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  1. Article ; Online: TMT-Based Multiplexed Quantitation of

    Saraswat, Mayank / Mangalaparthi, Kiran Kumar / Garapati, Kishore / Pandey, Akhilesh

    ACS omega

    2022  Volume 7, Issue 13, Page(s) 11023–11032

    Abstract: Glycoproteomics, or the simultaneous characterization of glycans and their attached peptides, is increasingly being employed to generate catalogs of glycopeptides on a large scale. Nevertheless, quantitative glycoproteomics remains challenging even ... ...

    Abstract Glycoproteomics, or the simultaneous characterization of glycans and their attached peptides, is increasingly being employed to generate catalogs of glycopeptides on a large scale. Nevertheless, quantitative glycoproteomics remains challenging even though isobaric tagging reagents such as tandem mass tags (TMT) are routinely used for quantitative proteomics. Here, we present a workflow that combines the enrichment or fractionation of TMT-labeled glycopeptides with size-exclusion chromatography (SEC) for an in-depth and quantitative analysis of the glycoproteome. We applied this workflow to study the cellular glycoproteome of an isogenic mammary epithelial cell system that recapitulated oncogenic mutations in the
    Language English
    Publishing date 2022-03-25
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.1c06970
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Photochemistry of 3,6-Didehydropyridazine Biradical─An Untraceable

    Saraswat, Mayank / Ravi, Satyam / Shamasundar, K R / Venkataramani, Sugumar

    The journal of physical chemistry. A

    2022  Volume 126, Issue 4, Page(s) 557–567

    Abstract: We report matrix isolation infrared spectroscopic studies to characterize 3,6- ... ...

    Abstract We report matrix isolation infrared spectroscopic studies to characterize 3,6-didehydropyridazine
    Language English
    Publishing date 2022-01-20
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/acs.jpca.1c09317
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Proteomic alterations in extracellular vesicles induced by oncogenic PIK3CA mutations.

    Saraswat, Mayank / Garapati, Kishore / Kim, Jinyong / Budhraja, Rohit / Pandey, Akhilesh

    Proteomics

    2022  Volume 22, Issue 19-20, Page(s) e2200077

    Abstract: PIK3CA is one of the most frequently mutated genes in human cancers, with the two most prevalent activating mutations being E545K and H1047R. Although the altered intracellular signaling pathways in these cells have been described, the effect of these ... ...

    Abstract PIK3CA is one of the most frequently mutated genes in human cancers, with the two most prevalent activating mutations being E545K and H1047R. Although the altered intracellular signaling pathways in these cells have been described, the effect of these mutations on their extracellular vesicles (EVs) has not yet been reported. To study altered cellular physiology and intercellular communication through proteomic analysis of EVs, MCF10A cells and their isogenic mutant versions (PIK3CA E545K and H1047R) were cultured and their EVs enriched by differential ultracentrifugation. Proteins were extracted, digested with trypsin and the peptides labeled with tandem mass tag (TMT) reagents and analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Four thousand six hundred and fifty-five peptides were identified from 579 proteins of which 522 proteins have been previously described in EVs. Relative quantitation revealed altered levels of EV proteins including several cell adhesion molecules. Mesothelin, E-cadherin, and epithelial cell adhesion molecule were elevated in both mutant cell-derived EVs. Markers of tumor invasion and progression like galectin-3 and transforming growth factor beta induced protein were increased in both mutants. Overall, activating mutations in PIK3CA result in altered EV composition with characteristic changes associated with these hotspot mutations.
    MeSH term(s) Humans ; Proteomics/methods ; Chromatography, Liquid/methods ; Tandem Mass Spectrometry ; Trypsin/metabolism ; Epithelial Cell Adhesion Molecule/analysis ; Epithelial Cell Adhesion Molecule/metabolism ; Galectin 3/analysis ; Galectin 3/metabolism ; Class I Phosphatidylinositol 3-Kinases/genetics ; Extracellular Vesicles/genetics ; Extracellular Vesicles/metabolism ; Cadherins/metabolism ; Transforming Growth Factor beta/metabolism
    Chemical Substances Trypsin (EC 3.4.21.4) ; Epithelial Cell Adhesion Molecule ; Galectin 3 ; Class I Phosphatidylinositol 3-Kinases (EC 2.7.1.137) ; Cadherins ; Transforming Growth Factor beta ; PIK3CA protein, human (EC 2.7.1.137)
    Language English
    Publishing date 2022-07-14
    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.202200077
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
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    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
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  4. Article ; Online: Photoelectron spectroscopic study of 2-naphthylnitrene and its thermal rearrangement to cyanoindenes.

