone, which displays homology with the glycosyltransferases, have still not been described for this crop. Nevertheless, results showed that several clones obtained in this study are associated with cell wall proteins, wall-modifying enzymes and lipid transfer proteins directly involved in fiber development.

C-reactive protein levels in patients with aggressive periodontitis.

Science.gov (United States)

Salzberg, Trang N; Overstreet, Benjamin T; Rogers, Jeffrey D; Califano, Joseph V; Best, Al M; Schenkein, Harvey A

2006-06-01

Sera from patients with periodontal infections contain elevated levels of C-reactive protein (CRP) compared to periodontally healthy individuals. Most studies to date have included patients with chronic periodontitis, and few investigators have studied CRP levels in subjects with aggressive periodontitis (AgP). The purpose of this study was to determine the relative levels of serum CRP in AgP patients and periodontally healthy subjects and to examine patients' characteristics that might account for intergroup differences. Serum samples were collected from 93 patients with generalized AgP (GAgP), from 97 patients with localized AgP (LAgP), and from 91 healthy controls (non-periodontitis [NP]). Periodontal examination consisted of plaque index, gingival index, probing depth, bleeding index, and attachment loss measurements. Current smoking was assessed by determination of serum cotinine levels by enzyme-linked immunosorbent assay (ELISA), and serum CRP levels were determined using a high-sensitivity ELISA assay. The three groups were significantly different from one another (P periodontal and demographic variables and current smoking, both mean probing depth and periodontal diagnosis remained correlated with CRP levels. Patients with AgP have statistically significant elevations in serum CRP levels compared to subjects without periodontitis. Elevated CRP in these subjects might represent a contribution of periodontal infections to systemic inflammation in relatively young individuals.

Cellular and molecular changes associated with somatic embryogenesis induction in Agave tequilana.

Science.gov (United States)

Portillo, L; Olmedilla, A; Santacruz-Ruvalcaba, F

2012-10-01

In spite of the importance of somatic embryogenesis for basic research in plant embryology as well as for crop improvement and plant propagation, it is still unclear which mechanisms and cell signals are involved in acquiring embryogenic competence by a somatic cell. The aim of this work was to study cellular and molecular changes involved in the induction stage in calli of Agave tequilana Weber cultivar azul in order to gain more information on the initial stages of somatic embryogenesis in this species. Cytochemical and immunocytochemical techniques were used to identify differences between embryogenic and non-embryogenic cells from several genotypes. Presence of granular structures was detected after somatic embryogenesis induction in embryogenic cells; composition of these structures as well as changes in protein and polysaccharide distribution was studied using Coomassie brilliant blue and Periodic Acid-Schiff stains. Distribution of arabinogalactan proteins (AGPs) and pectins was investigated in embryogenic and non-embryogenic cells by immunolabelling using anti-AGP monoclonal antibodies (JIM4, JIM8 and JIM13) as well as an anti-methyl-esterified pectin-antibody (JIM7), in order to evaluate major modifications in cell wall composition in the initial stages of somatic embryogenesis. Our observations pointed out that induction of somatic embryogenesis produced accumulation of proteins and polysaccharides in embryogenic cells. Presence of JIM8, JIM13 and JIM7 epitopes were detected exclusively in embryogenic cells, which supports the idea that specific changes in cell wall are involved in the acquisition of embryogenic competence of A. tequilana.

Structural characterization of a rhamnogalacturonan I-arabinan-type I arabinogalactan macromolecule from starfruit (Averrhoa carambola L.).

Science.gov (United States)

Leivas, Carolina Lopes; Iacomini, Marcello; Cordeiro, Lucimara M C

2015-05-05

A structural characterization of polysaccharides obtained from edible tropical fruit named starfruit (Averrhoa carambola L.) was carried out. After fractionation by freeze-thaw and Fehling precipitation, a pectic polysaccharide was obtained. It was composed of rhamnose, arabinose, galactose and uronic acid in the 5.0:72.5:12.1:10.4 molar ratios, respectively. A combination of monosaccharide, GPC, methylation and NMR analysis and enzymatic hydrolysis with endo-β-(1→4)-D-galactanase showed the presence of a rhamnogalacturonan I to which a branched arabinan and a type I arabinogalactan are attached. The arabinan moiety was formed by (1→5)-linked α-L-Araf units in the backbone, branched only at O-3 by (1→2)- and (1→3)-linked α-L-Araf units, while the type I arabinogalactan was formed by (1→4)- and (1→4,6)-linked β-D-Galp units in the backbone with (1→5)-, (1→3,5)- and (1→3)-linked α-L-Araf units as side chains. Copyright © 2014 Elsevier Ltd. All rights reserved.

Open-source implementation of an ad-hoc IEEE802.11a/g/p software-defined radio on low-power and low-cost general purpose processors

Directory of Open Access Journals (Sweden)

S. Ciccia

2017-12-01

Full Text Available This work proposes a low-cost and low-power software-defined radio open-source platform with IEEE 802.11 a/g/p wireless communication capability. A state-of-the-art version of the IEEE 802.11 a/g/p software for GNU Radio (a free and open-source software development framework is available online, but we show here that its computational complexity prevents operations in low-power general purpose processors, even at throughputs below the standard. We therefore propose an evolution of this software that achieves a faster and lighter IEEE 802.11 a/g/p transmitter and receiver, suitable for low-power general purpose processors, for which GNU Radio provides very limited support; we discuss and describe the software radio processing structuring that is necessary to achieve the goal, providing a review of signal processing techniques. In particular, we emphasize the advanced reduced-instruction set (RISC machine (ARM study case, for which we also optimize some of the processing libraries. The presented software will remain open-source.

A Physicochemical and Pharmacological Study of the Newly Synthesized Complex of Albendazole and the Polysaccharide Arabinogalactan from Larch Wood.

Science.gov (United States)

Chistyachenko, Yulia S; Meteleva, Elizaveta S; Pakharukova, Maria Y; Katokhin, Aleksey V; Khvostov, Mikhail V; Varlamova, Anastasiya I; Glamazdin, Igor I; Khalikov, Salavat S; Polyakov, Nikolay E; Arkhipov, Ivan A; Tolstikova, Tatyana G; Mordvinov, Viatcheslav A; Dushkin, Alexander V; Lyakhov, Nikolay Z

2015-01-01

Inclusion complexes of albendazole (ABZ) with the polysaccharide arabinogalactan from larch wood Larix sibirica and Larix gmelinii were synthesized using a solid-state mechanochemical technology. We investigated physicochemical properties of the synthesized complexes in the solid state and in aqueous solutions as well as their anthelmintic activity against Trichinella spiralis, Hymenolepis nаna, Fasciola hepatica, Opisthorchis felineus, and mixed nematodoses of sheep. Formation of the complexes was demonstrated by means of intrinsic solubility and the NMR relaxation method. The mechanochemically synthesized complexes were more stable in comparison with the complex produced by mixing solutions of the components. The complexes of ABZ showed anthelmintic activity at 10-fold lower doses than did free ABZ. The complexes also showed lower acute toxicity and hepatotoxicity. These results suggest that it is possible to design new drugs on the basis of the ABZ:arabinogalactan complex that are safer and more effective than albendazole.

The exploit of cereal embryo structure for productive reasons by in vitro techniques

Science.gov (United States)

Savaskan, C.

2017-07-01

There are two main sides of our works exploiting embryo structure in durum wheat and some other cereals. First is haploid (or doubled haploid) embryo production using anther or microspore culture or intergeneric crosses, to ameliorate desirable characters genetically homozygote. Secondly, to develope convenient embryo culture technique in order to be stored and cultivated longer time of genotypes without being alien pollination etc. in field conditions. For that reason, two different auxin and also their combination with kinetin were used for mature embryos of wheat genotypes (hexaploid and tetraploid), to understand efficient dose for calli production and plant regeneration in plant tissue culture. Modified MS media were used adding a single dose of arabinogalactan protein (AGP) and without adding for regeneration. In further step of this study, most efficient auxin+kinetin combination which is determined previous research, it was used in the same modified MS medium to produce calli production and plant regeneration in three different genotypes (hexaploid and tetraploid wheat and diploid barley). Data were calculated in five different developmental stages of treatments. All statistical analysis of data were performed and means were compared with Duncan's test. Genetics and morphological effects of AGP on genotypes were discussed with the results of variance analysis. Simple correlation coefficient (r) was calculated base on the main values of replications.

Characterization and emulsifying properties of β-lactoglobulin-gum Acacia Seyal conjugates prepared via the Maillard reaction.

Science.gov (United States)

Bi, Binwei; Yang, Hao; Fang, Yapeng; Nishinari, Katsuyoshi; Phillips, Glyn O

2017-01-01

Gum Acacia Seyal (ASY) is less valued than is gum Acacia Senegal, due to its poor emulsifying ability. The present study investigated the Maillard reaction between ASY and β-lactoglobulin (BLG) and its impact on the emulsifying properties of ASY. The reaction products of BLG/ASY mixture (r=1/4), prepared by dry-heating at 60°C and a relative humidity of 79%, as a function of incubation time, were characterized by SDS-PAGE, GPC-MALLS and DSC. The results showed that 12-24h of dry-heating under the given conditions was sufficient for conjugation, meanwhile avoiding the formation of deeply coloured and insoluble melanoidins. More than 64% of the protein was incorporated into ASY, resulting in a two-fold increase in arabinogalactan-protein (AGP) content and 3.5 times increase in weight-average molecular mass of ASY. The conjugation with BLG markedly improved the stability of ASY-stabilized emulsions and their resistance against severe conditions, such as low pH and high saline conditions. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Crystal Structures of the N-terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-parallel Dimers*

Science.gov (United States)

Nagano, Soshichiro; Scheerer, Patrick; Zubow, Kristina; Michael, Norbert; Inomata, Katsuhiko; Lamparter, Tilman; Krauß, Norbert

2016-01-01

Agp1 is a canonical biliverdin-binding bacteriophytochrome from the soil bacterium Agrobacterium fabrum that acts as a light-regulated histidine kinase. Crystal structures of the photosensory core modules (PCMs) of homologous phytochromes have provided a consistent picture of the structural changes that these proteins undergo during photoconversion between the parent red light-absorbing state (Pr) and the far-red light-absorbing state (Pfr). These changes include secondary structure rearrangements in the so-called tongue of the phytochrome-specific (PHY) domain and structural rearrangements within the long α-helix that connects the cGMP-specific phosphodiesterase, adenylyl cyclase, and FhlA (GAF) and the PHY domains. We present the crystal structures of the PCM of Agp1 at 2.70 Å resolution and of a surface-engineered mutant of this PCM at 1.85 Å resolution in the dark-adapted Pr states. Whereas in the mutant structure the dimer subunits are in anti-parallel orientation, the wild-type structure contains parallel subunits. The relative orientations between the PAS-GAF bidomain and the PHY domain are different in the two structures, due to movement involving two hinge regions in the GAF-PHY connecting α-helix and the tongue, indicating pronounced structural flexibility that may give rise to a dynamic Pr state. The resolution of the mutant structure enabled us to detect a sterically strained conformation of the chromophore at ring A that we attribute to the tight interaction with Pro-461 of the conserved PRXSF motif in the tongue. Based on this observation and on data from mutants where residues in the tongue region were replaced by alanine, we discuss the crucial roles of those residues in Pr-to-Pfr photoconversion. PMID:27466363

The Crystal Structures of the N-terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-parallel Dimers.

Science.gov (United States)

Nagano, Soshichiro; Scheerer, Patrick; Zubow, Kristina; Michael, Norbert; Inomata, Katsuhiko; Lamparter, Tilman; Krauß, Norbert

2016-09-23

Agp1 is a canonical biliverdin-binding bacteriophytochrome from the soil bacterium Agrobacterium fabrum that acts as a light-regulated histidine kinase. Crystal structures of the photosensory core modules (PCMs) of homologous phytochromes have provided a consistent picture of the structural changes that these proteins undergo during photoconversion between the parent red light-absorbing state (Pr) and the far-red light-absorbing state (Pfr). These changes include secondary structure rearrangements in the so-called tongue of the phytochrome-specific (PHY) domain and structural rearrangements within the long α-helix that connects the cGMP-specific phosphodiesterase, adenylyl cyclase, and FhlA (GAF) and the PHY domains. We present the crystal structures of the PCM of Agp1 at 2.70 Å resolution and of a surface-engineered mutant of this PCM at 1.85 Å resolution in the dark-adapted Pr states. Whereas in the mutant structure the dimer subunits are in anti-parallel orientation, the wild-type structure contains parallel subunits. The relative orientations between the PAS-GAF bidomain and the PHY domain are different in the two structures, due to movement involving two hinge regions in the GAF-PHY connecting α-helix and the tongue, indicating pronounced structural flexibility that may give rise to a dynamic Pr state. The resolution of the mutant structure enabled us to detect a sterically strained conformation of the chromophore at ring A that we attribute to the tight interaction with Pro-461 of the conserved PRXSF motif in the tongue. Based on this observation and on data from mutants where residues in the tongue region were replaced by alanine, we discuss the crucial roles of those residues in Pr-to-Pfr photoconversion. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Environmental temperature and stocking density effects on acute phase proteins, heat shock protein 70, circulating corticosterone and performance in broiler chickens

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Najafi, Pardis; Zulkifli, Idrus; Amat Jajuli, Nurfarahin; Farjam, Abdoreza Soleimani; Ramiah, Suriya Kumari; Amir, Anna Aryani; O'Reily, Emily; Eckersall, David

2015-11-01

An experiment was conducted to determine the effect of different stocking densities on serum corticosterone (CORT), ovotransferrin (OVT), α1-acid glycoprotein (AGP) and ceruloplasmin (CP) concentrations, brain heat shock protein (HSP) 70 expression and performance in broiler chickens exposed to unheated and heated conditions. Day-old chicks were stocked at 0.100 m2/bird (low density (LD)) or 0.063 m2/bird (high density (HD)), in battery cages and housed in environmentally controlled rooms. From 21 to 35 days of age, birds from each stocking density group were exposed to either 24 or 32 °C. Growth performance was recorded during the heat treatment period, and blood and brain samples were collected to determine CORT, OVT, AGP, CP and HSP 70 levels on day 35. Heat treatment but not stocking density was detrimental to growth performance. There were significant temperature × density interactions for CORT, CP and OVT on day 35. Although HD elevated CORT, CP and OVT when compared to LD, the effects of the former were more obvious under heated condition. Both temperature and density had significant effect on AGP and HSP 70. In conclusion, irrespective of temperature, high stocking density was physiologically stressful to broiler chickens, as indicated by CORT, AGP, CP, OVT and HSP 70, but not detrimental to growth performance and survivability. As it was shown in the present study, AGP, CP and OVT could be useful biomarkers to determine the effect of overcrowding and high temperature on the welfare of broiler chickens.

PRODUCTION AND CHARACTERIZATION OF AN ALKALOTHERMOSTABLE, ORGANIC SOLVENT TOLERANT AND SURFACTANT TOLERANT ESTERASE PRODUCED BY A THERMOPHILIC BACTERIUM GEOBACILLUS SP. AGP-04, ISOLATED FROM BAKRESHWAR HOT SPRING, INDIA

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Amit Ghati

2013-10-01

Full Text Available A thermophilic bacteria, Geobacillus sp. AGP-04, isolated from Surya Kund hot spring, Bakreshwar, West Bengal, India was studied in terms of capability of tributyrin hydrolysis and characterization of its thermostable esterase activity using p-nitrophenyl butyrate (PNPB as substrate. The extracellular crude preparation was characterized in terms of pH and temperature optima and stability, organic solvent tolerance capacity and stability, substrate specificity, surfactant tolerance capacity, kinetic parameters and activation/inhibition behavior towards some metal ions and chemicals. Tributyrin agar assay exhibited that Geobacillus sp. AGP-04 secretes an extracellular esterase. The Vmax and Km values of the esterase were found to be 5099 U/Land 103.5µM, respectively in the presence of PNPB as substrate. The optimum temperature and pH, for Geobacillus sp. AGP-04 esterase was 60oC and 8.0, respectively. Although the enzyme activity was not significantly altered by incubating crude extract solution at 20-70oC for 1 hour, the enzyme activity was fully lost at 90oC for same incubation period. The pH stability profile showed that original crude esterase activity is stable at a broad range (pH 5.0-10.0. Moreover, the enzyme was highly organic solvent and surfactant tolerant. The effect of some chemical on crude esterase activity indicated that Geobacillus sp. AGP-04 produce an esterase which contains a serine residue in active site and for its activity -SH groups are essential. Besides, enzyme production was highly induced if fermentation medium contain polysaccharides and oil as carbon source.

Complexes of lutein with bovine and caprine caseins and their impact on lutein chemical stability in emulsion systems: Effect of arabinogalactan.

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Mora-Gutierrez, A; Attaie, R; Núñez de González, M T; Jung, Y; Woldesenbet, S; Marquez, S A

2018-01-01

Lutein is an important xanthophyll carotenoid with many benefits to human health. Factors affecting the application of lutein as a functional ingredient in low-fat dairy-like beverages (pH 6.0-7.0) are not well understood. The interactions of bovine and caprine caseins with hydrophobic lutein were studied using UV/visible spectroscopy as well as fluorescence. Our studies confirmed that the aqueous solubility of lutein is improved after binding with bovine and caprine caseins. The rates of lutein solubilization by the binding to bovine and caprine caseins were as follows: caprine α S1 -II-casein 34%, caprine α S1 -I-casein 10%, and bovine casein 7% at 100 μM lutein. Fluorescence of the protein was quenched on binding supporting complex formation. The fluorescence experiments showed that the binding involves tryptophan residues and some nonspecific interactions. Scatchard plots of lutein binding to the caseins demonstrated competitive binding between the caseins and their sites of interaction with lutein. Competition experiments suggest that caprine α S1 -II casein will bind a larger number of lutein molecules with higher affinity than other caseins. The chemical stability of lutein was largely dependent on casein type and significant increases occurred in the chemical stability of lutein with the following pattern: caprine α S1 -II-casein > caprine α S1 -I-casein > bovine casein. Addition of arabinogalactan to lutein-enriched emulsions increases the chemical stability of lutein-casein complexes during storage under accelerated photo-oxidation conditions at 25°C. Therefore, caprine α S1 -II-casein alone and in combination with arabinogalactan can have important applications in the beverage industry as carrier of this xanthophyll carotenoid (lutein). Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Frost Grape Polysaccharide (FGP), an emulsion-forming arabinogalactan gum from the stems of native North American grape species Vitis riparia Michx

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A new arabinogalactan is described that is produced in large quantity from the cut stems of the North American grape species Vitis riparia (Frost grape). The sugar composition consists of L-arabinofuranose (L-Araf, 55.2 %) and D-galactopyranose (D-Galp 30.1%), with smaller components of D-xylose (11...

The onset of the progression of acute phase response mechanisms induced by extreme impacts can be followed by the decrease in blood levels of positive acute phase proteins.

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Larina, Olga; Bekker, Anna

Studies performed at space flights and earth-based simulation models detected the plasma indices of acute phase reaction (APR), i.e. the increase of APR cytokine mediators and alterations in the production of blood acute phase proteins (APP) at the initial stages of adaptation to altered gravity conditions. Acute phase response is the principal constituent of the functional activity of innate immunity system. Changes in plasma APPs contents are considered to serve the restoration of homeostasis state. According to trends of their concentration shifts at the evolving of acute phase reaction APPs are denoted as positive, neutral, or negative. Plasma concentrations of positive acute phase proteins α1-acid glycoprotein (α1-AGP), α1-antitrypsin (α1-AT), and neutral α2-macroglobulin (α2-M) were measured in human study at 12-hour antiorthostatic position (AOP) with 15° head down tilt and hypoxia experiments at 14% oxygen in pressure chamber. Both of these impacts were shown to produce alterations in the APP levels indicative for acute phase response. Nevertheless, in AOP experiment noticeable decrease in α1-AGP concentration occurred by hour 12, and even more pronounced decline of α1-AGP and α1-AT were found on hypoxia hours 12 and 36. Acute phase proteins α1-AGP and α2-M possess the features of proteinase inhibitors. This function is implemented by the formation of complexes with the molecules of proteolytic enzymes which subsequently are removed from the blood flow. Transient decrease in plasma concentrations of protease inhibitors on early phases of APR development was reported to result from the growth of plasma protease activity due to cathepsin release from activated leukocytes, which had not yet been compensated by enhanced APP synthesis. Being a carrier protein for positively charged and neutral substances, α1-AGP shows pronounced elevation in its blood content during APR development. As assumed, it is required for the transportation of the increased

A Type II Arabinogalactan from Anoectochilus formosanus for G-CSF Production in Macrophages and Leukopenia Improvement in CT26-Bearing Mice Treated with 5-Fluorouracil.

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Yang, Li-Chan; Lu, Ting-Jang; Lin, Wen-Chuan

2013-01-01

Anoectochilus formosanus is an herb well known in Asian countries. The polysaccharide isolated from A. formosanus consists of type II arabinogalactan (AGAF), with branched 3,6-Gal as the major moiety. In this study, AGAF was examined for the granulocyte colony-stimulating factor (G-CSF) production and related protein expression in RAW 264.7 murine macrophages. The signaling pathway of G-CSF production involves AGAF and mitogen-activated protein kinases (MAPKs) inhibitors and pattern-recognition receptor antibodies. AGAF was evaluated to ease the leukopenia in CT26-colon-cancer-bearing mice treated with 5-fluorouracil (5-FU). The results of this study showed that AGAF was a stimulant for Toll-like receptor 2 and Dectin-1 and that it induced G-CSF production, through p38 and ERK MAPK, and NF- κ B pathways. In vivo examination showed that the oral administration of AGAF mitigated the side effects of leukopenia caused by 5-FU in colon-cancer-bearing mice. In conclusion, the botanic type II AGAF in this study was a potent G-CSF inducer in vivo and in vitro.

A Type II Arabinogalactan from Anoectochilus formosanus for G-CSF Production in Macrophages and Leukopenia Improvement in CT26-Bearing Mice Treated with 5-Fluorouracil

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Li-Chan Yang

2013-01-01

Full Text Available Anoectochilus formosanus is an herb well known in Asian countries. The polysaccharide isolated from A. formosanus consists of type II arabinogalactan (AGAF, with branched 3,6-Gal as the major moiety. In this study, AGAF was examined for the granulocyte colony-stimulating factor (G-CSF production and related protein expression in RAW 264.7 murine macrophages. The signaling pathway of G-CSF production involves AGAF and mitogen-activated protein kinases (MAPKs inhibitors and pattern-recognition receptor antibodies. AGAF was evaluated to ease the leukopenia in CT26-colon-cancer-bearing mice treated with 5-fluorouracil (5-FU. The results of this study showed that AGAF was a stimulant for Toll-like receptor 2 and Dectin-1 and that it induced G-CSF production, through p38 and ERK MAPK, and NF-κB pathways. In vivo examination showed that the oral administration of AGAF mitigated the side effects of leukopenia caused by 5-FU in colon-cancer-bearing mice. In conclusion, the botanic type II AGAF in this study was a potent G-CSF inducer in vivo and in vitro.

Changes in cell wall properties coincide with overexpression of extensin fusion proteins in suspension cultured tobacco cells.

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Tan, Li; Pu, Yunqiao; Pattathil, Sivakumar; Avci, Utku; Qian, Jin; Arter, Allison; Chen, Liwei; Hahn, Michael G; Ragauskas, Arthur J; Kieliszewski, Marcia J

2014-01-01

Extensins are one subfamily of the cell wall hydroxyproline-rich glycoproteins, containing characteristic SerHyp4 glycosylation motifs and intermolecular cross-linking motifs such as the TyrXaaTyr sequence. Extensins are believed to form a cross-linked network in the plant cell wall through the tyrosine-derivatives isodityrosine, pulcherosine, and di-isodityrosine. Overexpression of three synthetic genes encoding different elastin-arabinogalactan protein-extensin hybrids in tobacco suspension cultured cells yielded novel cross-linking glycoproteins that shared features of the extensins, arabinogalactan proteins and elastin. The cell wall properties of the three transgenic cell lines were all changed, but in different ways. One transgenic cell line showed decreased cellulose crystallinity and increased wall xyloglucan content; the second transgenic cell line contained dramatically increased hydration capacity and notably increased cell wall biomass, increased di-isodityrosine, and increased protein content; the third transgenic cell line displayed wall phenotypes similar to wild type cells, except changed xyloglucan epitope extractability. These data indicate that overexpression of modified extensins may be a route to engineer plants for bioenergy and biomaterial production.

Effects of p-chlorophenoxyisobutyric acid, arabinogalactan, and activated charcoal on microspore embryogenesis in kale.

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Niu, R Q; Zhang, Y; Tong, Y; Liu, Z Y; Wang, Y H; Feng, H

2015-04-27

To improve embryogenesis in microspore cultures of kale (Brassica oleracea L. var. acephala DC.), 6-benzylaminopurine (6-BA), naphthaleneacetic acid (NAA), arabinogalactan (AG), p-chlorophenoxyisobutyric acid (PCIB), and activated charcoal (AC) were added to the medium using four varieties of kale. The results showed that the addition of AG (0.1-0.2 g/L), AC (0.1-0.2 g/L) or a combination of 6-BA (0.1-0.2 mg/L) and NAA (0.1-0.2 mg/L) promoted embryo-genesis. Adding 40 μM PCIB or a combination of 40 μM PCIB and 0.2 g/L AC to NLN-13 medium at pH 5.8 effectively enhanced embryogenesis. Treatment with a combination of 40 μM PCIB and 10 mg/L AG gave the highest rate of embryonic induction, especially in genotype "Y007," which showed a twelve-fold increase in yield.

Allergy-Protective Arabinogalactan Modulates Human Dendritic Cells via C-Type Lectins and Inhibition of NF-κB.

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Peters, Marcus; Guidato, Patrick M; Peters, Karin; Megger, Dominik A; Sitek, Barbara; Classen, Birgit; Heise, Esther M; Bufe, Albrecht

2016-02-15

Arabinogalactan (AG) isolated from dust of a traditional farm prevents disease in murine models of allergy. However, it is unclear whether this polysaccharide has immune regulatory properties in humans. The aim of this study was to test the influence of AG on the immune-stimulating properties of human dendritic cells (DCs). Moreover, we sought to identify the receptor to which AG binds. AG was produced from plant callus tissue under sterile conditions to avoid the influence of pathogen-associated molecular patterns in subsequent experiments. The influence of AG on the human immune system was investigated by analyzing its impact on monocyte-derived DCs. To analyze whether the T cell stimulatory capacity of AG-stimulated DCs is altered, an MLR with naive Th cells was performed. We revealed that AG reduced T cell proliferation in a human MLR. In the search for a molecular mechanism, we found that AG binds to the immune modulatory receptors DC-specific ICAM-3 -: grabbing non integrin (DC-SIGN) and macrophage mannose receptor 1 (MMR-1). Stimulation of these receptors with AG simultaneously with TLR4 stimulation with LPS increased the expression of the E3 ubiquitin-protein ligase tripartite motif -: containing protein 21 and decreased the phosphorylation of NF-κB p65 in DCs. This led to a reduced activation profile with reduced costimulatory molecules and proinflammatory cytokine production. Blocking of MMR-1 or DC-SIGN with neutralizing Abs partially inhibits this effect. We conclude that AG dampens the activation of human DCs by LPS via binding to DC-SIGN and MMR-1, leading to attenuated TLR signaling. This results in a reduced T cell activation capacity of DCs. Copyright © 2016 by The American Association of Immunologists, Inc.

Detection of Aggregatibacter actinomycetemcomitans leukotoxin and fimbria-associated protein gene genotypes among periodontitis patients and healthy controls: A case–control study

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Mahalakshmi, Krishnan; Krishnan, Padma; Chandrasekaran, S. C.

2018-01-01

Background: Aggregatibacter actinomycetemcomitans has been reported in higher proportions in subgingival microbiota of individuals with aggressive periodontitis (AgP) compared with those with chronic periodontitis (ChP) and healthy controls. The major virulence factors are the ones that help in colonization and evasion of host's defenses. Hence, this study was aimed to assess the prevalence of A. actinomycetemcomitans 16S rRNA and its virulent genotypes (leukotoxin [lktA] and fimbria-associated protein [fap]). Materials and Methods: In this case– control study We performed periodontal examination and measured probing depth and clinical attachment level (CAL). Subgingival plaque samples from 200 (ChP: n = 128 and AgP: n = 72) periodontitis patients and 200 healthy controls were screened for the presence of A. actinomycetemcomitans 16S rRNA, lktA, and fap genotypes by polymerase chain reaction. The prevalence of genotypes between periodontitis patients and healthy controls was compared with Pearson's Chi-square test. P periodontitis patients, while A. actinomycetemcomitans fap genotype showed 31.8% prevalence. The prevalence of these genotypes was insignificant in healthy controls. Conclusion: The high odds ratio for A. actinomycetemcomitans prevalence suggests its strong link to periodontitis. Detection of A. actinomycetemcomitans lktA + genotype may be a useful marker for AgP as its prevalence was found to be high in AgP. PMID:29922337

Embryogenic potential and the expression of arabinogalactanproteins (AGPs in embryogenic cell aggregates of Coffea arabica cv. Caturra rojo under influence of CO2

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Raúl Barbón

2002-07-01

Full Text Available The establishment and optimization of regeneration systems via somatic embryogenesis has centered traditionally on the study of the culture medium components, with little attention to other factors of the in vitro environment like the composition of the gaseous atmosphere. This work was realized with the aim to determine the embryogenic potential and the expression of arabinogalactanproteins (AGPs in embryogenic cell aggregates of Coffea arabica cv. Caturra Rojo under influence of carbon dioxide (CO2. Concentrations of 2.5% and 5.0% of CO2 stimulated a greater formation of somatic embryos (307 ES/50mgMF and 277 ES/50mgMF respectively in semisolid culture medium with better results to the controls with passive interchange and forced ventilation (195 ES/50mgMF and 107 ES/50mgMF whereas a concentration of 10.0% of CO2 inhibited the process of somatic embryogenesis (95 ES/50mgMF. In cell suspensions the formation of somatic embryos was greater with a concentration of 2.5% of CO2 (130x103 ES.l-1 in comparison with 5.0% and 10.0% of CO2 (116x103 ESl-1 and 15x103 ES.l-1 and the controls with passive interchange and forced ventilation. With a concentration of 2.5% CO2 there was a greater synthesis of Arabinogalactanproteins (AGPs at the cellular level (0.068 mg.gMF-1 and the excretion in the culture medium (2.10 mg.l-1, which coincided with the highest values of production of somatic embryos. Key Words: embryogenic cell suspensions, in vitro environment, molecular markers, somatic embryo, somatic embryogenesis

The immune system modulator a1-acid glycoprotein inhibits insulin and IGF1 induced protein synthesis in C2C12 myotubes

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Alpha-1 acid glycoprotein (AGP) has previously been demonstrated by our laboratory to be negatively correlated with growth rate in newborn piglets. However, a mechanism of action for AGP in growth has not been identified. Previous research has demonstrated that AGP can modify adipose tissue metabo...

Reversed-Phase UHPLC Enantiomeric Separation of Rasagiline Salts Using a Chiralpak® AGP Column

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Nagarajan Balaji

2017-07-01

Full Text Available We report the first rapid ultra-high performance liquid chromatographic (UHPLC enantiomeric reversed-phase separation of rasagiline mesylate and its tartrate salts using a Chiralpak® AGP column (50 mm × 2.1 mm, 5 μm as a stationary phase. This method was developed as an alternative to the usage of previously reported normal-phase chiral LC columns for isomer separation. Our method is based on an isocratic approach using a mixture of ammonium acetate and isopropyl alcohol (90:10, v/v as the mobile phase (0.6 mL/min flow rate. The detection limit (at a detection wavelength of 210 nm and quantification limit for the rasagiline enantiomers were 0.06 and 0.2 μg/mL, respectively. This method is compatible with the UHPLC-MS technique. The successful separation of rasagiline and its enantiomer was confirmed by determining the corresponding specific optical rotation values. Our method will be applicable for detecting rasagiline enantiomers during the control of manufacturing processes, and for use in rapid analysis for quality control in pharmaceutical industry to obtain optically pure pharmaceutical substances. This method was validated in terms of its precision, limit of detection, limit of quantification, linearity, accuracy, robustness, ruggedness, specificity, forced degradation, and solution stability, according to International Council on Harmonization Validation Guidelines Q2 (R1.

Intersubunit distances in full-length, dimeric, bacterial phytochrome Agp1, as measured by pulsed electron-electron double resonance (PELDOR) between different spin label positions, remain unchanged upon photoconversion.

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Kacprzak, Sylwia; Njimona, Ibrahim; Renz, Anja; Feng, Juan; Reijerse, Edward; Lubitz, Wolfgang; Krauss, Norbert; Scheerer, Patrick; Nagano, Soshichiro; Lamparter, Tilman; Weber, Stefan

2017-05-05

Bacterial phytochromes are dimeric light-regulated histidine kinases that convert red light into signaling events. Light absorption by the N-terminal photosensory core module (PCM) causes the proteins to switch between two spectrally distinct forms, Pr and Pfr, thus resulting in a conformational change that modulates the C-terminal histidine kinase region. To provide further insights into structural details of photoactivation, we investigated the full-length Agp1 bacteriophytochrome from the soil bacterium Agrobacterium fabrum using a combined spectroscopic and modeling approach. We generated seven mutants suitable for spin labeling to enable application of pulsed EPR techniques. The distances between attached spin labels were measured using pulsed electron-electron double resonance spectroscopy to probe the arrangement of the subunits within the dimer. We found very good agreement of experimental and calculated distances for the histidine-kinase region when both subunits are in a parallel orientation. However, experimental distance distributions surprisingly showed only limited agreement with either parallel- or antiparallel-arranged dimer structures when spin labels were placed into the PCM region. This observation indicates that the arrangements of the PCM subunits in the full-length protein dimer in solution differ significantly from that in the PCM crystals. The pulsed electron-electron double resonance data presented here revealed either no or only minor changes of distance distributions upon Pr-to-Pfr photoconversion. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Influence of wine pectic polysaccharides on the interactions between condensed tannins and salivary proteins.

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Carvalho, Elisabete; Mateus, Nuno; Plet, Benoit; Pianet, Isabelle; Dufourc, Erick; De Freitas, Victor

2006-11-15

Alpha-amylase, a major human salivary protein, and IB8c, a representative of the proline-rich proteins, were obtained by isolation from saliva and by solid-phase synthesis, respectively. The interactions between these proteins and condensed tannins isolated from grape seeds were studied at different protein and tannin concentrations by measuring their aggregation. Pectic polysaccharides were isolated from wine, and their effect on protein tannin aggregation was assessed. The results presented in this study showed that the most acidic fractions of arabinogalactan proteins have the ability to inhibit the formation of aggregates between the grape seed tannins and the two different salivary proteins. Rhamnogalacturonan II has the same ability toward alpha-amylase but not IB8c under the conditions of the present study. Polysaccharides show effects at concentrations at which they are present in wine, which could mean an influence in wine astringency. The interaction between condensed tannins and alpha-amylase is differently affected by ionic strength when compared with IB8c.

Non-surgical periodontal therapy decreases serum elastase levels in aggressive but not in chronic periodontitis.

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Eickholz, Peter; Siegelin, Yasemin; Scharf, Susanne; Schacher, Beate; Oremek, Gerhard M; Sauer-Eppel, Hildegund; Schubert, Ralf; Wohlfeil, Martin

2013-04-01

Assessment of the effect of non-surgical periodontal therapy (SRP) on serum inflammatory parameters in patients with untreated aggressive (AgP) and chronic (ChP) periodontitis. Overall, 31 ChP and 29 AgP were examined clinically prior to and 12 weeks after SRP (subgingival scaling of all pockets within 2 days) with systemic antibiotics for patients positive for Aggregatibacter actinomycetemcomitans (14 AgP, 9 ChP). Blood was sampled prior to, one day, 6, and 12 weeks after the first SRP visit. Serum elastase, C-reactive protein (CRP), lipopolysaccharide-binding protein (LBP), interleukin (IL) 6, 8, and leukocyte counts were assessed. At baseline, serum elastase, CRP, and LBP were significantly (p < 0.01) higher in AgP than ChP. Serum elastase, CRP, LBP, and IL-6 were significantly (p < 0.001) elevated one day after scaling in both groups. Both groups showed significant clinical improvement (p < 0.001). A significant difference was observed regarding change of serum elastase 12 weeks after SRP between AgP and ChP (p = 0.015). Multiple regression analysis revealed AgP, African origin, and bleeding on probing to be associated with more pronounced elastase reduction. CRP reduction was associated with African origin, systemic antibiotics, and baseline probing pocket depth. SRP results in serum elastase reduction in AgP but not in ChP. © 2013 John Wiley & Sons A/S.

[Examination of acute phase proteins concentrations in children with allergic rhinitis].

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Steiner, Iwona; Sobieska, Magdalena; Pucher, Beata; Grzegorowski, Michał; Samborski, Włodzimierz

2006-01-01

Allergic rhinitis is an inflammatory disorder of upper respiratory tract (about 15 per cent of the population in industrialized countries suffer from this condition), characterized by frequent sneezing and a runny or stuffy nose sometimes accompanied by watery eyes. As the most common allergic condition, allergic rhinitis affects people of all ages. Boys are twice as likely to get allergic rhinitis than girls. The median age of onset of the condition is 10 years old, meaning that equal numbers of children develop the condition before and after age 10. Symptoms usually appear in childhood first and then lessen by the age of 30 or 40. Seasonal allergic rhinitis usually results from tree, grass or weed pollen. With this type of rhinitis, symptoms will decrease with the arrival of cold weather. Perennial allergic rhinitis can cause year-round symptoms. This allergic reaction is the result of indoor irritants such as feathers, mold spores, animal dander (hair and skin shed by pets) or dust mites. It is often aggravated by a food allergy, the most common being an allergy to milk. Acute phase proteins (APP) belong to the most ancient part of the unspecific immunity and contribute markedly to the keeping of homeostasis. As much as 30 various proteins are for the moment regarded as APP. Being multifunctional regulators and effectors APP stay in multiple relations to practically all types of cells and molecules. Among APP following functional groups may be described: transport proteins (transferrin, ceruloplasmin and haptoglobin), clotting factors (fibrinogen), antiproteases (alpha1-antitrypsin, alpha1-antichymotrypsin, alpha2-macroglobulin), complement components (C3, C4) and several proteins of hardly known function, like C-reactive protein (CRP), serum amyloid A, acid alpha1-glycoprotein (AGP) and others. From a group of 32 children, aged from 5 to 14 years, with symptoms of seasonal allergic rhinitis, and from a control group of 10 healthy children sex and age matched

Quantitation of mRNAs for α₁-acid glycoprotein and for serum albumin in livers of normal, stressed, fasted, and refed rats. [¹²⁵I or ¹³¹I radioimmunoassay for protein products of specific mRNA activity

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Harris, Linda Jean [Univ. of Rochester, NY (United States)

1978-01-01

A new procedure for determining the relative levels of a specific mRNA species was developed and applied to mRNA for rat serum albumin (RSA) and α₁-AGP) in rat liver. The method is a radioimmunoassay (¹²⁵In or ¹³¹I) for the completed protein, but which also detects antigenic determinants in nascent polypeptide chains on plysomes synthesizing the specific protein. Results show that 24 hs after stressing the rat by turpentine injection the total number of polysomes per mg DNA has increased by 20 to 25%; however, the number of RSA synthesizing polysomes per mg DNA has decreased slightly. In rats fasted for 6 days, the number of RSA synthesizing polysomes per mg polysomal RNA is only slightly below normal, but the total number of RSA synthesizing polysomes per mg DNA has decreased by 40%. Again, it is seen that RSA mRNA levels do not decrease as sharply as the rate of RSA synthesis. Twelve hours after refeeding the rats, the number of RSA synthesizing polysomes begins to increase, reaching a peak two to three times normal levels 24 to 48 hours after commencement of refeeding. During the first 24 hs after turpentine injection, there is a linear increase in the number of α₁-AGP synthesizing polysomes. The increase is smaller during the next 24 hs and there is a small decrease between 48 and 72 hs. The serum concentrations of α₁-AGP following turpentine treatment reflect these changes in polysome levels. It was not possible to compare the number of α₁-AGP synthesizing polysomes in livers of normal, fasted, and refed rats because the levels detected were only slightly higher than those seen in rat and rat kidney polysome controls. This background activity must be eliminated before the technique can be applied to quantitating mRNA for proteins synthesized in very small quantities. This technique offers several advantages over other procedures commonly used to quantitate mRNA. (ERB)

Effect of Complexation with Arabinogalactan on Pharmacokinetics of “Guest” Drugs in Rats: For Example, Warfarin

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Mikhail V. Khvostov

2013-01-01

Full Text Available A pharmacokinetic study of the warfarin (WF : arabinogalactan (AG complex with the 1 : 10 mass ratio after its intragastric introduction to Wistar rats at a dose of 5 mg/kg (WF dose in the complex was 0.5 mg/kg once a day for three days was conducted. It was found that Cmax, T1/2, and AUC of WF in the complex form were lower than after the introduction of blank WF at the same dose, but its elimination (Cl, MRT was much faster. Significant accumulation (Cmin and an abrupt increase in plasma concentration after the third introduction were observed for blank WF, whereas the complex showed a much more moderate increase in concentration at this point. However, despite obvious differences in pharmacokinetic parameters, the efficacies of both agents were virtually identical; the complex differed from blank WF by only 15%. This value is rather insignificant and does not impair its anticoagulant activity. Thus, we can conclude that introduction of the WF : AG complex is safe in terms of reduction of the bleeding risk and accumulation.

Synthesis and Characterization of the Rubidium Thiophosphate Rb 6 (PS 5 )(P 2 S 10 ) and the Rubidium Silver Thiophosphates Rb 2 AgPS 4 , RbAg 5 (PS 4 ) 2 and Rb 3 Ag 9 (PS 4 ) 4

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Alahmary, Fatimah S.; Davaasuren, Bambar; Khanderi, Jayaprakash; Rothenberger, Alexander

2016-01-01

The metal thiophosphates Rb2AgPS4 (2), RbAg5(PS4)2 (3), and Rb3Ag9(PS4)4 (4) were synthesized by stoichiometric reactions, whereas Rb6(PS5)(P2S10) (1) was prepared with excess amount of sulfur. The compounds crystallize as follows: 1 monoclinic, P21

Identification and characterization of polymorphisms at the HSA a1-acid glycoprotein (ORM* gene locus in Caucasians

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Owczarek Catherine M.

2002-01-01

Full Text Available Human alpha1-acid glycoprotein (AGP or orosomucoid (ORM is a major acute phase protein that is thought to play a crucial role in maintaining homeostasis. Human AGP is the product of a cluster of at least two adjacent genes located on HSA chromosome 9. Using a range of restriction endonucleases we have investigated DNA variation at the locus encoding the AGP genes in a panel of healthy Caucasians. Polymorphisms were identified using BamHI, EcoRI, BglII, PvuII, HindIII, TaqI and MspI. Non-random associations were found between the BamHI, EcoRI, BglII RFLPs. The RFLPs detected with PvuII, TaqI and MspI were all located in exon 6 of both AGP genes. The duplication of an AGP gene was observed in 11% of the indiviuals studied and was in linkage disequilibrium with the TaqI RFLP. The identification and characterization of these polymorphisms will prove useful for other population and forensic studies.

