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Article ; Online: Digging deep—implementation, standardisation and interpretation of a total oxidisable precursor (TOP) assay within the regulatory context of per- and polyfluoroalkyl substances (PFASs) in soil

Göckener, Bernd / Lange, Frank Thomas / Lesmeister, Lukas / Gökçe, Emine / Dahme, Hans Ulrich / Bandow, Nicole / Biegel-Engler, Annegret

Environ Sci Eur. 2022 Dec., v. 34, no. 1 p.52-52

2022

Abstract: Over the past decades, thousands of different per- and polyfluoroalkyl substances (PFASs) have been produced and applied in various industrial processes and consumer products. Their structural diversity has reached a level that cannot be covered by ... ...

Abstract	Over the past decades, thousands of different per- and polyfluoroalkyl substances (PFASs) have been produced and applied in various industrial processes and consumer products. Their structural diversity has reached a level that cannot be covered by classical target screening methods for individual compounds. Large-scale contaminations of soil, however, require the need to adapt new analytical methods that can describe a contamination more comprehensively. While sum parameters such as the total oxidisable precursor (TOP) assay have been developed in the past years, they are not yet applied in the regulatory context of PFASs.In this commentary, we provide an overview on different approaches of the TOP assay as well as its benefits and disadvantages to other sum parameters for PFASs in soil samples. Furthermore, we elaborate its opportunities and its challenges that need to be tackled to implement the TOP assay as a regulatory tool. With several different approaches of the TOP assay being available, a sound and standardised method needs to be agreed upon and more research is necessary to better describe the method. Although the complexity of PFAS contaminations in soil cannot be fully covered by any analytical method alone, the TOP assay can provide valuable data to detect and characterise soil contamination as an inventory for subsequent remediation measures. Therefore, the TOP assay should be implemented as a useful tool both in research and in the regulatory context of PFASs.
Keywords	analytical methods ; inventories ; remediation ; soil ; soil pollution ; Europe
Language	English
Dates of publication	2022-12
Size	p. 52.
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
Note	Letter
ZDB-ID	2593962-2
ISSN	2190-4715 ; 2190-4707
ISSN (online)	2190-4715
ISSN	2190-4707
DOI	10.1186/s12302-022-00631-1
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The Effect of Distant Reiki Sessions on Holistic Well-Being.

Özcan Yüce, Ulviye / Arpacı, Afey / Kütmeç Yılmaz, Cemile / Yurtsever, Dilek / Üstün Gökçe, Emine / Burkev, Fatma Gönül / Yıldırım, Gülcihan / Gökşin, İlknur / Ünal Aslan, Kevser Sevgi / Bektaş Akpınar, Nilay / Altınbaş Akkaş, Özlem / Yurtsever, Sabire

Holistic nursing practice

2022 Volume 38, Issue 1, Page(s) 50–57

Abstract: This study investigated the effect of distant Reiki sessions on the holistic well-being of people without no acute/chronic diseases. The study was conducted between February 1 and March 31, 2022. The sample consisted of 180 healthy people living in a ... ...

Abstract	This study investigated the effect of distant Reiki sessions on the holistic well-being of people without no acute/chronic diseases. The study was conducted between February 1 and March 31, 2022. The sample consisted of 180 healthy people living in a city in Turkey. Participants attended 20-minute distant Reiki sessions (intervention) for 4 consecutive days. Pretest data were collected using a personal information form, the Holistic Well-Being Scale (HWBS), the Positive and Negative Affect Schedule (PANAS), and the Subjective Vitality Scale (SVS). Posttest data were collected 2 days (posttest I) and 1 week after the intervention (posttest II) using the HWBS, PANAS, and SVS. There was a statistically significant difference between pretest and posttest I and II HWBS subscale scores ( P < .05). There was a statistically significant difference between pretest and posttest PANAS and SVS scores ( P < .05). Distant Reiki sessions improved participants' holistic well-being. They also helped them develop a positive mood, experience and perceive less sadness, and develop subjective vitality and cognitive awareness.
MeSH term(s)	Humans ; Therapeutic Touch ; Affect ; Health Status ; Turkey
Language	English
Publishing date	2022-10-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	639032-8
ISSN	1550-5138 ; 0887-9311
ISSN (online)	1550-5138
ISSN	0887-9311
DOI	10.1097/HNP.0000000000000557
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Article ; Online: How persistent microbubbles shield nanoparticle productivity in laser synthesis of colloids - quantification of their volume, dwell dynamics, and gas composition.

