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  1. Article: Editorial: Proteomics of plant development and hormonal responses, volume II.

    Jones, Alexandra M E / De Smet, Ive

    Frontiers in plant science

    2023  Volume 14, Page(s) 1340170

    Language English
    Publishing date 2023-11-28
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2023.1340170
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Determination of Boron Content Using a Simple and Rapid Miniaturized Curcumin Assay.

    Mohan, Thotegowdanapalya C / Jones, Alexandra M E

    Bio-protocol

    2018  Volume 8, Issue 2

    Abstract: To determine boron quantity in soil, water and biological samples, several protocols are available. Colorimetric assays are the simplest and cheapest methods which can be used to determine boron concentration. However, published protocols do not give ... ...

    Abstract To determine boron quantity in soil, water and biological samples, several protocols are available. Colorimetric assays are the simplest and cheapest methods which can be used to determine boron concentration. However, published protocols do not give straightforward guidance for beginners to adopt these protocols for routine use in the laboratory. Based on a previously published available procedure, we present a detailed and modified version of a curcumin based colorimetric protocol to determine boron concentration extracted from any sample. Our modified protocol is able to determine up to 0.2 nmole of Boron in a sample volume of 300 μl.
    Language English
    Publishing date 2018-02-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2833269-6
    ISSN 2331-8325
    ISSN 2331-8325
    DOI 10.21769/BioProtoc.2703
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Identification of related peptides through the analysis of fragment ion mass shifts.

    Wilhelm, Thomas / Jones, Alexandra M E

    Journal of proteome research

    2014  Volume 13, Issue 9, Page(s) 4002–4011

    Abstract: Mass spectrometry (MS) has become the method of choice to identify and quantify proteins, typically by fragmenting peptides and inferring protein identification by reference to sequence databases. Well-established programs have largely solved the problem ...

    Abstract Mass spectrometry (MS) has become the method of choice to identify and quantify proteins, typically by fragmenting peptides and inferring protein identification by reference to sequence databases. Well-established programs have largely solved the problem of identifying peptides in complex mixtures. However, to prevent the search space from becoming prohibitively large, most search engines need a list of expected modifications. Therefore, unexpected modifications limit both the identification of proteins and peptide-based quantification. We developed mass spectrometry-peak shift analysis (MS-PSA) to rapidly identify related spectra in large data sets without reference to databases or specified modifications. Peptide identifications from established tools, such as MASCOT or SEQUEST, may be propagated onto MS-PSA results. Modification of a peptide alters the mass of the precursor ion and some of the fragmentation ions. MS-PSA identifies characteristic fragmentation masses from MS/MS spectra. Related spectra are identified by pattern matching of unchanged and mass-shifted fragment ions. We illustrate the use of MS-PSA with simple and complex mixtures with both high and low mass accuracy data sets. MS-PSA is not limited to the analysis of peptides but can be used for the identification of related groups of spectra in any set of fragmentation patterns.
    MeSH term(s) Databases, Protein ; Ions/analysis ; Ions/chemistry ; Molecular Weight ; Peptide Fragments/analysis ; Peptide Fragments/chemistry ; Proteomics/methods ; Tandem Mass Spectrometry/methods
    Chemical Substances Ions ; Peptide Fragments
    Language English
    Publishing date 2014-08-05
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/pr500347e
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6189: Show issues Location:
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  4. Article: Identification of Related Peptides through the Analysis of Fragment Ion Mass Shifts

    Wilhelm, Thomas / Jones Alexandra M. E

    Journal of Proteome Research. 2014 Sept. 05, v. 13, no. 9

    2014  

    Abstract: Mass spectrometry (MS) has become the method of choice to identify and quantify proteins, typically by fragmenting peptides and inferring protein identification by reference to sequence databases. Well-established programs have largely solved the problem ...