Alpha1-acid glycoprotein post-translational modifications: a comparative two dimensional electrophoresis based analysis

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P. Roncada

2010-04-01

Full Text Available Alpha1-acid glycoprotein (AGP is an immunomodulatory protein expressed by hepatocytes in response to the systemic reaction that follows tissue damage caused by inflammation, infection or trauma. A proteomic approach based on two dimensional electrophoresis, immunoblotting and staining of 2DE gels with dyes specific for post-translational modifications (PTMs such as glycosylation and phosphorylation has been used to evaluate the differential interspecific protein expression of AGP purified from human, bovine and ovine sera. By means of these techniques, several isoforms have been identified in the investigated species: they have been found to change both with regard to the number of isoforms expressed under physiological condition and with regard to the quality of PTMs (i.e. different oligosaccharidic chains, presence/absence of phosphorilations. In particular, it is suggested that bovine serum AGP may have one of the most complex pattern of PTMs among serum proteins of mammals studied so far.

Usefulness of acute phase proteins in differentiating between feline infectious peritonitis and other diseases in cats with body cavity effusions.

Science.gov (United States)

Hazuchova, Katarina; Held, Susanne; Neiger, Reto

2017-08-01

Objectives The aim of this study was to evaluate the measurement of acute phase proteins (APPs) as a diagnostic tool to differentiate between feline infectious peritonitis (FIP) and other diseases in cats with body cavity effusions. Methods Cats with pleural, abdominal or pericardial effusion were prospectively enrolled. Cats were classified as having or not having FIP based on immunohistochemistry (if available) or a sophisticated statistical method using machine learning methodology with concepts from game theory. Cats without FIP were further subdivided into three subgroups: cardiac disease, neoplasia and other diseases. Serum amyloid A (SAA), haptoglobin (Hp) and α 1 -acid glycoprotein (AGP) were measured in serum and effusion, using assays previously validated in cats. Results Serum and effusion samples were available for the measurement of APPs from 88 and 67 cats, respectively. Concentrations of the APPs in serum and effusion were significantly different in cats with and without FIP ( P <0.001 for all three APPs). The best APP to distinguish between cats with and without FIP was AGP in the effusion; a cut-off value of 1550 µg/ml had a sensitivity and specificity of 93% each for diagnosing FIP. Conclusions and relevance AGP, particularly if measured in effusion, was found to be useful in differentiating between FIP and other diseases, while SAA and Hp were not. The concentration of all three APPs in some diseases (eg, septic processes, disseminated neoplasia) was as high as in cats with FIP; therefore, none of these can be recommended as a single diagnostic test for FIP.

Quantitative analysis of N-glycans from human alfa-acid-glycoprotein using stable isotope labeling and zwitterionic hydrophilic interaction capillary liquid chromatography electrospray mass spectrometry as tool for pancreatic disease diagnosis

International Nuclear Information System (INIS)

Giménez, Estela; Balmaña, Meritxell; Figueras, Joan; Fort, Esther; Bolós, Carme de; Sanz-Nebot, Victòria; Peracaula, Rosa; Rizzi, Andreas

2015-01-01

Highlights: • The method enables relative quantitation of hAGP glycans from pathological samples • Pancreatic cancer samples clearly showed an increase of hAGP fucosylated glycans. • Fucosylated glycans could be potential biomarkers for diagnosing pancreatic cancer. • The established method could be extremely useful to find novel glycoprotein biomarkers - Abstract: In this work we demonstrate the potential of glycan reductive isotope labeling (GRIL) using [ 12 C]- and [ 13 C]-coded aniline and zwitterionic hydrophilic interaction capillary liquid chromatography electrospray mass spectrometry (μZIC-HILIC-ESI-MS) for relative quantitation of glycosylation variants in selected glycoproteins present in samples from cancer patients. Human α 1 -acid-glycoprotein (hAGP) is an acute phase serum glycoprotein whose glycosylation has been described to be altered in cancer and chronic inflammation. However, it is not clear yet whether some particular glycans in hAGP can be used as biomarker for differentiating between these two pathologies. In this work, hAGP was isolated by immunoaffinity chromatography (IAC) from serum samples of healthy individuals and from those suffering chronic pancreatitis and different stages of pancreatic cancer, respectively. After de-N-glycosylation, relative quantitation of the hAGP glycans was carried out using stable isotope labeling and μZIC-HILIC-ESI-MS analysis. First, protein denaturing conditions prior to PNGase F digestion were optimized to achieve quantitative digestion yields, and the reproducibility of the established methodology was evaluated with standard hAGP. Then, the proposed method was applied to the analysis of the clinical samples (control vs. pathological). Pancreatic cancer samples clearly showed an increase in the abundance of fucosylated glycans as the stage of the disease increases and this was unlike to samples from chronic pancreatitis. The results gained here indicate the mentioned glycan in hAGP as a

Serum protein binding displacement: theoretical analysis using a hypothetical radiopharmaceutical and experimental analysis with 123I-N-isopropyl-p-iodoamphetamine

International Nuclear Information System (INIS)

Kawai, Keiichi; Nishii, Ryuichi; Shikano, Naoto; Makino, Nobuo; Kuga, Noriyuki; Yoshimoto, Mitsuyoshi; Jinnouchi, Seishi; Nagamachi, Shigeki; Tamura, Shozo; Takamura, Norito

2009-01-01

Introduction: The binding of radiopharmaceutical to serum proteins is thought to be an important factor that restricts its excretion and accumulation in tissue. We calculated the effect of inhibitors of serum protein binding using a hypothetical radiopharmaceutical. In vitro experiments and protein binding inhibitor-loaded monkey scintigraphy were then conducted using 123 I-N-isopropyl-p-iodoamphetamine (IMP) as the radiopharmaceutical. Methods: Free fraction ratios of radiopharmaceutical were calculated with one radiopharmaceutical, two serum proteins and two specific inhibitors in the steady state at various serum protein concentrations. In vitro protein binding inhibition studies using human, rat and monkey sera were performed with site-selective displacers of specific binding sites: 400 μM 6-methoxy-2-naphthylacetic acid (6MNA; a major nabumeton metabolite) as a serum albumin Site II inhibitor and 400 μM erythromycin (ETC) as an α 1 -acid glycoprotein (AGP) site inhibitor. Scintigraphy with or without 6MNA loading of monkeys was performed. Results: The theoretical findings roughly corresponded to the experimental results. Approximately 75% of IMP bound to serum albumin Site II and AGP in the species examined. The free fraction of IMP (25.0±0.6% for human, 22.8±0.4% for monkey, 23.7±0.3% for rat) increased with loading of specific protein binding inhibitors (6MNA: 28.0±0.3% for human, 24.5±0.7% for monkey, 24.3±0.2% for rat; ETC: 26.3±0.4% for human, 29.5±1.1% for monkey, 26.0±0.7% for rat) and was serum protein concentration dependant based on the results of calculations. Simultaneous administration of 6MNA and ETC produced a higher free fraction ratio of IMP (31.9±1.0% for human, 34.6±0.4% for monkey, 27.0±0.3% for rat) than summation of the single administrations of 6MNA and ETC (domino effect) in human, rat and monkey sera. Rapid cerebral accumulation was observed with 6MNA loading in monkey scintigraphy. Conclusions: 6MNA appears to change

Quantitative analysis of N-glycans from human alfa-acid-glycoprotein using stable isotope labeling and zwitterionic hydrophilic interaction capillary liquid chromatography electrospray mass spectrometry as tool for pancreatic disease diagnosis

Energy Technology Data Exchange (ETDEWEB)

Giménez, Estela, E-mail: estelagimenez@ub.edu [Department of Analytical Chemistry, University of Barcelona, Diagonal 647, E-08028 Barcelona (Spain); Balmaña, Meritxell [Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, Campus Montilivi s/n, 17071 Girona (Spain); Figueras, Joan [Department of Surgery, Dr. Josep Trueta University Hospital, IdlBGi, 17007 Girona (Spain); Fort, Esther [Digestive Unit, Dr. Josep Trueta University Hospital, 17007 Girona (Spain); Bolós, Carme de [Gastroesophagic Cancer Research Group, Research Programme in Cancer, Hospital del Mar Medical Research Institute (IMIM), Dr. Aiguader, 88, 08003 Barcelona (Spain); Sanz-Nebot, Victòria [Department of Analytical Chemistry, University of Barcelona, Diagonal 647, E-08028 Barcelona (Spain); Peracaula, Rosa [Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, Campus Montilivi s/n, 17071 Girona (Spain); Rizzi, Andreas [Institute of Analytical Chemistry, University of Vienna, Währinger Straße 38, A-1090 Vienna (Austria)

2015-03-25

Highlights: • The method enables relative quantitation of hAGP glycans from pathological samples • Pancreatic cancer samples clearly showed an increase of hAGP fucosylated glycans. • Fucosylated glycans could be potential biomarkers for diagnosing pancreatic cancer. • The established method could be extremely useful to find novel glycoprotein biomarkers - Abstract: In this work we demonstrate the potential of glycan reductive isotope labeling (GRIL) using [{sup 12}C]- and [{sup 13}C]-coded aniline and zwitterionic hydrophilic interaction capillary liquid chromatography electrospray mass spectrometry (μZIC-HILIC-ESI-MS) for relative quantitation of glycosylation variants in selected glycoproteins present in samples from cancer patients. Human α{sub 1}-acid-glycoprotein (hAGP) is an acute phase serum glycoprotein whose glycosylation has been described to be altered in cancer and chronic inflammation. However, it is not clear yet whether some particular glycans in hAGP can be used as biomarker for differentiating between these two pathologies. In this work, hAGP was isolated by immunoaffinity chromatography (IAC) from serum samples of healthy individuals and from those suffering chronic pancreatitis and different stages of pancreatic cancer, respectively. After de-N-glycosylation, relative quantitation of the hAGP glycans was carried out using stable isotope labeling and μZIC-HILIC-ESI-MS analysis. First, protein denaturing conditions prior to PNGase F digestion were optimized to achieve quantitative digestion yields, and the reproducibility of the established methodology was evaluated with standard hAGP. Then, the proposed method was applied to the analysis of the clinical samples (control vs. pathological). Pancreatic cancer samples clearly showed an increase in the abundance of fucosylated glycans as the stage of the disease increases and this was unlike to samples from chronic pancreatitis. The results gained here indicate the mentioned glycan in hAGP

Plant glycosylphosphatidylinositol (GPI) anchored proteins at the plasma membrane-cell wall nexus.

Science.gov (United States)

Yeats, Trevor H; Bacic, Antony; Johnson, Kim L

2018-04-18

Approximately 1% of plant proteins are predicted to be post-translationally modified with a glycosylphosphatidylinositol (GPI) anchor that tethers the polypeptide to the outer leaflet of the plasma membrane. While the synthesis and structure of GPI anchors is largely conserved across eukaryotes, the repertoire of functional domains present in the GPI-anchored proteome has diverged substantially. In plants, this includes a large fraction of the GPI-anchored proteome being further modified with plant-specific arabinogalactan (AG) O-glycans. The importance of the GPI-anchored proteome to plant development is underscored by the fact that GPI biosynthetic null mutants exhibit embryo lethality. Mutations in genes encoding specific GPI-anchored proteins (GAPs) further supports their contribution to diverse biological processes occurring at the interface of the plasma membrane and cell wall, including signaling, cell wall metabolism, cell wall polymer cross-linking, and plasmodesmatal transport. Here, we review the literature concerning plant GPI-anchored proteins in the context of their potential to act as molecular hubs that mediate interactions between the plasma membrane and the cell wall and their potential to transduce the signal into the protoplast and thereby activate signal transduction pathways. This article is protected by copyright. All rights reserved.

ST proteins, a new family of plant tandem repeat proteins with a DUF2775 domain mainly found in Fabaceae and Asteraceae.

Science.gov (United States)

Albornos, Lucía; Martín, Ignacio; Iglesias, Rebeca; Jiménez, Teresa; Labrador, Emilia; Dopico, Berta

2012-11-07

Many proteins with tandem repeats in their sequence have been described and classified according to the length of the repeats: I) Repeats of short oligopeptides (from 2 to 20 amino acids), including structural cell wall proteins and arabinogalactan proteins. II) Repeats that range in length from 20 to 40 residues, including proteins with a well-established three-dimensional structure often involved in mediating protein-protein interactions. (III) Longer repeats in the order of 100 amino acids that constitute structurally and functionally independent units. Here we analyse ShooT specific (ST) proteins, a family of proteins with tandem repeats of unknown function that were first found in Leguminosae, and their possible similarities to other proteins with tandem repeats. ST protein sequences were only found in dicotyledonous plants, limited to several plant families, mainly the Fabaceae and the Asteraceae. ST mRNAs accumulate mainly in the roots and under biotic interactions. Most ST proteins have one or several Domain(s) of Unknown Function 2775 (DUF2775). All deduced ST proteins have a signal peptide, indicating that these proteins enter the secretory pathway, and the mature proteins have tandem repeat oligopeptides that share a hexapeptide (E/D)FEPRP followed by 4 partially conserved amino acids, which could determine a putative N-glycosylation signal, and a fully conserved tyrosine. In a phylogenetic tree, the sequences clade according to taxonomic group. A possible involvement in symbiosis and abiotic stress as well as in plant cell elongation is suggested, although different STs could play different roles in plant development. We describe a new family of proteins called ST whose presence is limited to the plant kingdom, specifically to a few families of dicotyledonous plants. They present 20 to 40 amino acid tandem repeat sequences with different characteristics (signal peptide, DUF2775 domain, conservative repeat regions) from the described group of 20 to 40

Plasma Proteome Biomarkers of Inflammation in School Aged Children in Nepal.

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Sun Eun Lee

Full Text Available Inflammation is a condition stemming from complex host defense and tissue repair mechanisms, often simply characterized by plasma levels of a single acute reactant. We attempted to identify candidate biomarkers of systemic inflammation within the plasma proteome. We applied quantitative proteomics using isobaric mass tags (iTRAQ tandem mass spectrometry to quantify proteins in plasma of 500 Nepalese children 6-8 years of age. We evaluated those that co-vary with inflammation, indexed by α-1-acid glycoprotein (AGP, a conventional biomarker of inflammation in population studies. Among 982 proteins quantified in >10% of samples, 99 were strongly associated with AGP at a family-wise error rate of 0.1%. Magnitude and significance of association varied more among proteins positively (n = 41 than negatively associated (n = 58 with AGP. The former included known positive acute phase proteins including C-reactive protein, serum amyloid A, complement components, protease inhibitors, transport proteins with anti-oxidative activity, and numerous unexpected intracellular signaling molecules. Negatively associated proteins exhibited distinct differences in abundance between secretory hepatic proteins involved in transporting or binding lipids, micronutrients (vitamin A and calcium, growth factors and sex hormones, and proteins of largely extra-hepatic origin involved in the formation and metabolic regulation of extracellular matrix. With the same analytical approach and the significance threshold, seventy-two out of the 99 proteins were commonly associated with CRP, an established biomarker of inflammation, suggesting the validity of the identified proteins. Our findings have revealed a vast plasma proteome within a free-living population of children that comprise functional biomarkers of homeostatic and induced host defense, nutrient metabolism and tissue repair, representing a set of plasma proteins that may be used to assess dynamics and extent of

Arabidopsis thaliana glucuronosyltransferase in family GT14

DEFF Research Database (Denmark)

Dilokpimol, Adiphol; Geshi, Naomi

2014-01-01

Arabinogalactan proteins are abundant cell-surface proteoglycans in plants and are involved in many cellular processes including somatic embryogenesis, cell-cell interactions, and cell elongation. We reported a glucuronosyltransferase encoded by Arabidopsis AtGlcAT14A, which catalyzes an addition...

Acute phase protein mRNA expressions and enhancement of antioxidant defense system in Black-meated Silkie Fowls supplemented with clove (Eugenia caryophyllus extracts under the influence of chronic heat stress

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Alhassan Usman Bello

2016-11-01

Full Text Available Abstract Background The current study investigates the anti-stress effects of clove (Eugenia caryophyllus extracts (0, 200, 400, and 600 mg/kg on serum antioxidant biomarkers, immune response, immunological organ growth index, and expression levels of acute phase proteins (APPs; ovotransferrin (OVT, ceruloplasmin (CP, ceruloplasmin (AGP, C-reactive protein (CRP, and serum amyloid-A (SAA mRNA in the immunological organs of 63-d-old male black-meated Silkie fowls subjected to 21 d chronic heat stress at 35 ± 2 °C. Results The results demonstrated that clove extract supplementation in the diet of Silkie fowls subjected to elevated temperature (ET improve growth performance, immune responses, and suppressed the activities of glutathion peroxidase (GSH-Px, superoxide dismutase (SOD, catalase (CAT, and thioredoxin reductase (TXNRD; reduced serum malonaldehyde (MDA and glutathione (GSH concentrations when compared with fowls raised under thermoneutral condition (TC. Upon chronic heat stress and supplementation of clove extracts, the Silkie fowls showed a linear increase in GSH-Px, SOD, CAT, and TXNRD activities (P = 0.01 compared with fowls fed diets without clove extract. ET decreased (P < 0.05 the growth index of the liver, spleen, bursa of Fabricius and thymus. However, the growth index of the liver, spleen, bursa of Fabricius and thymus increased significantly (P < 0.05 which corresponded to an increase in clove supplemented levels. The expression of OVT, CP, AGP, CRP, and SAA mRNA in the liver, spleen, bursa of Fabricius and thymus were elevated (P < 0.01 by ET compared with those maintained at TC. Nevertheless, clove mitigates heat stress-induced overexpression of OVT, CP, AGP, CRP and SAA mRNA in the immune organs of fowls fed 400 mg clove/kg compared to other groups. Conclusions The results showed that clove extracts supplementation decreased oxidative stress in the heat-stressed black-meated fowls by alleviating

Ultrasound-assisted extraction of arabinogalactan and dihydroquercetin simultaneously from Larix gmelinii as a pretreatment for pulping and papermaking.

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Chunhui Ma

Full Text Available An ultrasound-assisted extraction (UAE method using ethanol was applied for extracting arabinogalactan (AG and dihydroquercetin (DHQ simultaneously from larch wood, as a pretreatment for pulping and papermaking. The extraction parameters were optimized by a Box-Behnken experimental design with the yields of AG and DHQ as the response values. Under optimum conditions (three extractions, each using 40% ethanol, for 50 min, 200 W ultrasound power and 1∶18 solid-liquid ratio, the yields of AG and DHQ were 183.4 and 36.76 mg/g, respectively. After UAE pretreated, the wood chips were used for Kraft pulping (KP and high boiling solvent pulping (HBSP. The pulping yield after pretreatment was higher than that of untreated (the pulping yields of untreated HBSP and KP were 42.37% and 39.60%, and the pulping yields of HBSP and KP after UAE-pretreated were 44.23% and 41.50% respectively, as indicated by a lower kappa number (77.91 and 27.30 for untreated HBSP and KP; 77.01 and 26.83 for UAE-pretreated HBSP and KP. Furthermore, the characteristics of paper produced from pretreated wood chips were superior to those from the untreated chips: the basis weight was lower (85.67 and 82.48 g·cm(-2 for paper from untreated KP and HBSP; 79.94 and 80.25 g·cm(-2 for paper from UAE-pretreated KP and HBSP, and the tensile strengths, tearing strengths, bursting strengths, and folding strengths were higher than these of paper after UAE-pretreated, respectively.

Cell wall O-glycoproteins and N-glycoproteins: biosynthesis and some functional aspects.

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Eric eNguema-Ona

2014-10-01

Full Text Available Cell wall O-glycoproteins and N-glycoproteins are two types of glycomolecules whose glycans are structurally complex. They are both assembled and modified within the endomembrane system, i.e., the endoplasmic reticulum (ER and the Golgi apparatus, before their transport to their final locations within or outside the cell. In contrast to extensin, the O-glycan chains of arabinogalactan proteins are highly heterogeneous consisting mostly of (i a short oligo-arabinoside chain of three to four residues, and (ii a larger -1,3-linked galactan backbone with -1,6-linked side chains containing galactose, arabinose and, often, fucose, rhamnose or glucuronic acid. The fine structure of arabinogalactan chains varies between, and within plant species, and is important for the functional activities of the glycoproteins. With regards to N-glycans, ER-synthesizing events are highly conserved in all eukaryotes studied so far since they are essential for efficient protein folding. In contrast, evolutionary adaptation of N-glycan processing in the Golgi apparatus has given rise to a variety of organism-specific complex structures. Therefore, plant complex-type N-glycans contain specific glyco-epitopes such as core 1,2-xylose, core 1,3-fucose residues and Lewisa substitutions on the terminal position of the antenna. Like O-glycans, N-glycans of proteins are essential for their stability and function. Mutants affected in the glycan metabolic pathways have provided valuable information on the role of N-/O-glycoproteins in the control of growth, morphogenesis and adaptation to biotic and abiotic stresses. With regards to O-glycoproteins only extensin and arabinogalactan proteins are considered herein. The biosynthesis of these glycoproteins and functional aspects are presented and discussed in this review.

SETH1 and SETH2, two components of the glycosylphosphatidylinositol anchor biosynthetic pathway, are required for pollen germination and tube growth in arabidopsis

Czech Academy of Sciences Publication Activity Database

Lalanne, E.; Honys, David; Johnson, A.; Borner, G. H. H.; Lilley, K. S.; Dupree, P.; Grossniklaus, U.; Twell, D.

2004-01-01

Roč. 16, č. 1 (2004), s. 229-240 ISSN 1040-4651 R&D Projects: GA AV ČR IAA5038207 Institutional research plan: CEZ:AV0Z5038910 Keywords : ARABINOGALACTAN PROTEIN * LEISHMANIA -MEXICANA * GENOMIC ANALYSIS Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 11.295, year: 2004

Biomimetic chromatographic analysis of selenium species: Application for the estimation of their pharmacokinetic properties

Energy Technology Data Exchange (ETDEWEB)

Tsopelas, Fotios [National Technical University of Athens, Laboratory of Inorganic and Analytical Chemistry, School of Chemical Engineering, Athens (Greece); University of Athens, Laboratory of Pharmaceutical Chemistry, School of Pharmacy, Athens (Greece); Tsantili-Kakoulidou, Anna [University of Athens, Laboratory of Pharmaceutical Chemistry, School of Pharmacy, Athens (Greece); Ochsenkuehn-Petropoulou, Maria [National Technical University of Athens, Laboratory of Inorganic and Analytical Chemistry, School of Chemical Engineering, Athens (Greece)

2010-07-15

The retention behavior of selenites, selenates, seleno-dl-methionine, selenocystine, selenocystamine, selenourea, dimethyl selenide, and dimethyl diselenide was investigated by means of biomimetic liquid chromatography. For this purpose, two immobilized artificial membrane (IAM) columns, namely, IAM.PC.DD2 and IAM.PC.MG, and two immobilized plasma protein columns, human serum albumin (HSA) and {alpha}{sub 1}-acid glycoprotein (AGP) columns, were employed using different mobile phase conditions in respect to pH and buffer composition. In general, satisfactory interrelations between retention factors obtained with the two IAM stationary phases and HSA/AGP columns were obtained. Large differences were observed between biomimetic retention factors and octanol-water logD values, since the latter fail to describe electrostatic interactions. In contrast, despite the column diversity, the net retention outcome on all four biomimetic columns was quite similar, especially in the presence of phosphate-buffered saline, which by its effective shielding alleviates the differences between the stationary phases. Of the two IAM columns, IAM.PC.DD2 showed better performance when compared with HSA and AGP columns as well as to octanol-water partitioning. Biomimetic chromatographic indices were further used to estimate the percentage of human oral absorption and plasma protein binding of the eight selenium species investigated, according to equations previously reported in the literature. The estimated values of human oral absorption imply moderate absorption only for dimethyl diselenide, which also may exhibit considerable plasma protein binding. Moderate affinity for plasma proteins should also be expected for dimethyl selenide and selenocystamine. (orig.)

A Novel Biomarker Panel to Identify Steroid Resistance in Childhood Idiopathic Nephrotic Syndrome

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Michael R Bennett

2017-03-01

Full Text Available Idiopathic nephrotic syndrome (NS is the most common glomerular disorder of childhood. Response to initial treatment with corticosteroids is an indicator of prognosis, as resistant patients often present more progressive disease. In this cross-sectional pilot study, we set out to discover a panel of noninvasive biomarkers that could distinguish steroid-resistant nephrotic syndrome (SRNS from steroid-sensitive nephrotic syndrome (SSNS. Information gleaned from such a panel could yield more individualized treatment plans and prevent unnecessary steroid exposure in patients unlikely to respond. Urine was collected from 50 pediatric patients diagnosed with idiopathic NS at Cincinnati Children’s Hospital Medical Center. Isobaric tags for relative and absolute quantitation (iTRAQ was used to discover 13 proteins that were differentially expressed in SSNS vs SRNS in a small 5 × 5 discovery cohort. Suitable assays were found for 9 of the 13 markers identified by iTRAQ and were used in a 25 SRNS × 25 SSNS validation cohort. Vitamin D–binding protein (VDBP, alpha-1 acid glycoprotein 1 (AGP1, alpha-1 acid glycoprotein 2 (AGP2, alpha-1-B glycoprotein (A1BG, fetuin-A, prealbumin, thyroxine-binding globulin and hemopexin, and alpha-2 macroglobulin were measured and combined with urine neutrophil gelatinase–associated lipocalin (NGAL, which had been previously shown to distinguish patients with SRNS. Urinary VDBP, prealbumin, NGAL, fetuin-A, and AGP2 were found to be significantly elevated in SRNS using univariate analysis, with area under the receiver operating characteristic curves (AUCs ranging from 0.65 to 0.81. Multivariate analysis revealed a panel of all 10 markers that yielded an AUC of 0.92 for identification of SRNS. A subset of 5 markers (including VDBP, NGAL, fetuin-A, prealbumin, and AGP2 showed significant associations with SRNS and yielded an AUC of 0.85.

Arabinose-rich polymers as an evolutionary strategy to plasticize resurrection plant cell walls against desiccation

DEFF Research Database (Denmark)

Moore, John P.; Nguema-Ona, Eric E.; Vicré-Gibouin, Mäite

2013-01-01

A variety of Southern African resurrection plants were surveyed using high-throughput cell wall profiling tools. Species evaluated were the dicotyledons, Myrothamnus flabellifolia and Craterostigma plantagineum; the monocotyledons, Xerophyta viscosa, Xerophyta schlecterii, Xerophyta humilis and t......-arabinans, arabinogalactan proteins and arabinoxylans) as the major contributors in ensuring flexibility is maintained and rehydration is facilitated in these plants....

Effects of balneotherapy on the reactants of acute inflammation phase in Ankylosing spondylitis

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Stamenković Bojana

2009-01-01

Full Text Available Introduction. Ankylosing spondylitis (AS is a chronic inflammatory disease that affects sacroiliac joints, spinal column and peripheral joints. Beside medication therapy, physical and balneotherapy play an important role in its complex treatment. Objective. The aim of the research was to establish serum concentrations of C-reactive protein (CRP, α 1-acid glycoprotein (α 1-AGP, ceruloplasmine (CP and erythrocyte sedimentation rate (SE before and after the balneotherapy in ankylosing spondylitis. Methods. The research included 50 AS patients according to the revised New York criteria, of mean age 43 years, who were treated for 14 days on the average at the Clinic for Rheumatology of the Institute 'Niška Banja'. All the patients received medications and balneotherapy (radioactive oligomineral baths, peloid, massage, kinesitherapy; the serum concentrations of CRP, α1-AGP, CP and SE were measured before and after balneotherapy. Serum proteins were determined using original Nor Partigen plates Boehringer. Erythrocyte sedimentation rate was measured by Westergreen method. Balneotherapy was applied individually, intensively or mildly, depending on the AS stage and activity phase. Results. After dosed balneotherapy, a significant decrease in the concentrations of CP (p<0.05, α1-AGP (p<0.01 and CRP (p<0.05 was registered in the serums of AS patients. ESR was not significantly reduced. Conclusion. The research proved that α 1-acid glycoprotein, ceruloplasmine and C-reactive protein represent more sensitive inflammation markers as compared to erythrocyte sedimentation rate. The identification of acute phase reactants is important in the evaluation of dosed balneotherapy efficiency in the treatment of ankylosing spondylitis.

Proteomic Analysis of the Follicular Fluid of Tianzhu White Yak during Diestrus

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Jinzhong Tao

2014-03-01

Full Text Available The aim of this study was to identify differentially expressed proteins in the follicular fluid of Tianzhu white yak during diestrus. Follicles obtained from female yak were divided into four groups according to their diameter: 0–2, 2–4, 4–6 mm, and greater than 6 mm. The follicular fluid was directly aspirated from the follicles and mixed according to follicular size, and two-dimensional gel electrophoresis was carried out on the crude follicular fluid samples. Thirty-four differentially expressed spots were generated from these four sizes of follicles. Fourteen of these spots were analyzed by MALDI-TOF/TOF-MS and identified as: AS3MT, VDP, ANKRD6, C10orf107 protein, MRP4, MAPKAP1, AGO3, profilin-β-actin, SPT2 homolog, AGP, AR, RNF20, obscurin-like-1, and one unnamed protein. These proteins were first reported in follicular fluid, in addition to VDP and AGP. Based on existing knowledge of their function and patterns of expression, we hypothesize that most of these differentially expressed proteins play a role in ovarian follicular growth and development, dominant follicle selection, or follicular atresia and development of oocytes; however, the function of the other differentially expressed proteins in reproduction remains ambiguous.

Anticoagulant Activity and Structural Characterization of Polysaccharide from Abalone (Haliotis discus hannai Ino Gonad

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Jun Zhao

2016-06-01

Full Text Available In this study, we aimed at characterizing the structure and the anticoagulant activity of a polysaccharide fraction (AGP33 isolated from the gonads of Haliotis discus hannai Ino. AGP33 was extracted by enzymatic hydrolysis and purified by ion-exchange and gel-filtration chromatography. The backbone fraction of AGP33 (BAGP33, which appeared to contain of mannose, glucose and galactose, was prepared by partial acid hydrolysis. According to methylation and nuclear magnetic resonance (NMR spectroscopy, the backbone of AGP33 was identified as mainly consisting of 1→3-linked, 1→4-linked, and 1→6-linked monosaccharides. AGP33 is a sulfated polysaccharide with sulfates occur at 3-O- and 4-O-positions. It prolonged thromboplastin time (APTT, thrombin time (TT and prothrombin time (PT compared to a saline control solution in a dosage-dependent manner. AGP33 exhibited an extension (p < 0.01 of APTT compared to the saline group at concentrations higher than 5 μg/mL. AGP33 exhibited higher anticoagulant activity than its desulfated product (AGP33-des and BAGP33. The results showed that polysaccharide with higher molecular weight and sulfate content demonstrated greater anticoagulant activity.

Assessment of regression models for adjustment of iron status biomarkers for inflammation in children with moderate acute malnutrition in Burkina Faso

DEFF Research Database (Denmark)

Cichon, Bernardette; Ritz, Christian; Fabiansen, Christian

2017-01-01

approach. METHODS: Morbidity data were collected during clinical examinations with morbidity recalls in a cross-sectional study in children aged 6-23 mo with moderate acute malnutrition. C-reactive protein (CRP), α1-acid glycoprotein (AGP), serum ferritin (SF), and soluble transferrin receptor (sTfR) were...

Cytokine and acute phase protein gene expression in liver biopsies from dairy cows with a lipopolysaccharide - induced mastitis

DEFF Research Database (Denmark)

Vels, J; Røntved, Christine M.; Bjerring, Martin

2009-01-01

A minimally invasive liver biopsy technique was tested for its applicability to study the hepatic acute phase response (APR) in dairy cows with Escherichia coli lipopolysaccharide (LPS)-induced mastitis. The hepatic mRNA expression profiles of the inflammatory cytokines, tumor necrosis factor (TNF......, a minimally invasive liver biopsy technique can be used for studying the hepatic APR in diseased cattle. Lipopolysaccharide-induced mastitis resulted in a time-dependent production of inflammatory cytokines and SAA and Hp in the liver of dairy cows.......- ), IL-1β, IL-6, and IL-10, and the acute phase proteins serum amyloid A isoform 3 (SAA3), haptoglobin (Hp), and 1-acid glycoprotein (AGP) were determined by real-time reverse transcription-PCR. Fourteen primiparous cows in mid lactation were challenged with 200 µg of LPS (n = 8) or NaCl solution (n = 6...

Novel Glucose-1-Phosphatase with High Phytase Activity and Unusual Metal Ion Activation from Soil Bacterium Pantoea sp. Strain 3.5.1.

Science.gov (United States)

Suleimanova, Aliya D; Beinhauer, Astrid; Valeeva, Liia R; Chastukhina, Inna B; Balaban, Nelly P; Shakirov, Eugene V; Greiner, Ralf; Sharipova, Margarita R

2015-10-01

Phosphorus is an important macronutrient, but its availability in soil is limited. Many soil microorganisms improve the bioavailability of phosphate by releasing it from various organic compounds, including phytate. To investigate the diversity of phytate-hydrolyzing bacteria in soil, we sampled soils of various ecological habitats, including forest, private homesteads, large agricultural complexes, and urban landscapes. Bacterial isolate Pantoea sp. strain 3.5.1 with the highest level of phytase activity was isolated from forest soil and investigated further. The Pantoea sp. 3.5.1 agpP gene encoding a novel glucose-1-phosphatase with high phytase activity was identified, and the corresponding protein was purified to apparent homogeneity, sequenced by mass spectroscopy, and biochemically characterized. The AgpP enzyme exhibits maximum activity and stability at pH 4.5 and at 37°C. The enzyme belongs to a group of histidine acid phosphatases and has the lowest Km values toward phytate, glucose-6-phosphate, and glucose-1-phosphate. Unexpectedly, stimulation of enzymatic activity by several divalent metal ions was observed for the AgpP enzyme. High-performance liquid chromatography (HPLC) and high-performance ion chromatography (HPIC) analyses of phytate hydrolysis products identify dl-myo-inositol 1,2,4,5,6-pentakisphosphate as the final product of the reaction, indicating that the Pantoea sp. AgpP glucose-1-phosphatase can be classified as a 3-phytase. The identification of the Pantoea sp. AgpP phytase and its unusual regulation by metal ions highlight the remarkable diversity of phosphorus metabolism regulation in soil bacteria. Furthermore, our data indicate that natural forest soils harbor rich reservoirs of novel phytate-hydrolyzing enzymes with unique biochemical features. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

A microculture technique for the evaluation of corneal cell metabolism in vitro.

Science.gov (United States)

BenEzra, D

1977-10-01

A microculture technique for the evaluation of the metabolic activity of corneal cells is described and analyzed. The extent of DNA synthesis in microcultures with 10(3) to 2.5 X 10(3) cells per well was initially low during day 1, increasing steadily thereafter. Higher initial concentration of 10(4) to 2 X 10(4) cells per microculture demonstrated a high metabolic activity during days 1 and 2 in culture, followed by a rapid and marked decrease on days 3 and 4. The origin and concentration of serum in the system have been found to be crucial. Xenogeneic serum (fetal calf serum--FCS) had the most potent stimulatory effect on DNA and protein synthesis. Syngeneic serum (guinea pig serum, strain 13--SGpS) or allogeneic serum (guinea pig serum strain 2--AGpS) had a generally less stimulatory effect on the metabolic activity. However, both sera had a relatively much stronger effect on the protein synthesis.

Risk factors for and management of graft pancreatitis.

Science.gov (United States)

Nadalin, Silvio; Girotti, Paolo; Königsrainer, Alfred

2013-02-01

Systematic and detailed analysis of risk factors, pathophysiology, clinical manifestation, diagnosis and management of graft pancreatitis in its different forms, that is acute and chronic graft pancreatitis (A-GP and C-GP), and A-GP being further distinguished into: physiological (P-AGP), early (E-AGP) and late AP (L-AGP). Graft pancreatitis is the second most-frequent complication following pancreas transplantation. P-AGP is an unavoidable entity related to ischemic reperfusion injury. It is usually clinically silent. It is a timely and prognostically self-limited process. E-AGP occurs within 3 months after pancreas transplantation (PTx) in 35% of cases and is associated with high rates of graft loss (78-91%). Clinical signs are pain, systemic inflammatory response (SIRS) and haematuria. Therapy can be medical, interventional and surgical. L-AGP occurs 3 months following PTx in 14-25% of cases and represents an uncommon cause of graft loss. Typical clinical signs are pain, abdominal tenderness and fever. Typical laboratory signs are hyperamylasaemia, hyperglycaemia and hypercreatininaemia. Therapy is usually conservative. C-GP is difficult to be distinguished from chronic rejection and is associated to graft loss in 4-10% of cases. Recurrent A-GPs and infections are the main risk factors. Specific symptoms are chronic abdominal malaise, constipation and recurrence of DM. Isolated hyperglycaemia is typical of C-GP. The therapy is usually conservative. This systematic analysis of different manifestations of graft pancreatitis provides the basis for a clinical approach to tackling this complex entity.

Relations between the occurrence of resistance to antimicrobial growth promoters among Enterococcus faecium isolated from broilers and broiler meat

DEFF Research Database (Denmark)

Emborg, Hanne-Dorthe; Andersen, J. S.; Seyfarth, Anne Mette

2003-01-01

and streptogramin. By February 1998, all antimicrobial growth promoters (AGPs) were withdrawn from the Danish broiler production. The present study investigates, by logistic regression analyses, the (1) changes in the occurrence of AGP resistance among E. faecium from broilers and broiler meat from the fourth...... quarter of 1995 to the fourth quarter of 2001 and (2) relations between the occurrence of AGP resistance among E. faecium isolates from Danish broilers and AGP resistance among E. faecium isolates from the broiler meat of Danish and unknown origin collected in the same quarter within the year....... In the present study, we showed that after the AGP withdrawal, a significant decline in resistance to avilamycin, erythromycin, vancomycin and virginiamycin was observed among E. faecium from broilers and broiler meat. In addition, a decline in the occurrence of AGP resistance among E. faecium from Danish...

Axial Globe Position Measurement: A Prospective Multi-center Study by the International Thyroid Eye Disease Society

Science.gov (United States)

Bingham, Chad M.; Sivak-Callcott, Jennifer A.; Gurka, Matthew J.; Nguyen, John; Hogg, Jeffery P.; Feldon, Steve E.; Fay, Aaron; Seah, Lay-Leng; Strianese, Diego; Durairaj, Vikram D.; Uddin, Jimmy; Devoto, Martin H.; Harris, Matheson; Saunders, Justin; Osaki, Tammy H.; Looi, Audrey; Teo, Livia; Davies, Brett W.; Elefante, Andrea; Shen, Sunny; Realini, Tony; Fischer, William; Kazim, Michael

2015-01-01

Purpose Identify a reproducible measure of axial globe position (AGP) for multicenter studies of patients with thyroid eye disease (TED). Methods This is a prospective, international, multicenter, observational study in which 3 types of AGP evaluation were examined: radiologic, clinical, and photographic. In this study, computed tomography (CT) was the modality to which all other methods were compared. CT AGP was measured from an orthogonal line between the anterior lateral orbital rims to the cornea. All CT measurements were made at a single institution by 3 individual clinicians. Clinical evaluation was performed with exophthalmometry. Three clinicians from each clinical site assessed AGP with 3 different exophthalmometers and horizontal palpebral width using a ruler. Each physician made 3 separate measurements with each type of exophthalmometer, not in succession. All photographic measurements were made at a single institution. AGP was measured from lateral photographs in which a standard marker was placed at the anterior lateral orbital rim. Horizontal and vertical palpebral fissure were measured from frontal photographs. Three trained readers measured 3 separate times, not in succession. Exophthalmometry and photography method validity was assessed by agreement with CT (mean differences calculation, ICC’s, Bland-Altman figures). Correlation between palpebral fissure and CT AGP was assessed with Pearson correlation. Intraclinician and interclinician reliability was evaluated using intraclass correlation coefficients (ICC). Results Sixty-eight patients from 7 centers participated. CT mean AGP was 21.37mm (15.96 – 28.90mm) right, 21.22mm (15.87 – 28.70mm) left (ICC 0.996 and 0.995). Exophthalmometry AGP fell between 18mm and 25mm. Intraclinician agreement across exophthalmometers was ideal (ICC 0.948 – 0.983). Agreement between clinicians was greater than 0.85 for all upright exophthalmometry measurements. Photographic mean AGP was 20.47mm (10.92 – 30

A recombinant Anticarsia gemmatalis MNPV harboring chiA and v-cath genes from Choristoneura fumiferana defective NPV induce host liquefaction and increased insecticidal activity.

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Anabele Azevedo Lima

Full Text Available One of the interesting features of Anticarsia gemmatalis multiple nucleopolyhedrovirus isolate 2D (AgMNPV-2D genome is the absence of chitinase (chiA and cathepsin (v-cath genes. This characteristic may be responsible for the lack of liquefaction and melanization in A. gemmatalis larvae killed by AgMNPV-2D infection. This study aimed to test the hypothesis that CHIA and V-CATH proteins from Choristonera fumiferana DEF multiple nucleopolyhedrovirus (CfDEFNPV are able to liquefy and melanize the cuticle of A. gemmatalis larvae infected by a recombinant AgMNPV containing chiA and v-cath genes inserted in its genome. A fragment from the CfDefNPV genome containing chiA and v-cath genes was inserted into the genome of AgMNPV-2D. The recombinant virus (vAgp2100Cf.chiA/v-cath was purified and used to infect insect cells and larvae. Transcripts of v-cath and chiA genes were detected along the infection of insect cells by qRT-PCR, from early to late phases of infection. The analysis of A. gemmatalis larvae killed by vAgp2100Cf.chiA/v-cath infection confirmed the hypothesis proposed. The vAgp2100Cf.chiA/v-cath showed higher insecticidal activity against third instar A. gemmatalis larvae when compared to AgMNPV-2D. The mean time to death was also lower for the vAgp2100Cf.chiA/v-cath when compared to AgMNPV-2D at 10 days post infection. Occlusion body production was higher in A. gemmatalis larvae infected with vAgp2100Cf.chiA/v-cath when compared to AgMNPV-2D. Enzyme assays showed higher chitinase and cysteine protease activities in insect cells and insects infected with vAgp2100Cf.chiA/v-cath when compared to AgMNPV-2D. The introduction of chiA and v-cath genes into the genome of AgMNPV improves its insecticidal activity against A. gemmatalis larvae and this recombinant virus could be used as an alternative to the wild type virus to control this important insect pest.

Anti-angiogenic activity of a new andrographolide derivative in zebrafish and HUVECs.

Science.gov (United States)

Li, Jingjing; Peng, Yuran; Li, Shang; Sun, Yicheng; Chan, Judy Yuet-Wa; Cui, Guozhen; Wang, Decai; Zhou, Guo-Chun; Lee, Simon Ming-Yuen

2016-10-15

Andrographolide is among the most promising anti-tumor and anti-angiogenic components in Andrographis paniculata but its poor bioavailability and limited efficacy pose difficulties for its therapeutic development. Therefore, improving its pharmaceutical features and potency, by modifying its chemical structure, is desirable. In the present study, a new andrographolide derivative (AGP-40) was synthesized and characterized for its anti-angiogenic properties. Human umbilical vein endothelial cells (HUVECs) and zebrafish models were used to identify the anti-angiogenic activity of AGP-40. AGP-40 significantly suppressed the formation of blood vessels in zebrafish and inhibited proliferation, migration and tube formation in vitro. The anti-angiogenic effects of AGP-40 are at least partially mediated via the PI3K/Akt and MEK/Erk(1/2) signaling pathways. Furthermore, AGP-40 exhibited stronger anti-proliferative effects than andrographolide against A549, HepG2, Hela cancer cell lines. This study is the first to demonstrate the promising anti-angiogenic activity of the new andrographolide derivative AGP-40. Our results indicate that AGP-40 could serve as a potential therapeutic agent for the treatment and prevention of diseases associated with excessive angiogenesis. Copyright © 2016 Elsevier B.V. All rights reserved.