Kalus, Mark-Robert / Bärsch, Niko / Streubel, René / Gökce, Emine / Barcikowski, Stephan / Gökce, Bilal

Physical chemistry chemical physics : PCCP

2017 Volume 19, Issue 10, Page(s) 7112–7123

Abstract: During laser synthesis of colloids, cavitation bubbles with lifetimes in the microsecond-scale form and shield the laser pulse leading to a decrease in nanoparticle output. A second type of productivity-limiting bubble that severely affects the ... ...

Abstract	During laser synthesis of colloids, cavitation bubbles with lifetimes in the microsecond-scale form and shield the laser pulse leading to a decrease in nanoparticle output. A second type of productivity-limiting bubble that severely affects the productivity of the process is often neglected. With lifetimes from milliseconds to seconds, these persistent bubbles are systematically studied in this work by quantifying their composition, amount, size and dwell time in liquids with different viscosities and by relating the results to the nanoparticle productivities. It is found that during synthesis in water, water splitting occurs leading to persistent bubbles consisting of hydrogen and oxygen. In glycols, hydrogen and molecular carbon species containing microbubbles are formed. These persistent microbubbles shield up to 65% of the incoming laser beam depending on the liquid as well as the laser fluence and require attention by means of reducing their dwell time in the ablation zone and enhancing the nanoparticle output by liquid flow. The highest productivities and monodisperse quality are achieved in liquids with the lowest viscosities.
Language	English
Publishing date	2017-03-08
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/c6cp07011f
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Article: Phosphoproteome Analysis Links Protein Phosphorylation to Cellular Remodeling and Metabolic Adaptation during Magnaporthe oryzae Appressorium Development

Franck, WilliamL / Gokce Emine / Randall Shan M / Oh Yeonyee / Eyre Alex / Muddiman David C / Dean Ralph A

Journal of Proteome Research. 2015 June 05, v. 14, no. 6

2015

Abstract: The rice pathogen, Magnaporthe oryzae, undergoes a complex developmental process leading to formation of an appressorium prior to plant infection. In an effort to better understand phosphoregulation during appressorium development, a mass spectrometry ... ...

Abstract	The rice pathogen, Magnaporthe oryzae, undergoes a complex developmental process leading to formation of an appressorium prior to plant infection. In an effort to better understand phosphoregulation during appressorium development, a mass spectrometry based phosphoproteomics study was undertaken. A total of 2924 class I phosphosites were identified from 1514 phosphoproteins from mycelia, conidia, germlings, and appressoria of the wild type and a protein kinase A (PKA) mutant. Phosphoregulation during appressorium development was observed for 448 phosphosites on 320 phosphoproteins. In addition, a set of candidate PKA targets was identified encompassing 253 phosphosites on 227 phosphoproteins. Network analysis incorporating regulation from transcriptomic, proteomic, and phosphoproteomic data revealed new insights into the regulation of the metabolism of conidial storage reserves and phospholipids, autophagy, actin dynamics, and cell wall metabolism during appressorium formation. In particular, protein phosphorylation appears to play a central role in the regulation of autophagic recycling and actin dynamics during appressorium formation. Changes in phosphorylation were observed in multiple components of the cell wall integrity pathway providing evidence that this pathway is highly active during appressorium development. Several transcription factors were phosphoregulated during appressorium formation including the bHLH domain transcription factor MGG_05709. Functional analysis of MGG_05709 provided further evidence for the role of protein phosphorylation in regulation of glycerol metabolism and the metabolic reprogramming characteristic of appressorium formation. The data presented here represent a comprehensive investigation of the M. oryzae phosphoproteome and provide key insights on the role of protein phosphorylation during infection-related development.
Keywords	Magnaporthe oryzae ; actin ; appressoria ; autophagy ; cAMP-dependent protein kinase ; cell walls ; conidia ; glycerol ; mass spectrometry ; metabolism ; mutants ; mycelium ; pathogens ; phospholipids ; phosphoproteins ; protein phosphorylation ; proteome ; proteomics ; rice ; transcription (genetics) ; transcription factors ; transcriptomics
Language	English
Dates of publication	2015-0605
Size	p. 2408-2424.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021%2Fpr501064q
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Article ; Online: Increasing proteome coverage with offline RP HPLC coupled to online RP nanoLC-MS.