    Abstract Mass spectrometry (MS) has become the method of choice to identify and quantify proteins, typically by fragmenting peptides and inferring protein identification by reference to sequence databases. Well-established programs have largely solved the problem of identifying peptides in complex mixtures. However, to prevent the search space from becoming prohibitively large, most search engines need a list of expected modifications. Therefore, unexpected modifications limit both the identification of proteins and peptide-based quantification. We developed mass spectrometry–peak shift analysis (MS-PSA) to rapidly identify related spectra in large data sets without reference to databases or specified modifications. Peptide identifications from established tools, such as MASCOT or SEQUEST, may be propagated onto MS-PSA results. Modification of a peptide alters the mass of the precursor ion and some of the fragmentation ions. MS-PSA identifies characteristic fragmentation masses from MS/MS spectra. Related spectra are identified by pattern matching of unchanged and mass-shifted fragment ions. We illustrate the use of MS-PSA with simple and complex mixtures with both high and low mass accuracy data sets. MS-PSA is not limited to the analysis of peptides but can be used for the identification of related groups of spectra in any set of fragmentation patterns.
    Keywords data collection ; databases ; ions ; mass spectrometry ; peptides ; proteins ; proteome
    Language English
    Dates of publication 2014-0905
    Size p. 4002-4011.
    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%2Fpr500347e
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: SNAREs SYP121 and SYP122 Mediate the Secretion of Distinct Cargo Subsets.

    Waghmare, Sakharam / Lileikyte, Edita / Karnik, Rucha / Goodman, Jennifer K / Blatt, Michael R / Jones, Alexandra M E

    Plant physiology

    2018  Volume 178, Issue 4, Page(s) 1679–1688

    Abstract: ... SNARE ( ... ...

    Abstract SNARE (soluble
    MeSH term(s) Arabidopsis/genetics ; Arabidopsis/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Cell Membrane ; Glycosyltransferases/genetics ; Glycosyltransferases/metabolism ; Mass Spectrometry ; Mutation ; Plants, Genetically Modified ; Protein Transport ; Qa-SNARE Proteins/genetics ; Qa-SNARE Proteins/metabolism ; Reproducibility of Results
    Chemical Substances Arabidopsis Proteins ; PEN1 protein, Arabidopsis ; Qa-SNARE Proteins ; SYP122 protein, Arabidopsis ; Glycosyltransferases (EC 2.4.-) ; XTH24 protein, Arabidopsis (EC 2.4.1.207)
    Language English
    Publishing date 2018-10-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 208914-2
    ISSN 1532-2548 ; 0032-0889
    ISSN (online) 1532-2548
    ISSN 0032-0889
    DOI 10.1104/pp.18.00832
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Bonn / Germany

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  6. Article ; Online: Updates of the In-Gel Digestion Method for Protein Analysis by Mass Spectrometry.

    Goodman, Jennifer K / Zampronio, Cleidiane G / Jones, Alexandra M E / Hernandez-Fernaud, Juan R

    Proteomics

    2018  Volume 18, Issue 23, Page(s) e1800236

    Abstract: The in-gel digestion of proteins for analysis by liquid chromatograph mass spectrometry has been used since the early 1990s. Although several improvements have contributed to increasing the quality of the data obtained, many recent publications still use ...