Employees’ Satisfaction on Training & Development of Atlantic, Gulf, & Pacific Company of Manila, Inc.

OpenAIRE

ZALDY S. QUIZON

2014-01-01

–The need for quality human resources in AG&P is greatly felt. This is because of several factors directly and indirectly affecting the organization. The study aimed to describe the demographic profile of AG&P employees in terms of age, gender, educational attainment, employee type, and length of service in AG&P; to determine the level of employee’s satisfaction on Training & Development of AG&P with regard to the following: Its Nature and Essential, Training Program and Traine...

Improvement of broiler meat quality due to dietary inclusion of soybean oligosaccharide derived from soybean meal extract

Science.gov (United States)

Suthama, N.; Pramono, Y. B.; Sukamto, B.

2018-01-01

Dietary inclusion of antibiotics as growth promoters (AGPs) in poultry production has been applied for decades worldwide, but recently AGPs have been banned due to the negative consequences for health and food safety. Soybean oligosccharide (SOS) derived from soybean meal extract is one of natural compound without carrying-over the residue to product and is consumer’s health friendly. The purpose of the present study was to evaluate dietary inclusion of SOS on broiler meat quality. A total of 120 broilers of 7-day-old were allocated into 3 treatments with 4 replications (10 birds each) in completely randomized design. Treatments applied were D1: diet without SOS, D2: D1 plus 0.15% SOS, and D3: D1 plus 0.30% SOS. Intestinal lactic acid bacteria (LAB), protein digestibility, meat protein and fat depositions, and meat cholesterol were the parameters observed. Data were statistically tested using analysis of variance and Duncan test. Dietary SOS inclusion at 0.30% (D3) significantly (P<0.05) increased LAB population (7.21x104 cfu/g), protein digestibility (72.80%), and meat protein deposition (90.83 g/bird), but it decreased meat fat (8.27 g/bird) and meat cholesterol (37.28 mg/100 g). In conclusion, dietary SOS inclusion at 0.30% improves meat quality of broiler based on the increase in meat protein deposition with lower fat and cholesterol.

PCR amplification and sequences of cDNA clones for the small and large subunits of ADP-glucose pyrophosphorylase from barley tissues.

Science.gov (United States)

Villand, P; Aalen, R; Olsen, O A; Lüthi, E; Lönneborg, A; Kleczkowski, L A

1992-06-01

Several cDNAs encoding the small and large subunit of ADP-glucose pyrophosphorylase (AGP) were isolated from total RNA of the starchy endosperm, roots and leaves of barley by polymerase chain reaction (PCR). Sets of degenerate oligonucleotide primers, based on previously published conserved amino acid sequences of plant AGP, were used for synthesis and amplification of the cDNAs. For either the endosperm, roots and leaves, the restriction analysis of PCR products (ca. 550 nucleotides each) has revealed heterogeneity, suggesting presence of three transcripts for AGP in the endosperm and roots, and up to two AGP transcripts in the leaf tissue. Based on the derived amino acid sequences, two clones from the endosperm, beps and bepl, were identified as coding for the small and large subunit of AGP, respectively, while a leaf transcript (blpl) encoded the putative large subunit of AGP. There was about 50% identity between the endosperm clones, and both of them were about 60% identical to the leaf cDNA. Northern blot analysis has indicated that beps and bepl are expressed in both the endosperm and roots, while blpl is detectable only in leaves. Application of the PCR technique in studies on gene structure and gene expression of plant AGP is discussed.

Predictors of Inflammation in a Cohort of Bolivian Infants and Toddlers

Science.gov (United States)

Burke, Rachel M.; Suchdev, Parminder S.; Rebolledo, Paulina A.; Fabiszewski de Aceituno, Anna M.; Revollo, Rita; Iñiguez, Volga; Klein, Mitchel; Drews-Botsch, Carolyn; Leon, Juan S.

2016-01-01

Inflammation has been associated with cardiovascular disease and other health outcomes in children and adults, yet few longitudinal data are available on prevalence and predictors of inflammation in infants. We aimed to identify the prevalence of inflammation in a cohort of Bolivian infants and estimate its association with acute (recent illnesses) and chronic (overweight, stunting) morbidities and potential pathogen exposure (represented by water, sanitation, and hygiene [WASH] resources). We measured plasma concentrations of two acute phase proteins (C-reactive protein [CRP], marking acute inflammation, and alpha(1)-acid-glycoprotein [AGP], marking chronic inflammation) at three time points (target 2, 6–8, and 12–18 months). Of 451 singleton infants enrolled in the parent study, 272 had the first blood draw and complete data. Anthropometry and sociodemographic and recent illness data (2-week recall of cough, diarrhea, and fever) were collected at each visit. Inflammation was defined as CRP > 5 mg/L or AGP > 1 g/L. The prevalence of inflammation increased from early infancy (3% at first blood draw) to later infancy (15–22% at later blood draws). Recent cough, recent fever, and age in months were significantly associated with relative increases in CRP (7–44%) and AGP (5–23%), whereas recent diarrhea was only significantly associated with an increase in CRP (48%). Neither anthropometry nor WASH was significantly associated with inflammation. Results confirm the role of recent acute illness in inflammation in infants, and indicate that adiposity and WASH are not as important to inflammation in this age category. PMID:27527627

Microheterogeneity of alpha 1-acid glycoprotein in healthy elderly subjects: patterns obtained by crossed affino-immunoelectrophoresis.

Science.gov (United States)

Kawerk, N; Succari-Aderschlag, M; Foglietti, M J

1991-10-14

Total serum alpha 1-acid glycoprotein (AGP) concentration and concanavalin A-dependent microheterogeneity were studied in 31 healthy elderly subjects (18 men, 13 women, 71 to 76 yr old). Crossed affino-immunoelectrophoresis (CAIE) revealed three microheterogeneity variants of AGP: non-reactive, weakly reactive and strongly reactive with ConA. Two patterns were found in both elderly men and women, i.e. a normal pattern and one with an increase in the non-reactive form. Mean serum AGP levels in the elderly subjects with slightly higher than in a reference group of younger subjects. The Con A non-reactive form of AGP was increased in 42% of the elderly population. An increase in the non-reactive form of AGP in CAIE should be considered as general expression of chronic inflammation which is of no clinical relevance.

Effect of alkylglycerone phosphate synthase on the expression profile of circRNAs in the human thyroid cancer cell line FRO.

Science.gov (United States)

Hou, Shasha; Tan, Jian; Yang, Bing; He, Lu; Zhu, Yu

2018-05-01

Thyroid cancer is a common primary tumor in China. Therefore, it is important to investigate the underlying molecular mechanism of thyroid cancer in order to achieve effective individualized treatments. In our previous study, a positive correlation between the expression of alkylglycerone phosphate synthase (AGPS) and the malignant phenotype of thyroid cancer cell lines was identified. The inactivation of AGPS was able to decrease the malignancy of cancer, and inhibit tumor growth and invasion. However, the function of AGPS on thyroid cancer was unclear. In the present study, it was revealed that AGPS was able to regulate the expression of circular RNAs (circRNAs), which may be the mechanism of its anticancer activity. Therefore, the effects of AGPS silencing and knockout on circRNA expression in the thyroid cancer cell line FRO were investigated using circRNAs microarray, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed in order to investigate the underlying molecular mechanism of AGPS for the regulation of thyroid cancer through circRNAs.

Bacteriophytochromes control conjugation in Agrobacterium fabrum.

Science.gov (United States)

Bai, Yingnan; Rottwinkel, Gregor; Feng, Juan; Liu, Yiyao; Lamparter, Tilman

2016-08-01

Bacterial conjugation, the transfer of single stranded plasmid DNA from donor to recipient cell, is mediated through the type IV secretion system. We performed conjugation assays using a transmissible artificial plasmid as reporter. With this assay, conjugation in Agrobacterium fabrum was modulated by the phytochromes Agp1 and Agp2, photoreceptors that are most sensitive in the red region of visible light. In conjugation studies with wild-type donor cells carrying a pBIN-GUSINT plasmid as reporter that lacked the Ti (tumor inducing) plasmid, no conjugation was observed. When either agp1(-) or agp2(-) knockout donor strains were used, plasmid DNA was delivered to the recipient, indicating that both phytochromes suppress conjugation in the wild type donor. In the recipient strains, the loss of Agp1 or Agp2 led to diminished conjugation. When wild type cells with Ti plasmid and pBIN-GUS reporter plasmid were used as donor, a high rate of conjugation was observed. The DNA transfer was down regulated by red or far-red light by a factor of 3.5. With agp1(-) or agp2(-) knockout donor cells, conjugation in the dark was about 10 times lower than with the wild type donor, and with the double knockout donor no conjugation was observed. These results imply that the phytochrome system has evolved to inhibit conjugation in the light. The decrease of conjugation under different temperature correlated with the decrease of phytochrome autophosphorylation. Copyright © 2015 Elsevier B.V. All rights reserved.

Characterization of hop pectins shows the presence of an arabinogalactan-protein

NARCIS (Netherlands)

Oosterveld, A.; Voragen, A.G.J.; Schols, H.A.

2002-01-01

Hop pectins were extracted from spent hops using acid extraction conditions and were characterized chemically. The acid extraction of spent hops resulted in a yield of 2°containing 59 f polysaccharides. The hop pectins under investigation had a relatively high molecular weight and an intrinsic

Comparison of the performance of laboratory tests in the diagnosis of feline infectious peritonitis.

Science.gov (United States)

Stranieri, Angelica; Giordano, Alessia; Paltrinieri, Saverio; Giudice, Chiara; Cannito, Valentina; Lauzi, Stefania

2018-05-01

We compared the performance of clinicopathologic and molecular tests used in the antemortem diagnosis of feline infectious peritonitis (FIP). From 16 FIP and 14 non-FIP cats, we evaluated retrospectively the sensitivity, specificity, and likelihood ratios (LRs) of serum protein electrophoresis, α 1 -acid glycoprotein (AGP) on peripheral blood, screening reverse-transcription nested PCR (RT-nPCR) on the 3'-untranslated region (3'-UTR), and spike (S) gene sequencing on peripheral blood, body cavity effusions, and tissue, as well as body cavity cytology and delta total nucleated cell count (ΔTNC). Any of these tests on blood, and especially the molecular tests, may support or confirm a clinical diagnosis of FIP. A negative result does not exclude the disease except for AGP. Cytology, 3'-UTR PCR, and ΔTNC may confirm a clinical diagnosis on effusions; cytology or 3'-UTR PCR may exclude FIP. Conversely, S gene sequencing is not recommended based on the LRs. On tissues, S gene sequencing is preferable when histology is highly consistent with FIP, and 3'-UTR PCR when FIP is unlikely. Combining one test with high LR+ with one with low LR- (e.g., molecular tests and AGP on blood, ΔTNC and cytology in effusions) may improve the diagnostic power of the most used laboratory tests.

Organ and Tissue-Specific Localisation of Selected Cell Wall Epitopes in the Zygotic Embryo of Brachypodium distachyon

Directory of Open Access Journals (Sweden)

Alexander Betekhtin

2018-03-01

Full Text Available The plant cell wall shows a great diversity regarding its chemical composition, which may vary significantly even during different developmental stages. In this study, we analysed the distribution of several cell wall epitopes in embryos of Brachypodium distachyon (Brachypodium. We also described the variations in the nucleus shape and the number of nucleoli that occurred in some embryo cells. The use of transmission electron microscopy, and histological and immunolocalisation techniques permitted the distribution of selected arabinogalactan proteins, extensins, pectins, and hemicelluloses on the embryo surface, internal cell compartments, and in the context of the cell wall ultrastructure to be demonstrated. We revealed that the majority of arabinogalactan proteins and extensins were distributed on the cell surface and that pectins were the main component of the seed coat and other parts, such as the mesocotyl cell walls and the radicula. Hemicelluloses were localised in the cell wall and outside of the radicula protodermis, respectively. The specific arrangement of those components may indicate their significance during embryo development and seed germination, thus suggesting the importance of their protective functions. Despite the differences in the cell wall composition, we found that some of the antibodies can be used as markers to identify specific cells and the parts of the developing Brachypodium embryo.

Differences between easy- and difficult-to-mill chickpea (Cicer arietinum L.) genotypes. Part III: free sugar and non-starch polysaccharide composition.

Science.gov (United States)

Wood, Jennifer A; Knights, Edmund J; Campbell, Grant M; Choct, Mingan

2014-05-01

Parts I and II of this series of papers identified several associations between the ease of milling and the chemical compositions of different chickpea seed fractions. Non-starch polysaccharides were implicated; hence, this study examines the free sugars and sugar residues. Difficult milling is associated with: (1) lower glucose and xylose residues (less cellulose and xyloglucans) and more arabinose, rhamnose and uronic acid in the seed coat, suggesting a more flexible seed coat that resists cracking and decortication; (2) a higher content of soluble and insoluble non-starch polysaccharide fractions in the cotyledon periphery, supporting a pectic polysaccharide mechanism comprising arabinogalacturonan, homogalacturonan, rhamnogalalcturonan, and glucuronan backbone structures; (3) higher glucose and mannose residues in the cotyledon periphery, supporting a lectin-mediated mechanism of adhesion; and (4) higher arabinose and glucose residues in the cotyledon periphery, supporting a mechanism involving arabinogalactan-proteins. This series has shown that the chemical composition of chickpea does vary in ways that are consistent with physical explanations of how seed structure and properties relate to milling behaviour. Seed coat strength and flexibility, pectic polysaccharide binding, lectins and arabinogalactan-proteins have been implicated. Increased understanding in these mechanisms will allow breeding programmes to optimise milling performance in new cultivars. © 2013 Society of Chemical Industry.

Risk indicators for aggressive periodontitis in an untreated isolated young population from Brazil

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Priscila Corraini

2009-06-01

Full Text Available This study aimed to assess the prevalence of aggressive periodontitis (AgP, and to investigate the association between demographic, socioeconomic and behavioral risk indicators with AgP in an untreated and isolated young population in Southeastern Brazil. For this cross-sectional survey, 134 subjects aged 12-29 years were selected by a census. Of those eligible, 101 subjects received a full-mouth clinical examination, and were interviewed using a structured written questionnaire. Cases were defined as individuals with 4 or more teeth with attachment loss > 4 mm or > 5 mm in the age groups 12-19 and 20-29, respectively. Overall, 9.9% of the subjects presented AgP (10.3% of the 12-19-year-olds and 9.7% of the 20-29-year-olds. The only risk indicator significantly associated with AgP in this isolated population was a high proportion of sites (> 30% presenting supragingival calculus [OR = 23.2]. Having experienced an urgency dental treatment was a protective factor for AgP [OR = 0.1]. The authors concluded that this isolated and untreated population from Brazil presented a high prevalence of AgP. Local plaque-retaining factors played a major role in the prevalence of AgP in this isolated population, and should be included in further studies evaluating this destructive periodontal disease form.

Studying Secondary Growth and Bast Fiber Development: The Hemp Hypocotyl Peeks behind the Wall

Czech Academy of Sciences Publication Activity Database

Behr, M.; Legay, S.; Žižková, Eva; Motyka, Václav; Dobrev, Petre; Hausman, J.F.; Lutts, S.; Guerriero, G.

2016-01-01

Roč. 7, NOV 18 (2016), č. článku 1733. ISSN 1664-462X R&D Projects: GA ČR(CZ) GA16-14649S Institutional support: RVO:61389030 Keywords : plant-cell-wall * arabidopsis-thaliana * cannabis-sativa * lignin biosynthesis * microarray analysis * gene-expression * in-silico * anthocyanin biosynthesis * arabinogalactan-protein * transcription factors * Cannabis sativa * hypocotyl * bast fibers * cell wall * RNA-Seq * immunohistochemistry * phytohormones Subject RIV: EF - Botanics Impact factor: 4.298, year: 2016

Arabidopsis thaliana FLA4 functions as a glycan-stabilized soluble factor via its carboxy-proximal Fasciclin 1 domain.

Science.gov (United States)

Xue, Hui; Veit, Christiane; Abas, Lindy; Tryfona, Theodora; Maresch, Daniel; Ricardi, Martiniano M; Estevez, José Manuel; Strasser, Richard; Seifert, Georg J

2017-08-01

Fasciclin-like arabinogalactan proteins (FLAs) are involved in numerous important functions in plants but the relevance of their complex structure to physiological function and cellular fate is unresolved. Using a fully functional fluorescent version of Arabidopsis thaliana FLA4 we show that this protein is localized at the plasma membrane as well as in endosomes and soluble in the apoplast. FLA4 is likely to be GPI-anchored, is highly N-glycosylated and carries two O-glycan epitopes previously associated with arabinogalactan proteins. The activity of FLA4 was resistant against deletion of the amino-proximal fasciclin 1 domain and was unaffected by removal of the GPI-modification signal, a highly conserved N-glycan or the deletion of predicted O-glycosylation sites. Nonetheless these structural changes dramatically decreased endoplasmic reticulum (ER)-exit and plasma membrane localization of FLA4, with N-glycosylation acting at the level of ER-exit and O-glycosylation influencing post-secretory fate. We show that FLA4 acts predominantly by molecular interactions involving its carboxy-proximal fasciclin 1 domain and that its amino-proximal fasciclin 1 domain is required for stabilization of plasma membrane localization. FLA4 functions as a soluble glycoprotein via its carboxy-proximal Fas1 domain and its normal cellular trafficking depends on N- and O-glycosylation. © 2017 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

Gingival Crevicular Fluid and Salivary Periostin Levels in Non-Smoker Subjects With Chronic and Aggressive Periodontitis : Periostin Levels in Chronic and Aggressive Periodontitis.

Science.gov (United States)

Aral, Cüneyt A; Köseoğlu, Serhat; Sağlam, Mehmet; Pekbağrıyanık, Tuğba; Savran, Levent

2016-06-01

Periostin, an extracellular matrix protein functioning as an important structural mediator and adhesion molecule, has been shown to be an important regulator of connective tissue integrity. This study aimed to evaluate the levels of periostin in chronic periodontitis (CP) and aggressive periodontitis (AgP) compared to non-periodontitis (NP). Individuals were submitted to gingival crevicular fluid (GCF) and saliva sampling. Periodontal examination consisted of plaque index (PI), gingival index (GI), probing depth (PD), bleeding on probing (BOP), and clinical attachment level (CAL) measurements. Assays for periostin were performed by an enzyme-linked immunosorbent assay. Periodontitis patients presented more severe clinical indices compared to the NP group (p periodontitis. The results suggest that subjects with CP and AgP exhibit a different periostin profile. Periostin in GCF may have a protective role against periodontal disease. Furthermore, salivary periostin concentrations may have a promising diagnostic potential for the aggressive forms of periodontal disease.

[Effects of balneotherapy on the reactants of acute inflammation phase in ankylosing spondylitis].

Science.gov (United States)

2009-01-01

Ankylosing spondylitis (AS) is a chronic inflammatory disease that affects sacroiliac joints, spinal column and peripheral joints. Beside medication therapy, physical and balneotherapy play an important role in its complex treatment. The aim of the research was to establish serum concentrations of C-reactive protein (CRP), alpha 1-acid glycoprotein (alpha 1-AGP), ceruloplasmine (CP) and erythrocyte sedimentation rate (SE) before and after the balneotherapy in ankylosing spondylitis. The research included 50 AS patients according to the revised New York criteria, of mean age 43 years, who were treated for 14 days on the average at the Clinic for Rheumatology of the Institute "Niska Banja". All the patients received medications and balneotherapy (radioactive oligomineral baths, peloid, massage, kinesitherapy); the serum concentrations of CRP, al-AGP, CP and SE were measured before and after balneotherapy. Serum proteins were determined using original Nor Partigen plates Boehringer. Erythrocyte sedimentation rate was measured by Westergreen method. Balneotherapy was applied individually, intensively or mildly, depending on the AS stage and activity phase. After dosed balneotherapy, a significant decrease in the concentrations of CP (p balneotherapy efficiency in the treatment of ankylosing spondylitis.

Distribution of primaquine in human blood: Drug-binding to alpha 1-glycoprotein

International Nuclear Information System (INIS)

Kennedy, E.; Frischer, H.

1990-01-01

To clarify the distribution of the antimalarial primaquine in human blood, we measured the drug separately in the liquid, cellular, and ultrafiltrate phases. Washed red cells resuspended at a hematocrit of 0.4 were exposed to a submaximal therapeutic level of 250 ng/ml of carbon 14-labeled primaquine. The tracer was recovered quantitatively in separated plasma and red cells. Over 75% of the total labeled drug was found in red cells suspended in saline solution, but only 10% to 30% in red cells suspended in plasma. The plasma effect was not mediated by albumin. Studies with alpha 1-acid glycoprotein (AGP), tris(2-butoxyethyl)phosphate, an agent that displaces AGP-bound drugs, and cord blood known to have decreased AGP established that primaquine binds to physiologic amounts of the glycoprotein in plasma. Red cell primaquine concentration increased linearly as AGP level fell and as the free drug fraction rose. We suggest that clinical blood levels of primaquine include the red cell fraction or whole blood level because (1) erythrocytic primaquine is a sizable and highly variable component of the total drug in blood; (2) this component reflects directly the free drug in plasma, and inversely the extent of binding to AGP; (3) the amount of free primaquine may influence drug transport into specific tissues in vivo; and (4) fluctuations of AGP, an acute-phase reactant that increases greatly in patients with malaria and other infections, markedly affect the partition of primaquine in blood. Because AGP binds many basic drugs, unrecognized primaquine-drug interactions may exist

Proteoglycans from Boswellia serrata Roxb. and B. carteri Birdw. and identification of a proteolytic plant basic secretory protein

DEFF Research Database (Denmark)

Herrmann, Andreas; König, Simone; Lechtenberg, Matthias

2012-01-01

Water-soluble high molecular weight compounds were isolated in yields of 21-22% from the oleogum of Boswellia serrata and B. carteri. Using anion exchange chromatography and gel permeation chromatography, different proteoglycans were purified and characterized, leading to four principally different...... for analytical quality control. The data also offer an insight into the plant response towards wound-closing by the formation of extensin and AGP-containing gum....

Alternative Growth Promoters Modulate Broiler Gut Microbiome and Enhance Body Weight Gain

Science.gov (United States)

Salaheen, Serajus; Kim, Seon-Woo; Haley, Bradd J.; Van Kessel, Jo Ann S.; Biswas, Debabrata

2017-01-01

Antibiotic growth promoters (AGPs) are frequently used to enhance weight-gain in poultry production. However, there has been increasing concern over the impact of AGP on the emergence of antibiotic resistance in zoonotic bacterial pathogens in the microbial community of the poultry gut. In this study, we adopted mass-spectrophotometric, phylogenetic, and shotgun-metagenomic approaches to evaluate bioactive phenolic extracts (BPE) from blueberry (Vaccinium corymbosum) and blackberry (Rubus fruticosus) pomaces as AGP alternatives in broilers. We conducted two trials with 100 Cobb-500 broiler chicks (in each trial) in four equal groups that were provided water with no supplementation, supplemented with AGP (tylosin, neomycin sulfate, bacitracin, erythromycin, and oxytetracycline), or supplemented with 0.1 g Gallic acid equivalent (GAE)/L or 1.0 g GAE/L (during the last 72 h before euthanasia) of BPE for 6 weeks. When compared with the control group (water only), the chickens supplemented with AGP and 0.1 g GAE/L of BPE gained 9.5 and 5.8% more body weight, respectively. The microbiomes of both the AGP- and BPE-treated chickens had higher Firmicutes to Bacteroidetes ratios. AGP supplementation appeared to be associated with higher relative abundance of bacteriophages and unique cecal resistomes compared with BPE supplementation or control. Functional characterization of cecal microbiomes revealed significant animal-to-animal variation in the relative abundance of genes involved in energy and carbohydrate metabolism. These findings established a baseline upon which mechanisms of plant-based performance enhancers in regulation of animal growth can be investigated. In addition, the data will aid in designing alternate strategies to improve animal growth performance and consequently production. PMID:29123512

Alternative Growth Promoters Modulate Broiler Gut Microbiome and Enhance Body Weight Gain

Directory of Open Access Journals (Sweden)

Serajus Salaheen

2017-10-01

Full Text Available Antibiotic growth promoters (AGPs are frequently used to enhance weight-gain in poultry production. However, there has been increasing concern over the impact of AGP on the emergence of antibiotic resistance in zoonotic bacterial pathogens in the microbial community of the poultry gut. In this study, we adopted mass-spectrophotometric, phylogenetic, and shotgun-metagenomic approaches to evaluate bioactive phenolic extracts (BPE from blueberry (Vaccinium corymbosum and blackberry (Rubus fruticosus pomaces as AGP alternatives in broilers. We conducted two trials with 100 Cobb-500 broiler chicks (in each trial in four equal groups that were provided water with no supplementation, supplemented with AGP (tylosin, neomycin sulfate, bacitracin, erythromycin, and oxytetracycline, or supplemented with 0.1 g Gallic acid equivalent (GAE/L or 1.0 g GAE/L (during the last 72 h before euthanasia of BPE for 6 weeks. When compared with the control group (water only, the chickens supplemented with AGP and 0.1 g GAE/L of BPE gained 9.5 and 5.8% more body weight, respectively. The microbiomes of both the AGP- and BPE-treated chickens had higher Firmicutes to Bacteroidetes ratios. AGP supplementation appeared to be associated with higher relative abundance of bacteriophages and unique cecal resistomes compared with BPE supplementation or control. Functional characterization of cecal microbiomes revealed significant animal-to-animal variation in the relative abundance of genes involved in energy and carbohydrate metabolism. These findings established a baseline upon which mechanisms of plant-based performance enhancers in regulation of animal growth can be investigated. In addition, the data will aid in designing alternate strategies to improve animal growth performance and consequently production.

Application of biomimetic HPLC to estimate lipophilicity, protein and phospholipid binding of potential peptide therapeutics

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Klara Livia Valko

2018-06-01

Full Text Available Peptide therapeutics are new modalities offering several challenges to drug discovery. They are generally less stable and permeable in vivo. The characterization of their lipophilicity cannot be carried out using the traditional in silico or wet octanol/water partition coefficients. The prediction of their in vivo distribution and permeability is also challenging. In this paper, it is demonstrated that the biomimetic properties such as lipophilicity, protein and phospholipid binding can be easily assessed by HPLC using chemically bonded protein and immobilized artificial membrane (IAM stationary phases. The obtained properties for a set of potential therapeutic peptides with 3 to 33 amino acids have been analysed and it was found that similar characteristics of the properties could be observed as for small molecule drugs. The albumin binding showed correlation with their measured lipophilicity on the C-18 stationary phase with acidic peptides showing stronger than expected albumin binding. The (IAM chromatography revealed peptide membrane affinity, which was stronger for positively charged peptides (containing arginine and showed correlation to the alpha-1-acid glycoprotein (AGP binding, which was also stronger for positively charged compounds. The in vivo volume of distribution and drug efficiency of the peptides have been estimated using the models developed for small molecules. One of the candidate linear peptides has been assessed in various cellular and in vivo assays and the results have confirmed the estimated cell partition and brain to plasma ratio. It can be demonstrated, that up to 21 amino acids, the peaks of the peptides obtained on the protein phase were symmetrical and narrow. The interaction of larger peptides with the protein stationary phases resulted in wide peaks showing multiple equilibrium processes with slow kinetics during chromatography. The larger peptides showed narrow and symmetrical peaks on the IAM column enabling

The crystal structure of an intermediate dimer of aspergilloglutamic peptidase that mimics the enzyme-activation product complex produced upon autoproteolysis.

Science.gov (United States)

Sasaki, Hiroshi; Kubota, Keiko; Lee, Woo C; Ohtsuka, Jun; Kojima, Masaki; Iwata, So; Nakagawa, Atsushi; Takahashi, Kenji; Tanokura, Masaru

2012-07-01

Aspergilloglutamic peptidase from Aspergillus niger var. macrosporus (AGP) is one of the so-called pepstatin-insensitive acid endopeptidases, which are distinct from the well-studied aspartic peptidases. Among the known homologues of the glutamic peptidases, AGP is a unique two-chain enzyme with a light chain and a heavy chain bound non-covalently with each other, and thus is an interesting target for protein structure-function relationship studies. In this article, we report the crystal structure of a dimeric form of the enzyme at a resolution of 1.6 Å. This form has a unique structure in which the C-terminal region of the light chain of one of the molecules binds to the active site cleft of the other molecule like a part of a substrate. This form mimics the enzyme-activation product complex produced upon autoproteolysis, and provides a structural clue that could help to clarify the activation mechanism. This type of dimeric structure of a peptidase is here reported for the first time.

Effect of -based Direct-fed Microbial on Performance, Nutrient Utilization, Intestinal Morphology and Cecal Microflora in Broiler Chickens

Directory of Open Access Journals (Sweden)

Xinjian Lei

2015-02-01

Full Text Available The present study was conducted to evaluate the effect of the dietary supplementation of Bacillus amyloliquefaciens-based direct-fed microbial (DFM on growth performance, nutrient utilization, intestinal morphology and cecal microflora in broiler chickens. A total of two hundred and eighty eight 1-d-old Arbor Acres male broilers were randomly allocated to one of four experimental treatments in a completely randomized design. Each treatment was fed to eight replicate cages, with nine birds per cage. Dietary treatments were composed of an antibiotic-free basal diet (control, and the basal diet supplemented with either 15 mg/kg of virginiamycin as antibiotic growth promoter (AGP, 30 mg/kg of Bacillus amyloliquefaciens-based DFM (DFM 30 or 60 mg/kg of Bacillus amyloliquefaciens-based DFM (DFM 60. Experimental diets were fed in two phases: starter (d 1 to 21 and finisher (d 22 to 42. Growth performance, nutrient utilization, morphological parameters of the small intestine and cecal microbial populations were measured at the end of the starter (d 21 and finisher (d 42 phases. During the starter phase, DFM and virginiamycin supplementation improved the feed conversion ratio (FCR; p<0.01 compared with the control group. For the finisher phase and the overall experiment (d 1 to 42 broilers fed diets with the DFM had better body weight gain (BWG and FCR than that of control (p<0.05. Supplementation of virginiamycin and DFM significantly increased the total tract apparent digestibility of crude protein (CP, dry matter (DM and gross energy during both starter and finisher phases (p<0.05 compared with the control group. On d 21, villus height, crypt depth and villus height to crypt depth ratio of duodenum, jejunum, and ileum were significantly increased for the birds fed with the DFM diets as compared with the control group (p<0.05. The DFM 30, DFM 60, and AGP groups decreased the Escherichia coli population in cecum at d 21 and d 42 compared with control

Characterisation of Atherogenic Effects of Low Carbohydrate, High Protein Diet (LCHP) in ApoE/LDLR-/- Mice.

Science.gov (United States)

Kostogrys, R B; Johann, C; Czyżyńska, I; Franczyk-Żarów, M; Drahun, A; Maślak, E; Jasztal, A; Gajda, M; Mateuszuk, Ł; Wrobel, T P; Baranska, M; Wybrańska, I; Jezkova, K; Nachtigal, P; Chlopicki, S

2015-08-01

Low Carbohydrate High Protein diet represents a popular strategy to achieve weight loss. The aim of this study was to characterize effects of low carbohydrate, high protein diet (LCHP) on atherosclerotic plaque development in brachiocephalic artery (BCA) in apoE/LDLR-/- mice and to elucidate mechanisms of proatherogenic effects of LCHP diet. Atherosclerosis plaques in brachiocephalic artery (BCA) as well as in aortic roots, lipoprotein profile, inflammation biomarkers, expression of SREBP-1 in the liver as well as mortality were analyzed in Control diet (AIN-93G) or LCHP (Low Carbohydrate High Protein) diet fed mice. Area of atherosclerotic plaques in aortic roots or BCA from LCHP diet fed mice was substantially increased as compared to mice fed control diet and was characterized by increased lipids and cholesterol contents (ORO staining, FT-IR analysis), increased macrophage infiltration (MOMA-2) and activity of MMPs (zymography). Pro-atherogenic phenotype of LCHP fed apoE/LDLR-/- mice was associated with increased plasma total cholesterol concentration, and in LDL and VLDL fractions, increased TG contents in VLDL, and a modest increase in plasma urea. LCHP diet increased SCD-1 index, activated SREBP-1 transcription factor in the liver and triggered acute phase response as evidence by an increased plasma concentration of haptoglobin, CRP or AGP. Finally, in long-term experiment survival of apoE/LDLR-/- mice fed LCHP diet was substantially reduced as compared to their counterparts fed control diet suggesting overall detrimental effects of LCHP diet on health. The pro-atherogenic effect of LCHP diet in apoE/LDLR-/- mice is associated with profound increase in LDL and VLDL cholesterol, VLDL triglicerides, liver SREBP-1 upregulation, and systemic inflammation.

Quantitative analysis of the intestinal bacterial community in one- to three-week-old commercially reared broiler chickens fed conventional or antibiotic-free vegetable-based diets.

Science.gov (United States)

Wise, M G; Siragusa, G R

2007-04-01

To explore the effect of drug-free poultry production on the intestinal microflora of broiler chickens, the bacterial community of this environment was quantitatively profiled in both conventionally reared birds and birds reared without antibiotic growth promotants (AGPs) on a vegetable-based diet. Quantitative, real-time PCR with group-specific 16S rDNA primer sets was used to enumerate the abundance of the following chicken gastrointestinal (GI) tract phylogenetic groups: the Clostridium leptum-Faecalibacterium prausnitzii subgroup (Clostridium genus cluster IV), the Clostridium coccoides - Eubacterium rectale subgroup (Clostridium cluster XIVa and XIVb), the Bacteroides group (including Prevotella and Porphyromonas), Bifidobacterium spp., the Enterobacteriaceae, the Lactobacillus group (including the genera Leuconostoc, Pediococcus, Aerococcus and Weissella), the Clostridium perfringens subgroup (Clostridium cluster I), Enterococcus spp., Veillonella spp., Atopobium spp., Campylobacter spp. and the domain Bacteria. A species-specific 5'-nuclease (Taqman) assay was also employed to specifically assess Cl. perfringens abundance. Ten birds were sampled from each of two commercial chicken houses, one in which feed was supplemented with AGPs and exogenous animal protein, and the other vegetable-based and drug-free, at 7, 14 and 21 days of age. The ileal community was dominated by two large populations, the lactobacilli and the Enterobacteriaceae, with those taxa much more numerous in drug-free vegetable-based diet fed birds than those conventionally reared at the 7- and 14-day time periods. The progressive changes in microflora in both the conventional and drug-free caeca were similar to each other, with the Enterobacteriaceae sequences dominating at day 7, but being replaced by obligate anaerobe signature sequences by day 14. Of note was the finding that all the day 14 and day 21 replicate caecal samples from the drug-free house were positive for Campylobacter spp

Plastid-to-Nucleus Retrograde Signals Are Essential for the Expression of Nuclear Starch Biosynthesis Genes during Amyloplast Differentiation in Tobacco BY-2 Cultured Cells1[W][OA

Science.gov (United States)

Enami, Kazuhiko; Ozawa, Tomoki; Motohashi, Noriko; Nakamura, Masayuki; Tanaka, Kan; Hanaoka, Mitsumasa

2011-01-01

Amyloplasts, a subtype of plastid, are found in nonphotosynthetic tissues responsible for starch synthesis and storage. When tobacco (Nicotiana tabacum) Bright Yellow-2 cells are cultured in the presence of cytokinin instead of auxin, their plastids differentiate from proplastids to amyloplasts. In this program, it is well known that the expression of nucleus-encoded starch biosynthesis genes, such as ADP-Glucose Pyrophosphorylase (AgpS) and Granule-Bound Starch Synthase (GBSS), is specifically induced. In this study, we investigated the roles of plastid gene expression in amyloplast differentiation. Microarray analysis of plastid genes revealed that no specific transcripts were induced in amyloplasts. Nevertheless, amyloplast development accompanied with starch biosynthesis was drastically inhibited in the presence of plastid transcription/translation inhibitors. Surprisingly, the expression of nuclear AgpS and GBSS was significantly repressed by the addition of these inhibitors, suggesting that a plastid-derived signal(s) that reflects normal plastid gene expression was essential for nuclear gene expression. A series of experiments was performed to examine the effects of intermediates and inhibitors of tetrapyrrole biosynthesis, since some of the intermediates have been characterized as candidates for plastid-to-nucleus retrograde signals. Addition of levulinic acid, an inhibitor of tetrapyrrole biosynthesis, resulted in the up-regulation of nuclear AgpS and GBSS gene expression as well as starch accumulation, while the addition of heme showed opposite effects. Thus, these results indicate that plastid transcription and/or translation are required for normal amyloplast differentiation, regulating the expression of specific nuclear genes by unknown signaling mechanisms that can be partly mediated by tetrapyrrole intermediates. PMID:21771917

Morbidity, Iron Status and Anaemia in Children With Moderate Acute Malnutrition

DEFF Research Database (Denmark)

Cichon, Bernardette

% of total protein). The trial was double blinded with regard to quality of soy and quantity of milk, but not matrix (CSB vs LNS). Haemoglobin (Hb), serum ferritin (SF), serum soluble transferrin receptor (sTfR), serum C-reactive protein (CRP) and serum α1-acid glycoprotein (AGP) were measured at inclusion...... and after supplementation. Furthermore, morbidity data were collected during clinical examinations carried out by nurses and maternal morbidity recalls. Results Between September 2013 and August 2014 1609 children were enrolled and 61 (3.8%) were lost to follow-up. At baseline, 38% of mothers reported...

Alternative growth promoters alter broiler gut microbiome and enhance body weight gain

Science.gov (United States)

Antibiotic growth promoters (AGPs) have commonly been used to enhance growth in poultry production. However, there has been increasing concern over the impact of AGPs use in food production on acquisition of antibiotic resistance in zoonotic bacterial pathogens through inter-bacterial transfer of an...

The effect of discontinuing the use of antimicrobial growth promoters on the productivity in the Danish broiler production

DEFF Research Database (Denmark)

Emborg, Hanne-Dorthe; Ersboll, A. K.; Heuer, Ole Eske

2001-01-01

On 15 February 1998, the Danish poultry industry voluntarily decided to discontinue the use of all antimicrobial growth promoters (AGPs). To investigate how the removal of AGPs influenced the broiler productivity in Denmark, data from 6815 flocks collected from November 1995 to July 1999...

Cell wall glycoproteins at interaction sites between parasitic giant dodder (Cuscuta reflexa) and its host Pelargonium zonale.

Science.gov (United States)

Striberny, Bernd; Krause, Kirsten

2015-01-01

The process of host plant penetration by parasitic dodder (genus Cuscuta) is accompanied by molecular and structural changes at the host/parasite interface. Recently, changes in pectin methyl esterification levels in the host cell walls abutting parasitic cells in established infection sites were reported. In addition to that, we show here that the composition of cell wall glycoproteins in Cuscuta-infected Pelargonium zonale undergoes substantial changes. While several arabinogalactan protein epitopes exhibit decreased abundances in the vicinity of the Cuscuta reflexa haustorium, extensins tend to increase in the infected areas.

High-throughput screening of monoclonal antibodies against plant cell wall glycans by hierarchical clustering of their carbohydrate microarray binding profiles

DEFF Research Database (Denmark)

Moller, Isabel Eva; Marcus, Susan E.; Haeger, Ash

2008-01-01

Antibody-producing hybridoma cell lines were created following immunisation with a crude extract of cell wall polymers from the plant Arabidopsis thaliana. In order to rapidly screen the specificities of individual monoclonal antibodies (mAbs), their binding to microarrays containing 50 cell wall...... investigated using subsequent immunochemical and biochemical analyses and two novel mAbs are described in detail. mAb LM13 binds to an arabinanase-sensitive pectic epitope and mAb LM14, binds to an epitope occurring on arabinogalactan-proteins. Both mAbs display novel patterns of recognition of cell walls...

Productino of KSR-III Airglow Photometers to Measure MUV Airglows of the Upper Atmosphere Above the Korean Peninsular

Directory of Open Access Journals (Sweden)

T. H. Oh

2002-12-01

Full Text Available We have constructed two flight models of airglow photometer system (AGP to be onboard Korea Sounding Rocket-III (KSR-III for detection of MUV dayglow above the Korean peninsular. The AGP system is designed to detect dayglow emissions of OI 2972 Å, N_2 VK (0,6 2780Å, N_2 2PG 3150Å and background 3070Å toward the horizon at altitudes between 100 km and 300 km. The AGP system consists of a photometer body, a baffle, an electronic control unit and a battery unit. The MUV dayglow emissions enter through a narrow band interference filter and focusing lens of the photometer, which contains an ultraviolet sensitive photomultiplier tube. The photometer is equipped with an in-flight calibration light source on a circular plane that will rotate at the rocket's apogee. A baffle tube is installed at the entry of the photometer in order to block strong scattering lights from the lower atmosphere. We have carried out laboratory measurements of sensitivity and in-flight calibration light source for the AGP flight models. Although absolute sensitivities of the AGP flight models could not be determined in the country, relative sensitivities among channels are well measured so that observation data during rocket flight in the future can be analyzed with confidence.

Progress of the ITER NBI acceleration grid power supply reference design

International Nuclear Information System (INIS)

Toigo, Vanni; Zanotto, Loris; Bigi, Marco; Decamps, Hans; Ferro, Alberto; Gaio, Elena; Gutiérrez, Daniel; Tsuchida, Kazuki; Watanabe, Kazuhiro

2013-01-01

Highlights: ► This paper reports the progress in the reference design of the Acceleration Grid Power Supply (AGPS) of the ITER Neutral Beam Injector (NBI) ► A critical revision of the main design choices is presented in light of the definition of some key interface parameters between the two AGPS subsystems. ► The verification of the fulfillment of the requirements in any operational conditions is reported and discussed. -- Abstract: This paper reports the progress in the reference design of the Acceleration Grid Power Supply (AGPS) of the ITER Neutral Beam Injector (NBI). The design of the AGPS is very challenging, as it shall be rated to provide about 55 MW at 1 MV dc in quasi steady-state conditions; moreover, the procurement of the system is shared between the European Domestic Agency (F4E) and the Japanese Domestic Agency (JADA), resulting in additional design complication due to the need of a common definition of the interface parameters. A critical revision of the main design choices is presented also in light of the definition of some key interface parameters between the two AGPS subsystems. Moreover, the verification of the fulfillment of the requirements in any operational conditions taking into account the tolerance of the different parameters is also reported and discussed

Usage of veterinary therapeutic antimicrobials in Denmark, Norway and Sweden following termination of antimicrobial growth promoter use

DEFF Research Database (Denmark)

Grave, K.; Jensen, Vibeke Frøkjær; Odensvik, K.

2006-01-01

Antimicrobial growth promoters (AGPs) were phased out in Denmark, Norway and Sweden in 1998-1999, 1995 and 1986, respectively. The annual usage of therapeutic antimicrobials in animals in Denmark almost doubled during the period when AGPs were phased out (1988-1999) and in the subsequent 2 years....