Gokce, Emine / Andrews, Genna L / Dean, Ralph A / Muddiman, David C

Journal of chromatography. B, Analytical technologies in the biomedical and life sciences

2011 Volume 879, Issue 9-10, Page(s) 610–614

Abstract: Fractionation prior to mass spectrometry is an indispensable step in proteomics. In this paper we report the success of performing offline reversed phase high pressure liquid chromatography (HPLC) fractionation on a C18 2.0 mm×150 mm column at the ... ...

Abstract	Fractionation prior to mass spectrometry is an indispensable step in proteomics. In this paper we report the success of performing offline reversed phase high pressure liquid chromatography (HPLC) fractionation on a C18 2.0 mm×150 mm column at the peptide level with microliter per minute flow rates prior to online nano-flow reversed phase liquid chromatography mass spectrometry (nanoLC-MS) using the well-studied fungus Saccharomyces cerevisiae. A C18 75 μm×150 mm column was used online and the online elution gradients for each fraction were adjusted in order to obtain well resolved separation. Comparing this method directly to only performing nanoLC-MS we observed a 61.6% increase in the number of identified proteins. At a 1% false discovery rate 1028 proteins were identified using two dimensions of RPLC versus 636 proteins identified in a single nano-flow separation. The majority of proteins identified by one dimension of nano-LC were present in the proteins identified in our two dimensional strategy. Although increasing analysis time, this non-orthogonal and facile pre-fractionation method affords a more comprehensive examination of the proteome.
MeSH term(s)	Chromatography, High Pressure Liquid/methods ; Chromatography, Reverse-Phase/methods ; Mass Spectrometry/methods ; Nanotechnology ; Peptide Fragments/analysis ; Peptide Fragments/metabolism ; Proteome/analysis ; Proteome/metabolism ; Proteomics/methods ; Saccharomyces cerevisiae Proteins/analysis ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	Peptide Fragments ; Proteome ; Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2011-02-04
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1180823-8
ISSN	1873-376X ; 0378-4347 ; 1570-0232 ; 1387-2273
ISSN (online)	1873-376X
ISSN	0378-4347 ; 1570-0232 ; 1387-2273
DOI	10.1016/j.jchromb.2011.01.032
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Article: In-Depth Analysis of the Magnaporthe oryzae Conidial Proteome

Gokce, Emine / Franck, William L / Oh, Yeonyee / Dean, RalphA / Muddiman, David C

Journal of Proteome Research. 2012 Dec. 07, v. 11, no. 12

2012

Abstract: The filamentous fungus Magnaporthe oryzae (M. oryzae) is the causative agent of rice blast disease and presents a significant threat to worldwide rice production. To establish the groundwork for future research on the pathogenic development of M. oryzae, ...

Abstract	The filamentous fungus Magnaporthe oryzae (M. oryzae) is the causative agent of rice blast disease and presents a significant threat to worldwide rice production. To establish the groundwork for future research on the pathogenic development of M. oryzae, a global proteomic study of conidia was performed. The filter aided sample preparation method (FASP) and anion StageTip fractionation combined with long, optimized shallow 210 min nanoLC gradients prior to mass spectrometry analysis on an Orbitrap XL was applied, which resulted in a doubling of protein identifications in comparison to our previous GeLC analysis. Herein, we report the identification of 2912 conidial proteins at a 1% protein false discovery rate (FDR) and we present the most extensive study performed on M. oryzae conidia to date. A similar distribution between identified proteins and the predicted proteome was observed when subcellular localization analysis was performed, suggesting the detected proteins build a representative portion of the predicted proteome. A higher percentage of cytoplasmic proteins (associated with translation, energy, and metabolism) were observed in the conidial proteome relative to the whole predicted proteome. Conversely, nuclear and extracellular proteins were less well represented in the conidial proteome. Further analysis by gene ontology revealed biological insights into identified proteins important for central metabolic processes and the physiology of conidia.
Keywords	Magnaporthe oryzae ; blast disease ; conidia ; crop production ; energy ; fractionation ; fungi ; gene ontology ; mass spectrometry ; metabolism ; protein content ; proteins ; proteome ; proteomics ; translation (genetics)
Language	English
Dates of publication	2012-1207
Size	p. 5827-5835.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021%2Fpr300604s
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Article ; Online: Temporal analysis of the magnaporthe oryzae proteome during conidial germination and cyclic AMP (cAMP)-mediated appressorium formation.