    Abstract The in-gel digestion of proteins for analysis by liquid chromatograph mass spectrometry has been used since the early 1990s. Although several improvements have contributed to increasing the quality of the data obtained, many recent publications still use sub-optimal approaches. Updates of the in-gel digestion protocol has been presented in the study. It has been shown that alternative reducing, alkylating agent reactions, and tryptic digestion buffers increase peptide and protein identification and reduce incubation times. The results indicate that a simultaneous and short, high temperature reduction and alkylation reaction using Tris(2-carboxyethyl)phosphine hydrochloride and chloroacetamide with a subsequent gel wash improve protein identification and sequence coverage, and diminish peptide side reactions. Additionally, use of 4-(2-hydroxyethyl)piperazine-1-ethanesulfonic acid buffer allows a significant reduction in the digestion time improving trypsin performance and increasing the peptide recovery. The updates of the in-gel digestion protocol described here are efficient and offer flexibility to be incorporated in any proteomic laboratory.
    MeSH term(s) Mass Spectrometry ; Proteomics/methods ; Temperature ; Trypsin/chemistry
    Chemical Substances Trypsin (EC 3.4.21.4)
    Language English
    Publishing date 2018-11-25
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2032093-0
    ISSN 1615-9861 ; 1615-9853
    ISSN (online) 1615-9861
    ISSN 1615-9853
    DOI 10.1002/pmic.201800236
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 5386: Show issues Location:
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  7. Article ; Online: Structural and functional insights into the mechanism of action of plant borate transporters.

    Saouros, Savvas / Mohan, Thotegowdanapalya C / Cecchetti, Cristina / Lehmann, Silke / Barrit, Joseph D / Scull, Nicola J / Simpson, Paul / Alguel, Yilmaz / Cameron, Alexander D / Jones, Alexandra M E / Byrne, Bernadette

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 12328

    Abstract: Boron has essential roles in plant growth and development. BOR proteins are key in the active uptake and distribution of boron, and regulation of intracellular boron concentrations. However, their mechanism of action remains poorly studied. BOR proteins ... ...

    Abstract Boron has essential roles in plant growth and development. BOR proteins are key in the active uptake and distribution of boron, and regulation of intracellular boron concentrations. However, their mechanism of action remains poorly studied. BOR proteins are homologues of the human SLC4 family of transporters, which includes well studied mammalian transporters such as the human Anion Exchanger 1 (hAE1). Here we generated Arabidopsis thaliana BOR1 (AtBOR1) variants based (i) on known disease causing mutations of hAE1 (S466R, A500R) and (ii) a loss of function mutation (D311A) identified in the yeast BOR protein, ScBOR1p. The AtBOR1 variants express in yeast and localise to the plasma membrane, although both S466R and A500R exhibit lower expression than the WT AtBOR1 and D311A. The D311A, S466R and A500R mutations result in a loss of borate efflux activity in a yeast bor1p knockout strain. A. thaliana plants containing these three individual mutations exhibit substantially decreased growth phenotypes in soil under conditions of low boron. These data confirm an important role for D311 in the function of the protein and show that mutations equivalent to disease-causing mutations in hAE1 have major effects in AtBOR1. We also obtained a low resolution cryo-EM structure of a BOR protein from Oryza sativa, OsBOR3, lacking the 30 C-terminal amino acid residues. This structure confirms the gate and core domain organisation previously observed for related proteins, and is strongly suggestive of an inward facing conformation.
    MeSH term(s) Anion Exchange Protein 1, Erythrocyte/genetics ; Antiporters/genetics ; Antiporters/ultrastructure ; Arabidopsis/genetics ; Arabidopsis/growth & development ; Arabidopsis/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/ultrastructure ; Borates/metabolism ; Boron/metabolism ; Gene Expression Regulation, Plant ; Humans ; Ion Transport/genetics ; Membrane Transport Proteins/genetics ; Mutation ; Oryza/genetics ; Oryza/growth & development ; Plant Development/genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics
    Chemical Substances Anion Exchange Protein 1, Erythrocyte ; Antiporters ; Arabidopsis Proteins ; BOR1 protein, Arabidopsis ; Bor1 protein, S cerevisiae ; Borates ; Membrane Transport Proteins ; SLC4A1 protein, human ; Saccharomyces cerevisiae Proteins ; Boron (N9E3X5056Q)
    Language English
    Publishing date 2021-06-10
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-91763-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Expanding the Zebrafish Genetic Code through Site-Specific Introduction of Azido-lysine, Bicyclononyne-lysine, and Diazirine-lysine.