Lectin-like receptor for alpha 1-acid glycoprotein in the epithelium of the rat prostate gland and seminal vesicles

DEFF Research Database (Denmark)

Andersen, U O; Bøg-Hansen, T C; Kirkeby, S

1996-01-01

by mannose and N-Acetyl-D-glucosamine. RESULTS: In vitro the receptor was also inhibited by the steroid hormones cortisone, aldosterone, progesterone, and estradiol, but not by testosterone. A significant regional variation in the expression of AGP-lectin receptor and in the localization of AGP was seen...

Robust Design in Multiobjective Systems using Taguchi’s Parameter Design Approach and a Pareto Genetic Algorithm

Directory of Open Access Journals (Sweden)

Enrique Canessa

2014-01-01

Full Text Available Se presenta un Algoritmo Genético de Pareto (AGP, que encuentra la frontera de Pareto en problemas de diseño robusto para sistemas multiobjetivo. El AGP fue diseñado para ser aplicado usando el método de Diseño de Parámetros de Taguchi, el cual es el método más frecuentemente empleado por profesionales para ejecutar diseño robusto. El AGP se probó con datos obtenidos de un sistema real con una respuesta y de un simulador de procesos multiobjetivo con muchos factores de control y ruido. En todos los casos, el AGP entregó soluciones óptimas que cumplen con los objetivos del diseño robusto. Además, la discusión de resultados muestra que tener dichas soluciones ayuda en la selección de las mejores a ser implementadas en el sistema bajo estudio, especialmente cuando el sistema tiene muchos factores de control y salidas.

Validation of reported genetic risk factors for periodontitis in a large-scale replication study

NARCIS (Netherlands)

Schaefer, A.S.; Bochenek, G.; Manke, T.; Nothnagel, M.; Graetz, C.; Thien, A.; Jockel-Schneider, Y.; Harks, I.; Staufenbiel, I.; Wijmenga, C.; Eberhard, J.; Guzeldemir-Akcakanat, E.; Cine, N.; Folwaczny, M.; Noack, B.; Meyle, J.; Eickholz, P.; Trombelli, L.; Scapoli, C.; Nohutcu, R.; Bruckmann, C.; Doerfer, C.; Jepsen, S.; Loos, B.G.; Schreiber, S.

2013-01-01

Aim Many studies investigated the role of genetic variants in periodontitis, but few were established as risk factors. We aimed to validate the associations of recent candidate genes in aggressive periodontitis (AgP). Material and Methods We analysed 23 genes in 600 German AgP patients and 1441

Validation of reported genetic risk factors for periodontitis in a large-scale replication study

NARCIS (Netherlands)

Schaefer, Arne S.; Bochenek, Gregor; Manke, Thomas; Nothnagel, Michael; Graetz, Christian; Thien, Anneke; Jockel-Schneider, Yvonne; Harks, Inga; Staufenbiel, Ingmar; Wijmenga, Cisca; Eberhard, Joerg; Guzeldemir-Akcakanat, Esra; Cine, Naci; Folwaczny, Mathias; Noack, Barbara; Meyle, Joerg; Eickholz, Peter; Trombelli, Leonardo; Scapoli, Chiara; Nohutcu, Rahime; Bruckmann, Corinna; Doerfer, Christof; Jepsen, Soren; Loos, Bruno G.; Schreiber, Stefan

Aim Many studies investigated the role of genetic variants in periodontitis, but few were established as risk factors. We aimed to validate the associations of recent candidate genes in aggressive periodontitis (AgP). Material and Methods We analysed 23 genes in 600 German AgP patients and 1441

Anemia and Iron Deficiency in Vietnamese Children, 6 to 11 Years Old.

Science.gov (United States)

Le Nguyen Bao, Khanh; Tran Thuy, Nga; Nguyen Huu, Chinh; Khouw, Ilse; Deurenberg, Paul

2016-07-01

In a population sample of 385 children, 6 to 11 years old, venous blood parameters-hemoglobin (Hb), ferritin, red blood cell count (RBC), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), C-reactive protein (CRP), and α1-acid glycoprotein (AGP)-were determined to get insight into the iron status. The prevalence of anemia was 11.4%; 5.6% had iron deficiency (ID), whereas 0.4% had ID anemia. Correction for inflammation based on CRP and AGP did not markedly change the overall prevalence of ID and ID anemia. Stunted children had lower Hb and ferritin values compared with nonstunted children, and thin children had lower values compared with normal-weight or overweight and obese children. Many nonanemic children had alert values for RBC, MCV, MCH, and MCHC. It is concluded that although the prevalence of anemia is of the magnitude of a mild public health problem, the iron status of many nonanemic children is borderline, as indicated by a high number of children with low values for red blood cytology. © 2016 APJPH.

Support vector machine-based differentiation between aggressive and chronic periodontitis using microbial profiles.

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Feres, Magda; Louzoun, Yoram; Haber, Simi; Faveri, Marcelo; Figueiredo, Luciene C; Levin, Liran

2018-02-01

The existence of specific microbial profiles for different periodontal conditions is still a matter of debate. The aim of this study was to test the hypothesis that 40 bacterial species could be used to classify patients, utilising machine learning, into generalised chronic periodontitis (ChP), generalised aggressive periodontitis (AgP) and periodontal health (PH). Subgingival biofilm samples were collected from patients with AgP, ChP and PH and analysed for their content of 40 bacterial species using checkerboard DNA-DNA hybridisation. Two stages of machine learning were then performed. First of all, we tested whether there was a difference between the composition of bacterial communities in PH and in disease, and then we tested whether a difference existed in the composition of bacterial communities between ChP and AgP. The data were split in each analysis to 70% train and 30% test. A support vector machine (SVM) classifier was used with a linear kernel and a Box constraint of 1. The analysis was divided into two parts. Overall, 435 patients (3,915 samples) were included in the analysis (PH = 53; ChP = 308; AgP = 74). The variance of the healthy samples in all principal component analysis (PCA) directions was smaller than that of the periodontally diseased samples, suggesting that PH is characterised by a uniform bacterial composition and that the bacterial composition of periodontally diseased samples is much more diverse. The relative bacterial load could distinguish between AgP and ChP. An SVC classifier using a panel of 40 bacterial species was able to distinguish between PH, AgP in young individuals and ChP. © 2017 FDI World Dental Federation.

Genetic Basis of Variation in Rice Seed Storage Protein (Albumin, Globulin, Prolamin, and Glutelin) Content Revealed by Genome-Wide Association Analysis.

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Chen, Pingli; Shen, Zhikang; Ming, Luchang; Li, Yibo; Dan, Wenhan; Lou, Guangming; Peng, Bo; Wu, Bian; Li, Yanhua; Zhao, Da; Gao, Guanjun; Zhang, Qinglu; Xiao, Jinghua; Li, Xianghua; Wang, Gongwei; He, Yuqing

2018-01-01

Rice seed storage protein (SSP) is an important source of nutrition and energy. Understanding the genetic basis of SSP content and mining favorable alleles that control it will be helpful for breeding new improved cultivars. An association analysis for SSP content was performed to identify underlying genes using 527 diverse Oryza sativa accessions grown in two environments. We identified more than 107 associations for five different traits, including the contents of albumin (Alb), globulin (Glo), prolamin (Pro), glutelin (Glu), and total SSP (Total). A total of 28 associations were located at previously reported QTLs or intervals. A lead SNP sf0709447538, associated for Glu content in the indica subpopulation in 2015, was further validated in near isogenic lines NIL(Zhenshan97) and NIL(Delong208), and the Glu phenotype had significantly difference between two NILs. The association region could be target for map-based cloning of the candidate genes. There were 13 associations in regions close to grain-quality-related genes; five lead single nucleotide polymorphisms (SNPs) were located less than 20 kb upstream from grain-quality-related genes ( PG5a , Wx , AGPS2a , RP6 , and, RM1 ). Several starch-metabolism-related genes ( AGPS2a , OsACS6 , PUL , GBSSII , and ISA2 ) were also associated with SSP content. We identified favorable alleles of functional candidate genes, such as RP6 , RM1 , Wx , and other four candidate genes by haplotype analysis and expression pattern. Genotypes of RP6 and RM1 with higher Pro were not identified in japonica and exhibited much higher expression levels in indica group. The lead SNP sf0601764762, repeatedly detected for Alb content in 2 years in the whole association population, was located in the Wx locus that controls the synthesis of amylose. And Alb content was significantly and negatively correlated with amylose content and the level of 2.3 kb Wx pre-mRNA examined in this study. The associations or candidate genes identified would

Genetic Basis of Variation in Rice Seed Storage Protein (Albumin, Globulin, Prolamin, and Glutelin Content Revealed by Genome-Wide Association Analysis

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Pingli Chen

2018-05-01

Full Text Available Rice seed storage protein (SSP is an important source of nutrition and energy. Understanding the genetic basis of SSP content and mining favorable alleles that control it will be helpful for breeding new improved cultivars. An association analysis for SSP content was performed to identify underlying genes using 527 diverse Oryza sativa accessions grown in two environments. We identified more than 107 associations for five different traits, including the contents of albumin (Alb, globulin (Glo, prolamin (Pro, glutelin (Glu, and total SSP (Total. A total of 28 associations were located at previously reported QTLs or intervals. A lead SNP sf0709447538, associated for Glu content in the indica subpopulation in 2015, was further validated in near isogenic lines NIL(Zhenshan97 and NIL(Delong208, and the Glu phenotype had significantly difference between two NILs. The association region could be target for map-based cloning of the candidate genes. There were 13 associations in regions close to grain-quality-related genes; five lead single nucleotide polymorphisms (SNPs were located less than 20 kb upstream from grain-quality-related genes (PG5a, Wx, AGPS2a, RP6, and, RM1. Several starch-metabolism-related genes (AGPS2a, OsACS6, PUL, GBSSII, and ISA2 were also associated with SSP content. We identified favorable alleles of functional candidate genes, such as RP6, RM1, Wx, and other four candidate genes by haplotype analysis and expression pattern. Genotypes of RP6 and RM1 with higher Pro were not identified in japonica and exhibited much higher expression levels in indica group. The lead SNP sf0601764762, repeatedly detected for Alb content in 2 years in the whole association population, was located in the Wx locus that controls the synthesis of amylose. And Alb content was significantly and negatively correlated with amylose content and the level of 2.3 kb Wx pre-mRNA examined in this study. The associations or candidate genes identified would provide

Tysnd1 deficiency in mice interferes with the peroxisomal localization of PTS2 enzymes, causing lipid metabolic abnormalities and male infertility.

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Yumi Mizuno

Full Text Available Peroxisomes are subcellular organelles involved in lipid metabolic processes, including those of very-long-chain fatty acids and branched-chain fatty acids, among others. Peroxisome matrix proteins are synthesized in the cytoplasm. Targeting signals (PTS or peroxisomal targeting signal at the C-terminus (PTS1 or N-terminus (PTS2 of peroxisomal matrix proteins mediate their import into the organelle. In the case of PTS2-containing proteins, the PTS2 signal is cleaved from the protein when transported into peroxisomes. The functional mechanism of PTS2 processing, however, is poorly understood. Previously we identified Tysnd1 (Trypsin domain containing 1 and biochemically characterized it as a peroxisomal cysteine endopeptidase that directly processes PTS2-containing prethiolase Acaa1 and PTS1-containing Acox1, Hsd17b4, and ScpX. The latter three enzymes are crucial components of the very-long-chain fatty acids β-oxidation pathway. To clarify the in vivo functions and physiological role of Tysnd1, we analyzed the phenotype of Tysnd1(-/- mice. Male Tysnd1(-/- mice are infertile, and the epididymal sperms lack the acrosomal cap. These phenotypic features are most likely the result of changes in the molecular species composition of choline and ethanolamine plasmalogens. Tysnd1(-/- mice also developed liver dysfunctions when the phytanic acid precursor phytol was orally administered. Phyh and Agps are known PTS2-containing proteins, but were identified as novel Tysnd1 substrates. Loss of Tysnd1 interferes with the peroxisomal localization of Acaa1, Phyh, and Agps, which might cause the mild Zellweger syndrome spectrum-resembling phenotypes. Our data established that peroxisomal processing protease Tysnd1 is necessary to mediate the physiological functions of PTS2-containing substrates.

First Clinical Experience with Retrospective Flash Glucose Monitoring (FGM) Analysis in South Africa: Characterizing Glycemic Control with Ambulatory Glucose Profile.

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Distiller, Larry A; Cranston, Iain; Mazze, Roger

2016-11-01

In 2014, an innovative blinded continuous glucose monitoring system was introduced with automated ambulatory glucose profile (AGP) reporting. The clinical use and interpretation of this new technology has not previously been described. Therefore we wanted to understand its use in characterizing key factors related to glycemic control: glucose exposure, variability, and stability, and risk of hypoglycemia in clinical practice. Clinicians representing affiliated diabetes centers throughout South Africa were trained and subsequently were given flash glucose monitoring readers and 2-week glucose sensors to use at their discretion. After patient use, sensor data were collected and uploaded for AGP reporting. Complete data (sensor AGP with corresponding clinical information) were obtained for 50 patients with type 1 (70%) and type 2 diabetes (30%), irrespective of therapy. Aggregated analysis of AGP data comparing patients with type 1 versus type 2 diabetes, revealed that despite similar HbA1c values between both groups (8.4 ± 2 vs 8.6 ± 1.7%, respectively), those with type 2 diabetes had lower mean glucose levels (9.2 ± 3 vs 10.3 mmol/l [166 ± 54 vs 185 mg/dl]) and lower indices of glucose variability (3.0 ± 1.5 vs 5.0 ± 1.9 mmol/l [54 ± 27 vs 90 ± 34.2 mg/dl]). This highlights key areas for future focus. Using AGP, the characteristics of glucose exposure, variability, stability, and hypoglycemia risk and occurrence were obtained within a short time and with minimal provider and patient input. In a survey at the time of the follow-up visit, clinicians indicated that aggregated AGP data analysis provided important new clinical information and insights. © 2016 Diabetes Technology Society.

First Clinical Experience with Retrospective Flash Glucose Monitoring (FGM) Analysis in South Africa

Science.gov (United States)

Distiller, Larry A.; Cranston, Iain; Mazze, Roger

2016-01-01

Background: In 2014, an innovative blinded continuous glucose monitoring system was introduced with automated ambulatory glucose profile (AGP) reporting. The clinical use and interpretation of this new technology has not previously been described. Therefore we wanted to understand its use in characterizing key factors related to glycemic control: glucose exposure, variability, and stability, and risk of hypoglycemia in clinical practice. Methods: Clinicians representing affiliated diabetes centers throughout South Africa were trained and subsequently were given flash glucose monitoring readers and 2-week glucose sensors to use at their discretion. After patient use, sensor data were collected and uploaded for AGP reporting. Results: Complete data (sensor AGP with corresponding clinical information) were obtained for 50 patients with type 1 (70%) and type 2 diabetes (30%), irrespective of therapy. Aggregated analysis of AGP data comparing patients with type 1 versus type 2 diabetes, revealed that despite similar HbA1c values between both groups (8.4 ± 2 vs 8.6 ± 1.7%, respectively), those with type 2 diabetes had lower mean glucose levels (9.2 ± 3 vs 10.3 mmol/l [166 ± 54 vs 185 mg/dl]) and lower indices of glucose variability (3.0 ± 1.5 vs 5.0 ± 1.9 mmol/l [54 ± 27 vs 90 ± 34.2 mg/dl]). This highlights key areas for future focus. Conclusions: Using AGP, the characteristics of glucose exposure, variability, stability, and hypoglycemia risk and occurrence were obtained within a short time and with minimal provider and patient input. In a survey at the time of the follow-up visit, clinicians indicated that aggregated AGP data analysis provided important new clinical information and insights. PMID:27154973

Identification and characterization of a bile salt hydrolase from Lactobacillus salivarius for development of novel alternatives to antibiotic growth promoters.

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Wang, Zhong; Zeng, Ximin; Mo, Yiming; Smith, Katie; Guo, Yuming; Lin, Jun

2012-12-01

Antibiotic growth promoters (AGPs) have been used as feed additives to improve average body weight gain and feed efficiency in food animals for more than 5 decades. However, there is a worldwide trend to limit AGP use to protect food safety and public health, which raises an urgent need to discover effective alternatives to AGPs. The growth-promoting effect of AGPs has been shown to be highly correlated with the decreased activity of intestinal bile salt hydrolase (BSH), an enzyme that is produced by various gut microflora and involved in host lipid metabolism. Thus, BSH inhibitors are likely promising feed additives to AGPs to improve animal growth performance. In this study, the genome of Lactobacillus salivarius NRRL B-30514, a BSH-producing strain isolated from chicken, was sequenced by a 454 GS FLX sequencer. A BSH gene identified by genome analysis was cloned and expressed in an Escherichia coli expression system for enzymatic analyses. The BSH displayed efficient hydrolysis activity for both glycoconjugated and tauroconjugated bile salts, with slightly higher catalytic efficiencies (k(cat)/K(m)) on glycoconjugated bile salts. The optimal pH and temperature for the BSH activity were 5.5 and 41°C, respectively. Examination of a panel of dietary compounds using the purified BSH identified some potent BSH inhibitors, in which copper and zinc have been recently demonstrated to promote feed digestion and body weight gain in different food animals. In sum, this study identified and characterized a BSH with broad substrate specificity from a chicken L. salivarius strain and established a solid platform for us to discover novel BSH inhibitors, the promising feed additives to replace AGPs for enhancing the productivity and sustainability of food animals.

Vitamin A deficiency and inflammatory markers among preschool children in the Republic of the Marshall Islands

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Ricks Michelle O

2004-12-01

Full Text Available Abstract Background The exclusion of individuals with elevated acute phase proteins has been advocated in order to improve prevalence estimates of vitamin A deficiency in surveys, but it is unclear whether this will lead to sampling bias. The purpose of the study was to determine whether the exclusion of individuals with elevated acute phase proteins is associated with sampling bias and to characterize inflammation in children with night blindness. Methods In a survey in the Republic of the Marshall Islands involving 281 children, aged 1–5 years, serum retinol, C-reactive protein (CRP, and α1-acid glycoprotein (AGP were measured. Results Of 281 children, 24 (8.5% had night blindness and 165 (58.7% had serum retinol 5 mg/L and/or AGP >1000 mg/L. Among children with and without night blindness, the proportion with serum retinol P = 0.03 and with anemia was 58.3% and 35.7% (P = 0.029, respectively. The proportion of children with serum retinol P = 0.016, the proportion of boys was 43.1% vs. 54.3% (P = 0.075, with no hospitalizations in the last year was 11.0% vs 23.6% (P = 0.024, and with anemia was 43.8% vs 31.7% (P = 0.05, respectively. Conclusions Exclusion of children with inflammation in this survey of vitamin A deficiency does not improve prevalence estimates for vitamin A deficiency and instead leads to sampling bias for variables such as age, gender, anemia, and hospitalization history.

SUPL support for mobile devices

Science.gov (United States)

Narisetty, Jayanthi; Soghoyan, Arpine; Sundaramurthy, Mohanapriya; Akopian, David

2012-02-01

Conventional Global Positioning System (GPS) receivers operate well in open-sky environments. But their performance degrades in urban canyons, indoors and underground due to multipath, foliage, dissipation, etc. To overcome such situations, several enhancements have been suggested such as Assisted GPS (A-GPS). Using this approach, orbital parameters including ephemeris and almanac along with reference time and coarse location information are provided to GPS receivers to assist in acquisition of weak signals. To test A-GPS enabled receivers high-end simulators are used, which are not affordable by many academic institutions. This paper presents an economical A-GPS supplement for inexpensive simulators which operates on application layer. Particularly proposed solution is integrated with National Instruments' (NI) GPS Simulation Toolkit and implemented using NI's Labview environment. This A-GPS support works for J2ME and Android platforms. The communication between the simulator and the receiver is in accordance with the Secure User Plane Location (SUPL) protocol encapsulated with Radio Resource Location Protocol (RRLP) applies to Global System for Mobile Communications (GSM) and Universal Mobile Telecommunications System (UMTS) cellular networks.

Consumo alimentar da população adulta segundo perfil sócio-econômico e demográfico: Projeto Bambuí Food intake according to socioeconomic and demographic profile: the Bambuí Project

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Élido Bonomo

2003-10-01

Full Text Available Foi realizado inquérito nutricional em amostra probabilística de 546 indivíduos (idade > 18 anos, residentes na cidade de Bambuí (15 mil habitantes, Minas Gerais, Brasil, utilizando-se o Questionário Semiquantitativo de Freqüência Alimentar (QSFA. A mediana de ingestão calórica entre mulheres e homens foi de 2.807 e 3.775kcal, respectivamente. Homens ingeriram quatro vezes mais álcool que mulheres e estas, mais carboidratos, fibras e ácidos graxos polinsaturados (AGP. A distribuição de proteínas (15%, carboidratos (57% e lipídios (28% foi adequada. As proporções médias de inadequação da participação de lipídios, ácidos graxos saturados (AGS, AGP e colesterol na energia total foram, respectivamente, 36%, 50% e 90%, sendo mais pronunciadas entre os homens. A ingestão de lipídios, AGS e AGP, entre mulheres, e de lipídios e AGS entre homens, aumentou de acordo com a renda. A ingestão de AGP e fibras e a relação AGP/AGS estavam abaixo do recomendado nos dois gêneros. A dieta apresentou proporções de inadequação diferenciais, sugerindo possíveis agregados de risco à saúde da população para doenças cardiovasculares.A nutritional survey was performed in a random sample of 546 individuals (ages 18 and over in a city named Bambuí (15,000 inhabitants in Minas Gerais State, Brazil, using the Semi-Quantitative Food Frequency Questionnaire (SFFQ. Median calorie intakes for women and men were 2,807 and 3,775kcal, respectively. Men consumed four times more alcohol than women, and women consumed more carbohydrates, fiber, and polyunsaturated fatty acids (PUFA. The relative consumption of proteins (15%, carbohydrates (57%, and lipids (28% were adequate in both genders. The average proportions, for all participants, of an inadequate share of lipids, saturated fatty acids (SFA, PUFA, and cholesterol in the total calorie intake were, respectively, 36%, 90%, and 50%, and were more pronounced in men than in women. The lipid

Effects of replacing a dietary antibacterial agent (zinc bacitracin) with copper salts in Cherry Valley Pekin meat ducks.

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Wu, D W; Wang, L C; Wen, C; Hooge, D M; Liang, C; Zhou, Y M

2013-01-01

1. A study was conducted to investigate the effectiveness of high dietary copper concentrations obtained from tribasic copper chloride (TBCC, 58% copper) and copper sulphate pentahydrate (CuSO4, 25% copper) in replacing antibiotic growth promoters (AGP) in duck diets. 2. A total of 960 one-day-old Cherry Valley meat-strain ducks were divided into 3 treatment groups, with 8 replicates per treatment, in a 6-week feeding trial. The ducks were fed a basal diet supplemented with AGP (40 mg zinc bacitracin/kg and 40 mg garlicin/kg of diet) or 150 mg of Cu/kg of diet, given as either CuSO4 or TBCC. 3. The body weight, average daily gain, average daily feed intake and mortality of ducks were not affected by the dietary treatments. However, the feed/gain ratio of ducks that were fed TBCC diets was significantly lower than those of ducks that were fed CuSO4 diets and were similar to those in the AGP group. 4. TBCC increased the Cu content in the liver tissue of ducks compared with the content in those that were fed the diet supplemented with AGP. TBCC also increased the Fe and Zn content in breast muscles compared with that in ducks that were fed the diet supplemented with CuSO4. 5. The activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) were significantly higher in the serum of ducks that received the diet supplemented with TBCC than AGP or CuSO4. TBCC treatment decreased the malondialdehyde (MDA) content in serum of ducks compared with groups supplemented with CuSO4. 6. No significant difference was observed in liver or muscle fat content among the different dietary treatment groups. The serum low-density lipoprotein cholesterol concentration was lower in ducks fed AGP diets than those fed CuSO4 diets. 7. It was concluded that the replacement of AGP with 150 mg of Cu/kg of feed from TBCC improved the feed efficiency, trace mineral deposition and antioxidant status more than when the source of copper was CuSO4.

Consumo alimentar da população adulta segundo perfil sócio-econômico e demográfico: Projeto Bambuí

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Bonomo Élido

2003-01-01

Full Text Available Foi realizado inquérito nutricional em amostra probabilística de 546 indivíduos (idade > 18 anos, residentes na cidade de Bambuí (15 mil habitantes, Minas Gerais, Brasil, utilizando-se o Questionário Semiquantitativo de Freqüência Alimentar (QSFA. A mediana de ingestão calórica entre mulheres e homens foi de 2.807 e 3.775kcal, respectivamente. Homens ingeriram quatro vezes mais álcool que mulheres e estas, mais carboidratos, fibras e ácidos graxos polinsaturados (AGP. A distribuição de proteínas (15%, carboidratos (57% e lipídios (28% foi adequada. As proporções médias de inadequação da participação de lipídios, ácidos graxos saturados (AGS, AGP e colesterol na energia total foram, respectivamente, 36%, 50% e 90%, sendo mais pronunciadas entre os homens. A ingestão de lipídios, AGS e AGP, entre mulheres, e de lipídios e AGS entre homens, aumentou de acordo com a renda. A ingestão de AGP e fibras e a relação AGP/AGS estavam abaixo do recomendado nos dois gêneros. A dieta apresentou proporções de inadequação diferenciais, sugerindo possíveis agregados de risco à saúde da população para doenças cardiovasculares.

Prohibition of antibiotic growth promoters has affected the genomic profiles of Lactobacillus salivarius inhabiting the swine intestine.

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Jun-Yeong Lee

Full Text Available After the introduction of a ban on the use of antibiotic growth promoters (AGPs for livestock, the feeding environment, including the composition of animal intestinal microbiota, has changed rapidly. We hypothesized that the microbial genomes have also been affected by this legal prohibition, and investigated an important member of the swine gut microbiota, Lactobacillus salivarius, with a pan-genomic approach. Here, we isolated 21 L. salivarius strains composed of 6 strains isolated before the AGP prohibition (SBPs and 15 strains isolated after the AGP prohibition (SAPs at an interval of a decade, and the draft genomes were generated de novo. Several genomic differences between SBPs and SAPs were identified, although the number and function of antibiotic resistance genes were not different. SBPs showed larger genome size and a higher number of orthologs, as well as lower genetic diversity, than SAPs. SBPs had genes associated with the utilization of L-rhamnose and D-tagatose for energy production. Because these sugars are also used in exopolysaccharide (EPS synthesis, we tried to identify differences in biofilm formation-associated genes. The genes for the production of EPSs and extracellular proteins were different in terms of amino acid sequences. Indeed, SAPs formed dense biofilm and survived better than SBPs in the swine intestinal environment. These results suggest that SAPs have evolved and adapted to protect themselves from new selection pressure of the swine intestinal microenvironment by forming dense biofilms, adopting a distinct antibiotic resistance strategy. This finding is particularly important to understand the evolutionary changes in host-microbe interaction and provide detailed insight for the development of effective probiotics for livestock.

Prohibition of antibiotic growth promoters has affected the genomic profiles of Lactobacillus salivarius inhabiting the swine intestine.

Science.gov (United States)

Lee, Jun-Yeong; Han, Geon Goo; Lee, Ho-Bin; Lee, Sang-Mok; Kang, Sang-Kee; Jin, Gwi-Deuk; Park, Jongbin; Chae, Byung Jo; Choi, Yo Han; Kim, Eun Bae; Choi, Yun-Jaie

2017-01-01

After the introduction of a ban on the use of antibiotic growth promoters (AGPs) for livestock, the feeding environment, including the composition of animal intestinal microbiota, has changed rapidly. We hypothesized that the microbial genomes have also been affected by this legal prohibition, and investigated an important member of the swine gut microbiota, Lactobacillus salivarius, with a pan-genomic approach. Here, we isolated 21 L. salivarius strains composed of 6 strains isolated before the AGP prohibition (SBPs) and 15 strains isolated after the AGP prohibition (SAPs) at an interval of a decade, and the draft genomes were generated de novo. Several genomic differences between SBPs and SAPs were identified, although the number and function of antibiotic resistance genes were not different. SBPs showed larger genome size and a higher number of orthologs, as well as lower genetic diversity, than SAPs. SBPs had genes associated with the utilization of L-rhamnose and D-tagatose for energy production. Because these sugars are also used in exopolysaccharide (EPS) synthesis, we tried to identify differences in biofilm formation-associated genes. The genes for the production of EPSs and extracellular proteins were different in terms of amino acid sequences. Indeed, SAPs formed dense biofilm and survived better than SBPs in the swine intestinal environment. These results suggest that SAPs have evolved and adapted to protect themselves from new selection pressure of the swine intestinal microenvironment by forming dense biofilms, adopting a distinct antibiotic resistance strategy. This finding is particularly important to understand the evolutionary changes in host-microbe interaction and provide detailed insight for the development of effective probiotics for livestock.

Effect of vitamin D3 supplementation and influence of BsmI polymorphism of the VDR gene of the inflammatory profile and oxidative stress in elderly women with vitamin D insufficiency: Vitamin D3 megadose reduces inflammatory markers.

Science.gov (United States)

de Medeiros Cavalcante, Isa Gabriela; Silva, Alexandre Sérgio; Costa, Maria José Carvalho; Persuhn, Darlene Camati; Issa, Chahira Taha Mahd Ibrahim; Issa, ChariraTahaMad Ibraim; de Luna Freire, Tiago Lima; da Conceição Rodrigues Gonçalves, Maria

2015-06-01

This study aimed to evaluate the effect of vitamin D3 megadose supplementation and influence of BsmI polymorphism in the VDR gene on the inflammatory profile and oxidative stress in elderly women with vitamin D deficiency. A double blind, randomized, placebo-controlled trial was conducted with 40 elderly women (aged 68±6 years) diagnosed with vitamin D insufficiency (24.7±3.1 ng/mL). Participants were distributed into a supplementation group that received 200,000 IU of vitamin D3 (SG; n=20) and a placebo group (PG; n=20). Blood samples were collected at baseline and after intervention to analyse the 25(OH)D, parathyroid hormone, serum calcium, ultra-sensitive C-reactive protein (us-CRP), alpha 1-acid glycoprotein (AGP-A), total antioxidant capacity (TAC), and malondialdehyde (MDA) levels, as well as the renal and hepatic function, and genotyping was performed for BsmI polymorphism. Four weeks after supplementation, elderly women in the SG group showed a significant increase in the serum concentration of 25(OH)D (25.29±2.8 to 31.48±6.0; p=0.0001), which was followed by increased TAC (65.25±15.66 to 71.83±10.71; p=0.03) and decreased serum PTH (46.32±13.2 to 35.45±11.0; p=0.009), us-CRP (0.38±0.3 to 0.19±0.1; p=0.007) and AGP-A levels (75.3±15.4 to 61.1±5.9; p=0.005). Changes in BP, ANAC and MDA were not observed. The 25(OH)D and PTH, us-CRP and AGP-A levels of participants with the BB/Bb genotype were more responsive to supplementation, but their other markers did not change. Supplementation with a vitamin D3 megadose reduced inflammatory markers and increased the total antioxidant capacity in elderly women with vitamin D insufficiency. The 25(OH)D, PTH, us-CRP and AGP-A levels of elderly patients with the BB/Bb genotype were more responsive to supplementation compared with those with the bb genotype. Copyright © 2015 Elsevier Inc. All rights reserved.

Synthesis and Characterization of the Rubidium Thiophosphate Rb 6 (PS 5 )(P 2 S 10 ) and the Rubidium Silver Thiophosphates Rb 2 AgPS 4 , RbAg 5 (PS 4 ) 2 and Rb 3 Ag 9 (PS 4 ) 4

KAUST Repository

Alahmary, Fatimah S.

2016-02-18

The metal thiophosphates Rb2AgPS4 (2), RbAg5(PS4)2 (3), and Rb3Ag9(PS4)4 (4) were synthesized by stoichiometric reactions, whereas Rb6(PS5)(P2S10) (1) was prepared with excess amount of sulfur. The compounds crystallize as follows: 1 monoclinic, P21/c (no. 14), a = 17.0123(7) Å, b = 6.9102(2) Å, c = 23.179(1) Å, β = 94.399(4)°; 2 triclinic, P ¯ (no. 2), a = 6.600(1) Å, b = 6.856(1) Å, c = 10.943(3) Å, α = 95.150(2)°, β = 107.338(2)°, γ = 111.383(2)°; 3 orthorhombic, Pbca (no. 61), a = 12.607(1) Å, b = 12.612(1) Å, c = 17.759(2) Å; 4 orthorhombic, Pbcm (no. 57), a = 6.3481(2) Å, b = 12.5782(4) Å, c = 35.975(1) Å. The crystal structures contain discrete units, chains, and 3D polyanionic frameworks composed of PS4 tetrahedral units arranged and connected in different manner. Compounds 1-3 melt congruently, whereas incongruent melting behavior was observed for compound 4. 1-4 are semiconductors with bandgaps between 2.3 and 2.6 eV and thermally stable up to 450 °C in an inert atmosphere. Copyright © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparative Efficacy of an Organic Acid Blend and Bacitracin Methylene Disalicylate as Growth Promoters in Broiler Chickens: Effects on Performance, Gut Histology, and Small Intestinal Milieu

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Saikat Samanta

2010-01-01

Full Text Available This study evaluated the efficacy of organic acids as a growth promoter for broiler chickens relative to antibiotic growth promoters (AGPs. Broiler chickens were supplemented with graded doses of an organic acid blend (OAB, 1 g and 2 g/kg diet and bacitracin methylene disalicylate (BMD, 0.5 g and 1 g/kg diet for 35 days. Supplementation of OAB improved (<.001 feed conversion ratio (FCR and increased protein accretion (<.001. Dietary acidification caused pH of the gizzard to decline linearly (<.01 with the dose of supplemental OAB. In the lower intestine, pH remained unaffected by dietary treatments. Unlike BMD, supplemental OAB selectively promoted growth of lactobacilli in the small intestine. Moreover, compared to BMD, OAB tended to maintain the villi in the small intestine at a greater height. Although benefits of exceeding the dose of supplemental organic acids more than 1 g/kg diet are not always conspicuous, based on the live weight and feed conversion data, supplementation of 2 g organic acid per kg diet may be recommended for total replacement of AGPs in broiler diet.

ADP-glucose pyrophosphorylase gene plays a key role in the quality of corm and yield of cormels in gladiolus

International Nuclear Information System (INIS)

Seng, Shanshan; Wu, Jian; Sui, Juanjuan; Wu, Chenyu; Zhong, Xionghui; Liu, Chen; Liu, Chao; Gong, Benhe; Zhang, Fengqin; He, Junna; Yi, Mingfang

2016-01-01

Starch is the main storage compound in underground organs like corms. ADP-glucose pyrophosphorylase (AGPase) plays a key role in regulating starch biosynthesis in storage organs and is likely one of the most important determinant of sink strength. Here, we identify an AGPase gene (GhAGPS1) from gladiolus. The highest transcriptional levels of GhAGPS1 were observed in cormels and corms. Transformation of GhAGPS1 into Arabidopsis rescued the phenotype of aps1 mutant. Silencing GhAGPS1 in gladiolus corms by virus-induced gene silencing (VIGS) decreased the transcriptional levels of two genes and starch content. Transmission electron microscopy analyses of leaf and corm sections confirmed that starch biosynthesis was inhibited. Corm weight and cormel number reduced significantly in the silenced plants. Taken together, these results indicate that inhibiting the expression of AGPase gene could impair starch synthesis, which results in the lowered corm quality and cormel yield in gladiolus. -- Highlights: •Cormel quantity was reduced significantly in silenced Gladiolus plants. •Corm quality was declined significantly in silenced Gladiolus plants. •Starch synthesis was inhibited in silenced Gladiolus plants.

ADP-glucose pyrophosphorylase gene plays a key role in the quality of corm and yield of cormels in gladiolus

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Seng, Shanshan, E-mail: seshsh108@126.com [Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Yuan Mingyuan Western Road 2#, Beijing 100193 (China); Wu, Jian [Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Yuan Mingyuan Western Road 2#, Beijing 100193 (China); Sui, Juanjuan [Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Yuan Mingyuan Western Road 2#, Beijing 100193 (China); College of Biology, Fuyang Normal College, Qinghe Western Road 100#, Fuyang 236037, Anhui (China); Wu, Chenyu; Zhong, Xionghui; Liu, Chen; Liu, Chao; Gong, Benhe; Zhang, Fengqin; He, Junna [Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Yuan Mingyuan Western Road 2#, Beijing 100193 (China); Yi, Mingfang, E-mail: ymfang@cau.edu.cn [Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Yuan Mingyuan Western Road 2#, Beijing 100193 (China)

2016-05-20

Starch is the main storage compound in underground organs like corms. ADP-glucose pyrophosphorylase (AGPase) plays a key role in regulating starch biosynthesis in storage organs and is likely one of the most important determinant of sink strength. Here, we identify an AGPase gene (GhAGPS1) from gladiolus. The highest transcriptional levels of GhAGPS1 were observed in cormels and corms. Transformation of GhAGPS1 into Arabidopsis rescued the phenotype of aps1 mutant. Silencing GhAGPS1 in gladiolus corms by virus-induced gene silencing (VIGS) decreased the transcriptional levels of two genes and starch content. Transmission electron microscopy analyses of leaf and corm sections confirmed that starch biosynthesis was inhibited. Corm weight and cormel number reduced significantly in the silenced plants. Taken together, these results indicate that inhibiting the expression of AGPase gene could impair starch synthesis, which results in the lowered corm quality and cormel yield in gladiolus. -- Highlights: •Cormel quantity was reduced significantly in silenced Gladiolus plants. •Corm quality was declined significantly in silenced Gladiolus plants. •Starch synthesis was inhibited in silenced Gladiolus plants.

Plasma and salivary total antioxidant capacity in healthy controls compared with aggressive and chronic periodontitis patients.

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Baser, Ulku; Gamsiz-Isik, Hikmet; Cifcibasi, Emine; Ademoglu, Evin; Yalcin, Funda

2015-07-01

To evaluate the plasma and salivary total antioxidant capacity (TAOC) in patients with generalized chronic periodontitis (CP), generalized aggressive periodontitis (AgP), and periodontally healthy controls. This cross-sectional study includes of 88 individuals seeking dental treatment at the Faculty of Dentistry, Istanbul University, Istanbul, Turkey between January 2011 and March 2012. Fifteen AgP patients were compared with 21 healthy controls (C1), while 36 CP patients were compared with 16 healthy controls (C2). Clinical periodontal measurements were recorded, and plasma and saliva samples were collected. The TAOC of the plasma and saliva samples were determined using a commercially available colorimetric kit. The plasma TAOC of both AgP and CP patients was significantly lower for C1 and C2. The salivary TAOC of CP patients was significantly lower for C2, but there was no significant difference between AgP patients and C1. Our results demonstrate that severe periodontitis may be associated with a lower plasma antioxidant capacity. The reduced antioxidant capacity in patients with severe periodontitis, especially with aggressive forms may be an important contributing factor to severe tissue destruction.

Effects of Fe and Mn deficiencies on the protein profiles of tomato (Solanum lycopersicum) xylem sap as revealed by shotgun analyses.

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Ceballos-Laita, Laura; Gutierrez-Carbonell, Elain; Takahashi, Daisuke; Abadía, Anunciación; Uemura, Matsuo; Abadía, Javier; López-Millán, Ana Flor

2018-01-06

The aim of this work was to study the effects of Fe and Mn deficiencies on the xylem sap proteome of tomato using a shotgun proteomic approach, with the final goal of elucidating plant response mechanisms to these stresses. This approach yielded 643 proteins reliably identified and quantified with 70% of them predicted as secretory. Iron and Mn deficiencies caused statistically significant and biologically relevant abundance changes in 119 and 118 xylem sap proteins, respectively. In both deficiencies, metabolic pathways most affected were protein metabolism, stress/oxidoreductases and cell wall modifications. First, results suggest that Fe deficiency elicited more stress responses than Mn deficiency, based on the changes in oxidative and proteolytic enzymes. Second, both nutrient deficiencies affect the secondary cell wall metabolism, with changes in Fe deficiency occurring via peroxidase activity, and in Mn deficiency involving peroxidase, Cu-oxidase and fasciclin-like arabinogalactan proteins. Third, the primary cell wall metabolism was affected by both nutrient deficiencies, with changes following opposite directions as judged from the abundances of several glycoside-hydrolases with endo-glycolytic activities and pectin esterases. Fourth, signaling pathways via xylem involving CLE and/or lipids as well as changes in phosphorylation and N-glycosylation also play a role in the responses to these stresses. Biological significance In spite of being essential for the delivery of nutrients to the shoots, our knowledge of xylem responses to nutrient deficiencies is very limited. The present work applies a shotgun proteomic approach to unravel the effects of Fe and Mn deficiencies on the xylem sap proteome. Overall, Fe deficiency seems to elicit more stress in the xylem sap proteome than Mn deficiency, based on the changes measured in proteolytic and oxido-reductase proteins, whereas both nutrients exert modifications in the composition of the primary and secondary

Assessment of goals and priorities in patients with a chronic condition: a secondary quantitative analysis of determinants across 11 countries.

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Vermunt, Neeltje P C A; Westert, Gert P; Olde Rikkert, Marcel G M; Faber, Marjan J

2018-03-01

To assess the impact of patient characteristics, patient-professional engagement, communication and context on the probability that healthcare professionals will discuss goals or priorities with older patients. Secondary analysis of cross-sectional data from the 2014 Commonwealth Fund International Health Policy Survey of Older Adults. 11 western countries. Community-dwelling adults, aged 55 or older. Assessment of goals and priorities. The final sample size consisted of 17,222 respondents, 54% of whom reported an assessment of their goals and priorities (AGP) by healthcare professionals. In logistic regression model 1, which was used to analyse the entire population, the determinants found to have moderate to large effects on the likelihood of AGP were information exchange on stress, diet or exercise, or both. Country (living in Sweden) and continuity of care (no regular professional or organisation) had moderate to large negative effects on the likelihood of AGP. In model 2, which focussed on respondents who experienced continuity of care, country and information exchange on stress and lifestyle were the main determinants of AGP, with comparable odds ratios to model 1. Furthermore, a professional asking questions also increased the likelihood of AGP. Continuity of care and information exchange is associated with a higher probability of AGP, while people living in Sweden are less likely to experience these assessments. Further study is required to determine whether increasing information exchange and professionals asking more questions may improve goal setting with older patients. Key points   A patient goal-oriented approach can be beneficial for older patients with chronic conditions or multimorbidity; however, discussing goals with these patients is not a common practice. The likelihood of discussing goals varies by country, occurring most commonly in the USA, and least often in Sweden. Country-level differences in continuity of care and questions asked by a

Four-body correlation embedded in antisymmetrized geminal power wave function.

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Kawasaki, Airi; Sugino, Osamu

2016-12-28

We extend the Coleman's antisymmetrized geminal power (AGP) to develop a wave function theory that can incorporate up to four-body correlation in a region of strong correlation. To facilitate the variational determination of the wave function, the total energy is rewritten in terms of the traces of geminals. This novel trace formula is applied to a simple model system consisting of one dimensional Hubbard ring with a site of strong correlation. Our scheme significantly improves the result obtained by the AGP-configuration interaction scheme of Uemura et al. and also achieves more efficient compression of the degrees of freedom of the wave function. We regard the result as a step toward a first-principles wave function theory for a strongly correlated point defect or adsorbate embedded in an AGP-based mean-field medium.

Use of Plant Extracts as an Effective Manner to Control Clostridium perfringens Induced Necrotic Enteritis in Poultry

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Dominguez, J. E.; Chacana, A. P.