Franck, William L / Gokce, Emine / Oh, Yeonyee / Muddiman, David C / Dean, Ralph A

Molecular & cellular proteomics : MCP

2013 Volume 12, Issue 8, Page(s) 2249–2265

Abstract: Rice blast disease caused by Magnaporthe oryzae is one of the most serious threats to global rice production. During the earliest stages of rice infection, M. oryzae conidia germinate on the leaf surface and form a specialized infection structure termed ... ...

Abstract	Rice blast disease caused by Magnaporthe oryzae is one of the most serious threats to global rice production. During the earliest stages of rice infection, M. oryzae conidia germinate on the leaf surface and form a specialized infection structure termed the appressorium. The development of the appressorium represents the first critical stage of infectious development. A total of 3200 unique proteins were identified by nanoLC-MS/MS in a temporal study of conidial germination and cAMP-induced appressorium formation in M. oryzae. Using spectral counting based label free quantification, observed changes in relative protein abundance during the developmental process revealed changes in the cell wall biosynthetic machinery, transport functions, and production of extracellular proteins in developing appressoria. One hundred and sixty-six up-regulated and 208 down-regulated proteins were identified in response to cAMP treatment. Proteomic analysis of a cAMP-dependent protein kinase A mutant that is compromised in the ability to form appressoria identified proteins whose developmental regulation is dependent on cAMP signaling. Selected reaction monitoring was used for absolute quantification of four regulated proteins to validate the global proteomics data and confirmed the germination or appressorium specific regulation of these proteins. Finally, a comparison of the proteome and transcriptome was performed and revealed little correlation between transcript and protein regulation. A subset of regulated proteins were identified whose transcripts show similar regulation patterns and include many of the most strongly regulated proteins indicating a central role in appressorium formation. A temporal quantitative RT-PCR analysis confirmed a strong correlation between transcript and protein abundance for some but not all genes. Collectively, the data presented here provide the first comprehensive view of the M. oryzae proteome during early infection-related development and highlight biological processes important for pathogenicity.
MeSH term(s)	Cyclic AMP/metabolism ; Fungal Proteins/metabolism ; Magnaporthe/growth & development ; Magnaporthe/metabolism ; Mitochondrial Proteins/metabolism ; Peptide Hydrolases/metabolism ; Proteome ; Spores, Fungal/growth & development ; Spores, Fungal/metabolism
Chemical Substances	Fungal Proteins ; Mitochondrial Proteins ; Proteome ; Cyclic AMP (E0399OZS9N) ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2013-05-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1074/mcp.M112.025874
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Article: Increasing proteome coverage with offline RP HPLC coupled to online RP nanoLC–MS

Gokce, Emine / Andrews, Genna L / Dean, Ralph A / Muddiman, David C

Journal of chromatography. 2011 Mar. 15, v. 879, no. 9-10

2011

Abstract	Fractionation prior to mass spectrometry is an indispensable step in proteomics. In this paper we report the success of performing offline reversed phase high pressure liquid chromatography (HPLC) fractionation on a C18 2.0mm×150mm column at the peptide level with microliter per minute flow rates prior to online nano-flow reversed phase liquid chromatography mass spectrometry (nanoLC–MS) using the well-studied fungus Saccharomyces cerevisiae. A C18 75μm×150mm column was used online and the online elution gradients for each fraction were adjusted in order to obtain well resolved separation. Comparing this method directly to only performing nanoLC–MS we observed a 61.6% increase in the number of identified proteins. At a 1% false discovery rate 1028 proteins were identified using two dimensions of RPLC versus 636 proteins identified in a single nano-flow separation. The majority of proteins identified by one dimension of nano-LC were present in the proteins identified in our two dimensional strategy. Although increasing analysis time, this non-orthogonal and facile pre-fractionation method affords a more comprehensive examination of the proteome.
Keywords	Saccharomyces cerevisiae ; fractionation ; fungal proteins ; mass spectrometry ; proteome ; proteomics ; reversed-phase high performance liquid chromatography ; reversed-phase liquid chromatography
Language	English
Dates of publication	2011-0315
Size	p. 610-614.
Publishing place	Elsevier B.V.
Document type	Article
ISSN	1570-0232
DOI	10.1016/j.jchromb.2011.01.032
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Article: Comparative Proteomic Analysis and IgE Binding Properties of Peanut Seed and Testa (Skin)

White, Brittany L / Gökce, Emine / Nepomuceno, Angeliot I / Muddiman, David C / Sanders, Timothy H / Davis, Jack P

Journal of agricultural and food chemistry. 2013 Apr. 24, v. 61, no. 16

2013

Abstract: To investigate the protein composition and potential allergenicity of peanut testae or skins, proteome analysis was conducted using nanoLC-MS/MS sequencing. Initial amino acid analysis suggested differences in protein compositions between the blanched ... ...