    Syed, Junetha / Palani, Saravanan / Clarke, Scott T / Asad, Zainab / Bottrill, Andrew R / Jones, Alexandra M E / Sampath, Karuna / Balasubramanian, Mohan K

    International journal of molecular sciences

    2019  Volume 20, Issue 10

    Abstract: Site-specific incorporation of un-natural amino acids (UNAA) is a powerful approach to engineer and understand protein function. Site-specific incorporation of UNAAs is achieved through repurposing the amber codon (UAG) as a sense codon for the UNAA, ... ...

    Abstract Site-specific incorporation of un-natural amino acids (UNAA) is a powerful approach to engineer and understand protein function. Site-specific incorporation of UNAAs is achieved through repurposing the amber codon (UAG) as a sense codon for the UNAA, using a tRNA
    MeSH term(s) Animals ; Codon, Terminator/genetics ; Genetic Code ; Glutathione Transferase/genetics ; Green Fluorescent Proteins/genetics ; Lysine/analogs & derivatives ; Lysine/genetics ; Protein Engineering/methods ; Zebrafish/genetics ; Zebrafish Proteins/genetics
    Chemical Substances Codon, Terminator ; Zebrafish Proteins ; Green Fluorescent Proteins (147336-22-9) ; Glutathione Transferase (EC 2.5.1.18) ; Lysine (K3Z4F929H6)
    Language English
    Publishing date 2019-05-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms20102577
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Editorial: Mechanisms regulating immunity in plants.

    Jones, Alexandra M E / Monaghan, Jacqueline / Ntoukakis, Vardis

    Frontiers in plant science

    2013  Volume 4, Page(s) 64

    Language English
    Publishing date 2013-03-27
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2013.00064
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Dynamic changes of the Prf/Pto tomato resistance complex following effector recognition.

    Sheikh, Arsheed H / Zacharia, Iosif / Pardal, Alonso J / Dominguez-Ferreras, Ana / Sueldo, Daniela J / Kim, Jung-Gun / Balmuth, Alexi / Gutierrez, Jose R / Conlan, Brendon F / Ullah, Najeeb / Nippe, Olivia M / Girija, Anil M / Wu, Chih-Hang / Sessa, Guido / Jones, Alexandra M E / Grant, Murray R / Gifford, Miriam L / Mudgett, Mary Beth / Rathjen, John P /
    Ntoukakis, Vardis

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 2568

    Abstract: In both plants and animals, nucleotide-binding leucine-rich repeat (NLR) immune receptors play critical roles in pathogen recognition and activation of innate immunity. In plants, NLRs recognise pathogen-derived effector proteins and initiate effector- ... ...

    Abstract In both plants and animals, nucleotide-binding leucine-rich repeat (NLR) immune receptors play critical roles in pathogen recognition and activation of innate immunity. In plants, NLRs recognise pathogen-derived effector proteins and initiate effector-triggered immunity (ETI). However, the molecular mechanisms that link NLR-mediated effector recognition and downstream signalling are not fully understood. By exploiting the well-characterised tomato Prf/Pto NLR resistance complex, we identified the 14-3-3 proteins TFT1 and TFT3 as interacting partners of both the NLR complex and the protein kinase MAPKKKα. Moreover, we identified the helper NRC proteins (NLR-required for cell death) as integral components of the Prf /Pto NLR recognition complex. Notably our studies revealed that TFTs and NRCs interact with distinct modules of the NLR complex and, following effector recognition, dissociate facilitating downstream signalling. Thus, our data provide a mechanistic link between activation of immune receptors and initiation of downstream signalling cascades.
    MeSH term(s) Animals ; Solanum lycopersicum ; Proteins ; Signal Transduction ; Immunity, Innate ; Plants/metabolism ; Receptors, Immunologic ; Plant Immunity ; Plant Proteins/metabolism ; Plant Diseases
    Chemical Substances Proteins ; Receptors, Immunologic ; Plant Proteins
    Language English
    Publishing date 2023-05-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-38103-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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