2016-01-01

Necrotic enteritis (NE) is an important concern in poultry industry since it causes economic losses, increased mortality, reduction of bird welfare, and contamination of chicken products for human consumption. For decades, the use of in-feed antimicrobial growth promoters (AGPs) has been the main strategy to control intestinal pathogens including Clostridium perfringens (CP), the causative agent of NE. However, the use of AGPs in animal diet has been linked to the emergence and transmission of antimicrobial resistance through food-borne microorganisms, which has led to the ban of AGPs in many countries. This scenario has challenged the poultry industry to search for safer alternative products in order to prevent NE. In this context, the utilization of natural plant extracts with antimicrobial properties appears as a promising and feasible tool to control NE in chicken. In this paper, we review the scientific studies analyzing the potential of plant extracts as alternative feed additives to reduce NE in poultry, with focus on two types of plant products that arise as promising candidates: tannins and essential oils. Some of these products showed antimicrobial activity against CP and coccidia in vitro and in vivo and are able to increase productive performance, emulating the bioactive properties of AGPs. PMID:27747227

PROFESSIONAL FLASH CONTINUOUS GLUCOSE MONITORING WITH AMBULATORY GLUCOSE PROFILE REPORTING TO SUPPLEMENT A1C: RATIONALE AND PRACTICAL IMPLEMENTATION.

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Hirsch, Irl B; Verderese, Carol A

2017-11-01

Recent consensus statements strongly advocate downloading and interpreting continuous glucose data for diabetes management in patients with type 1 or 2 diabetes. Supplementing periodic glycated hemoglobin (A1C) testing with intermittent continuous glucose monitoring (CGM) using a standardized report form known as the ambulatory glucose profile (AGP) is an evolving standard of care. The rationale for this approach and its implementation with a recently approved novel monitoring technology are explored. Search of the medical literature, professional guidelines, and real-world evidence guided this introduction of an integrative practice framework that uses AGP in conjunction with intermittent flash continuous glucose monitoring (FCGM) as a supplement to A1C testing. The combination of intermittent continuous glucose pattern analysis, standardized glucose metrics, and a readily interpretable data report has the potential to practically extend the recognized benefits of CGM to more patients and clarify the relationship between A1C and average glucose levels in individual cases. Novel FCGM technologies portend greater use of continuous forms of glucose monitoring and wider adoption of AGP report analysis. Additional formal and empirical evidence is needed to more fully characterize best practice. A1C = glycated hemoglobin; AGP = ambulatory glucose profile; CGM = continuous glucose monitoring; FCGM = flash continuous glucose monitoring; IQR = interquartile range; SMBG = self-monitoring of blood glucose.

Role of nutraceuticals in gut health and growth performance of poultry

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Sugiharto Sugiharto

2016-06-01

Full Text Available The gut is a fundamental organ system which makes up two equally important functions, i.e., the digestion and host defence. To elicit the well-functioning and healthy gut, the dynamic balance of gut ecosystem is of importance. A wide range of factors related to diets and infectious disease agents seem to affect this balance, and subsequently affect the health status and production performance of the chicken. With the ban and/or reduction of the use of antibiotic growth promoters (AGPs in poultry production, the alternatives to AGP are needed especially to preserve the balance of gut microbiota in chicken. This review provides a summary of the potentials and possible mechanisms of action of some alternatives to AGP (referred as nutraceuticals in improving the gut microbial ecosystem and immune system as well as growth performance of poultry.

Proteome analysis of Physcomitrella patens exposed to progressive dehydration and rehydration

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Cui, Suxia; Hu, Jia; Guo, Shilei; Wang, Jie; Cheng, Yali; Dang, Xinxing; Wu, Lili; He, Yikun

2012-01-01

Physcomitrella patens is an extremely dehydration-tolerant moss. However, the molecular basis of its responses to loss of cellular water remains unclear. A comprehensive proteomic analysis of dehydration- and rehydration-responsive proteins has been conducted using quantitative two-dimensional difference in-gel electrophoresis (2D-DIGE), and traditional 2-D gel electrophoresis (2-DE) combined with MALDI TOF/TOF MS. Of the 216 differentially-expressed protein spots, 112 and 104 were dehydration- and rehydration-responsive proteins, respectively. The functional categories of the most differentially-expressed proteins were seed maturation, defence, protein synthesis and quality control, and energy production. Strikingly, most of the late embryogenesis abundant (LEA) proteins were expressed at a basal level under control conditions and their synthesis was strongly enhanced by dehydration, a pattern that was confirmed by RT-PCR. Actinoporins, phosphatidylethanolamine-binding protein, arabinogalactan protein, and phospholipase are the likely dominant players in the defence system. In addition, 24 proteins of unknown function were identified as novel dehydration- or rehydration-responsive proteins. Our data indicate that Physcomitrella adopts a rapid protein response mechanism to cope with dehydration in its leafy-shoot and basal expression levels of desiccation-tolerant proteins are rapidly upgraded at high levels under stress. This mechanism appears similar to that seen in angiosperm seeds. PMID:21994173

Edible mushroom powder (Agaricus bisporus) and flavophospholipol improve performance and blood parameters of broilers

OpenAIRE

Shamsi, Sepideh; Seidavi, Alireza; Rahati, Maliheh; G Nieto, José Ángel

2015-01-01

Background: flavophospholipol is an antibiotic growth promoter (AGP). The current ban of AGP in some countries is controversial because their benefits on the environment and economy by saving feed and reducing nitrogen excretion have been overlooked. White button mushrooms have important nutritional properties and the industry discards large quantities of waste that could be fed to animals. Objective: to evaluate the effect of dietary inclusion of five levels of edible mushroom powder (EMP) a...

Recurring Necrotic Enteritis Outbreaks in Commercial Broiler Chicken Flocks Strongly Influence Toxin Gene Carriage and Species Richness in the Resident Clostridium perfringens Population

OpenAIRE

Marie-Lou Gaucher; Marie-Lou Gaucher; Marie-Lou Gaucher; Gabriel G. Perron; Julie Arsenault; Ann Letellier; Martine Boulianne; Sylvain Quessy

2017-01-01

Extensive use of antibiotic growth promoters (AGPs) in food animals has been questioned due to the globally increasing problem of antibiotic resistance. For the poultry industry, digestive health management following AGP withdrawal in Europe has been a challenge, especially the control of necrotic enteritis. Much research work has focused on gut health in commercial broiler chicken husbandry. Understanding the behavior of Clostridium perfringens in its ecological niche, the poultry barn, is k...

Pan-Genomic Approaches in Lactobacillus reuteri as a Porcine Probiotic: Investigation of Host Adaptation and Antipathogenic Activity.

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Lee, Jun-Yeong; Han, Geon Goo; Choi, Jaeyun; Jin, Gwi-Deuk; Kang, Sang-Kee; Chae, Byung Jo; Kim, Eun Bae; Choi, Yun-Jaie

2017-10-01

After the introduction of a ban on the use of antibiotic growth promoters (AGPs) for livestock, reuterin-producing Lactobacillus reuteri is getting attention as an alternative to AGPs. In this study, we investigated genetic features of L. reuteri associated with host specificity and antipathogenic effect. We isolated 104 L. reuteri strains from porcine feces, and 16 strains, composed of eight strains exhibiting the higher antipathogenic effect (group HS) and eight strains exhibiting the lower effect (group LS), were selected for genomic comparison. We generated draft genomes of the 16 isolates and investigated their pan-genome together with the 26 National Center for Biotechnology Information-registered genomes. L. reuteri genomes organized six clades with multi-locus sequence analysis, and the clade IV includes the 16 isolates. First, we identified six L. reuteri clade IV-specific genes including three hypothetical protein-coding genes. The three annotated genes encode transposases and cell surface proteins, indicating that these genes are the result of adaptation to the host gastrointestinal epithelia and that these host-specific traits were acquired by horizontal gene transfer. We also identified differences between groups HS and LS in the pdu-cbi-cob-hem gene cluster, which is essential for reuterin and cobalamin synthesis, and six genes specific to group HS are revealed. While the strains of group HS possessed all genes of this cluster, LS strains have lost many genes of the cluster. This study provides a deeper understanding of the relationship between probiotic properties and genomic features of L. reuteri.

Genetic hemoglobin disorders rather than iron deficiency are a major predictor of hemoglobin concentration in women of reproductive age in rural prey Veng, Cambodia.

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Karakochuk, Crystal D; Whitfield, Kyly C; Barr, Susan I; Lamers, Yvonne; Devlin, Angela M; Vercauteren, Suzanne M; Kroeun, Hou; Talukder, Aminuzzaman; McLean, Judy; Green, Timothy J

2015-01-01

Anemia is common in Cambodian women. Potential causes include micronutrient deficiencies, genetic hemoglobin disorders, inflammation, and disease. We aimed to investigate factors associated with anemia (low hemoglobin concentration) in rural Cambodian women (18-45 y) and to investigate the relations between hemoglobin disorders and other iron biomarkers. Blood samples were obtained from 450 women. A complete blood count was conducted, and serum and plasma were analyzed for ferritin, soluble transferrin receptor (sTfR), folate, vitamin B-12, retinol binding protein (RBP), C-reactive protein (CRP), and α1 acid glycoprotein (AGP). Hemoglobin electrophoresis and multiplex polymerase chain reaction were used to determine the prevalence and type of genetic hemoglobin disorders. Overall, 54% of women had a genetic hemoglobin disorder, which included 25 different genotypes (most commonly, hemoglobin E variants and α(3.7)-thalassemia). Of the 420 nonpregnant women, 29.5% had anemia (hemoglobin 8.3 mg/L), hemoglobin disorders, respectively. There was no biochemical evidence of vitamin A deficiency (RBP 5 mg/L) and 26% (AGP >1 g/L) of nonpregnant women, respectively. By using an adjusted linear regression model, the strongest predictors of hemoglobin concentration were hemoglobin E homozygous disorder and pregnancy status. Other predictors were 2 other heterozygous traits (hemoglobin E and Constant Spring), parity, RBP, log ferritin, and vitamin B-12. Multiple biomarkers for anemia and iron deficiency were significantly influenced by the presence of hemoglobin disorders, hence reducing their diagnostic sensitivity. Further investigation of the unexpectedly low prevalence of IDA in Cambodian women is warranted. © 2015 American Society for Nutrition.

Excitation functions for the formation of some short-lived products in proton-induced reactions on silver

International Nuclear Information System (INIS)

Uddin, M.S.; Latif, S.K.A.; Baba, M.; Hagiwara, M.; Qaim, S.M.

2008-01-01

Excitation functions of the nat Ag(p, xn) 104, 105 Cd and nat Ag(p, pxn) 103, 104m,g, 104g Ag reactions were measured for the first time over the proton energy range of 32 to about 60 MeV. The data were compared with the results of precompound-hybrid model calculations, whereby only partial agreement was obtained. The contribution of the 103 Ag precursor decay to the total formation of the therapeutic radionuclide 103 Pd in proton activation of silver was estimated: it amounted to about 70%. The various possible routes for the production of 103 Pd were also considered: the nat Ag(p, x) 103 Pd and 103 Rh(p, n) 103 Pd processes were found to be most interesting. Despite its somewhat lower yield, the latter process is preferred because it can be applied at a low-energy cyclotron. (orig.)

Atlas-guided prostate intensity modulated radiation therapy (IMRT) planning

International Nuclear Information System (INIS)

Sheng, Yang; Li, Taoran; Zhang, You; Lee, W Robert; Yin, Fang-Fang; Wu, Q Jackie; Ge, Yaorong

2015-01-01

An atlas-based IMRT planning technique for prostate cancer was developed and evaluated. A multi-dose atlas was built based on the anatomy patterns of the patients, more specifically, the percent distance to the prostate and the concaveness angle formed by the seminal vesicles relative to the anterior-posterior axis. A 70-case dataset was classified using a k-medoids clustering analysis to recognize anatomy pattern variations in the dataset. The best classification, defined by the number of classes or medoids, was determined by the largest value of the average silhouette width. Reference plans from each class formed a multi-dose atlas. The atlas-guided planning (AGP) technique started with matching the new case anatomy pattern to one of the reference cases in the atlas; then a deformable registration between the atlas and new case anatomies transferred the dose from the atlas to the new case to guide inverse planning with full automation. 20 additional clinical cases were re-planned to evaluate the AGP technique. Dosimetric properties between AGP and clinical plans were evaluated. The classification analysis determined that the 5-case atlas would best represent anatomy patterns for the patient cohort. AGP took approximately 1 min on average (corresponding to 70 iterations of optimization) for all cases. When dosimetric parameters were compared, the differences between AGP and clinical plans were less than 3.5%, albeit some statistical significances observed: homogeneity index (p  >  0.05), conformity index (p  <  0.01), bladder gEUD (p  <  0.01), and rectum gEUD (p  =  0.02). Atlas-guided treatment planning is feasible and efficient. Atlas predicted dose can effectively guide the optimizer to achieve plan quality comparable to that of clinical plans. (paper)

Segal’s Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project

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James B. Pettengill

2017-06-01

Full Text Available Obtaining human population level estimates of the prevalence of foodborne pathogens is critical for understanding outbreaks and ameliorating such threats to public health. Estimates are difficult to obtain due to logistic and financial constraints, but citizen science initiatives like that of the American Gut Project (AGP represent a potential source of information concerning enteric pathogens. With an emphasis on genera Listeria and Salmonella, we sought to document the prevalence of those two taxa within the AGP samples. The results provided by AGP suggest a surprising 14% and 2% of samples contained Salmonella and Listeria, respectively. However, a reanalysis of those AGP sequences described here indicated that results depend greatly on the algorithm for assigning taxonomy and differences persisted across both a range of parameter settings and different reference databases (i.e., Greengenes and HITdb. These results are perhaps to be expected given that AGP sequenced the V4 region of 16S rRNA gene, which may not provide good resolution at the lower taxonomic levels (e.g., species, but it was surprising how often methods differ in classifying reads—even at higher taxonomic ranks (e.g., family. This highlights the misleading conclusions that can be reached when relying on a single method that is not a gold standard; this is the essence of Segal’s Law: an individual with one watch knows what time it is but an individual with two is never sure. Our results point to the need for an appropriate molecular marker for the taxonomic resolution of interest, and calls for the development of more conservative classification methods that are fit for purpose. Thus, with 16S rRNA gene datasets, one must be cautious regarding the detection of taxonomic groups of public health interest (e.g., culture independent identification of foodborne pathogens or taxa associated with a given phenotype.

Segal's Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project.

Science.gov (United States)

Pettengill, James B; Rand, Hugh

2017-01-01

Obtaining human population level estimates of the prevalence of foodborne pathogens is critical for understanding outbreaks and ameliorating such threats to public health. Estimates are difficult to obtain due to logistic and financial constraints, but citizen science initiatives like that of the American Gut Project (AGP) represent a potential source of information concerning enteric pathogens. With an emphasis on genera Listeria and Salmonella , we sought to document the prevalence of those two taxa within the AGP samples. The results provided by AGP suggest a surprising 14% and 2% of samples contained Salmonella and Listeria , respectively. However, a reanalysis of those AGP sequences described here indicated that results depend greatly on the algorithm for assigning taxonomy and differences persisted across both a range of parameter settings and different reference databases (i.e., Greengenes and HITdb). These results are perhaps to be expected given that AGP sequenced the V4 region of 16S rRNA gene, which may not provide good resolution at the lower taxonomic levels (e.g., species), but it was surprising how often methods differ in classifying reads-even at higher taxonomic ranks (e.g., family). This highlights the misleading conclusions that can be reached when relying on a single method that is not a gold standard; this is the essence of Segal's Law: an individual with one watch knows what time it is but an individual with two is never sure. Our results point to the need for an appropriate molecular marker for the taxonomic resolution of interest, and calls for the development of more conservative classification methods that are fit for purpose. Thus, with 16S rRNA gene datasets, one must be cautious regarding the detection of taxonomic groups of public health interest (e.g., culture independent identification of foodborne pathogens or taxa associated with a given phenotype).

Antioxidant and immunomodulatory properties of polysaccharides from Allanblackia floribunda Oliv stem bark and Chromolaena odorata (L.) King and H.E. Robins leaves.

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Boudjeko, Thaddée; Megnekou, Rosette; Woguia, Alice Louise; Kegne, Francine Mediesse; Ngomoyogoli, Judith Emery Kanemoto; Tchapoum, Christiane Danielle Nounga; Koum, Olga

2015-12-09

Many plant polysaccharides have shown high antioxidant and immunostimulating properties and can be explored as novel molecules with biological properties that can potentially improve immune function. The objective of this work was to characterize soluble and cell wall polysaccharides isolated from the stem bark of Allanblackia floribunda and Chromolaena odorata leaves and to evaluate their antioxidant and immunomodulatory properties. Three polysaccharide fractions: soluble polysaccharides (PoS), pectins (Pec) and hemicelluloses (Hem) were extracted from A. floribunda stem bark and C. odorata leaves. These samples were analysed for their proteins, phenolic compounds and total sugar contents. The monosaccharide composition was determined by gas chromatography and arabinogalactan proteins content in PoS was evaluated by rocket electrophoresis. The in vitro antioxidant activities were evaluated by 1, 1-diphenyl-2-picryl hydrazyl (DPPH) and 2,2'-azino-bis-3-éthylbenzylthiazoline-6-sulphonic acid (ABTS) radical scavenging assays and ferrous ions chelating activity. Immunomodulatory activities were performed on the peripheral blood mononuclear cells (PBMCs) using proliferation and enzyme linked immunospot (ELISPOT) method to determine the production of an interferon-gamma. The characterization of the various fractions showed varied metabolites in each plant. In PoS fractions, Ara and Gal were the major monosaccharides found, indicating that arabinogalactans are the primary macromolecules. Hem fractions contained predominantly Xyl and GalA for A. floribunda and Xyl (upto 80 %) for and C. odorata. A. floribunda Hem fraction and C. odorata PoS fraction showed significant DPPH and ABTS radical scavenging activities and immunostimulatory activity via stimulation of PBMC and production of IFN-γ in a dose-dependent manner. The results obtained from this study support the ethnomedicinal use of the stem bark of A. floribunda and leaves of C. odorata. Further research is

Preparation and characterization of 1,6 anhydrous Β-D-Glucopyranose from starch

International Nuclear Information System (INIS)

Alvarez Lopez, M.S.

1991-01-01

In order to prepare 2-deoxi-2-fluoride-D-glucosa (2FDG) in an inert form there are several synthesis methods, but the more interesting one for our study is based in a reaction from the 1,6 anhydrous, Β-D-glucopyranose (1,6AGP), in an attempt to compare the labelling efficiency rate of 2FDG with F-18, which is highly used in nuclear medicine. In the present paper the attainment of starch from white potatoe, infrared analysis of this starch and fusion point are included. Also results are compared with an analytical reactive standard. The process of preparation of 1,6AGP by pyrolysis of starch under reduced pressure, its separation and purification by crystallization and infrared characterization of 1,6AGP, nuclear magnetic resonance and mass spectrometry are also included. 10 kg. of potatoes were used, and 93059 g. ±5.8 of starch with an efficiency rate of 9.32 ±0.631; fusion point was 272 o C and there was a 9.83 ± 1.48 % of humidity. After the pyrolysis, crystallization an purification processes, 1.71 ±0.54 % of 1,6AGP were obtained. Later results of compound characterization, nuclear magnetic resonance, infrared and mass spectrometry were compared with a commercial product and it was proved that it corresponds to such pure compound. (Author)

Prevalence and risk indicators of gingivitis and periodontitis in a Multi-Centre study in North Jordan: a cross sectional study

Science.gov (United States)

2012-01-01

Background There are limited data about the epidemiology and risk factors/indicators of gingivitis, aggressive periodontitis (AgP) and chronic periodontitis (CP) in Jordan. The aim of this study was to assess the prevalence and risk indicators of gingivitis, AgP and CP. Methods A sample of 595 subjects was randomly selected from subjects escorting out-patients attending a Medical Center, a Dental Teaching Hospital, and 2 private dental clinics. The socio-demographic variables, oral hygiene habits, income, smoking and Body Mass Index (BMI) were recorded. Full mouth periodontal examination was performed, and radiographs were taken for sites with probing depth > 3 mm. Results About 76% had gingivitis, 2.2% had AgP and 5.5% had CP. Periodontitis was more frequent among males than females with a M: F ratio of 1.6:1 and the prevalence increased with age. Subjects who reported not using a tooth brush, smokers and subjects with BMI > 30 kg/m2 had significantly higher prevalence of periodontitis. The risk for periodontitis was greater among subjects who reported positive family history and subjects with ≤ 12 years of education. Conclusions This is the first study to report on the prevalence of gingivitis, CP and AgP in North Jordanian. Age, low education, low frequency of tooth brushing and family history were significantly associated with increased risk of periodontitis. PMID:22214223

Adsorption of histones on natural polysaccharides: The potential as agent for multiple organ failure in sepsis.

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Isobe, Takashi; Kofuji, Kyoko; Okada, Kenji; Fujimori, Junya; Murata, Mikio; Shigeyama, Masato; Hanioka, Nobumitsu; Murata, Yoshifumi

2016-03-01

Histones are intracellular proteins that are structural elements of nuclear chromatin and regulate gene transcription. However, the extracellular histones released in response to bacterial challenges have been identified as mediators contributing to endothelial dysfunction, organ failure, and death during sepsis. In the present study, the adsorption of histones as well as plasma proteins (α1-acid glycoprotein (AGP), albumin, and γ-globulin) on alginic acid, pectin, dextran, and chitosan was examined in order to evaluate the potential of natural polysaccharides as therapeutic agents for multiple organ failure in sepsis. Alginic acid and pectin strongly adsorbed histones, whereas the adsorption abilities of dextran and chitosan toward histones were very low or negligible. Among the natural polysaccharides examined, only alginic acid did not adsorb any of the plasma proteins. These results demonstrated that alginic acid strongly adsorbed histones, but not plasma proteins; therefore, it has potential as a candidate drug for the treatment of multiple organ failure in sepsis. Copyright © 2015 Elsevier B.V. All rights reserved.

Development of a Menu Driven Materials Data Base for Use on Personal Computers

Science.gov (United States)

1992-07-01

written permission. Copyright Is the responsibility of the Director Publishing and Marketing , AGPS. Enquiries should be directed to the Manager, AGPS...PROGRAM LISTING A-2-1 Program MOB; uses crt; label levell,level2,level3,shutdown,dis;play; var options,code, nlines ,nmeflitemp,i,j4,k :integer; w,chl,ch2,ch3...char; menus :array [I. .1001 of st~ring[801; nline :array [l. .100] of integer; s2 :string[21; control :string[4]; aline :string[801; inm,iflt :text

Density matrix embedding in an antisymmetrized geminal power bath

International Nuclear Information System (INIS)

Tsuchimochi, Takashi; Welborn, Matthew; Van Voorhis, Troy

2015-01-01

Density matrix embedding theory (DMET) has emerged as a powerful tool for performing wave function-in-wave function embedding for strongly correlated systems. In traditional DMET, an accurate calculation is performed on a small impurity embedded in a mean field bath. Here, we extend the original DMET equations to account for correlation in the bath via an antisymmetrized geminal power (AGP) wave function. The resulting formalism has a number of advantages. First, it allows one to properly treat the weak correlation limit of independent pairs, which DMET is unable to do with a mean-field bath. Second, it associates a size extensive correlation energy with a given density matrix (for the models tested), which AGP by itself is incapable of providing. Third, it provides a reasonable description of charge redistribution in strongly correlated but non-periodic systems. Thus, AGP-DMET appears to be a good starting point for describing electron correlation in molecules, which are aperiodic and possess both strong and weak electron correlation

21 CFR 172.610 - Arabinogalactan.

Science.gov (United States)

2010-04-01

... Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN CONSUMPTION (CONTINUED) FOOD ADDITIVES PERMITTED FOR DIRECT ADDITION TO FOOD FOR HUMAN CONSUMPTION Gums... water from Western larch wood, having galactose units and arabinose units in the approximate ratio of...

Effects of a large-scale micronutrient powder and young child feeding education program on the micronutrient status of children 6-24 months of age in the Kyrgyz Republic.

Science.gov (United States)

Serdula, M K; Lundeen, E; Nichols, E K; Imanalieva, C; Minbaev, M; Mamyrbaeva, T; Timmer, A; Aburto, N J

2013-07-01

To combat iron and other micronutrient deficiencies, the Ministry of Health of the Kyrgyz Republic launched a regional Infant and Young Child Nutrition (IYCN) program in 2009, which included promotion of home fortification with micronutrient powder (MNP) containing iron (12.5 mg elemental iron), vitamin A (300 μg) and other micronutrients. Every 2 months children aged 6-24 months were provided 30 sachets to be taken on a flexible schedule. The objective was to assess biochemical indicators of iron and vitamin A status among children aged 6-24 months at the baseline and follow-up surveys. Cross-sectional representative cluster surveys were conducted in 2008 (n=571 children) and 2010 (n=541). Data collected included measurement of hemoglobin, serum ferritin, soluble transferrin receptor (sTfR), retinol-binding protein, C-reactive protein (CRP) and α1-glycoprotein acid (AGP). Among all children, declines were observed in the prevalence of: anemia, 50.6% versus 43.8% (P=0.05); total iron deficiency (either low ferritin or high sTfR), 77.3% versus 63.7% (P<0.01); and iron deficiency anemia, 45.5% versus 33.4% (P<0.01). Among children without inflammation as measured by CRP and AGP, similar declines were observed, but only declines in total iron deficiency and iron deficiency anemia reached statistical significance. Among all children and those without inflammation, the prevalence of vitamin A deficiency remained the same. One year after the introduction of home fortification with MNP, within a larger IYCN program, the prevalence of anemia, iron deficiency and iron deficiency anemia declined, but vitamin A deficiency remained unchanged.

Comparison between the diagnostic accuracy of clinico-pathological and molecular tests for feline infectious peritonitis (FIP

Directory of Open Access Journals (Sweden)

Angelica Stranieri

2015-07-01

Full Text Available The aim of this study was to compare the diagnostic accuracy for feline infectious peritonitis (FIP of conventional clinic-pathological tests with that of molecular tests such as routine PCR and PCR followed by the sequencing of the Spike (S gene. Blood, effusion and tissues specimens were collected from 21 FIP suspected cats. In vivo examination consisted of CBC, serum protein electrophoresis, AGP measurement, cytological and biochemical examination and the evaluation of the ΔTNC on effusions, and of molecular tests such the screening PCR (target: 3’UTR region and the PCR directed towards the S gene followed by the amplification products sequencing in order to detect the aminoacidic substitution recently considered diagnostic for FIP1. These molecular techniques were applied to tissues collected during necropsy, which also allowed forming an FIP group (13 cats and a non-FIP group (5 cats based on histology and immunohistochemistry. The best test on tissues was immunohistochemistry (sens: 92.3%; spec: 100%, while the screening PCR suffered of low specificity (spec: 33.3% and the S gene sequencing showed low sensitivity (sens: 69.2%.On effusions, the best tests resulted screening PCR and cytology (sens and spec: 100% in comparison with the ΔTNC measurement (sens: 85.7 %; spec: 100% and the S gene sequencing (sens: 42.8%; spec: 100%.On blood, the best test resulted AGP measurement (sens: 81.8%; spec: 100%, while serum protein electrophoresis showed a surprisingly low sensitivity (sens: 41.7%. Screening PCR (sens: 55.6%; spec: 100% and S gene sequencing (sens: 33.3%; spec: 100% proved again low accuracy.

Egg quality and blood parameters of “Bianca di Saluzzo” and Isa Brown hens kept under free range conditions

Directory of Open Access Journals (Sweden)

Luca Doglione

2010-01-01

Full Text Available Egg quality traits and some blood parameters of Bianca di Saluzzo hen (BSh were compared to Isa Brown hen (IBh. Birds were reared in free range conditions. Weightofthewholeegg Weight of the whole egg was higher (P≤0.01 for IBh, due to its higher amount of albumen (P≤0.01 whereas BSh egg showed the highest weight and relative percentage of yolk (PP≤0.01. IBh and BSh egg chemical composition was similar.Totalredcellsdidnotshowstatisticaldifferencesbetweengroups,whiletotalleucocytes Total red cells did not show statistical differences between groups, while total leucocytes were lower (P≤0.05 forBShhens. Heterophyl/Lymphocyte(H/L ratioof BShwaslower (P for BSh hens. Heterophyl/Lymphocyte(H/L ratioof BShwaslower (P . Heterophyl/Lymphocyte(H/L ratioof BShwaslower (P Heterophyl/Lymphocyte (H/L ratio of BSh was lower (P (PP≤0.01 than IBh(0.33 IBh (0.33 (0.33 vs. 0.82.IBh 0.82. IBh IBh α-1 acid glycoprotein (AGPmeanconcentrationswereaffectedbytime: (AGP mean concentrations were affected by time: the values registered after 15 d (T1 and 2 months (T2 of observation were similar (345±132 and 279±58 μg/mlrespectively,whileAGPvalueregisteredafter4months(T3weresignificantlyhigher μg/ml respectively,whileAGPvalueregisteredafter4months(T3weresignificantlyhigher , while AGP value registered after 4 months (T3 were significantly higher (700±487 μg/ml;BShdidnotdisplayanyAGPstatisticalvariationovertime.IBhalbuminmeancon- μg/ml; BShdidnotdisplayanyAGPstatisticalvariationovertime.IBhalbuminmeancon- BSh did not display any AGP statistical variation over time. IBh albumin mean con- centration (1.62 g/dL was statistically lower than BSh values (1.89 g/dL; in both groups no effect of time of sampling was recorded. Acutephaseprotein(APPvaluesofBShsuggestedamoreadaptive Acute phase protein (APPvaluesofBShsuggestedamoreadaptive (APP values of BSh suggested a more adaptive attitude to free range conditions and appeared more constant over time. The present

The Orosomucoid 1 protein is involved in the vitamin D – mediated macrophage de-activation process

Energy Technology Data Exchange (ETDEWEB)

Gemelli, Claudia, E-mail: claudia.gemelli@unimore.it [Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena (Italy); Center for Regenerative Medicine, University of Modena and Reggio Emilia, Via Gottardi 100, 41125 Modena (Italy); Martello, Andrea; Montanari, Monica; Zanocco Marani, Tommaso; Salsi, Valentina; Zappavigna, Vincenzo; Parenti, Sandra; Vignudelli, Tatiana; Selmi, Tommaso; Ferrari, Sergio; Grande, Alexis [Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena (Italy)

2013-12-10

Orosomucoid 1 (ORM1), also named Alpha 1 acid glycoprotein A (AGP-A), is an abundant plasma protein characterized by anti-inflammatory and immune-modulating properties. The present study was designed to identify a possible correlation between ORM1 and Vitamin D3 (1,25(OH)2D3), a hormone exerting a widespread effect on cell proliferation, differentiation and regulation of the immune system. In particular, the data described here indicated that ORM1 is a 1,25(OH)2D3 primary response gene, characterized by the presence of a VDRE element inside the 1 kb sequence of its proximal promoter region. This finding was demonstrated with gene expression studies, Chromatin Immunoprecipitation and luciferase transactivation experiments and confirmed by VDR full length and dominant negative over-expression. In addition, several experiments carried out in human normal monocytes demonstrated that the 1,25(OH)2D3 – VDR – ORM1 pathway plays a functional role inside the macrophage de-activation process and that ORM1 may be considered as a signaling molecule involved in the maintenance of tissue homeostasis and remodeling. - Highlights: • ORM1 is a Vitamin D primary response gene. • VD and its receptor VDR are involved in the de-activation process mediated by human resident macrophages. • The signaling pathway VD-VDR-ORM1 plays an important role in the control of macrophage de-activation process. • ORM1 may be defined as a signaling molecule implicated in the maintenance of tissue homeostasis and remodeling.

The Orosomucoid 1 protein is involved in the vitamin D – mediated macrophage de-activation process

International Nuclear Information System (INIS)

Gemelli, Claudia; Martello, Andrea; Montanari, Monica; Zanocco Marani, Tommaso; Salsi, Valentina; Zappavigna, Vincenzo; Parenti, Sandra; Vignudelli, Tatiana; Selmi, Tommaso; Ferrari, Sergio; Grande, Alexis

2013-01-01

Orosomucoid 1 (ORM1), also named Alpha 1 acid glycoprotein A (AGP-A), is an abundant plasma protein characterized by anti-inflammatory and immune-modulating properties. The present study was designed to identify a possible correlation between ORM1 and Vitamin D3 (1,25(OH)2D3), a hormone exerting a widespread effect on cell proliferation, differentiation and regulation of the immune system. In particular, the data described here indicated that ORM1 is a 1,25(OH)2D3 primary response gene, characterized by the presence of a VDRE element inside the 1 kb sequence of its proximal promoter region. This finding was demonstrated with gene expression studies, Chromatin Immunoprecipitation and luciferase transactivation experiments and confirmed by VDR full length and dominant negative over-expression. In addition, several experiments carried out in human normal monocytes demonstrated that the 1,25(OH)2D3 – VDR – ORM1 pathway plays a functional role inside the macrophage de-activation process and that ORM1 may be considered as a signaling molecule involved in the maintenance of tissue homeostasis and remodeling. - Highlights: • ORM1 is a Vitamin D primary response gene. • VD and its receptor VDR are involved in the de-activation process mediated by human resident macrophages. • The signaling pathway VD-VDR-ORM1 plays an important role in the control of macrophage de-activation process. • ORM1 may be defined as a signaling molecule implicated in the maintenance of tissue homeostasis and remodeling

Environ: E00817 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available E00817 Marshmallow Medicinal herb Starch [CPD:C00369], Arabinogalactan [CPD:C00569...], Flavonoid [CPD:C01579], Phenolic acid Althaea officinalis [TAX:145745] ... Malvaceae (mallow family) Marshmallow root ...

Generation of recombinant European bat lyssavirus type 1 and inter-genotypic compatibility of lyssavirus genotype 1 and 5 antigenome promoters.

Science.gov (United States)

Orbanz, Jeannette; Finke, Stefan

2010-10-01

Bat lyssaviruses (Fam. Rhabdoviridae) represent a source for the infection of terrestial mammals and the development of rabies disease. Molecular differences in the replication of bat and non-bat lyssaviruses and their contribution to pathogenicity, however, are unknown. One reason for this is the lack of reverse genetics systems for bat-restricted lyssaviruses. To investigate bat lyssavirus replication and host adaptation, we developed a reverse genetics system for European bat lyssavirus type 1 (EBLV-1; genotype 5). This was achieved by co-transfection of HEK-293T cells with a full-length EBLV-1 genome cDNA and expression plasmids for EBLV-1 proteins, resulting in recombinant EBLV-1 (rEBLV-1). Replication of rEBLV-1 was comparable to that of parental virus, showing that rEBLV-1 is a valid tool to investigate EBLV-1 replication functions. In a first approach, we tested whether the terminal promoter sequences of EBLV-1 are genotype-specific. Although genotype 1 (rabies virus) minigenomes were successfully amplified by EBLV-1 helper virus, in the context of the complete virus, only the antigenome promoter (AGP) sequence of EBLV-1 was replaceable, as indicated by comparable replication of rEBLV-1 and the chimeric virus. These analyses demonstrate that the terminal AGPs of genotype 1 and genotype 5 lyssaviruses are compatible with those of the heterologous genotype.

Influence of drinking water containing Aloe vera (Aloe barbadensis Miller) gel on growth performance, intestinal microflora, and humoral immune responses of broilers.

Science.gov (United States)

Shokraneh, Meisam; Ghalamkari, Gholamreza; Toghyani, Majid; Landy, Nasir

2016-11-01

The risk of bacteria resistance to specific antibiotics possibly by continuous subtherapeutical administration of antibiotic growth promoters (AGPs) in poultry feed led to a ban on the use of AGP in poultry production. As a result of this ban, alternative substances for poultry growth promotion and disease prevention are being investigated, among which phytogenic and herbal products have received increased attention as natural additives because they have been accepted by consumers as natural additives. The effect of water supplementation of Aloe vera (AV) as an AGP substitute on performance, intestinal microflora, and immune responses of broilers. The five experimental treatments were allocated to four replicates. The following treatments were applied (1) a basal broiler diet (C) and normal drinking water, (2) 0.5% AV gel in drinking water, (3) 0.75% AV gel in drinking water, (4) 1% AV gel in drinking water, and (5) diet C supplemented with flavophospholipol at 4.5 mg/kg and drinking normal water. Vaccines against influenza disease and sheep red blood cell (SRBC) were administrated to immunological stimuli. The populations of Lactobacilli spp. and coliforms were enumerated in ileum. Body weight of broilers supplemented with different levels of AV increased compared with control group (pantibiotic had the best feed-to-gain ratio (F:G) in different periods. Supplementation of 0.5% and 0.75% AV improved F: G entire experimental period compared with control group (pantibiotic (pantibiotic significantly was higher than other groups (pwater with 1% AV gel as an alternative for AGP substitution.

Long-term effects of dietary supplementation with an essential oil mixture on the growth and laying performance of two layer strains

Directory of Open Access Journals (Sweden)

Abdullah U. Çatli

2012-01-01

Full Text Available One thousand two hundred 1-day-old Lohmann LSL white and Lohmann Brown layer chickens were fed diets supplemented with either an antibiotic growth promoter (AGP or an herbal essential oil mixture (EOM till 58 wk of age to reveal the long-term effects of those additives on growth, performance and wholesome egg quality parameters. The study was arranged in a 2x3 factorial design with two layer strains and three feed additive regimens. Thus, the layer birds of both strains were randomly assigned to the three dietary treatments, i.e., standard basal diet (control, control with AGP (specifically, avilamycin, 10 mg/kg diet and control with EOM (24 mg/kg diet. The data regarding egg production were recorded between 22 to 58 weeks of age. Neither the dietary treatments nor the bird strain influenced the body weight and mortality of the birds in both the growing and laying period. AGP or EOM supplementation to the laying hen diet significantly increased the egg production rate and egg weight as compared to the control  diet alone, but egg mass output, feed consumption, and feed conversion ratio were not effected  by the dietary treatments. Neither dietary treatment created any statistically significantly differences in egg quality parameters with the exception of Haugh unit. The research findings have confirmed the beneficial effects of supplementation with feed-grade EOM on the laying rate and egg weight of both white and brown layers. Indeed, EOM, being a novel feed additive natural origin, proved to be as efficacious as AGP in promoting egg yield.

Management of aggressive periodontitis patient with implant supported prosthesis

Directory of Open Access Journals (Sweden)

Garima Jain

2015-01-01

Full Text Available Aggressive periodontitis (AgP comprises a group of rare, often severe, rapidly progressive forms of periodontitis which is characterized by an early age of clinical manifestations. It usually affects people under 30 years of age, but patients may be older. Microbiota associated are Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis. The presence of highly pathogenic bacteria, severe periodontal bone destruction and the refractory nature of this disease tends to deter the clinician from placing implants in these patients. This case report demonstrates the placement of implants in a patient with AgP with successful 18 months follow-up.

Involvement of activated leukocytes in the regulation of plasma levels of acute phase proteins in microgravity simulation experiments

Science.gov (United States)

Larina, Olga; Bekker, Anna; Turin-Kuzmin, Alexey

2016-07-01

Earth-based studies of microgravity effects showed the induction of the mechanisms of acute phase reaction (APR). APR comprises the transition of stress-sensitive protein kinases of macrophages and other responsive cells into the active state and the phosphorylation of transcription factors which in turn stimulate the production of acute-phase reaction cytokines. Leukocyte activation is accompanied by the acceleration of the formation of oxygen radicals which can serve a functional indice of leukocyte cell state. The series of events at acute phase response result in selective changes in the synthesis of a number of secretory blood proteins (acute phase proteins, APPs) in liver cells thus contributing the recovery of homeostasis state in the organism. Earlier experiment with head-down tilt showed the increase in plasma concentrations of two cytokine mediators of acute phase response, tumor necrosis factor-alpha (TNF-alpha) and interleukin-6 (IL-6) being the outcome of the activation of producer cells, foremost, leukocytes. In experiment with 4-day dry immersion chemiluminescent (ChL) reply of the whole blood samples to a test stimulus were studied along with the measurements of plasma levels of APPs, namely, alpha1-antitrypsin (alpha1-AT), alpha1-acid glycoprotein (alpha1-AGP), alpha2-macroglobulin (alpha2-M), ceruloplasmin (Cer), haptoglobin (Hp), C3-complement component (C3), C-reactive protein (CRP). Eight individuals aged 21.2 ± 3.2 years were the test subjects in the investigation. Protein studies showed a noticeable increase in the mean plasma levels of all APPs measured in experiment thus producing the evidence of the activation of acute phase response mechanisms while individual patterns revealed variability during the immersion period. The overall trends were similar to these in the previous immersion series. The augment in the strength of signal in stimulated light emission tests was higher after 1- and 2-day of immersion exposure than before the

Membrane nanodomains in plants: capturing form, function, and movement.

Science.gov (United States)

Tapken, Wiebke; Murphy, Angus S

2015-03-01

The plasma membrane is the interface between the cell and the external environment. Plasma membrane lipids provide scaffolds for proteins and protein complexes that are involved in cell to cell communication, signal transduction, immune responses, and transport of small molecules. In animals, fungi, and plants, a substantial subset of these plasma membrane proteins function within ordered sterol- and sphingolipid-rich nanodomains. High-resolution microscopy, lipid dyes, pharmacological inhibitors of lipid biosynthesis, and lipid biosynthetic mutants have been employed to examine the relationship between the lipid environment and protein activity in plants. They have also been used to identify proteins associated with nanodomains and the pathways by which nanodomain-associated proteins are trafficked to their plasma membrane destinations. These studies suggest that plant membrane nanodomains function in a context-specific manner, analogous to similar structures in animals and fungi. In addition to the highly conserved flotillin and remorin markers, some members of the B and G subclasses of ATP binding cassette transporters have emerged as functional markers for plant nanodomains. Further, the glycophosphatidylinositol-anchored fasciclin-like arabinogalactan proteins, that are often associated with detergent-resistant membranes, appear also to have a functional role in membrane nanodomains. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Estimation of pentraxin-3 levels in the gingival tissues of chronic and aggressive periodontitis participants: an in vivo study.

Science.gov (United States)

Lakshmanan, Reema; Jayakumar, N D; Sankari, Malaiappan; Padmalatha, Ogoti; Varghese, Sheeja

2014-02-01

Pentraxins are acute-phase proteins that belong to a family of evolutionarily conserved proteins, and they are considered markers of inflammation. Pentraxin-3 (PTX3) is a prototype of the long pentraxin group. It is suggested to play an important role in innate resistance against pathogens, regulation of inflammation, and clearance of apoptotic cells. The aim of this study is to estimate the level of PTX3 in gingival tissues of individuals with chronic (CP) and aggressive (AgP) periodontitis and control participants and further correlate the level of PTX3 with clinical parameters. The study population consisted of 50 participants ranging in age from 20 to 55 years and attending the outpatient section of Department of Periodontics, Saveetha Dental College and Hospital, Chennai, India. The study groups included the following: 1) group A, patients with generalized CP (n = 20); 2) group B (n = 20), patients with generalized AgP (GAgP); and 3) group C (n = 10), healthy controls. Tissue samples from participants were assayed for PTX3 levels using enzyme-linked immunosorbent assay. Gingival tissues from patients with GAgP (8.349 ± 5.076 ng/mL) had a higher mean concentration of PTX3 than tissues from patients with generalized CP (5.068 ± 3.274 ng/mL) and controls (0.251 ± 0.277). The PTX3 levels in the gingival tissues correlated positively with clinical parameters in all the groups. Among the parameters, probing depth was the most significant predictor variable associated with PTX3 in cases with periodontitis. PTX3 concentration in gingival tissues of patients with GAgP was higher than in tissues from patients with CP, and the levels correlated positively with clinical parameters. Hence, tissue PTX3 level can be considered a marker of inflammation in periodontal disease.