Abstract	To investigate the protein composition and potential allergenicity of peanut testae or skins, proteome analysis was conducted using nanoLC-MS/MS sequencing. Initial amino acid analysis suggested differences in protein compositions between the blanched seed (skins removed) and skin. Phenolic compounds hindered analysis of proteins in skins when the conventional extraction method was used; therefore, phenol extraction of proteins was necessary. A total of 123 proteins were identified in blanched seed and skins, and 83 of the proteins were common between the two structures. The skins contained all of the known peanut allergens in addition to 38 proteins not identified in the seed. Multiple defense proteins with antifungal activity were identified in the skins. Western blotting using sera from peanut-allergic patients revealed that proteins extracted from both the blanched seed and skin bound significant levels of IgE. However, when phenolic compounds were present in the skin protein extract, no IgE binding was observed. These findings indicate that peanut skins contain potentially allergenic proteins; however, the presence of phenolic compounds may attenuate this effect.
Keywords	Western blotting ; allergens ; amino acid composition ; antifungal properties ; antifungal proteins ; binding properties ; immunoglobulin E ; peanuts ; phenol ; proteomics ; testa
Language	English
Size	p. 3957-3968.
Document type	Article
ZDB-ID	241619-0
ISSN	1520-5118 ; 0021-8561
ISSN (online)	1520-5118
ISSN	0021-8561
DOI	10.1021/jf400184y
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Article ; Online: Phosphoproteome Analysis Links Protein Phosphorylation to Cellular Remodeling and Metabolic Adaptation during Magnaporthe oryzae Appressorium Development.

Franck, William L / Gokce, Emine / Randall, Shan M / Oh, Yeonyee / Eyre, Alex / Muddiman, David C / Dean, Ralph A

Journal of proteome research

2015 Volume 14, Issue 6, Page(s) 2408–2424

Abstract	The rice pathogen, Magnaporthe oryzae, undergoes a complex developmental process leading to formation of an appressorium prior to plant infection. In an effort to better understand phosphoregulation during appressorium development, a mass spectrometry based phosphoproteomics study was undertaken. A total of 2924 class I phosphosites were identified from 1514 phosphoproteins from mycelia, conidia, germlings, and appressoria of the wild type and a protein kinase A (PKA) mutant. Phosphoregulation during appressorium development was observed for 448 phosphosites on 320 phosphoproteins. In addition, a set of candidate PKA targets was identified encompassing 253 phosphosites on 227 phosphoproteins. Network analysis incorporating regulation from transcriptomic, proteomic, and phosphoproteomic data revealed new insights into the regulation of the metabolism of conidial storage reserves and phospholipids, autophagy, actin dynamics, and cell wall metabolism during appressorium formation. In particular, protein phosphorylation appears to play a central role in the regulation of autophagic recycling and actin dynamics during appressorium formation. Changes in phosphorylation were observed in multiple components of the cell wall integrity pathway providing evidence that this pathway is highly active during appressorium development. Several transcription factors were phosphoregulated during appressorium formation including the bHLH domain transcription factor MGG_05709. Functional analysis of MGG_05709 provided further evidence for the role of protein phosphorylation in regulation of glycerol metabolism and the metabolic reprogramming characteristic of appressorium formation. The data presented here represent a comprehensive investigation of the M. oryzae phosphoproteome and provide key insights on the role of protein phosphorylation during infection-related development.
MeSH term(s)	Adaptation, Physiological ; Basic Helix-Loop-Helix Transcription Factors/metabolism ; Chromatography, Liquid ; Fungal Proteins/metabolism ; Magnaporthe/metabolism ; Magnaporthe/physiology ; Oryza/microbiology ; Phosphoproteins/metabolism ; Phosphorylation ; Proteomics ; Signal Transduction ; Tandem Mass Spectrometry
Chemical Substances	Basic Helix-Loop-Helix Transcription Factors ; Fungal Proteins ; Phosphoproteins
Language	English
Publishing date	2015-05-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/pr501064q
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