Urinary Biomarkers in Relapsing Antineutrophil Cytoplasmic Antibody-associated Vasculitis

Science.gov (United States)

Lieberthal, Jason G.; Cuthbertson, David; Carette, Simon; Hoffman, Gary S.; Khalidi, Nader A.; Koening, Curry L.; Langford, Carol A.; Maksimowicz-McKinnon, Kathleen; Seo, Philip; Specks, Ulrich; Ytterberg, Steven R.; Merkel, Peter A.; Monach, Paul A.

2015-01-01

Objective Glomerulonephritis (GN) is common in antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV), but tools for early detection of renal involvement are imperfect. We investigated 4 urinary proteins as markers of active renal AAV: alpha-1 acid glycoprotein (AGP), kidney injury molecule-1 (KIM-1), monocyte chemoattractant protein-1 (MCP-1), and neutrophil gelatinase-associated lipocalin (NGAL). Methods Patients with active renal AAV (n = 20), active nonrenal AAV (n = 16), and AAV in longterm remission (n = 14) were identified within a longitudinal cohort. Urinary biomarker concentrations (by ELISA) were normalized for urine creatinine. Marker levels during active AAV were compared to baseline remission levels (from 1–4 visits) for each patient. Areas under receiver-operating characteristic curves (AUC), sensitivities, specificities, and likelihood ratios (LR) comparing disease states were calculated. Results Baseline biomarker levels varied among patients. All 4 markers increased during renal flares (p < 0.05). MCP-1 discriminated best between active renal disease and remission: a 1.3-fold increase in MCP-1 had 94% sensitivity and 89% specificity for active renal disease (AUC = 0.93, positive LR 8.5, negative LR 0.07). Increased MCP-1 also characterized 50% of apparently nonrenal flares. Change in AGP, KIM-1, or NGAL showed more modest ability to distinguish active renal disease from remission (AUC 0.71–0.75). Hematuria was noted in 83% of active renal episodes, but also 43% of nonrenal flares and 25% of remission samples. Conclusion Either urinary MCP-1 is not specific for GN in AAV, or it identifies early GN not detected by standard assessment and thus has potential to improve care. A followup study with kidney biopsy as the gold standard is needed. PMID:23547217

Formation of water-soluble soybean polysaccharides from spent flakes by hydrogen peroxide treatment

DEFF Research Database (Denmark)

Pierce, Brian; Wichmann, Jesper; Tran, Tam H.

2016-01-01

70% of the original insoluble material as high molar mass soluble polysaccharides. A design of experiment was used to quantify the effects of pH, reaction time, and hydrogen peroxide concentration on the reaction yield, average molar mass, and free monosaccharides generated. The resulting product......In this paper we propose a novel chemical process for the generation of water-soluble polysaccharides from soy spent flake, a by-product of the soy food industry. This process entails treatment of spent flake with hydrogen peroxide at an elevated temperature, resulting in the release of more than...... is low in protein, fat, and minerals and contains predominantly water-soluble polysaccharides of high molar mass, including arabinan, type I arabinogalactan, homogalacturonan, xyloglucan, rhamnogalacturonan, and (glucurono)arabinoxylan. This treatment provides a straightforward approach for generation...

Establishment and conventional cytogenetic characterization of three gastric cancer cell lines.

Science.gov (United States)

Leal, Mariana Ferreira; Martins do Nascimento, José Luiz; da Silva, Carla Elvira Araújo; Vita Lamarão, Maria Fernanda; Calcagno, Danielle Queiroz; Khayat, André Salim; Assumpção, Paulo Pimentel; Cabral, Isabel Rosa; de Arruda Cardoso Smith, Marília; Burbano, Rommel Rodríguez

2009-11-01

Gastric cancer is the fourth most frequent type of cancer and the second most frequent cause of cancer mortality worldwide. Only a modest number of gastric carcinoma cell lines have been isolated thus far. Here we describe the establishment and cytogenetic characterization of three new gastric cancer cell lines obtained from primary gastric adenocarcinoma (ACP02 and ACP03) and cancerous ascitic fluid (AGP01) of individuals from northern Brazil. ACP02, ACP03, and AGP01 cell lines are presently in the 60th passage. The cell lines grew in a disorganized single layer with some agglomerations and heterogeneous divisions (bipolar and multipolar). All cell lines exhibited a composite karyotype with several clonal chromosome alterations. Trisomy 8 was the most frequent alteration. Chromosome 8 aneusomy was confirmed by fluorescence in situ hybridization. All cell lines also exhibited trisomy 7 and deletion of chromosome arm 17p. These results suggest that, although frequent chromosome alterations are commonly observed due to culture process, the ACP02, ACP03, and AGP01 cell lines and primary gastric cancer from individuals of northern Brazil share genetic alterations, supporting use of these cell lines as a model of gastric carcinogenesis in this population.

Systemic antibiotics in the treatment of aggressive periodontitis. A systematic review and a Bayesian Network meta-analysis.

Science.gov (United States)

Rabelo, Cleverton Correa; Feres, Magda; Gonçalves, Cristiane; Figueiredo, Luciene C; Faveri, Marcelo; Tu, Yu-Kang; Chambrone, Leandro

2015-07-01

The aim of this study was to assess the effect of systemic antibiotic therapy on the treatment of aggressive periodontitis (AgP). This study was conducted and reported in accordance with the PRISMA statement. The MEDLINE, EMBASE and CENTRAL databases were searched up to June 2014 for randomized clinical trials comparing the treatment of subjects with AgP with either scaling and root planing (SRP) alone or associated with systemic antibiotics. Bayesian network meta-analysis was prepared using the Bayesian random-effects hierarchical models and the outcomes reported at 6-month post-treatment. Out of 350 papers identified, 14 studies were eligible. Greater gain in clinical attachment (CA) (mean difference [MD]: 1.08 mm; p benefits in CA gain and PD reduction when SRP was associated with systemic antibiotics. SRP plus systemic antibiotics led to an additional clinical effect compared with SRP alone in the treatment of AgP. Of the antibiotic protocols available for inclusion into the Bayesian network meta-analysis, Mtz and Mtz/Amx provided to the most beneficial outcomes. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Three-Dimensionally Functionalized Reverse Phase Glycoprotein Array for Cancer Biomarker Discovery and Validation.

Science.gov (United States)

Pan, Li; Aguilar, Hillary Andaluz; Wang, Linna; Iliuk, Anton; Tao, W Andy

2016-11-30

Glycoproteins have vast structural diversity that plays an important role in many biological processes and have great potential as disease biomarkers. Here, we report a novel functionalized reverse phase protein array (RPPA), termed polymer-based reverse phase glycoprotein array (polyGPA), to capture and profile glycoproteomes specifically, and validate glycoproteins. Nitrocellulose membrane functionalized with globular hydroxyaminodendrimers was used to covalently capture preoxidized glycans on glycoproteins from complex protein samples such as biofluids. The captured glycoproteins were subsequently detected using the same validated antibodies as in RPPA. We demonstrated the outstanding specificity, sensitivity, and quantitative capabilities of polyGPA by capturing and detecting purified as well as endogenous α-1-acid glycoprotein (AGP) in human plasma. We further applied quantitative N-glycoproteomics and the strategy to validate a panel of glycoproteins identified as potential biomarkers for bladder cancer by analyzing urine glycoproteins from bladder cancer patients or matched healthy individuals.

Finland: construction of the first geological storage of the world; Finlandia: construccion del primer almacen geologico del mundo

Energy Technology Data Exchange (ETDEWEB)

Garcia Neri, E.

2015-07-01

Finland has become the first country in the world granting a construction license for a store deep geological (AGP) for radioactive waste, as reported last November 12 Posiva, the agency management of these materials in the Baltic country. After more than 40 years of research, Posiva begin construction of this facility in Olkiluoto, which will house so end spent fuel generated in power stations Olkiluoto and Loviisa and could start operating in 2023. As noted Janne Mokka, president of Posiva, this pioneering project is not only important for Finland, but for everyone because it is the first AGP enters under construction in the world. (Author)

Finland: construction of the first geological storage of the world

International Nuclear Information System (INIS)

Garcia Neri, E.

2015-01-01

Finland has become the first country in the world granting a construction license for a store deep geological (AGP) for radioactive waste, as reported last November 12 Posiva, the agency management of these materials in the Baltic country. After more than 40 years of research, Posiva begin construction of this facility in Olkiluoto, which will house so end spent fuel generated in power stations Olkiluoto and Loviisa and could start operating in 2023. As noted Janne Mokka, president of Posiva, this pioneering project is not only important for Finland, but for everyone because it is the first AGP enters under construction in the world. (Author)

Efficiency of serum protein removal from skim milk with ceramic and polymeric membranes at 50 degrees C.

Science.gov (United States)

Zulewska, J; Newbold, M; Barbano, D M

2009-04-01

Raw milk (2,710 kg) was separated at 4 degrees C, the skim milk was pasteurized (72 degrees C, 16 s), split into 3 batches, and microfiltered using pilot-scale ceramic uniform transmembrane pressure (UTP; Membralox model EP1940GL0.1microA, 0.1 microm alumina, Pall Corp., East Hills, NY), ceramic graded permeability (GP; Membralox model EP1940GL0.1microAGP1020, 0.1 microm alumina, Pall Corp.), and polymeric spiral-wound (SW; model FG7838-OS0x-S, 0.3 microm polyvinylidene fluoride, Parker-Hannifin, Process Advanced Filtration Division, Tell City, IN) membranes. There were differences in flux among ceramic UTP, ceramic GP, and polymeric SW microfiltration membranes (54.08, 71.79, and 16.21 kg/m2 per hour, respectively) when processing skim milk at 50 degrees C in a continuous bleed-and-feed 3x process. These differences in flux among the membranes would influence the amount of membrane surface area required to process a given volume of milk in a given time. Further work is needed to determine if these differences in flux are maintained over longer processing times. The true protein contents of the microfiltration permeates from UTP and GP membranes were higher than from SW membranes (0.57, 0.56, and 0.38%, respectively). Sodium-dodecyl-sulfate-PAGE gels for permeates revealed a higher casein proportion in GP and SW permeate than in UTP permeate, with the highest passage of casein through the GP membrane under the operational conditions used in this study. The slight cloudiness of the permeates produced using the GP and SW systems may have been due to the presence of a small amount of casein, which may present an obstacle in their use in applications when clarity is an important functional characteristic. More beta-lactoglobulin passed through the ceramic membranes than through the polymeric membrane. The efficiency of removal of serum proteins in a continuous bleed-and-feed 3x process at 50 degrees C was 64.40% for UTP, 61.04% for GP, and 38.62% for SW microfiltration

Assessment of iron status in settings of inflammation: challenges and potential approaches.

Science.gov (United States)

Suchdev, Parminder S; Williams, Anne M; Mei, Zuguo; Flores-Ayala, Rafael; Pasricha, Sant-Rayn; Rogers, Lisa M; Namaste, Sorrel Ml

2017-12-01

The determination of iron status is challenging when concomitant infection and inflammation are present because of confounding effects of the acute-phase response on the interpretation of most iron indicators. This review summarizes the effects of inflammation on indicators of iron status and assesses the impact of a regression analysis to adjust for inflammation on estimates of iron deficiency (ID) in low- and high-infection-burden settings. We overviewed cross-sectional data from 16 surveys for preschool children (PSC) ( n = 29,765) and from 10 surveys for nonpregnant women of reproductive age (WRA) ( n = 25,731) from the Biomarkers Reflecting the Inflammation and Nutritional Determinants of Anemia (BRINDA) project. Effects of C-reactive protein (CRP) and α1-acid glycoprotein (AGP) concentrations on estimates of ID according to serum ferritin (SF) (used generically to include plasma ferritin), soluble transferrin receptor (sTfR), and total body iron (TBI) were summarized in relation to infection burden (in the United States compared with other countries) and population group (PSC compared with WRA). Effects of the concentrations of CRP and AGP on SF, sTfR, and TBI were generally linear, especially in PSC. Overall, regression correction changed the estimated prevalence of ID in PSC by a median of +25 percentage points (pps) when SF concentrations were used, by -15 pps when sTfR concentrations were used, and by +14 pps when TBI was used; the estimated prevalence of ID in WRA changed by a median of +8 pps when SF concentrations were used, by -10 pps when sTfR concentrations were used, and by +3 pps when TBI was used. In the United States, inflammation correction was done only for CRP concentrations because AGP concentrations were not measured; regression correction for CRP concentrations increased the estimated prevalence of ID when SF concentrations were used by 3 pps in PSC and by 7 pps in WRA. The correction of iron-status indicators for inflammation with the

Athletic groin pain (part 2): a prospective cohort study on the biomechanical evaluation of change of direction identifies three clusters of movement patterns

Science.gov (United States)

Franklyn-Miller, A; Richter, C; King, E; Gore, S; Moran, K; Strike, S; Falvey, E C

2017-01-01

Background Athletic groin pain (AGP) is prevalent in sports involving repeated accelerations, decelerations, kicking and change-of-direction movements. Clinical and radiological examinations lack the ability to assess pathomechanics of AGP, but three-dimensional biomechanical movement analysis may be an important innovation. Aim The primary aim was to describe and analyse movements used by patients with AGP during a maximum effort change-of-direction task. The secondary aim was to determine if specific anatomical diagnoses were related to a distinct movement strategy. Methods 322 athletes with a current symptom of chronic AGP participated. Structured and standardised clinical assessments and radiological examinations were performed on all participants. Additionally, each participant performed multiple repetitions of a planned maximum effort change-of-direction task during which whole body kinematics were recorded. Kinematic and kinetic data were examined using continuous waveform analysis techniques in combination with a subgroup design that used gap statistic and hierarchical clustering. Results Three subgroups (clusters) were identified. Kinematic and kinetic measures of the clusters differed strongly in patterns observed in thorax, pelvis, hip, knee and ankle. Cluster 1 (40%) was characterised by increased ankle eversion, external rotation and knee internal rotation and greater knee work. Cluster 2 (15%) was characterised by increased hip flexion, pelvis contralateral drop, thorax tilt and increased hip work. Cluster 3 (45%) was characterised by high ankle dorsiflexion, thorax contralateral drop, ankle work and prolonged ground contact time. No correlation was observed between movement clusters and clinically palpated location of the participant's pain. Conclusions We identified three distinct movement strategies among athletes with long-standing groin pain during a maximum effort change-of-direction task These movement strategies were not related to clinical

Building a State without the Nation? “Peace-through-Statebuilding” in Southern Sudan, 2005-2011

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Aleksi Ylönen

2013-10-01

Full Text Available En enero de 2005 la firma del Acuerdo General de Paz (AGP puso fin oficialmente a la guerra civil más larga de África, en el Sur de Sudán. El AGP es en esencia un tratado para compartir el poder entre el Gobierno de Sudán y la mayor organización rebelde en el Sur de Sudán, el Movimiento/Ejército de Liberación del Pueblo de Sudán (M/ELPS. Si bien el AGP proporcionó una hoja de ruta para la paz entre las principales partes en conflicto y facilitó la secesión de Sudán del Sur en julio de 2011, se vio afectado por una serie de dificultades derivadas de su imposición a un panorama complejo de actores políticos locales. En este artículo se analiza la intervención externa durante la implementación del AGP en el Sur de Sudán en el período 2005-2011. Se abordan por separado los temas de construcción del Estado y construcción de la nación, con el fin de demostrar los límites de la intervención actual destinada a la construcción de un Estado legítimo y con autoridad. El artículo sostiene que la intervención externa en el Sur de Sudán, que se caracteriza por el enfoque de “paz a través del proceso de construcción del Estado”, no fue capaz de garantizar la paz durante el período investigado debido a su falta de atención al proceso de construcción de la nación.

Impact of Denmark's ban on antimicrobials for growth promotion.

Science.gov (United States)

Jensen, Helen H; Hayes, Dermot J

2014-06-01

Denmark was among the first countries to ban the use of antimicrobials for growth promotion (AGPs) in animal production through an on-going series of actions and regulations since 1995. In 2010 the Yellow Card scheme was adopted to decrease total antimicrobial consumption in pig production through additional restrictions on pig farmers. The withdrawal of AGPs and other restrictions have reduced total antimicrobial use, but at the same time therapeutic drug use has increased and resistance in key zoonotic bacteria has not decreased. Improved use of vaccines and management practices can help reduce losses especially for weaner pigs, but come with additional costs to producers. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effect of probiotic supplementation on organic feed to alternative antibiotic growth promoter on production performance and economics analysis of quail.

Science.gov (United States)

Lokapirnasari, W P; Dewi, A R; Fathinah, A; Hidanah, S; Harijani, N; Soeharsono; Karimah, B; Andriani, A D

2017-12-01

The purpose of this study was to know the production performance and economic analysis in quail which use probiotic supplementation to alternate antibiotic growth promoter (AGP) to feed consumption, water consumption, egg production, egg mass, feed conversion, and feed efficiency. About 240 quails ( Coturnix coturnix japonica) at 14 weeks of age were completely randomized into four treatments, each treatment consisted of six replications and each replication consisted by 10 heads. The treatment was T0 (organic feed without AGP and without probiotic), T1 (organic feed + 0.001% AGP), T2 (organic feed + 0.005% probiotic in feed), and T3 (organic feed + 0.005% probiotic in drinking water). The probiotic consist of 1.2×10 5 CFU/g of Lactobacillus casei and Lactobacillus rhamnosus . The results showed that the probiotic supplementation both in feed and water give a significant impact to feed consumption, water intake, feed conversion, feed efficiency, and quail day production, but no statistical difference of egg mass. The T3 also show the most profitable business analysis, which has the best result in income, profit, break-even point, return cost ratio, benefit-cost ratio, and return on investment. It can be concluded that giving 0.005% probiotic in drinking water to get the best egg production and profit.

Standardization versus customization of glucose reporting.

Science.gov (United States)

Rodbard, David

2013-05-01

Bergenstal et al. (Diabetes Technol Ther 2013;15:198-211) described an important approach toward standardization of reporting and analysis of continuous glucose monitoring and self-monitoring of blood glucose (SMBG) data. The ambulatory glucose profile (AGP), a composite display of glucose by time of day that superimposes data from multiple days, is perhaps the most informative and useful of the many graphical approaches to display glucose data. However, the AGP has limitations; some variations are desirable and useful. Synchronization with respect to meals, traditionally used in glucose profiles for SMBG data, can improve characterization of postprandial glucose excursions. Several other types of graphical display are available, and recently developed ones can augment the information provided by the AGP. There is a need to standardize the parameters describing glycemic variability and cross-validate the available computer programs that calculate glycemic variability. Clinical decision support software can identify and prioritize clinical problems, make recommendations for modifications of therapy, and explain its justification for those recommendations. The goal of standardization is challenging in view of the diversity of clinical situations and of computing and display platforms and software. Standardization is desirable but must be done in a manner that permits flexibility and fosters innovation.

Mannan oligosaccharides as growth promoter in finishing rabbit: effect on in vivo performance and carcass traits

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Antonino Nizza

2010-01-01

Full Text Available Four groups each consisting in 440, 60 days old rabbits, were fed, respectively, four experimental diets: (1 MOS_0.5 (Bio-Mos® at 0.5 g/kg; (2 MOS_1.0 (Bio-Mos® at 1.0 g/kg; (3 MOS_ 1.5 (Bio-Mos® at 1.5 g/kg and (4 antibiotics (AGP, colistin sulphate 144 mg/kg; tylosin 100 mg/kg and oxytetracyclin 1000 mg/kg. Up to slaughter age (82 days of age mortality rate was recorded daily. For each group, 64 rabbits were controlled weekly for live weight to calculate daily weight gain (DWG. Feed intake (and, by consequence feed conversion ratio was measured, weekly, per group. At 82 days 16 rabbits per group were slaughtered and carcass traits were recorded. No differences were recorded among groups in live weight at different age and in daily weight gain but, in particular during the last week, AGP and MOS_0.5 groups showed higher feed intake and less favourable feed conversion ratio. MOS_1.0 group showed significantly higher incidence of empty gastro-intestinal tract but not differences were found for dressing out percentage. Perirenal fat showed a lower incidence in MOS than in AGP groups.

Effects of Some Plant Extracts in Triticale-Based Broiler Diets on Growth Performance, E.Coli Counts in Intestine and Blood Parameters

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Ergun Demir

2016-10-01

Full Text Available This study was conducted to determine the effect of using plant essential oils in triticale-based broiler diets as alternative to antimicrobial growth promotors (AGPs on growth, E.coli counts in small intestine and blood parameters. 720 male broiler chicks were randomly distributed to nine experimental groups with four replicates. The control group received the triticale-soybean meal basal diet. In the other treatment groups the basal diet was supplemented with one of the following; flavomycin, enzyme, flavomycin+enzyme, enzyme+thyme oil, enzyme+fennel oil, enzyme+bay leaf oil, enzyme+thyme oil+fennel oil and enzyme+thyme oil+fennel oil+bay leaf oil. Results showed that the weight gain and feed intake were not influenced by the treatments (P>0,05. The use of the combination of plant extracts significantly improved the feed conversion. Use of plant extracts in triticale-based broiler diets as an alternative to AGPs had no regular effect on E.coli count in small intestine segments (P>0,05. Feeding broiler chickens with the enzyme+thyme oil supplemented diets increased eritrocyte level in serum (P0,05 by the treatments. In conclusion, these plant ectracts can be also used with enzyme in triticale-based broiler diets as alternative to AGPs.

Isolation and identification of bioactive compounds in Andrographis paniculata (Chuanxinlian

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Lin Bi-Fong

2010-05-01

Full Text Available Abstract Andrographis paniculata (Burm. f. Nees (Acanthaceae is a medicinal plant used in many countries. Its major constituents are diterpenoids, flavonoids and polyphenols. Among the single compounds extracted from A. paniculata, andrographolide is the major one in terms of bioactive properties and abundance. Among the andrographolide analogues, 14-deoxy-11,12-didehydroandrographolide is immunostimulatory, anti-infective and anti-atherosclerotic; neoandrographolide is anti-inflammatory, anti-infective and anti-hepatotoxic; 14-deoxyandrographolide is immunomodulatory and anti-atherosclerotic. Among the less abundant compounds from A. paniculata, andrograpanin is both anti-inflammatory and anti-infective; 14-deoxy-14,15-dehydroandrographolide is anti-inflammatory; isoandrographolide, 3,19-isopropylideneandrographolide and 14-acetylandrographolide are tumor suppressive; arabinogalactan proteins are anti-hepatotoxic. The four flavonoids from A. paniculata, namely 7-O-methylwogonin, apigenin, onysilin and 3,4-dicaffeoylquinic acid are anti-atherosclerotic.

Effects by periodontitis on pristane-induced arthritis in rats.

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Eriksson, Kaja; Lönnblom, Erik; Tour, Gregory; Kats, Anna; Mydel, Piotr; Georgsson, Pierre; Hultgren, Catharina; Kharlamova, Nastya; Norin, Ulrika; Jönsson, Jörgen; Lundmark, Anna; Hellvard, Annelie; Lundberg, Karin; Jansson, Leif; Holmdahl, Rikard; Yucel-Lindberg, Tülay

2016-11-03

An infection-immune association of periodontal disease with rheumatoid arthritis has been suggested. This study aimed to investigate the effect of pre-existing periodontitis on the development and the immune/inflammatory response of pristane-induced arthritis. We investigated the effect of periodontitis induced by ligature placement and Porphyromonas gingivalis (P. gingivalis) infection, in combination with Fusobacterium nucleatum to promote its colonization, on the development of pristane-induced arthritis (PIA) in rats (Dark Agouti). Disease progression and severity of periodontitis and arthritis was monitored using clinical assessment, micro-computed tomography (micro-CT)/intraoral radiographs, antibody response, the inflammatory markers such as α-1-acid glycoprotein (α-1-AGP) and c-reactive protein (CRP) as well as cytokine multiplex profiling at different time intervals after induction. Experimentally induced periodontitis manifested clinically (P periodontitis-induction led to severe arthritis in all rats demonstrating that the severity of arthritis was not affected by the pre-existence of periodontitis. Endpoint analysis showed that 89% of the periodontitis-affected animals were positive for antibodies against arginine gingipain B and furthermore, the plasma antibody levels to a citrullinated P. gingivalis peptidylarginine deiminase (PPAD) peptide (denoted CPP3) were significantly (P periodontitis rats with PIA. Additionally, there was a trend towards increased pro-inflammatory and anti-inflammatory cytokine levels, and increased α-1-AGP levels in plasma from periodontitis-challenged PIA rats. Pre-existence of periodontitis induced antibodies against citrullinated peptide derived from PPAD in rats with PIA. However, there were no differences in the development or severity of PIA between periodontitis challenged and periodontitis free rats.

Reduced-molecular-weight derivatives of frost grape polysaccharide

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A new Type II arabinogalactan was recently described as an abundant gum exudate from stems of wildfrost grape (Vitus riparia Michx.). The purpose of the current study is to more thoroughly characterize the physical properties of this frost grape polysaccharide (FGP), and develop methods to modify th...

Water holding capacity and enzymatic modification of pressed potato fibres

NARCIS (Netherlands)

Ramasamy, U.

2014-01-01

Cell wall polysaccharides (CWPs) contribute to the water holding capacity (WHC) of fibre rich feeds, such as pressed potato fibres (PPF). However, the role of CWPs on the WHC of PPF was unidentified so far.

PPF was characterized to be abundant in arabinogalactan (AG) linked

Recurring Necrotic Enteritis Outbreaks in Commercial Broiler Chicken Flocks Strongly Influence Toxin Gene Carriage and Species Richness in the Resident Clostridium perfringens Population

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Marie-Lou Gaucher

2017-05-01

Full Text Available Extensive use of antibiotic growth promoters (AGPs in food animals has been questioned due to the globally increasing problem of antibiotic resistance. For the poultry industry, digestive health management following AGP withdrawal in Europe has been a challenge, especially the control of necrotic enteritis. Much research work has focused on gut health in commercial broiler chicken husbandry. Understanding the behavior of Clostridium perfringens in its ecological niche, the poultry barn, is key to a sustainable and cost-effective production in the absence of AGPs. Using polymerase chain reaction and pulsed-field gel electrophoresis, we evaluated how the C. perfringens population evolved in drug-free commercial broiler chicken farms, either healthy or affected with recurring clinical necrotic enteritis outbreaks, over a 14-month period. We show that a high genotypic richness was associated with an increased risk of clinical necrotic enteritis. Also, necrotic enteritis-affected farms had a significant reduction of C. perfringens genotypic richness over time, an increase in the proportion of C. perfringens strains harboring the cpb2 gene, the netB gene, or both. Thus, necrotic enteritis occurrence is correlated with the presence of an initial highly diverse C. perfringens population, increasing the opportunity for the selective sweep of particularly virulent genotypes. Disease outbreaks also appear to largely influence the evolution of this bacterial species in poultry farms over time.

Genetic Variation of Myeloperoxidase Gene Contributes to Aggressive Periodontitis: A Preliminary Association Study in Turkish Population

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Kamile Erciyas

2010-01-01

Full Text Available Myeloperoxidase (MPO is a lysosomal enzyme found in the azurophilic granules of polymorphonuclear leukocytes. It is involved in the defense against periodontal bacteria, and is also able to mediate inflammatory tissue destruction in aggressive and chronic periodontitis. The aim of this study was to explore the association between MPO-463G/A gene polymorphism and aggressive periodontitis (AgP and chronic periodontitis (CP. The study included 147 subjects. Probing depth (PD, clinical attachment loss (CAL, plaque index (PI, and gingival index (GI were recorded as the clinical parameters. Genomic DNA was obtained from the peripheral blood of 32 subjects with AgP, 25 with CP, and 90 reference controls. We genotyped the MPO-463G/A polymorphism using the PCR-RFLP method. All data were analyzed using SPSS version 13.0 for windows. There were no significant differences between the CP patients and controls regarding MPO-463A/G gene polymorphism either in terms of allele frequency or genotype frequency of MPO-463A/G. However, either in terms of allele frequency or genotype frequency of MPO-463A/G, there were significant differences between the AgP patients and the controls. In conclusion, our data suggest that MPO-463G/A may be associated with increased risk of aggressive periodontitis in Turkish patients.

Recurring Necrotic Enteritis Outbreaks in Commercial Broiler Chicken Flocks Strongly Influence Toxin Gene Carriage and Species Richness in the Resident Clostridium perfringens Population

Science.gov (United States)

Gaucher, Marie-Lou; Perron, Gabriel G.; Arsenault, Julie; Letellier, Ann; Boulianne, Martine; Quessy, Sylvain

2017-01-01

Extensive use of antibiotic growth promoters (AGPs) in food animals has been questioned due to the globally increasing problem of antibiotic resistance. For the poultry industry, digestive health management following AGP withdrawal in Europe has been a challenge, especially the control of necrotic enteritis. Much research work has focused on gut health in commercial broiler chicken husbandry. Understanding the behavior of Clostridium perfringens in its ecological niche, the poultry barn, is key to a sustainable and cost-effective production in the absence of AGPs. Using polymerase chain reaction and pulsed-field gel electrophoresis, we evaluated how the C. perfringens population evolved in drug-free commercial broiler chicken farms, either healthy or affected with recurring clinical necrotic enteritis outbreaks, over a 14-month period. We show that a high genotypic richness was associated with an increased risk of clinical necrotic enteritis. Also, necrotic enteritis-affected farms had a significant reduction of C. perfringens genotypic richness over time, an increase in the proportion of C. perfringens strains harboring the cpb2 gene, the netB gene, or both. Thus, necrotic enteritis occurrence is correlated with the presence of an initial highly diverse C. perfringens population, increasing the opportunity for the selective sweep of particularly virulent genotypes. Disease outbreaks also appear to largely influence the evolution of this bacterial species in poultry farms over time. PMID:28567032

Recurring Necrotic Enteritis Outbreaks in Commercial Broiler Chicken Flocks Strongly Influence Toxin Gene Carriage and Species Richness in the Resident Clostridium perfringens Population.

Science.gov (United States)

Gaucher, Marie-Lou; Perron, Gabriel G; Arsenault, Julie; Letellier, Ann; Boulianne, Martine; Quessy, Sylvain

2017-01-01

Extensive use of antibiotic growth promoters (AGPs) in food animals has been questioned due to the globally increasing problem of antibiotic resistance. For the poultry industry, digestive health management following AGP withdrawal in Europe has been a challenge, especially the control of necrotic enteritis. Much research work has focused on gut health in commercial broiler chicken husbandry. Understanding the behavior of Clostridium perfringens in its ecological niche, the poultry barn, is key to a sustainable and cost-effective production in the absence of AGPs. Using polymerase chain reaction and pulsed-field gel electrophoresis, we evaluated how the C. perfringens population evolved in drug-free commercial broiler chicken farms, either healthy or affected with recurring clinical necrotic enteritis outbreaks, over a 14-month period. We show that a high genotypic richness was associated with an increased risk of clinical necrotic enteritis. Also, necrotic enteritis-affected farms had a significant reduction of C. perfringens genotypic richness over time, an increase in the proportion of C. perfringens strains harboring the cpb2 gene, the netB gene, or both. Thus, necrotic enteritis occurrence is correlated with the presence of an initial highly diverse C. perfringens population, increasing the opportunity for the selective sweep of particularly virulent genotypes. Disease outbreaks also appear to largely influence the evolution of this bacterial species in poultry farms over time.

Plant Reproduction: AMOR Enables Males to Respond to Female Signals.

Science.gov (United States)

Dresselhaus, Thomas; Coimbra, Silvia

2016-04-25

The pollen tube of flowering plants undertakes a long journey to transport two sperm cells for double fertilization. New work on pollen tube guidance has identified an arabinogalactan-derived ovular factor that primes tubes to respond to female gametophyte-secreted attraction signals. Copyright © 2016 Elsevier Ltd. All rights reserved.

Use of Bacillus Subtilis PB6 as a potential antibiotic growth promoter replacement in improving performance of broiler birds.

Science.gov (United States)

Jayaraman, Sathishkumar; Das, Partha Pratim; Saini, Prakash Chandra; Roy, Barun; Chatterjee, Paresh Nath

2017-08-01

The intestinal gut health is one of the primary determinants of broiler growth and performance. Among the various enteric diseases, necrotic enteritis (NE) is an enterotoxemic disease caused by Clostridium perfringens, which can result in severe economic losses in poultry farming. Antibiotics like bacitracin methylene disalicylate (BMD) and avilamycin (AVL) are commonly used antibiotic growth promoters (AGP) in poultry feed to control necrotic enteritis in birds. Bacillus subtilis PB6 was reported to prevent necrotic enteritis and improve performance in birds. This paper investigated the influence of Bacillus subtilis PB6 in improving the performance of broiler birds in comparison with BMD and avilamycin. A 35 day trial was conducted with 240 day-old commercial broiler chicks (VenCobb 400), which were divided into four treatment groups, where each treatment group was composed of 6 replicates each containing 10 birds, for a total of 60 birds per treatment. The treatment groups included a negative control (no AGP), Bacillus subtilis PB6, BMD, and avilamycin. The parameters analyzed included body weight, feed conversion ratio (FCR), mortality, villus histomorphometry, and European efficiency factor (EEF). Bacillus subtilis PB6 significantly (P < 0.05) improved body weight and FCR (8 points) compared to the control. The group supplemented with B. subtilis PB6 or BMD had higher (P < 0.05) body weight compared to all other treatment groups. The supplementation of B. subtilis PB6 significantly improved the villus height (P < 0.05) compared to control and other AGP groups. The EEF was found to be the highest in the B. subtilis PB6 supplemented group at 35th day as compared to other treatment groups. The combined data from this study indicate that supplementation of B. subtilis PB6 improves overall performance of broilers compared to BMD and avilamycin, and can be used as potential AGP replacement in poultry farming. © 2017 Poultry Science Association Inc.

Influence of drinking water containing Aloe vera (Aloe barbadensis Miller gel on growth performance, intestinal microflora, and humoral immune responses of broilers

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Meisam Shokraneh

2016-11-01

Full Text Available Aim: The risk of bacteria resistance to specific antibiotics possibly by continuous subtherapeutical administration of antibiotic growth promoters (AGPs in poultry feed led to a ban on the use of AGP in poultry production. As a result of this ban, alternative substances for poultry growth promotion and disease prevention are being investigated, among which phytogenic and herbal products have received increased attention as natural additives because they have been accepted by consumers as natural additives. The effect of water supplementation of Aloe vera (AV as an AGP substitute on performance, intestinal microflora, and immune responses of broilers. Materials and Methods: The five experimental treatments were allocated to four replicates. The following treatments were applied (1 a basal broiler diet (C and normal drinking water, (2 0.5% AV gel in drinking water, (3 0.75% AV gel in drinking water, (4 1% AV gel in drinking water, and (5 diet C supplemented with flavophospholipol at 4.5 mg/kg and drinking normal water. Vaccines against influenza disease and sheep red blood cell (SRBC were administrated to immunological stimuli. The populations of Lactobacilli spp. and coliforms were enumerated in ileum. Results: Body weight of broilers supplemented with different levels of AV increased compared with control group (p<0.05. Birds supplemented with antibiotic had the best feed-to-gain ratio (F:G in different periods. Supplementation of 0.5% and 0.75% AV improved F:G entire experimental period compared with control group (p<0.05. Coliform bacteria were reduced in broilers supplemented with different levels of AV or antibiotic (p<0.05. The Lactobacilli spp. population in birds supplemented with 0.75%, 1% AV or antibiotic significantly was higher than other groups (p<0.05. Supplementation with 1% AV led to greater antibody titers against SRBC compared with other groups (p<0.05. Conclusion: These findings demonstrated a possibility of supplementing

Gas transport in the bentonite barrier of AGP and their interfaces; Transporte de gas en la barrera de bentonita de un AGP y sus interfases

Energy Technology Data Exchange (ETDEWEB)

Gutierrez Rodrigo, V.; Villar Gelicia, M. V.; Martin Martin, P. L.; Romero Alvarez, F. J.

2014-07-01

The research of gas transport processes through the barriers is of great relevance in the assessment of the behaviour of the repository. The main objective of this study is to determine the properties of gas transport in saturated bentonite samples and the interfaces between them. (Author)

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.

Immunomodulatory dietary polysaccharides: a systematic review of the literature

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Nelson Erika D

2010-11-01

Full Text Available Abstract Background A large body of literature suggests that certain polysaccharides affect immune system function. Much of this literature, however, consists of in vitro studies or studies in which polysaccharides were injected. Their immunologic effects following oral administration is less clear. The purpose of this systematic review was to consolidate and evaluate the available data regarding the specific immunologic effects of dietary polysaccharides. Methods Studies were identified by conducting PubMed and Google Scholar electronic searches and through reviews of polysaccharide article bibliographies. Only articles published in English were included in this review. Two researchers reviewed data on study design, control, sample size, results, and nature of outcome measures. Subsequent searches were conducted to gather information about polysaccharide safety, structure and composition, and disposition. Results We found 62 publications reporting statistically significant effects of orally ingested glucans, pectins, heteroglycans, glucomannans, fucoidans, galactomannans, arabinogalactans and mixed polysaccharide products in rodents. Fifteen controlled human studies reported that oral glucans, arabinogalactans, heteroglycans, and fucoidans exerted significant effects. Although some studies investigated anti-inflammatory effects, most studies investigated the ability of oral polysaccharides to stimulate the immune system. These studies, as well as safety and toxicity studies, suggest that these polysaccharide products appear to be largely well-tolerated. Conclusions Taken as a whole, the oral polysaccharide literature is highly heterogenous and is not sufficient to support broad product structure/function generalizations. Numerous dietary polysaccharides, particularly glucans, appear to elicit diverse immunomodulatory effects in numerous animal tissues, including the blood, GI tract and spleen. Glucan extracts from the Trametes versicolor

The composition and metabolism of faecal microbiota is specifically modulated by different dietary polysaccharides and mucin: an isothermal microcalorimetry study.

Science.gov (United States)

Adamberg, K; Kolk, K; Jaagura, M; Vilu, R; Adamberg, S

2018-01-29

The metabolic activity of colon microbiota is specifically affected by fibres with various monomer compositions, degree of polymerisation and branching. The supply of a variety of dietary fibres assures the diversity of gut microbial communities considered important for the well-being of the host. The aim of this study was to compare the impact of different oligo- and polysaccharides (galacto- and fructooligosaccharides, resistant starch, levan, inulin, arabinogalactan, xylan, pectin and chitin), and a glycoprotein mucin on the growth and metabolism of faecal microbiota in vitro by using isothermal microcalorimetry (IMC). Faecal samples from healthy donors were incubated in a phosphate-buffered defined medium with or without supplementation of a single substrate. The generation of heat was followed on-line, microbiota composition (V3-V4 region of the 16S rRNA using Illumina MiSeq v2) and concentrations of metabolites (HPLC) were determined at the end of growth. The multiauxic power-time curves obtained were substrate-specific. More than 70% of all substrates except chitin were fermented by faecal microbiota with total heat generation of up to 8 J/ml. The final metabolite patterns were in accordance with the microbiota changes. For arabinogalactan, xylan and levan, the fibre-affected distribution of bacterial taxa showed clear similarities (e.g. increase of Bacteroides ovatus and decrease of Bifidobacterium adolescentis). The formation of propionic acid, an important colon metabolite, was enhanced by arabinogalactan, xylan and mucin but not by galacto- and fructooligosaccharides or inulin. Mucin fermentation resulted in acetate, propionate and butyrate production in ratios previously observed for faecal samples, indicating that mucins may serve as major substrates for colon microbial population. IMC combined with analytical methods was shown to be an effective method for screening the impact of specific dietary fibres on functional changes in faecal microbiota.

Protein docking prediction using predicted protein-protein interface

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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.

Increasing the productivity of glycopeptides analysis by using higher-energy collision dissociation-accurate mass-product-dependent electron transfer dissociation.

Science.gov (United States)

Saba, Julian; Dutta, Sucharita; Hemenway, Eric; Viner, Rosa

2012-01-01

Currently, glycans are attracting attention from the scientific community as potential biomarkers or as posttranslational modifications (PTMs) of therapeutic proteins. However, structural characterization of glycoproteins and glycopeptides remains analytically challenging. Here, we report on the implementation of a novel acquisition strategy termed higher-energy collision dissociation-accurate mass-product-dependent electron transfer dissociation (HCD-PD-ETD) on a hybrid linear ion trap-orbitrap mass spectrometer. This acquisition strategy uses the complementary fragmentations of ETD and HCD for glycopeptides analysis in an intelligent fashion. Furthermore, the approach minimizes user input for optimizing instrumental parameters and enables straightforward detection of glycopeptides. ETD spectra are only acquired when glycan oxonium ions from MS/MS HCD are detected. The advantage of this approach is that it streamlines data analysis and improves dynamic range and duty cycle. Here, we present the benefits of HCD-PD-ETD relative to the traditional alternating HCD/ETD for a trainer set containing twelve-protein mixture with two glycoproteins: human serotransferrin, ovalbumin and contaminations of two other: bovine alpha 1 acid glycoprotein (bAGP) and bovine fetuin.

Non-cellulosic polysaccharides from the leaves of small balsam (Impatiens parviflora DC.)

Czech Academy of Sciences Publication Activity Database

Hromádková, Z.; Košťálová, Z.; Vrchotová, Naděžda; Ebringerová, A.

2014-01-01

Roč. 389, May 7 (2014), s. 147-153 ISSN 0008-6215 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0073; GA MŠk(CZ) LD11014 Institutional support: RVO:67179843 Keywords : impatiens parviflora DC * leaves * pectin * Glucuronoxylan * Arabinogalactan Subject RIV: EH - Ecology, Behaviour Impact factor: 1.929, year: 2014

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

Directory of Open Access Journals (Sweden)

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.

Environmentally safe oil-field reagents for development and operation of oil-gas deposits

Science.gov (United States)

Fakhreeva, A. V.; Manaure, D. A.; Dokichev, V. A.; Voloshin, A. I.; Telin, A. G.; Tomilov, Yu V.; Nifantiev, N. E.

2018-04-01

Sodium-carboxymethylcellulose and arabinogalactane inhibits the crystallization of calcium carbonate from a supersaturated aqueous solution at 80°C. The sizes of formed crystals CaCO3 in the presence of arabinogalactane, sodium-carboxymethylcellulose and neonol AF 9-10 decrease on an average 7-12 μm and a change of their structure. It is expected, that the mechanism of inhibitionis in specific adsorption polysaccharides and neonol on occurring crystalline surface of the calcium carbonate, both at the expense of electrostatic interaction of functional groups with Ca2+ ions, located on the surface of the crystal, and due to coordination and hydrogen bonds with oxygen atoms and HO-groups of additives. Oil-water emulsion rheology in the presence of neonol AF 9-10 has been studied. It is shown that neonol AF 9-10 decrease viscosity natural water-oil emulsion by 25 times. Addition of 5% neonol to water-oil emulsion leads to formation more than 20 stable emulsion forms of different density and composition. New highly effective “green” oilfield reagents have been developed on the basis of neonol and natural polysaccharides.

Characterization of silver/polystyrene nanocomposites prepared by in situ bulk radical polymerization

Energy Technology Data Exchange (ETDEWEB)

Vukoje, Ivana D., E-mail: ivanav@vinca.rs [Vinča Institute of Nuclear Sciences, University of Belgrade, P.O. Box 522, 11001 Belgrade (Serbia); Vodnik, Vesna V., E-mail: vodves@vinca.rs [Vinča Institute of Nuclear Sciences, University of Belgrade, P.O. Box 522, 11001 Belgrade (Serbia); Džunuzović, Jasna V., E-mail: jasnav2002@googlemail.com [Institute of Chemistry, Technology and Metallurgy (ICTM)-Center of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade (Serbia); Džunuzović, Enis S., E-mail: edzunuzovic@tmf.bg.ac.rs [Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, 11120 Belgrade (Serbia); Marinović-Cincović, Milena T., E-mail: milena@vinca.rs [Vinča Institute of Nuclear Sciences, University of Belgrade, P.O. Box 522, 11001 Belgrade (Serbia); Jeremić, Katarina, E-mail: kjeremic@tmf.bg.ac.rs [Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, 11120 Belgrade (Serbia); Nedeljković, Jovan M., E-mail: jovned@vinca.rs [Vinča Institute of Nuclear Sciences, University of Belgrade, P.O. Box 522, 11001 Belgrade (Serbia)

2014-01-01

Graphical abstract: - Highlights: • Synthesis and characterization of polystyrene nanocomposites based on Ag nanoparticles. • The glass transition temperature decreased in nanocomposites with respect to the pure polymer. • Resistance of the polymer to thermal degradation enhanced with Ag nanoparticles content. - Abstract: Nanocomposites (NCs) with different content of silver nanoparticles (Ag NPs) embeded in polystyrene (PS) matrix were prepared by in situ bulk radical polymerization. The nearly monodisperse Ag NPs protected with oleylamine were synthesized via organic solvo-thermal method and further used as a filler. The as-prepared spherical Ag NPs with diameter of 7.0 ± 1.5 nm were well dispersed in the PS matrix. The structural properties of the resulting Ag/PS NCs were characterized by transmission electron microscope (TEM) and Fourier transform infrared (FTIR) spectroscopy, while optical properties were characterized using optical absorption measurements. The gel permeation chromatography (GPC) measurements showed that the presence of Ag NPs stabilized with oleylamine has no influence on the molecular weight and polydispersity of the PS matrix. The influence of silver content on the thermal properties of Ag/PS NCs was investigated by thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). The results indicated that resistance of PS to thermal degradation was improved upon incorporation of Ag NPs. The Ag/PS NCs have lower glass transition temperatures than neat PS because loosely packed oleylamine molecules at the interface caused the increase of free volume and chain segments mobility near the surface of Ag NPs.

Performance, biochemical and haematological responses, and relative organ weights of laying hens fed diets supplemented with prebiotic, probiotic and synbiotic.

Science.gov (United States)

Tang, Shirley Gee Hoon; Sieo, Chin Chin; Ramasamy, Kalavathy; Saad, Wan Zuhainis; Wong, Hee Kum; Ho, Yin Wan

2017-08-17

The increasing trend of ban on the use of antibiotic growth promoters (AGPs) across the globe in the poultry industry has led to a growing need for alternatives to AGPs. Prebiotic, probiotic and their combination as a synbiotic have been considered as potential alternatives. This study aimed to investigate the effects of a prebiotic (isomaltooligosaccharide, IMO), a probiotic (PrimaLac®), and their combination (synbiotic) on hen performance, biochemical and haematological responses, and relative organ weights from 20 to 52 weeks of age. Supplementation of 1% IMO (PRE), 0.1% PrimaLac® (PRO) and 1% IMO + 0.1% PrimaLac® (SYN) improved (P feed intake and egg production at 20-36 weeks of age; body weight gain, feed conversion ratio and egg mass at 20-36 and 20-52 weeks of age; and egg weight at 20-36, 37-52 and 20-52 weeks of age. Compared to control-fed hens at 20-36 weeks of age, PRO- and SYN-fed hens produced less (P hens produced more large size eggs. From 37 to 52 weeks of age, PRE-, PRO- or SYN-fed hens produced less (P hens from 20 to 52 weeks of age. These results demonstrated the use of PRE, PRO and SYN as alternative feed additives to AGPs for improving the health and productivity of hens, while PRO is the best for commercial layer production to yield maximum profit.

Microbiota in fermented feed and swine gut.

Science.gov (United States)

Wang, Cheng; Shi, Changyou; Zhang, Yu; Song, Deguang; Lu, Zeqing; Wang, Yizhen

2018-04-01

Development of alternatives to antibiotic growth promoters (AGP) used in swine production requires a better understanding of their impacts on the gut microbiota. Supplementing fermented feed (FF) in swine diets as a novel nutritional strategy to reduce the use of AGP and feed price, can positively affect the porcine gut microbiota, thereby improving pig productivities. Previous studies have noted the potential effects of FF on the shift in benefit of the swine microbiota in different regions of the gastrointestinal tract (GIT). The positive influences of FF on swine gut microbiota may be due to the beneficial effects of both pre- and probiotics. Necessarily, some methods should be adopted to properly ferment and evaluate the feed and avoid undesired problems. In this mini-review, we mainly discuss the microbiota in both fermented feed and swine gut and how FF influences swine gut microbiota.

The study of antibacterial activity and stability of dyed cotton fabrics modified with different forms of silver

Directory of Open Access Journals (Sweden)

Lazić Vesna

2012-01-01

Full Text Available This study compares the effect of colloidal silver nanoparticles and commercial RUCO-BAC AGP agent with silver chloride as an active component on antibacterial activity of dyed cotton fabrics. Cotton fabrics were dyed with vat dyes Bezanthren olive T and Bezanthren grey FFB. Antibacterial activity of silver loaded dyed cotton fabrics was tested against Gram-positive bacterium Staphylococcus aureus and Gram-negative bacterium Escherichia coli. Unlike RUCO-BAC AGP synthesized silver nanoparticles deposited onto dyed cotton fabrics provided maximum bacteria reduction independently of applied dye. The stability of modified cotton fabrics was analyzed in artificial sweat at pH 5.5 and 8.0. Approximately the same amount of silver was released from differently modified cotton fabrics in artificial sweat. Larger amount of silver was released in the sweat at pH 8.0.

An efficient synthesis of linear β-(1→6)-galactan oligosaccharides related to plant cell wall glycans

DEFF Research Database (Denmark)

Andersen, Mathias Christian Franch; Arentoft, Camilla Anna Søholt; Boos, Irene

2017-01-01

Galactans are linear structures mainly found in arabinogalactan glycans and RG-I side chains. As a follow-up to our work on both β-(1→3)-linked and β-(1→4)-linked galactans, we herein report a convergent synthesis of β-(1→6)-galactan using our previously synthesized 4,6-benzylidene protected disa...

Assessment of regression models for adjustment of iron status biomarkers for inflammation in children with moderate acute malnutrition in Burkina Faso

DEFF Research Database (Denmark)

Cichon, Bernardette; Ritz, Christian; Fabiansen, Christian

2017-01-01

BACKGROUND: Biomarkers of iron status are affected by inflammation. In order to interpret them in individuals with inflammation, the use of correction factors (CFs) has been proposed. OBJECTIVE: The objective of this study was to investigate the use of regression models as an alternative to the CF...... approach. METHODS: Morbidity data were collected during clinical examinations with morbidity recalls in a cross-sectional study in children aged 6-23 mo with moderate acute malnutrition. C-reactive protein (CRP), α1-acid glycoprotein (AGP), serum ferritin (SF), and soluble transferrin receptor (sTfR) were......TfR with the use of the best-performing model led to a 17% point increase and iron deficiency. CONCLUSION: Regression analysis is an alternative to adjust SF and may be preferable in research settings, because it can take morbidity and severity...

A temperature-sensitive allele of a putative mRNA splicing helicase down-regulates many cell wall genes and causes radial swelling in Arabidopsis thaliana.

Science.gov (United States)

Howles, Paul A; Gebbie, Leigh K; Collings, David A; Varsani, Arvind; Broad, Ronan C; Ohms, Stephen; Birch, Rosemary J; Cork, Ann H; Arioli, Tony; Williamson, Richard E

2016-05-01

The putative RNA helicase encoded by the Arabidopsis gene At1g32490 is a homolog of the yeast splicing RNA helicases Prp2 and Prp22. We isolated a temperature-sensitive allele (rsw12) of the gene in a screen for root radial swelling mutants. Plants containing this allele grown at the restrictive temperature showed weak radial swelling, were stunted with reduced root elongation, and contained reduced levels of cellulose. The role of the protein was further explored by microarray analysis. By using both fold change cutoffs and a weighted gene coexpression network analysis (WGCNA) to investigate coexpression of genes, we found that the radial swelling phenotype was not linked to genes usually associated with primary cell wall biosynthesis. Instead, the mutation has strong effects on expression of secondary cell wall related genes. Many genes potentially associated with secondary walls were present in the most significant WGCNA module, as were genes coding for arabinogalactans and proteins with GPI anchors. The proportion of up-regulated genes that possess introns in rsw12 was above that expected if splicing was unrelated to the activity of the RNA helicase, suggesting that the helicase does indeed play a role in splicing in Arabidopsis. The phenotype may be due to a change in the expression of one or more genes coding for cell wall proteins.

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

Identification of PEG-induced water stress responsive transcripts using co-expression network in Eucalyptus grandis.

Science.gov (United States)

Ghosh Dasgupta, Modhumita; Dharanishanthi, Veeramuthu

2017-09-05

Ecophysiological studies in Eucalyptus have shown that water is the principal factor limiting stem growth. Effect of water deficit conditions on physiological and biochemical parameters has been extensively reported in Eucalyptus. The present study was conducted to identify major polyethylene glycol induced water stress responsive transcripts in Eucalyptus grandis using gene co-expression network. A customized array representing 3359 water stress responsive genes was designed to document their expression in leaves of E. grandis cuttings subjected to -0.225MPa of PEG treatment. The differentially expressed transcripts were documented and significantly co-expressed transcripts were used for construction of network. The co-expression network was constructed with 915 nodes and 3454 edges with degree ranging from 2 to 45. Ninety four GO categories and 117 functional pathways were identified in the network. MCODE analysis generated 27 modules and module 6 with 479 nodes and 1005 edges was identified as the biologically relevant network. The major water responsive transcripts represented in the module included dehydrin, osmotin, LEA protein, expansin, arabinogalactans, heat shock proteins, major facilitator proteins, ARM repeat proteins, raffinose synthase, tonoplast intrinsic protein and transcription factors like DREB2A, ARF9, AGL24, UNE12, WLIM1 and MYB66, MYB70, MYB 55, MYB 16 and MYB 103. The coordinated analysis of gene expression patterns and coexpression networks developed in this study identified an array of transcripts that may regulate PEG induced water stress responses in E. grandis. Copyright © 2017 Elsevier B.V. All rights reserved.

Stunting is characterized by chronic inflammation in Zimbabwean infants.

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Andrew J Prendergast

Full Text Available Stunting affects one-third of children in developing countries, but the causes remain unclear. We hypothesized that enteropathy leads to low-grade inflammation, which suppresses the growth hormone-IGF axis and mediates stunting.We conducted a case-control study of 202 HIV-unexposed Zimbabwean infants who were stunted (height-for-age Z-score (HAZ -0.5; controls at 18 months. We measured biomarkers of intestinal damage (I-FABP, inflammation (CRP, AGP, IL-6 and growth hormone-IGF axis (IGF-1, IGFBP3 in infant plasma at 6 weeks and 3, 6, 12 and 18 months, and in paired maternal-infant plasma at birth. Adjusted mean differences between biomarkers were estimated using regression models. Multivariate odds ratios of stunting were estimated by logistic regression.At birth, cases were shorter (median (IQR HAZ -1.00 (-1.53, -0.08 vs 0.03 (-0.57, 0.62,; P<0.001 than controls and their mothers had lower levels of IGF-1 (adjusted mean difference (95%CI -21.4 (-39.8, -3.1 ng/mL. From 6 weeks to 12 months of age, levels of CRP and AGP were consistently higher and IGF-1 and IGFBP3 lower in cases versus controls; IGF-1 correlated inversely with inflammatory markers at all time-points. I-FABP increased between 3-12 months, indicating extensive intestinal damage during infancy, which was similar in cases and controls. In multivariate analysis, higher log10 levels of CRP (aOR 3.06 (95%CI 1.34, 6.99; P = 0.008 and AGP (aOR 7.87 (95%CI 0.74, 83.74; P = 0.087 during infancy were associated with stunting. There were no associations between levels of I-FABP, IL-6, sCD14 or EndoCAb and stunting.Stunting began in utero and was associated with low maternal IGF-1 levels at birth. Inflammatory markers were higher in cases than controls from 6 weeks of age and were associated with lower levels of IGF-1 throughout infancy. Higher levels of CRP and AGP during infancy were associated with stunting. These findings suggest that an extensive enteropathy occurs during infancy

No association between a common single nucleotide polymorphism, rs4141463, in the MACROD2 gene and autism spectrum disorder.

NARCIS (Netherlands)

Curran, S.; Bolton, P.; Rozsnyai, K.; Chiocchetti, A.; Klauck, S.M.; Duketis, E.; Poustka, F.; Schlitt, S.; Freitag, C.M.; Lee, I. van der; Muglia, P.; Poot, M.; Staal, W.G.; Jonge, M.V. de; Ophoff, R.A.; Lewis, C.; Skuse, D.; Mandy, W.; Vassos, E.; Fossdal, R.; Magnusson, P.; Hreidarsson, S.; Saemundsen, E.; Stefansson, H.; Stefansson, K.; Collier, D.

2011-01-01

The Autism Genome Project (AGP) Consortium recently reported genome-wide significant association between autism and an intronic single nucleotide polymorphism marker, rs4141463, within the MACROD2 gene. In the present study we attempted to replicate this finding using an independent case-control

Banned antibacterial growth promoters in animal feed: Collaborative trial on the liquid chromatography-tandem mass spectrometry method developed in the feedstuffs-radius project

NARCIS (Netherlands)

Poucke, C.V.; Dumoulin, F.; Yakkundi, S.; Situ, C.; Elliott, C.T.; Grutters, E.M.; Verheijen, R.; Schilt, R.; Eriksson, S.; Peteghem, C.V.

2006-01-01

A chemical confirmation method for the identification and quantification of five banned antibacterial growth promoters (AGPs) in animal feed was developed and in-house validated as part of the European Feedstuffs-RADIUS project [1]. To complete the validation process a collaborative trial was

Protein nanoparticles for therapeutic protein delivery.

Science.gov (United States)

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.

Data envelopment analysis and Pareto genetic algorithm applied to robust design in multiresponse systems

Directory of Open Access Journals (Sweden)

Enrique Carlos Canessa-Terrazas

2016-01-01

Full Text Available Se presenta el uso de Análisis Envolvente de Datos (AED para priorizar y seleccionar soluciones encontradas por un Algoritmo Genético de Pareto (AGP a problemas de diseño robusto en sistemas multirespuesta con muchos factores de control y ruido. El análisis de eficiencia de las soluciones con AED muestra que el AGP encuentra una buena aproximación a la frontera eficiente. Además, se usa AED para determinar la combinación del nivel de ajuste de media y variación de las respuestas del sistema, y con la finalidad de minimizar el costo económico de alcanzar dichos objetivos. Al unir ese costo con otras consideraciones técnicas y/o económicas, la solución que mejor se ajuste con un nivel predeterminado de calidad puede ser seleccionada más apropiadamente.

A Quantitative Acetylomic Analysis of Early Seed Development in Rice (Oryza sativa L.).

Science.gov (United States)

Wang, Yifeng; Hou, Yuxuan; Qiu, Jiehua; Li, Zhiyong; Zhao, Juan; Tong, Xiaohong; Zhang, Jian

2017-06-27

PKA (protein lysine acetylation) is a critical post-translational modification that regulates various developmental processes, including seed development. However, the acetylation events and dynamics on a proteomic scale in this process remain largely unknown, especially in rice early seed development. We report the first quantitative acetylproteomic study focused on rice early seed development by employing a mass spectral-based (MS-based), label-free approach. A total of 1817 acetylsites on 1688 acetylpeptides from 972 acetylproteins were identified in pistils and seeds at three and seven days after pollination, including 268 acetyproteins differentially acetylated among the three stages. Motif-X analysis revealed that six significantly enriched motifs, such as (DxkK), (kH) and (kY) around the acetylsites of the identified rice seed acetylproteins. Differentially acetylated proteins among the three stages, including adenosine diphosphate (ADP) -glucose pyrophosphorylases (AGPs), PDIL1-1 (protein disulfide isomerase like 1-1), hexokinases, pyruvate dehydrogenase complex (PDC) and numerous other regulators that are extensively involved in the starch and sucrose metabolism, glycolysis/gluconeogenesis, tricarboxylic acid (TCA) cycle and photosynthesis pathways during early seed development. This study greatly expanded the rice acetylome dataset, and shed novel insight into the regulatory roles of PKA in rice early seed development.

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

Science.gov (United States)

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.

Rank restriction for the variational calculation of two-electron reduced density matrices of many-electron atoms and molecules

International Nuclear Information System (INIS)

Naftchi-Ardebili, Kasra; Hau, Nathania W.; Mazziotti, David A.

2011-01-01

Variational minimization of the ground-state energy as a function of the two-electron reduced density matrix (2-RDM), constrained by necessary N-representability conditions, provides a polynomial-scaling approach to studying strongly correlated molecules without computing the many-electron wave function. Here we introduce a route to enhancing necessary conditions for N representability through rank restriction of the 2-RDM. Rather than adding computationally more expensive N-representability conditions, we directly enhance the accuracy of two-particle (2-positivity) conditions through rank restriction, which removes degrees of freedom in the 2-RDM that are not sufficiently constrained. We select the rank of the particle-hole 2-RDM by deriving the ranks associated with model wave functions, including both mean-field and antisymmetrized geminal power (AGP) wave functions. Because the 2-positivity conditions are exact for quantum systems with AGP ground states, the rank of the particle-hole 2-RDM from the AGP ansatz provides a minimum for its value in variational 2-RDM calculations of general quantum systems. To implement the rank-restricted conditions, we extend a first-order algorithm for large-scale semidefinite programming. The rank-restricted conditions significantly improve the accuracy of the energies; for example, the percentages of correlation energies recovered for HF, CO, and N 2 improve from 115.2%, 121.7%, and 121.5% without rank restriction to 97.8%, 101.1%, and 100.0% with rank restriction. Similar results are found at both equilibrium and nonequilibrium geometries. While more accurate, the rank-restricted N-representability conditions are less expensive computationally than the full-rank conditions.

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

Fabrication of polystyrene/agave particle biocomposites using ...

Indian Academy of Sciences (India)

Polystyrene (PS) composites reinforced with ungrafted and acrylonitrile (AN) grafted agave particles (AgP) have been prepared with 10–30% particle content by weight using compression molding technique. The composite specimens thus prepared were subjected to the evaluation of mechanical, chemical, flammability and ...

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

Directory of Open Access Journals (Sweden)

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.

The beta-1,4-endogalactanase A gene from Aspergillus niger is specifically induced on arabinose and galacturonic acid and plays an important role in the degradation of pectic hairy regions.

Science.gov (United States)

De Vries, Ronald P; Parenicová, Lucie; Hinz, Sandra W A; Kester, Harry C M; Beldman, Gerrit; Benen, Jacques A E; Visser, Jaap

2002-10-01

The Aspergillus nigerbeta-1,4-endogalactanase encoding gene (galA) was cloned and characterized. The expression of galA in A. niger was only detected in the presence of sugar beet pectin, d-galacturonic acid and l-arabinose, suggesting that galA is coregulated with both the pectinolytic genes as well as the arabinanolytic genes. The corresponding enzyme, endogalactanase A (GALA), contains both active site residues identified previously for the Pseudomonas fluorescensbeta-1,4-endogalactanase. The galA gene was overexpressed to facilitate purification of GALA. The enzyme has a molecular mass of 48.5 kDa and a pH optimum between 4 and 4.5. Incubations of arabinogalactans of potato, onion and soy with GALA resulted initially in the release of d-galactotriose and d-galactotetraose, whereas prolonged incubation resulted in d-galactose and d-galactobiose, predominantly. MALDI-TOF analysis revealed the release of l-arabinose substituted d-galacto-oligosaccharides from soy arabinogalactan. This is the first report of the ability of a beta-1,4-endogalactanase to release substituted d-galacto-oligosaccharides. GALA was not active towards d-galacto-oligosaccharides that were substituted with d-glucose at the reducing end.

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.

Eutrophication levels of some South African impoundments III. Roodeplaat Dam

CSIR Research Space (South Africa)

Steyn, DJ

1976-01-01

Full Text Available Algal bioassays indicated that the waters of Roodeplaat dam are severely eutrophied since algal growth potentials (AGP) of up to 200 mg/l and batch culture algal growth rate of up to 2,2 d were registered with selemastrm capricornutum as test alga...

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.

Molecular convergence of the parasitic plant species Cuscuta reflexa and Phelipanche aegyptiaca.

Science.gov (United States)

Rehker, Jan; Lachnit, Magdalena; Kaldenhoff, Ralf

2012-08-01

The parasitic plant species Cuscuta reflexa and Phelipanche aegyptiaca have independently developed parasitism, the former parasitizing on shoots and the latter attaching to roots. Regardless of these differences, the two species use similar organs, termed haustoria, to attach to the host plant. In this study, we show that this morphological similarity can be extended to the molecular level. An attAGP-promoter from Solanum lycopersicum, which is activated by Cuscuta infections, was also induced after infection by P. aegyptiaca. Furthermore, we show by validation of transcriptome sequencing data that the Phelipanche orthologue of a haustorium-specific Cuscuta gene, which codes for a cysteine proteinase, was activated in the early stages of Phelipanche invasion. Inhibition of the Phelipanche cysteine proteinase was achieved by 35S- or attAGP-promoter-driven expression of its intrinsic inhibitory polypeptide. A reduction in P. aegyptiaca infection rates during experiments in flower pots and in an in vitro polybag system in comparison to controls was recorded.

The use of combined heart rate response and accelerometry to assess the level and predictors of physical activity in tuberculosis patients in Tanzania

DEFF Research Database (Denmark)

Faurholt-Jepsen, Maria; Faurholt-Jepsen, Daniel; Range, N

2014-01-01

, HIV and physical activity estimates were assessed in multivariable linear regression models adjusted for age, sex, haemoglobin and alpha-1-acid glycoprotein (AGP). Sputum-positive [eB 0·43, 95% confidence interval (CI) 0·29-0·64] and sputum-negative (eB 0·67, 95% CI 0·47-0·94) TB as well as HIV......SUMMARY: We assessed the role of tuberculosis (TB) disease and HIV infection on the level of physical activity. A combined heart rate and movement sensor was used to assess habitual physical activity in TB patients and non-TB controls. The association between sputum-negative TB, sputum-positive TB...... infection (eB 0·59, 95% CI 0·46-0·75) were associated with reduced activity compared to controls. Anaemia accounted for a substantial part of the effects of HIV, while elevated AGP primarily mediated the TB effect. The level of physical activity is highly influenced by TB and HIV, and mainly mediated...

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.

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)

Various alternatives-to-antibiotics for maximizing the efficiency of growth performance and feed efficiency in poultry: a review

Science.gov (United States)

With the increase in regulations regarding the use of antibiotic growth promoters (AGP) and the rise in consumer demand for poultry products from “Raised Without Antibiotics” or “No Antibiotics Ever” flocks, the quest for alternative products or approaches has intensified in recent years. A great d...

Sector- and economy-wide effects of terminating the use of anti-microbial growth promoters in Denmark

DEFF Research Database (Denmark)

Jacobsen, Lars-Bo; Jensen, Hans Grinsted; Lawson, Lartey

2006-01-01

calculates economy-wide effects of the removal of AGP using the Agricultural Applied General Equilibrium (AAGE) model of the Danish economy. The results show that the long-term effects are a moderate decline in the production and export of pig meat, and a positive indirect effect on other industries...

Two lectin-like receptors for alpha 1-acid glycoprotein in mouse testis

DEFF Research Database (Denmark)

Andersen, U O; Kirkeby, S; Bøg-Hansen, T C

1997-01-01

Three glycoforms of alpha 1-acid glycoprotein (AGP) were biotinylated to examine their binding in mouse testis by light microscopy. The transition from one stage to another in the spermatogenic cycle is marked with an appearance of a receptor for the Concanavalin A (Con A) non-reactive glycoform...

Polymorphisms in interleukins 17A and 17F genes and periodontitis: results from a meta-analysis.

Science.gov (United States)

da Silva, Felipe Rodolfo Pereira; Pessoa, Larissa Dos Santos; Vasconcelos, Any Carolina Cardoso Guimarães; de Aquino Lima, Weberson; Alves, Even Herlany Pereira; Vasconcelos, Daniel Fernando Pereira

2017-12-01

Polymorphisms in inflammatory genes such as interleukins 17A and 17F are associated with the risk of development of periodontitis, although the results remain contradictory. Hence, the aim of this study was perform a meta-analysis focusing on two polymorphisms (rs2275913 and rs763780) in interleukins 17A and 17F genes, respectively, in both chronic (CP) and aggressive periodontitis (AgP). A review in literature was performed in several databases for studies published before 25, September 2016. The meta-analysis was obtained through the review manager statistical software (version 5.2) with odds ratio (OR) calculation and funnel plot (P < 0.05) for heterogeneity, as well as the comprehensive meta-analysis software (version 3.3.070) for the assessment of publication bias. Seven articles with 1540 participants composed the results in which the mutant allele in the rs2275913 polymorphism did not present significant association with the risk of CP or AgP (OR 1.56, 95% CI 0.77, 3.15, P = 0.21; OR 1.12, 95% CI 0.05, 23.44, P = 0.94, respectively) nor was the mutant allele in rs763780 associated with the risk of CP (OR 1.19, 95% CI 0.80, 1.76, P = 0.39) or AgP (OR 1.07, 95% CI 0.63, 1.84, P = 0.79). No bias of publication was observed by Egger's and Begg's tests in any allelic evaluation. This meta-analysis showed a non-significant association between the polymorphisms rs2275913 and rs763780 in interleukins 17A and 17F genes and chronic and aggressive periodontitis in the allelic evaluation.

Perspectives in the use of tannins as alternative to antimicrobial growth promoter factors in poultry

Directory of Open Access Journals (Sweden)

Leandro M Redondo

2014-03-01

Full Text Available Antibiotics have been included in the formulation of feed for livestock production for more than 40 years as a strategy to improve feed conversion rates and to reduce costs. The use of antimicrobials as growth-promoting factors (AGP in sub-therapeutic doses for long periods is particularly favorable to select antimicrobial-resistant microorganisms. In the last years, global concern about development of antimicrobial resistance and transference of resistance genes from animal to human strains has been arising. Removal of AGP from animal diets involves a tremendous pressure on the livestock and poultry farmers, one of the main consequences being a substantial increase in the incidence of infectious diseases with the related increase in the use of antibiotics for therapy and, concomitantly, economic cost. Therefore, alternatives to AGP are urgently needed. The challenge is to implement new alternatives without affecting the production performances of livestock and also avoiding the increase of antimicrobial resistant microorganisms. Plant extracts and purified derived substances are showing promising results for food animal production, either from their efficacy as well as from an economical point of view. Tannins are plant derived compounds that are being successfully used as additives in feed poultry to control diseases and to improve animal performance. Successful use of any of these extracts as feed additive must ensure a product of consistent quality in enough quantities to fulfill the actual requirements of the poultry industry. Chestnut (hydrolizable and Quebracho (condennsed tannins are probably the most readily available commercial products that are covering those needs. The present report intends to analyze the available data supporting their use.

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

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.

A LARGE HUMAN CENTRIFUGE FOR EXPLORATION AND EXPLOITATION RESEARCH

Directory of Open Access Journals (Sweden)

Jack J.W.A. van Loon

2012-06-01

Full Text Available This paper addresses concepts regarding the development of an Altered Gravity Platform (AGP that will serve as a research platform for human space exploration. Space flight causes a multitude of physiological problems, many of which are due to gravity level transitions. Going from Earth's gravity to microgravity generates fluid shifts, space motion sickness, cardiovascular deconditioning among other changes, and returning to a gravity environment again puts the astronauts under similar stressors. A prolonged stay in microgravity provokes additional deleterious changes such as bone loss, muscle atrophy and loss of coordination or specific psychological stresses. To prepare for future manned space exploration missions, a ground-based research test bed for validating countermeasures against the deleterious effects of g-level transitions is needed. The proposed AGP is a large rotating facility (diameter > 150 m, where gravity levels ranging from 1.1 to 1.5g are generated, covering short episodes or during prolonged stays of weeks or even months. On this platform, facilities are built where a crew of 6 to 8 humans can live autonomously. Adaptation from 1 g to higher g levels can be studied extensively and monitored continuously. Similarly, re-adaptation back to 1 g, after a prolonged period of altered g can also be investigated. Study of the physiological and psychological adaptation to changing g-levels will provide instrumental and predictive knowledge to better define the ultimate countermeasures that are needed for future successful manned space exploration missions to the Moon, Mars and elsewhere. The AGP initiative will allow scientific top experts in Europe and worldwide to investigate the necessary scientific, operational, and engineering inputs required for such space missions. Because so many different physiological systems are involved in adaptation to gravity levels, a multidisciplinary approach is crucial. One of the final and crucial

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

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.

Effects of prebiotics and probiotics on the performance and bacterial ...

African Journals Online (AJOL)

A study was undertaken to evaluate the effects of Neoxyval (antimicrobial growth promoter (AGP)), TechnoMos (prebiotic), GalliPro (probiotic) and a mixture of TechnoMos and GalliPro (symbiotic) on growth performance, carcass yield, histomorphology and intestinal bacterial counts in broilers (0 d to 42 d). Two hundred ...

LuFLA1PRO and LuBGAL1PRO promote gene expression in the phloem fibres of flax (Linum usitatissimum).

Science.gov (United States)

Hobson, Neil; Deyholos, Michael K

2013-04-01

Cell type-specific promoters were identified that drive gene expression in an industrially important product. To identify flax (Linum usitatissimum) gene promoters, we analyzed the genomic regions upstream of a fasciclin-like arabinogalactan protein (LuFLA1) and a beta-galactosidase (LuBGAL1). Both of these genes encode transcripts that have been found to be highly enriched in tissues bearing phloem fibres. Using a beta-glucuronidase (GUS) reporter construct, we found that a 908-bp genomic sequence upstream of LuFLA1 (LuFLA1PRO) directed GUS expression with high specificity to phloem fibres undergoing secondary cell wall development. The DNA sequence upstream of LuBGAL1 (LuBGAL1PRO) likewise produced GUS staining in phloem fibres with developing secondary walls, as well as in tissues of developing flowers and seed bolls. These data provide further evidence of a specific role for LuFLA1 in phloem fibre development, and demonstrate the utility of LuFLA1PRO and LuBGAL1PRO as tools for biotechnology and further investigations of phloem fibre development.

Colds and influenza: a review of diagnosis and conventional, botanical, and nutritional considerations.

Science.gov (United States)

Roxas, Mario; Jurenka, Julie

2007-03-01

The common cold is the leading cause of doctor visits in the United States and annually results in 189 million lost school days. In the course of one year the U.S. population contracts approximately 1 billion colds. Influenza infection is still a leading cause of morbidity and mortality, accounting for 20-25 million doctor visits and 36,000 deaths per year in the United States. Conventional therapies for colds and flu focus primarily on temporary symptom relief and include over-the-counter antipyretics, anti-inflammatories, and decongestants. Treatment for influenza also includes prescription antiviral agents and vaccines for prevention. This article reviews the common cold and influenza viruses, presents the conventional treatment options, and highlights select botanicals (Echinacea spp., Sambucus nigra, larch arabinogalactan, Astragalus membranaceous, Baptisia tinctoria, Allium sativa, Panax quinquefolium, Eleutherococcus senticosus, Andrographis paniculata, olive leaf extract, and Isatis tinctoria) and nutritional considerations (vitamins A and C, zinc, high lactoferrin whey protein, N-acetylcysteine, and DHEA) that may help in the prevention and treatment of these conditions.

Chemical Methods for the Determination of Soluble and Insoluble Non-Starch Polysaccharides - Review

OpenAIRE

Rodica Căpriţă; Adrian Căpriţă

2011-01-01

Polysaccharides are macromolecules of monosaccharides linked by glycosidic bonds. Non-starch polysaccharides(NSP) are principally non-α-glucan polysaccharides of the plant cell wall. They are a heterogeneous group ofpolysaccharides with varying degrees of water solubility, size, and structure. The water insoluble fiber fractioninclude cellulose, galactomannans, xylans, xyloglucans, and lignin, while the water-soluble fibers are the pectins,arabinogalactans, arabinoxylans, and β-(1,3)(1,4)-D-g...

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

Principal results of uncertainty and sensibility analysis for generic spanish AGP-granite

International Nuclear Information System (INIS)

Bolado, R.; Moya, J.A.

1998-01-01

Recently, ENRESA published his Performance Assessment of a deep geologic repository in granite. This paper summarises the main results of the uncertainty and sensitivity analysis performed on the data generated for the main scenario in the ENRESA Performance Assessment. The uncertainty analysis allowed us to determine the most important radionuclides, which were ''129I, ''36 Cl, ''79 Se and ''126 Sn, and to estimate upper bounds for the risk due to each one of them and for the global risk. Since ''129 I was the most important radionuclide, the main efforts in the sensitivity study were done in studying the most influential parameters on the maximum dose due to that radionuclide. The analysis shows that the order of magnitude of the maximum dose is essentially related to geosphere transport parameters. Nevertheless, the most influential parameters, when considering only the highest values of the maximum doses, are those that control the total amount of contaminant that can be driven into the main path to biosphere. (Author) 3 refs

Synthesis report of geo technic assessment to clay-AGP design: reference concept

International Nuclear Information System (INIS)

Farina, P.; Pedraza, L.; Ruiz, F.

1995-01-01

This report summarizes the studies on clays for the storage of radioactive wastes. The study is focussed to the geotechnical assessment for the clays. The report presents the methodology analysis, the geotechnical feasibility, minimizing methods, costs and operation

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

The effect of discontinued use of antimicrobial growth promoters on the risk of therapeutic antibiotic treatment in Danish farrow-to-finish pig farms

DEFF Research Database (Denmark)

Vigre, Håkan; Larsen, P.B.; Andreasen, Morten

2008-01-01

) the proportion of days per farm where treatment was performed (PDT) and (2) the proportion of pigs treated per day per farm at days where treatment was performed (PPT) before and after duAGPs at 68 farrow-to-finish farms. The farms were selected using, a two-stage (veterinarian/farm) convenience sampling...

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.

Improving the stability of coal slurries: Quarterly progress report for the period June 15, 1987-September 15, 1987

Energy Technology Data Exchange (ETDEWEB)

Fogler, H.S.

1987-01-01

Gum tragacanth, GT is a polysaccharide containing tragacanthic acid and arabinogalactan. In order to find which polysaccharide is responsible for the stabilization, the arabinogalactan and polygalacturonic acid were used in the flocculation test. The polygalacturonic acid is a linear polysaccharide which constitutes the core of tragacanthic acid that is branched polysaccharide. The much greater stabilization effect by polygalacturonic acid indicated that the tragacanthic acid is responsible for the stabilization by GT. More interestingly, the similar pH dependence of the stability was found for polygalacturonic acid as had been found for GT. The binding study indicated that this pH effect for polygalacturonic acid is due to the difference in the amount of adsorption whereas the pH effect for GT is due to the difference in the steric layer thickness with about the same amount of adsorption. This relative pH independence of amount of adsorption for GT indicates that the binding mechanism of GT is hydrophobic. In order to verify this, the hydrophilic latex was used in the adsorption study as well as hydrophobic latex. It was found that the amount of adsorption of GT for the hydrophilic latex was less than that for the hydrophobic sulfate polystyrene latex. 10 refs., 6 figs., 2 tabs.

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

The experiences of working carers of older people regarding access to a web-based family care support network offered by a municipality.

Science.gov (United States)

Andersson, Stefan; Erlingsson, Christen; Magnusson, Lennart; Hanson, Elizabeth

2017-09-01

Policy makers in Sweden and other European Member States pay increasing attention as to how best support working carers; carers juggling providing unpaid family care for older family members while performing paid work. Exploring perceived benefits and challenges with web-based information and communication technologies as a means of supporting working carers' in their caregiving role, this paper draws on findings from a qualitative study. The study aimed to describe working carers' experiences of having access to the web-based family care support network 'A good place' (AGP) provided by the municipality to support those caring for an older family member. Content analysis of interviews with nine working carers revealed three themes: A support hub, connections to peers, personnel and knowledge; Experiencing ICT support as relevant in changing life circumstances; and Upholding one's personal firewall. Findings indicate that the web-based family care support network AGP is an accessible, complementary means of support. Utilising support while balancing caregiving, work obligations and responsibilities was made easier with access to AGP; enabling working carers to access information, psychosocial support and learning opportunities. In particular, it provided channels for carers to share experiences with others, to be informed, and to gain insights into medical and care issues. This reinforced working carers' sense of competence, helping them meet caregiving demands and see positive aspects in their situation. Carers' low levels of digital skills and anxieties about using computer-based support were barriers to utilising web-based support and could lead to deprioritising of this support. However, to help carers overcome these barriers and to better match web-based support to working carers' preferences and situations, web-based support must be introduced in a timely manner and must more accurately meet each working carer's unique caregiving needs. © 2016 Nordic College

Outcomes in Asymptomatic Severe Aortic Stenosis With Preserved Ejection Fraction Undergoing Rest and Treadmill Stress Echocardiography.

Science.gov (United States)

Huded, Chetan P; Masri, Ahmad; Kusunose, Kenya; Goodman, Andrew L; Grimm, Richard A; Gillinov, A Marc; Johnston, Douglas R; Rodriguez, L Leonardo; Popovic, Zoran B; Svensson, Lars G; Griffin, Brian P; Desai, Milind Y

2018-04-12

In asymptomatic patients with severe aortic stenosis and preserved left ventricular ejection fraction, we sought to assess the incremental prognostic value of resting valvuloarterial impedence (Zva) and left ventricular global longitudinal strain (LV-GLS) to treadmill stress echocardiography. We studied 504 such patients (66±12 years, 78% men, 32% with coronary artery disease who underwent treadmill stress echocardiography between 2001 and 2012. Clinical and exercise variables (% of age-sex predicted metabolic equivalents [%AGP-METs]) were recorded. Resting Zva ([systolic arterial pressure+mean aortic valve gradient]/[LV-stroke volume index]) and LV-GLS (measured offline using Velocity Vector Imaging, Siemens) were obtained from the baseline resting echocardiogram. Death was the primary outcome. There were no major adverse cardiac events during treadmill stress echocardiography. Indexed aortic valve area, Zva, and LV-GLS were 0.46±0.1 cm 2 /m 2 , 4.5±0.9 mm Hg/mL per m 2 and -16±4%, respectively; only 50% achieved >100% AGP-METs. Sixty-four percent underwent aortic valve replacement. Death occurred in 164 (33%) patients over 8.9±3.6 years (2 within 30 days of aortic valve replacement). On multivariable Cox survival analysis, higher Society of Thoracic Surgeons score (hazard ratio or HR 1.06), lower % AGP-METS (HR 1.16), higher Zva (HR 1.25) and lower LV-GLS (HR 1.12) were associated with higher longer-term mortality, while aortic valve replacement (HR 0.45) was associated with improved survival (all P statistic from 0.65 to 0.69 and 0.75, respectively, both P stress echocardiography, LV-GLS and ZVa offer incremental prognostic value. © 2018 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley.

Research Program Peer Review: Purposes, Principles, Practices, Protocols

Science.gov (United States)

2004-06-01

Statement 1994-95. Canberra: AGPS. Cook- Deegan , R.M. Merit Review for Federally Funded Science and Technology: A White Paper for the Council of the...18p. Craig -B, "SPE Peer-Review Critique", JOURNAL OF PETROLEUM TECHNOLOGY, 1994, Vol 46, Iss 7, pp 563-563 Cram-DL Stebbins-M Eom-HS Ratto-N

Grr1p is required for transcriptional induction of amino acid permease genes and proper transcriptional regulation of genes in carbon metabolism of Saccharomyces cerevisiae

DEFF Research Database (Denmark)

Eckert-Boulet, Nadine; Regenberg, Birgitte; Nielsen, Jens

2005-01-01

and a grr1 Delta strain and adding citrulline in the exponential phase. Whole-genome transcription analyses were performed on samples from each cultivation, both immediately before and 30 min after citrulline addition. Transcriptional induction of the AAP genes AGP1, BAP2, BAP3, DIP5, GNP1 and TAT1 is fully...

Isolation, purification and some structural features of the mucilaginous exudate from Musa paradisiaca.

Science.gov (United States)

Mondal, S K; Ray, B; Thakur, S; Ghosal, P K

2001-03-01

The water-soluble polysaccharides isolated from the vascular gel of Musa paradisiaca, were fractionated via anion exchange chromatography into four fractions. Fractionated polymers contained arabinose, xylose and galacturonic acid as major sugars, together with traces of galactose, rhamnose, mannose and glucose residues. Methylation analysis revealed the presence of a highly branched arabinoxylan with a significant amount of terminal arabinopyranosyl units and an arabinogalactan type I pectin. Periodate oxidation studies supported the results of methylation analysis.

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

Global restriction of using antibiotic growth promoters and alternative strategies in poultry production.

Science.gov (United States)

Salim, Hossan Md; Huque, Khan Shahidul; Kamaruddin, Kazi M; Beg, M D Anwarul Haque

2018-03-01

A growing global concern of antibiotic use in poultry diets due to its potential adverse effects on birds and human health, food safety and the environment has led to a complete ban or restricted use in some countries, and, at the same time, expanding options for the use of alternative feed additives. Multiple, rather than a single additive may replace antibiotic growth promoters (AGPs) in poultry. Blending of feeding additives and hygienic farm management, vaccination and biosecurity may help achieve good intestinal health, stabilise enteric ecosystems and result in sustainable and cost effective production performance of birds. Moreover, controlling unsolicited ingredients at the production level must have the support of different markets responsible for the supply of safe and quality poultry products for consumers. This requires the further increase and diversification of value added poultry products and the expansion of their markets through strategic planning and gradual limitation of live bird markets. More research is warranted in order to explore suitable, reliable and cost effective alternatives to AGPs for commercial use, and strategic poultry value chain development.

Characterization of Ag-porous silicon nanostructured layer formed by an electrochemical etching of p-type silicon surface for bio-application

Science.gov (United States)

Naddaf, M.; Al-Mariri, A.; Haj-Mhmoud, N.

2017-06-01

Nanostructured layers composed of silver-porous silicon (Ag-PS) have been formed by an electrochemical etching of p-type (1 1 1) silicon substrate in a AgNO3:HF:C2H5OH solution at different etching times (10 min-30 min). Scanning electron microscopy (SEM) and energy-dispersive x-ray spectroscopy (EDS) results reveal that the produced layers consist of Ag dendrites and a silicon-rich porous structure. The nanostructuring nature of the layer has been confirmed by spatial micro-Raman scattering and x-ray diffraction techniques. The Ag dendrites exhibit a surface-enhanced Raman scattering (SERS) spectrum, while the porous structure shows a typical PS Raman spectrum. Upon increasing the etching time, the average size of silicon nanocrystallite in the PS network decreases, while the average size of Ag nanocrystals is slightly affected. In addition, the immobilization of prokaryote Salmonella typhimurium DNA via physical adsorption onto the Ag-PS layer has been performed to demonstrate its efficiency as a platform for detection of biological molecules using SERS.

Activity of Antimicrobial Silver Polystyrene Nanocomposites

Directory of Open Access Journals (Sweden)

M. Palomba

2012-01-01

Full Text Available A simple technique based on doping polymers with in situ generated silver nanoparticles (Ag/PS films has been developed. In particular, an antiseptic material has been prepared by dissolving silver 1,5-cyclooctadiene-hexafluoroacetylacetonate in amorphous polystyrene, and the obtained solid solution has been heated for ca. 10 s at a convenient temperature (180°C. Under such conditions the metal precursor decomposes producing silver atoms that diffuse into the polymer and clusterize. The antimicrobial characteristics of the resulting polystyrene-based material have been accurately evaluated toward Escherichia coli (E. coli comparing the cytotoxicity effect of 10 wt.% and 30 wt.% (drastic and mild annealing silver-doped polystyrene to the corresponding pure micrometric silver powder. Two different bacterial viability assays were performed in order to demonstrate the cytotoxic effect of Ag/PS films on cultured E. coli: (1 turbidimetric determination of optical density; (2 BacLight fluorescence-based test. Both methods have shown that silver-doped polystyrene (30 wt.% provides higher antibacterial activity than pure Ag powder, under similar concentration and incubation conditions.

Aggregatibacter (Actinobacillus actimycetemcomitans leukotoxin and human periodontitis – A historic review with emphasis on JP2

Directory of Open Access Journals (Sweden)

Chi-Cheng Tsai

2018-04-01

Full Text Available Aggregatibacter (Actinobacillus actimycetemcomitans (Aa is a gram-negative bacterium that colonizes the human oral cavity and is causative agent for localized aggressive (juvenile periodontitis (AgP. In the middle of 1990s, a specific JP2 clone of belonging to the cluster of serotype b strains of Aa with highly leukotoxicity (leukotoxin, LtxA able to kill human immune cells was isolated. JP2 clone of Aa was strongly associated with in particularly in rapidly progressing forms of aggressive periodontitis. The JP2 clone of Aa is transmitted through close contacts. Therefore, AgP patients need intense monitoring of their periodontal status as the risk for developing severely progressing periodontitis lesions are relatively high. Furthermore, timely periodontal treatment, including periodontal surgery supplemented by the use of antibiotics, is warranted. More importantly, periodontal attachment loss should be prevented by early detection of the JP2 clone of Aa by microbial diagnosis testing and/or preventive means. Keywords: Aggregatibacter (Actinobacillus actinomycetemcomitans, Aggressive periodontitis, Leukotoxin (LtxA, Polymorphonuclear leukocytes (PMNs

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

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

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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

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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.

Study of Site Effect at Seismic Station Located in Undermined Area of Karviná Region (Czech Republic)

Czech Academy of Sciences Publication Activity Database

Lednická, Markéta; Kaláb, Zdeněk

2016-01-01

Roč. 64, č. 5 (2016), s. 1715-1730 ISSN 1895-7455 R&D Projects: GA ČR GP13-07027P Institutional support: RVO:68145535 Keywords : Karviná region * site effect * SSR * HVSR * mining induced seismicity Subject RIV: JM - Building Engineering Impact factor: 0.968, year: 2016 http://agp.igf.edu.pl/files/64/5/Lednicka-Kalab.pdf

Lower Devonian conodonts from the Karlík Valley and Na Branžovech sections in the Barrandian area, Czech Republic, and their significance for Pragian conodont zonation

Czech Academy of Sciences Publication Activity Database

Slavík, Ladislav

2001-01-01

Roč. 51, č. 3 (2001), s. 253-271 ISSN 0001-5709 R&D Projects: GA ČR GA205/98/0454; GA ČR GA205/98/1347 Institutional research plan: CEZ:AV0Z3013912 Keywords : Conodonts * Barrandian * Pragian Subject RIV: DB - Geology ; Mineralogy https://geojournals.pgi.gov.pl/agp/article/view/9913/8446

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

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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

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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*

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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.

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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

Science.gov (United States)

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

Science.gov (United States)

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.

Science.gov (United States)

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

Science.gov (United States)

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

Science.gov (United States)

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.

Science.gov (United States)

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

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

Energy Technology Data Exchange (ETDEWEB)

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.

Directory of Open Access Journals (Sweden)

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.

Science.gov (United States)

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.

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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.

Quantifying the molecular origins of opposite solvent effects on protein-protein interactions.

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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

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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

[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.

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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...

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.

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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

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....

Synthesis of Ag-coated polystyrene colloids by an improved surface seeding and shell growth technique

International Nuclear Information System (INIS)

Tian Chungui; Wang Enbo; Kang Zhenhui; Mao Baodong; Zhang Chao; Lan Yang; Wang Chunlei; Song Yanli

2006-01-01

In this paper, an improved surface seeding and shell growth technique was developed to prepare Ag-polystyrene core shell composite. Polyethyleneimine (PEI) could act as the linker between Ag ions (Ag nanoparticles) and polystyrene (PS) colloids and the reducing agent in the formation of Ag nanoparticles. Due to the multi-functional characteristic of PEI, Ag seeds formed in-situ and were immobilized on the surface of PEI-modified PS colloids and no free Ag clusters coexist with the Ag 'seeding' PS colloids in the system. Then, the additional agents could be added into the resulting dispersions straightly to produce a thick Ag nanoshell. The Ag nanoshell with controllable thickness was formed on the surface of PS by the 'one-pot' surface seeding and shell growth method. The Ag-coverage increased gradually with the increasing of mass ratio of AgNO 3 /PS. The optical properties of the Ag-PS colloids could be tailored by changing the coverage of Ag. - Graphical abstract: An improved surface seeding and shell growth technique was developed to prepare Ag-polystyrene core shell composite. The optical properties of the Ag-PS colloids could be tailored by changing the coverage of Ag. Display Omitted

Professional flash continuous glucose monitoring as a supplement to A1C in primary care.

Science.gov (United States)

Hirsch, Irl B

2017-11-01

Decreasing glycated hemoglobin (A1C) is the primary goal of current diabetes management due to intervention studies in type 1 and type 2 diabetes associating levels <7.0% (53 mmol/mol) with lower complication risk. Strategic self-monitoring of blood glucose (SMBG) is also recommended to achieve greater time in range, with fewer extremes of hypo- or hyperglycemia. Unlike A1C, SMBG can distinguish among fasting, prandial, and postprandial hyperglycemia; uncover glycemic variability, including potentially dangerous hypoglycemia; and provide feedback to patients about the effects of behavior and medication on glycemic control. However, it has the drawback of capturing only static glucose readings and users are often dependent on time-pressed clinicians to interpret numerous data points. A novel flash continuous glucose monitoring (FCGM) device used for a single 2-week period with a readily interpretable data report know as the ambulatory glucose profile (AGP) has the potential to overcome limitations of conventional technologies, with less cost and greater convenience. This review summarizes the rationale for using intermittent FCGM as a supplement to A1C in primary care, and provides a stepwise approach to interpreting the AGP visual display for efficient individualized therapy.

A model for the analysis of a normal evolution scenarios for a deep geological granite repository for high-level radioactive waste

International Nuclear Information System (INIS)

Cormenzana Lopez, J.L.; Cunado, M.A.; Lopez, M.T.

1996-01-01

The methodology usually used to evaluate the behaviour of deep geological repositories for high-level radioactive wastes comprises three phases: Identification of factors (processes, characteristics and events) that can affect the repository. Generation of scenarios. In general, a normal evolution scenario (Reference Scenario) and various disruptive scenarios (earthquake, human intrusion, etc) are considered. Evaluation of the behaviour of the repository in each scenario. The normal evolution scenario taking into account all factors with a high probability of occurrence is the first to be analysed. The performance assessment of behaviour being carried out by ENRESA for the AGP Granite has led to the identification of 63 of these factors. To analyse repository behaviour in the normal evolution scenario, it is necessary to first of all create an integrated model of the global system. This is a qualitative model including the 63 factors identified. For a global view of a such a complex system, it is very useful to graphically display the relationship between factors in an Influence Diagram. This paper shows the Influence Diagram used in the analysis of the AGP Granite Reference Scenario. (Author)

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.

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

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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.

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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.

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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.

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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.

Long-term Geomechanical Observation in the Jeroným Mine

Czech Academy of Sciences Publication Activity Database

Kaláb, Zdeněk; Lednická, Markéta

2016-01-01

Roč. 64, č. 5 (2016), s. 1513-1524 ISSN 1895-7455 R&D Projects: GA ČR GA105/09/0089 Institutional support: RVO:68145535 Keywords : abandoned mine * geomechanical observation * movements along fractures * stress tensor changes * mine water table fluctuation Subject RIV: DC - Siesmology, Volcanology, Earth Structure Impact factor: 0.968, year: 2016 http://agp.igf.edu.pl/files/64/5/Kalab-Lednicka.pdf

Vibration Effect of Near Earthquakes at Different Depths in a Shallow Medieval Mine

Czech Academy of Sciences Publication Activity Database

Lednická, Markéta; Kaláb, Zdeněk

2016-01-01

Roč. 64, č. 6 (2016), s. 2244-2263 ISSN 1895-7455 R&D Projects: GA ČR GA105/09/0089; GA MŠk LM2010008 Institutional support: RVO:68145535 Keywords : Jeroným mine * vibration * earthquake * seismic swarm * underground space Subject RIV: DC - Siesmology, Volcanology, Earth Structure Impact factor: 0.968, year: 2016 http://agp.igf.edu.pl/files/64/6/Lednicka-Kalab-2.pdf

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.

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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.

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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.

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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.

Interaction of IL1B and IL1RN polymorphisms, smoking habit, gender, and ethnicity with aggressive and chronic periodontitis susceptibility

Directory of Open Access Journals (Sweden)

Magali Silveira Monteiro Ribeiro

2016-01-01

Full Text Available Background: Although the interleukin-1 (IL-1 plays a critical role in the pathogenesis of periodontitis, associations between IL1 gene cluster polymorphisms and the disease remains unclear. Aims: To investigate the importance of IL1B-511C>T (rs16944, IL1B +3954C>T (rs1143634, and IL1RN intron 2 variable number tandem repeat (VNTR (rs2234663 polymorphisms, individually or in combination, as the risk factors of periodontitis in a Southeastern Brazilian population with a high degree of miscegenation. Subjects and Methods: A total of 145 individuals, with aggressive (aggressive periodontitis [AgP], n = 43 and chronic (chronic periodontitis [CP], n = 52 periodontitis, and controls (n = 50 were genotyped by polymerase chain reaction (PCR (IL1RN intron 2 VNTR or PCR-restriction fragment length polymorphism (PCR-RFLP (IL1B-511 C>T and IL1B + 3954C>T techniques. Statistical Analysis: The independent t-test, Chi-square, and Fisher′s exact tests were used. The SNPStats program was used for haplotype estimation and multiplicative interaction analyses. Results: The IL1B +3954T allele represented risk for CP (odds ratio [OR] = 2.84, particularly in smokers (OR = 4.43 and females (OR = 6.00. The minor alleles IL1RNFNx012 and FNx013 increased the risk of AgP (OR = 2.18, especially the IL1RNFNx012FNx012 genotype among  white Brazilians (OR = 7.80. Individuals with the combinations of the IL1B + 3954T and IL1RNFNx012 or FNx013-containing genotypes were at increased risk of developing CP (OR = 4.50. Considering the three polymorphisms (rs16944, rs1143634, and rs2234663, the haplotypes TC2 and CT1 represented risk for AgP (OR = 3.41 and CP (OR = 6.39, respectively. Conclusions: Our data suggest that the IL1B +3954C>T and IL1RN intron 2 VNTR polymorphisms are potential candidates for genetic biomarkers of periodontitis, particularly in specific groups of individuals.

Interaction of IL1B and IL1RN polymorphisms, smoking habit, gender, and ethnicity with aggressive and chronic periodontitis susceptibility.

Science.gov (United States)

Ribeiro, Magali Silveira Monteiro; Pacheco, Renata Botelho Antunes; Fischer, Ricardo Guimarães; Macedo, Jacyara Maria Brito

2016-01-01

Although the interleukin-1 (IL-1) plays a critical role in the pathogenesis of periodontitis, associations between IL1 gene cluster polymorphisms and the disease remains unclear. To investigate the importance of IL1B-511C>T (rs16944), IL1B +3954C>T (rs1143634), and IL1RN intron 2 variable number tandem repeat (VNTR) (rs2234663) polymorphisms, individually or in combination, as the risk factors of periodontitis in a Southeastern Brazilian population with a high degree of miscegenation. A total of 145 individuals, with aggressive (aggressive periodontitis [AgP], n = 43) and chronic (chronic periodontitis [CP], n = 52) periodontitis, and controls (n = 50) were genotyped by polymerase chain reaction (PCR) (IL1RN intron 2 VNTR) or PCR-restriction fragment length polymorphism (PCR-RFLP) (IL1B-511 C>T and IL1B + 3954C>T) techniques. The independent t-test, Chi-square, and Fisher's exact tests were used. The SNPStats program was used for haplotype estimation and multiplicative interaction analyses. The IL1B +3954T allele represented risk for CP (odds ratio [OR] = 2.84), particularly in smokers (OR = 4.43) and females (OR = 6.00). The minor alleles IL1RN*2 and *3 increased the risk of AgP (OR = 2.18), especially the IL1RN*2*2 genotype among  white Brazilians (OR = 7.80). Individuals with the combinations of the IL1B + 3954T and IL1RN*2 or *3-containing genotypes were at increased risk of developing CP (OR = 4.50). Considering the three polymorphisms (rs16944, rs1143634, and rs2234663), the haplotypes TC2 and CT1 represented risk for AgP (OR = 3.41) and CP (OR = 6.39), respectively. Our data suggest that the IL1B +3954C>T and IL1RN intron 2 VNTR polymorphisms are potential candidates for genetic biomarkers of periodontitis, particularly in specific groups of individuals.

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.

3DProIN: Protein-Protein Interaction Networks and Structure Visualization.

Science.gov (United States)

Li, Hui; Liu, Chunmei

2014-06-14

3DProIN is a computational tool to visualize protein-protein interaction networks in both two dimensional (2D) and three dimensional (3D) view. It models protein-protein interactions in a graph and explores the biologically relevant features of the tertiary structures of each protein in the network. Properties such as color, shape and name of each node (protein) of the network can be edited in either 2D or 3D views. 3DProIN is implemented using 3D Java and C programming languages. The internet crawl technique is also used to parse dynamically grasped protein interactions from protein data bank (PDB). It is a java applet component that is embedded in the web page and it can be used on different platforms including Linux, Mac and Window using web browsers such as Firefox, Internet Explorer, Chrome and Safari. It also was converted into a mac app and submitted to the App store as a free app. Mac users can also download the app from our website. 3DProIN is available for academic research at http://bicompute.appspot.com.

Racemic protein crystallography.

Science.gov (United States)

Yeates, Todd O; Kent, Stephen B H

2012-01-01

Although natural proteins are chiral and are all of one "handedness," their mirror image forms can be prepared by chemical synthesis. This opens up new opportunities for protein crystallography. A racemic mixture of the enantiomeric forms of a protein molecule can crystallize in ways that natural proteins cannot. Recent experimental data support a theoretical prediction that this should make racemic protein mixtures highly amenable to crystallization. Crystals obtained from racemic mixtures also offer advantages in structure determination strategies. The relevance of these potential advantages is heightened by advances in synthetic methods, which are extending the size limit for proteins that can be prepared by chemical synthesis. Recent ideas and results in the area of racemic protein crystallography are reviewed.

Modularity in protein structures: study on all-alpha proteins.

Science.gov (United States)

Khan, Taushif; Ghosh, Indira

2015-01-01

Modularity is known as one of the most important features of protein's robust and efficient design. The architecture and topology of proteins play a vital role by providing necessary robust scaffolds to support organism's growth and survival in constant evolutionary pressure. These complex biomolecules can be represented by several layers of modular architecture, but it is pivotal to understand and explore the smallest biologically relevant structural component. In the present study, we have developed a component-based method, using protein's secondary structures and their arrangements (i.e. patterns) in order to investigate its structural space. Our result on all-alpha protein shows that the known structural space is highly populated with limited set of structural patterns. We have also noticed that these frequently observed structural patterns are present as modules or "building blocks" in large proteins (i.e. higher secondary structure content). From structural descriptor analysis, observed patterns are found to be within similar deviation; however, frequent patterns are found to be distinctly occurring in diverse functions e.g. in enzymatic classes and reactions. In this study, we are introducing a simple approach to explore protein structural space using combinatorial- and graph-based geometry methods, which can be used to describe modularity in protein structures. Moreover, analysis indicates that protein function seems to be the driving force that shapes the known structure space.

Emergence of modularity and disassortativity in protein-protein interaction networks.

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Wan, Xi; Cai, Shuiming; Zhou, Jin; Liu, Zengrong

2010-12-01

In this paper, we present a simple evolution model of protein-protein interaction networks by introducing a rule of small-preference duplication of a node, meaning that the probability of a node chosen to duplicate is inversely proportional to its degree, and subsequent divergence plus nonuniform heterodimerization based on some plausible mechanisms in biology. We show that our model cannot only reproduce scale-free connectivity and small-world pattern, but also exhibit hierarchical modularity and disassortativity. After comparing the features of our model with those of real protein-protein interaction networks, we believe that our model can provide relevant insights into the mechanism underlying the evolution of protein-protein interaction networks. © 2010 American Institute of Physics.

HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy.

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Yan, Yumeng; Zhang, Di; Zhou, Pei; Li, Botong; Huang, Sheng-You

2017-07-03

Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein-protein and protein-DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10-20 min for a docking run. Tested on the cases with weakly homologous complexes of server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Aquaporin Protein-Protein Interactions

Directory of Open Access Journals (Sweden)

Jennifer Virginia Roche

2017-10-01

Full Text Available Aquaporins are tetrameric membrane-bound channels that facilitate transport of water and other small solutes across cell membranes. In eukaryotes, they are frequently regulated by gating or trafficking, allowing for the cell to control membrane permeability in a specific manner. Protein–protein interactions play crucial roles in both regulatory processes and also mediate alternative functions such as cell adhesion. In this review, we summarize recent knowledge about aquaporin protein–protein interactions; dividing the interactions into three types: (1 interactions between aquaporin tetramers; (2 interactions between aquaporin monomers within a tetramer (hetero-tetramerization; and (3 transient interactions with regulatory proteins. We particularly focus on the structural aspects of the interactions, discussing the small differences within a conserved overall fold that allow for aquaporins to be differentially regulated in an organism-, tissue- and trigger-specific manner. A deep knowledge about these differences is needed to fully understand aquaporin function and regulation in many physiological processes, and may enable design of compounds targeting specific aquaporins for treatment of human disease.

A method for investigating protein-protein interactions related to Salmonella typhimurium pathogenesis

Energy Technology Data Exchange (ETDEWEB)

Chowdhury, Saiful M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Shi, Liang [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Yoon, Hyunjin [Dartmouth College, Hanover, NH (United States); Ansong, Charles [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Rommereim, Leah M. [Dartmouth College, Hanover, NH (United States); Norbeck, Angela D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Auberry, Kenneth J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Moore, R. J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Adkins, Joshua N. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Heffron, Fred [Oregon Health and Science Univ., Portland, OR (United States); Smith, Richard D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2009-02-10

We successfully modified an existing method to investigate protein-protein interactions in the pathogenic bacterium Salmonella typhimurium (STM). This method includes i) addition of a histidine-biotin-histidine tag to the bait proteins via recombinant DNA techniques; ii) in vivo cross-linking with formaldehyde; iii) tandem affinity purification of bait proteins under fully denaturing conditions; and iv) identification of the proteins cross-linked to the bait proteins by liquid-chromatography in conjunction with tandem mass-spectrometry. In vivo cross-linking stabilized protein interactions permitted the subsequent two-step purification step conducted under denaturing conditions. The two-step purification greatly reduced nonspecific binding of non-cross-linked proteins to bait proteins. Two different negative controls were employed to reduce false-positive identification. In an initial demonstration of this approach, we tagged three selected STM proteins- HimD, PduB and PhoP- with known binding partners that ranged from stable (e.g., HimD) to transient (i.e., PhoP). Distinct sets of interacting proteins were identified with each bait protein, including the known binding partners such as HimA for HimD, as well as anticipated and unexpected binding partners. Our results suggest that novel protein-protein interactions may be critical to pathogenesis by Salmonella typhimurium. .

Exceptional heat stability of high protein content dispersions containing whey protein particles

NARCIS (Netherlands)

Saglam, D.; Venema, P.; Vries, de R.J.; Linden, van der E.

2014-01-01

Due to aggregation and/or gelation during thermal treatment, the amount of whey proteins that can be used in the formulation of high protein foods e.g. protein drinks, is limited. The aim of this study was to replace whey proteins with whey protein particles to increase the total protein content and

Directed Evolution of Proteins through In Vitro Protein Synthesis in Liposomes

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Takehiro Nishikawa

2012-01-01

Full Text Available Directed evolution of proteins is a technique used to modify protein functions through “Darwinian selection.” In vitro compartmentalization (IVC is an in vitro gene screening system for directed evolution of proteins. IVC establishes the link between genetic information (genotype and the protein translated from the information (phenotype, which is essential for all directed evolution methods, by encapsulating both in a nonliving microcompartment. Herein, we introduce a new liposome-based IVC system consisting of a liposome, the protein synthesis using recombinant elements (PURE system and a fluorescence-activated cell sorter (FACS used as a microcompartment, in vitro protein synthesis system, and high-throughput screen, respectively. Liposome-based IVC is characterized by in vitro protein synthesis from a single copy of a gene in a cell-sized unilamellar liposome and quantitative functional evaluation of the synthesized proteins. Examples of liposome-based IVC for screening proteins such as GFP and β-glucuronidase are described. We discuss the future directions for this method and its applications.

Categorizing Biases in High-Confidence High-Throughput Protein-Protein Interaction Data Sets*

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Yu, Xueping; Ivanic, Joseph; Memišević, Vesna; Wallqvist, Anders; Reifman, Jaques

2011-01-01

We characterized and evaluated the functional attributes of three yeast high-confidence protein-protein interaction data sets derived from affinity purification/mass spectrometry, protein-fragment complementation assay, and yeast two-hybrid experiments. The interacting proteins retrieved from these data sets formed distinct, partially overlapping sets with different protein-protein interaction characteristics. These differences were primarily a function of the deployed experimental technologies used to recover these interactions. This affected the total coverage of interactions and was especially evident in the recovery of interactions among different functional classes of proteins. We found that the interaction data obtained by the yeast two-hybrid method was the least biased toward any particular functional characterization. In contrast, interacting proteins in the affinity purification/mass spectrometry and protein-fragment complementation assay data sets were over- and under-represented among distinct and different functional categories. We delineated how these differences affected protein complex organization in the network of interactions, in particular for strongly interacting complexes (e.g. RNA and protein synthesis) versus weak and transient interacting complexes (e.g. protein transport). We quantified methodological differences in detecting protein interactions from larger protein complexes, in the correlation of protein abundance among interacting proteins, and in their connectivity of essential proteins. In the latter case, we showed that minimizing inherent methodology biases removed many of the ambiguous conclusions about protein essentiality and protein connectivity. We used these findings to rationalize how biological insights obtained by analyzing data sets originating from different sources sometimes do not agree or may even contradict each other. An important corollary of this work was that discrepancies in biological insights did not

With Protein Foods, Variety Is Key: 10 Tips for Choosing Protein

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... Dietary Guidelines Communicator’s Guide 10 Tips: Vary Your Protein Routine You are here Home 10 Tips: Vary ... Protein Routine Print Share 10 Tips: Vary Your Protein Routine Protein foods include both animal (meat, poultry, ...

Protein complex prediction based on k-connected subgraphs in protein interaction network

OpenAIRE

Habibi, Mahnaz; Eslahchi, Changiz; Wong, Limsoon

2010-01-01

Abstract Background Protein complexes play an important role in cellular mechanisms. Recently, several methods have been presented to predict protein complexes in a protein interaction network. In these methods, a protein complex is predicted as a dense subgraph of protein interactions. However, interactions data are incomplete and a protein complex does not have to be a complete or dense subgraph. Results We propose a more appropriate protein complex prediction method, CFA, that is based on ...

Karakteristik Protein dan Nitrogen Non Protein Daging Ikan Cucut Lanyam (Charcharhinus limbatus (Characteristics of Protein and Non Protein Nitrogen in Lanyam Shark Muscle

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Yuspihana Fitrial

2017-02-01

Based on protein solubility of Lanyam muscle at pH 1.5 to 12 obtained two points which is minimum solubility at pH 4.5 and pH 9. Based on the classification Osborn, Lanyam muscle contained albumin (28.64%, globulin (13:44%, prolamin (03.29%, glutelin (33.70%. Observation of non-protein nitrogen levels indicated that the washing process was very effective to reduce non-protein nitrogen levels up to 62.34% and urea levels up to 58% . Differential Scanning Calorimetry Study of Lanyam mince showed two types of protein that has a different stability to heat and after added 2.5% NaCl formed a peak which is a fusion of both these proteins

Protections Against Grid Breakdowns in the ITER Neutral Beam Injector Power Supplies

International Nuclear Information System (INIS)

Bigi, M.; Toigo, V.; Zanotto, L.

2006-01-01

The ITER Neutral Beam Injector (NBI) is designed to deliver 16.5 MW of additional heating power to the plasma, accelerating negative ions up to -1 MV with a current up to 40 A. Two main power supplies are foreseen to feed the system: the Acceleration Grid Power Supply (AGPS), which provides power to the acceleration grids, and the Ion Source Power Supply (ISPS), devoted to supplying the ion source components. For the accelerator, two different concepts are under investigation: the MAMuG (Multiple Aperture, Multiple Gap) and the SINGAP (SINgle Aperture). During operation of the NBI, the breakdown of the acceleration grids will occur regularly; as a consequence the AGPS is expected to experience frequent load short-circuits during a pulse. For each grid breakdown, energy and current peaks are delivered from the power supply systems that could damage the grids, if not limited. In previous NBI, rated for a lower accelerating voltage, the protection system in case of grid breakdowns was based on dc circuit breakers able to quickly disconnect the power supply from the grids. In the ITER case, a similar solution is not feasible, as the voltage level is too high for present dc breaker technology. Therefore, the protection strategy has to rely on fast switch-off of the power supplies, on the optimisation of the filter elements and core snubbers placed downstream the AGPS and on the introduction of additional passive elements. However, achieving a satisfactory protection against grid breakdowns is a challenging task, as the optimisation of each single provision can result in drawbacks for other aspects of the design; for instance, the optimisation of the filter elements, obtained by reducing the filter capacitance, produces an increase of the output voltage ripple. Therefore, the design of the protections must be carried out considering all the relevant aspects of the specifications, also those that are not strictly related to the limitations of the current peaks and energy

On the role of electrostatics on protein-protein interactions

Science.gov (United States)

Zhang, Zhe; Witham, Shawn; Alexov, Emil

2011-01-01

The role of electrostatics on protein-protein interactions and binding is reviewed in this article. A brief outline of the computational modeling, in the framework of continuum electrostatics, is presented and basic electrostatic effects occurring upon the formation of the complex are discussed. The role of the salt concentration and pH of the water phase on protein-protein binding free energy is demonstrated and indicates that the increase of the salt concentration tends to weaken the binding, an observation that is attributed to the optimization of the charge-charge interactions across the interface. It is pointed out that the pH-optimum (pH of optimal binding affinity) varies among the protein-protein complexes, and perhaps is a result of their adaptation to particular subcellular compartment. At the end, the similarities and differences between hetero- and homo-complexes are outlined and discussed with respect to the binding mode and charge complementarity. PMID:21572182

Tragacanth Gum: Structural Composition, Natural Functionality and Enxymatic Conversion as Source of Potential Prebiotic Activity

DEFF Research Database (Denmark)

Ahmadi Gavlighi, Hassan

very high viscosities when in aqueous solution, and is described as a complex, highly branched, heterogeneous hydrophilic polysaccharide. The gum contains pectinaceous arabinogalactans and fucose-substituted xylogalacturonans. The objective of this PhD study were to evaluate tragacanth samples from six...... and fractionated by centrifugation to soluble and insoluble. To examine correlation between composition structure, sugar composition and methoxyl and acetyl content was determined. The six gum samples varied with respect totheir levels and ratios of water-soluble and water-swellable fractions, their monosaccharide...

Synthesis of branched–backbone oligosaccharides of the pectic RG-I plant cell wall polysaccharide

DEFF Research Database (Denmark)

Awan, Shahid Iqbal; Clausen, Mads Hartvig

with numerous branches of galactan, arabinan, or arabinogalactan positioned at C-4 of the rhamnose residues. The use of defined oligosaccharides rather than isolated polysaccharides can aid in obtaining detailedinformation about biosynthetic pathways, plant evolution, and agronomical properties. Furthermore......,biological testing can provide new insight into plant biology; important for plant preservation, engineering,and utilization of plants as a source of bioenergy. Present work towards defined RG-I substructures involvesa [4+3]-coupling to furnish a heptasaccharide backbone unit (see Figure 1). Moreover, installation...

PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs

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Greenblatt Jack

2006-07-01

Full Text Available Abstract Background Identification of protein interaction networks has received considerable attention in the post-genomic era. The currently available biochemical approaches used to detect protein-protein interactions are all time and labour intensive. Consequently there is a growing need for the development of computational tools that are capable of effectively identifying such interactions. Results Here we explain the development and implementation of a novel Protein-Protein Interaction Prediction Engine termed PIPE. This tool is capable of predicting protein-protein interactions for any target pair of the yeast Saccharomyces cerevisiae proteins from their primary structure and without the need for any additional information or predictions about the proteins. PIPE showed a sensitivity of 61% for detecting any yeast protein interaction with 89% specificity and an overall accuracy of 75%. This rate of success is comparable to those associated with the most commonly used biochemical techniques. Using PIPE, we identified a novel interaction between YGL227W (vid30 and YMR135C (gid8 yeast proteins. This lead us to the identification of a novel yeast complex that here we term vid30 complex (vid30c. The observed interaction was confirmed by tandem affinity purification (TAP tag, verifying the ability of PIPE to predict novel protein-protein interactions. We then used PIPE analysis to investigate the internal architecture of vid30c. It appeared from PIPE analysis that vid30c may consist of a core and a secondary component. Generation of yeast gene deletion strains combined with TAP tagging analysis indicated that the deletion of a member of the core component interfered with the formation of vid30c, however, deletion of a member of the secondary component had little effect (if any on the formation of vid30c. Also, PIPE can be used to analyse yeast proteins for which TAP tagging fails, thereby allowing us to predict protein interactions that are not

Consumption of Milk Protein or Whey Protein Results in a Similar Increase in Muscle Protein Synthesis in Middle Aged Men.

Science.gov (United States)

Mitchell, Cameron J; McGregor, Robin A; D'Souza, Randall F; Thorstensen, Eric B; Markworth, James F; Fanning, Aaron C; Poppitt, Sally D; Cameron-Smith, David

2015-10-21

The differential ability of various milk protein fractions to stimulate muscle protein synthesis (MPS) has been previously described, with whey protein generally considered to be superior to other fractions. However, the relative ability of a whole milk protein to stimulate MPS has not been compared to whey. Sixteen healthy middle-aged males ingested either 20 g of milk protein (n = 8) or whey protein (n = 8) while undergoing a primed constant infusion of ring (13)C₆ phenylalanine. Muscle biopsies were obtained 120 min prior to consumption of the protein and 90 and 210 min afterwards. Resting myofibrillar fractional synthetic rates (FSR) were 0.019% ± 0.009% and 0.021% ± 0.018% h(-1) in the milk and whey groups respectively. For the first 90 min after protein ingestion the FSR increased (p whey groups respectively with no difference between groups (p = 0.810). FSR returned to baseline in both groups between 90 and 210 min after protein ingestion. Despite evidence of increased rate of digestion and leucine availability following the ingestion of whey protein, there was similar activation of MPS in middle-aged men with either 20 g of milk protein or whey protein.

Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes.

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Nillegoda, Nadinath B; Stank, Antonia; Malinverni, Duccio; Alberts, Niels; Szlachcic, Anna; Barducci, Alessandro; De Los Rios, Paolo; Wade, Rebecca C; Bukau, Bernd

2017-05-15

Hsp70 participates in a broad spectrum of protein folding processes extending from nascent chain folding to protein disaggregation. This versatility in function is achieved through a diverse family of J-protein cochaperones that select substrates for Hsp70. Substrate selection is further tuned by transient complexation between different classes of J-proteins, which expands the range of protein aggregates targeted by metazoan Hsp70 for disaggregation. We assessed the prevalence and evolutionary conservation of J-protein complexation and cooperation in disaggregation. We find the emergence of a eukaryote-specific signature for interclass complexation of canonical J-proteins. Consistently, complexes exist in yeast and human cells, but not in bacteria, and correlate with cooperative action in disaggregation in vitro. Signature alterations exclude some J-proteins from networking, which ensures correct J-protein pairing, functional network integrity and J-protein specialization. This fundamental change in J-protein biology during the prokaryote-to-eukaryote transition allows for increased fine-tuning and broadening of Hsp70 function in eukaryotes.

Globular and disordered-the non-identical twins in protein-protein interactions

DEFF Research Database (Denmark)

Teilum, Kaare; Olsen, Johan Gotthardt; Kragelund, Birthe Brandt

2015-01-01

as a strong determinant for their function. This has fostered the notion that IDP's bind with low affinity but high specificity. Here we have analyzed available detailed thermodynamic data for protein-protein interactions to put to the test if the thermodynamic profiles of IDP interactions differ from those...... of other protein-protein interactions. We find that ordered proteins and the disordered ones act as non-identical twins operating by similar principles but where the disordered proteins complexes are on average less stable by 2.5 kcal mol(-1)....

Neuromuscular electrical stimulation prior to presleep protein feeding stimulates the use of protein-derived amino acids for overnight muscle protein synthesis.

Science.gov (United States)

Dirks, Marlou L; Groen, Bart B L; Franssen, Rinske; van Kranenburg, Janneau; van Loon, Luc J C

2017-01-01

Short periods of muscle disuse result in substantial skeletal muscle atrophy. Recently, we showed that both neuromuscular electrical stimulation (NMES) as well as presleep dietary protein ingestion represent effective strategies to stimulate muscle protein synthesis rates. In this study, we test our hypothesis that NMES can augment the use of presleep protein-derived amino acids for overnight muscle protein synthesis in older men. Twenty healthy, older [69 ± 1 (SE) yr] men were subjected to 24 h of bed rest, starting at 8:00 AM. In the evening, volunteers were subjected to 70-min 1-legged NMES, while the other leg served as nonstimulated control (CON). Immediately following NMES, 40 g of intrinsically l-[1- 13 C]-phenylalanine labeled protein was ingested prior to sleep. Blood samples were taken throughout the night, and muscle biopsies were obtained from both legs in the evening and the following morning (8 h after protein ingestion) to assess dietary protein-derived l-[1- 13 C]-phenylalanine enrichments in myofibrillar protein. Plasma phenylalanine concentrations and plasma l-[1- 13 C]-phenylalanine enrichments increased significantly following protein ingestion and remained elevated for up to 6 h after protein ingestion (P protein-bound l-[1- 13 C]-phenylalanine enrichments (MPE) increased to a greater extent in the stimulated compared with the control leg (0.0344 ± 0.0019 vs. 0.0297 ± 0.0016 MPE, respectively; P protein-derived amino acids in the NMES compared with CON leg. In conclusion, application of NMES prior to presleep protein feeding stimulates the use of dietary protein-derived amino acids for overnight muscle protein synthesis in older men. Neuromuscular electrical stimulation (NMES) as well as presleep dietary protein ingestion represent effective strategies to stimulate muscle protein synthesis rates. Here we demonstrate that in older men after a day of bed rest, the application of NMES prior to presleep protein feeding stimulates the use of

A computational tool to predict the evolutionarily conserved protein-protein interaction hot-spot residues from the structure of the unbound protein.

Science.gov (United States)

Agrawal, Neeraj J; Helk, Bernhard; Trout, Bernhardt L

2014-01-21

Identifying hot-spot residues - residues that are critical to protein-protein binding - can help to elucidate a protein's function and assist in designing therapeutic molecules to target those residues. We present a novel computational tool, termed spatial-interaction-map (SIM), to predict the hot-spot residues of an evolutionarily conserved protein-protein interaction from the structure of an unbound protein alone. SIM can predict the protein hot-spot residues with an accuracy of 36-57%. Thus, the SIM tool can be used to predict the yet unknown hot-spot residues for many proteins for which the structure of the protein-protein complexes are not available, thereby providing a clue to their functions and an opportunity to design therapeutic molecules to target these proteins. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

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

KAUST Repository

Wang, Jim Jing-Yan; Gao, Xin; Wang, Quanquan; Li, Yongping

2012-01-01

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

Current strategies for protein production and purification enabling membrane protein structural biology.

Science.gov (United States)

Pandey, Aditya; Shin, Kyungsoo; Patterson, Robin E; Liu, Xiang-Qin; Rainey, Jan K

2016-12-01

Membrane proteins are still heavily under-represented in the protein data bank (PDB), owing to multiple bottlenecks. The typical low abundance of membrane proteins in their natural hosts makes it necessary to overexpress these proteins either in heterologous systems or through in vitro translation/cell-free expression. Heterologous expression of proteins, in turn, leads to multiple obstacles, owing to the unpredictability of compatibility of the target protein for expression in a given host. The highly hydrophobic and (or) amphipathic nature of membrane proteins also leads to challenges in producing a homogeneous, stable, and pure sample for structural studies. Circumventing these hurdles has become possible through the introduction of novel protein production protocols; efficient protein isolation and sample preparation methods; and, improvement in hardware and software for structural characterization. Combined, these advances have made the past 10-15 years very exciting and eventful for the field of membrane protein structural biology, with an exponential growth in the number of solved membrane protein structures. In this review, we focus on both the advances and diversity of protein production and purification methods that have allowed this growth in structural knowledge of membrane proteins through X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).

Fragment-based quantum mechanical calculation of protein-protein binding affinities.

Science.gov (United States)

Wang, Yaqian; Liu, Jinfeng; Li, Jinjin; He, Xiao

2018-04-29

The electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method has been successfully utilized for efficient linear-scaling quantum mechanical (QM) calculation of protein energies. In this work, we applied the EE-GMFCC method for calculation of binding affinity of Endonuclease colicin-immunity protein complex. The binding free energy changes between the wild-type and mutants of the complex calculated by EE-GMFCC are in good agreement with experimental results. The correlation coefficient (R) between the predicted binding energy changes and experimental values is 0.906 at the B3LYP/6-31G*-D level, based on the snapshot whose binding affinity is closest to the average result from the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) calculation. The inclusion of the QM effects is important for accurate prediction of protein-protein binding affinities. Moreover, the self-consistent calculation of PB solvation energy is required for accurate calculations of protein-protein binding free energies. This study demonstrates that the EE-GMFCC method is capable of providing reliable prediction of relative binding affinities for protein-protein complexes. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

PROTEIN FRACTIONS AND IN VITRO FERMENTATION OF PROTEIN FEEDS FOR RUMINANTS

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Angel L. Guevara-Mesa

2011-05-01

Full Text Available The objective of this study was to evaluate 20 protein feeds grouped in forages, vegetal by- products and animal by-products used for ruminant diets. Protein fractions (PF: A, non-protein nitrogen (NPN; B1, buffer-soluble protein; B2, buffer-insoluble, NDF-soluble protein; B3, NDF-insoluble, ADF-soluble protein; and C, ADF-insoluble protein, were determined for each ingredient.  Protein composition was correlated with total gas production in vitro (GP, gas production rate (S, lag time (L, DM disappearance (DMDIV and residual protein (RPIV. The completely randomised designed was analysed using mixed proc. and Tukey contrasts. Forages contained 18.29, 7.86, 66.00, 2.96, 4.89% of fractions A, B1, B2, B3 and C, respectively. Vegetable by-products contained 22.55, 4.55, 59.51, 8.84, 4.55% of each fraction, in the same order. Animal by-products contained 19.13, 4.52, 70.24, 3.74, 2.37% of each fraction, in the same order. Vetch, wheat bran and poultry litter had the greatest Vmax in each group. Vmax was correlated (P≤0.01 with total protein (r = -0.45, ADF (r = 0.27 and DMDIV (r = 0.61. In conclusion, there were differences in protein composition and kinetics of in vitro gas production among ingredients.

Selection of peptides interfering with protein-protein interaction.

Science.gov (United States)

Gaida, Annette; Hagemann, Urs B; Mattay, Dinah; Räuber, Christina; Müller, Kristian M; Arndt, Katja M

2009-01-01

Cell physiology depends on a fine-tuned network of protein-protein interactions, and misguided interactions are often associated with various diseases. Consequently, peptides, which are able to specifically interfere with such adventitious interactions, are of high interest for analytical as well as medical purposes. One of the most abundant protein interaction domains is the coiled-coil motif, and thus provides a premier target. Coiled coils, which consist of two or more alpha-helices wrapped around each other, have one of the simplest interaction interfaces, yet they are able to confer highly specific homo- and heterotypic interactions involved in virtually any cellular process. While there are several ways to generate interfering peptides, the combination of library design with a powerful selection system seems to be one of the most effective and promising approaches. This chapter guides through all steps of such a process, starting with library options and cloning, detailing suitable selection techniques and ending with purification for further down-stream characterization. Such generated peptides will function as versatile tools to interfere with the natural function of their targets thereby illuminating their down-stream signaling and, in general, promoting understanding of factors leading to specificity and stability in protein-protein interactions. Furthermore, peptides interfering with medically relevant proteins might become important diagnostics and therapeutics.

Phthalic Acid Chemical Probes Synthesized for Protein-Protein Interaction Analysis

Directory of Open Access Journals (Sweden)

Chin-Jen Wu

2013-06-01

Full Text Available Plasticizers are additives that are used to increase the flexibility of plastic during manufacturing. However, in injection molding processes, plasticizers cannot be generated with monomers because they can peel off from the plastics into the surrounding environment, water, or food, or become attached to skin. Among the various plasticizers that are used, 1,2-benzenedicarboxylic acid (phthalic acid is a typical precursor to generate phthalates. In addition, phthalic acid is a metabolite of diethylhexyl phthalate (DEHP. According to Gene_Ontology gene/protein database, phthalates can cause genital diseases, cardiotoxicity, hepatotoxicity, nephrotoxicity, etc. In this study, a silanized linker (3-aminopropyl triethoxyslane, APTES was deposited on silicon dioxides (SiO2 particles and phthalate chemical probes were manufactured from phthalic acid and APTES–SiO2. These probes could be used for detecting proteins that targeted phthalic acid and for protein-protein interactions. The phthalic acid chemical probes we produced were incubated with epithelioid cell lysates of normal rat kidney (NRK-52E cells to detect the interactions between phthalic acid and NRK-52E extracted proteins. These chemical probes interacted with a number of chaperones such as protein disulfide-isomerase A6, heat shock proteins, and Serpin H1. Ingenuity Pathways Analysis (IPA software showed that these chemical probes were a practical technique for protein-protein interaction analysis.

Protein-protein docking using region-based 3D Zernike descriptors.