    Saraswat, Mayank / Portela-Gonzalez, Adrian / Mendez-Vega, Enrique / Karir, Ginny / Sander, Wolfram / Hemberger, Patrick

    Physical chemistry chemical physics : PCCP

    2023  Volume 25, Issue 45, Page(s) 31146–31152

    Abstract: 2-Cyanoindene has recently been identified in the interstellar medium, however current models cannot fully account for its formation pathways. Herein, we identify and characterize 2-naphthylnitrene, which is prone to rearrange to 2- and 3-cyanoindene, in ...

    Abstract 2-Cyanoindene has recently been identified in the interstellar medium, however current models cannot fully account for its formation pathways. Herein, we identify and characterize 2-naphthylnitrene, which is prone to rearrange to 2- and 3-cyanoindene, in the gas phase using photoion mass-selective threshold photoelectron spectroscopy (ms-TPES). The adiabatic ionization energies (AIE) of triplet nitrene (
    Language English
    Publishing date 2023-11-22
    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/d3cp04064j
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  5. Article ; Online: Thermal Decomposition of 2- and 4-Iodobenzyl Iodide Yields Fulvenallene and Ethynylcyclopentadienes: A Joint Threshold Photoelectron and Matrix Isolation Spectroscopic Study.

    Saraswat, Mayank / Portela-Gonzalez, Adrian / Karir, Ginny / Mendez-Vega, Enrique / Sander, Wolfram / Hemberger, Patrick

    The journal of physical chemistry. A

    2023  Volume 127, Issue 41, Page(s) 8574–8583

    Abstract: The thermal decomposition of 2- and 4-iodobenzyl iodide at high temperatures was investigated by mass-selective threshold photoelectron spectroscopy (ms-TPES) in the gas phase, as well as by matrix isolation infrared spectroscopy in cryogenic matrices. ... ...

    Abstract The thermal decomposition of 2- and 4-iodobenzyl iodide at high temperatures was investigated by mass-selective threshold photoelectron spectroscopy (ms-TPES) in the gas phase, as well as by matrix isolation infrared spectroscopy in cryogenic matrices. Scission of the benzylic C-I bond in the precursors at 850 K affords 2- and 4-iodobenzyl radicals (
    Language English
    Publishing date 2023-09-21
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/acs.jpca.3c04688
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Through bond and through space interactions in dehydro-diazine radicals: a case study of 3c-5e interactions.

    Saraswat, Mayank / Venkataramani, Sugumar

    Physical chemistry chemical physics : PCCP

    2018  Volume 20, Issue 6, Page(s) 4386–4395

    Abstract: Owing to the 3c-5e (3-centred-5-electrons) interactions between two nitrogen lone pairs and a radical electron, the dehydrodiazine radical isomers are very interesting from the fundamental point of view. Among them, pyrimidine has three (1a-1c), ... ...

    Abstract Owing to the 3c-5e (3-centred-5-electrons) interactions between two nitrogen lone pairs and a radical electron, the dehydrodiazine radical isomers are very interesting from the fundamental point of view. Among them, pyrimidine has three (1a-1c), pyridazine has two (2a and 2b) and pyrazine has only one (3a) radical isomer. Based on quantum chemical calculations at the (U)B3LYP, (U)M06-2X, (U)BLYP, CBS-QB3 and (U)CCSD(T) levels with cc-pVTZ as the basis set, we found the 4-dehydropyrimidine (1b) radical to be the most stable isomer among the three pyrimidine radicals, followed by the 2-dehydropyrimidine (1a) and 5-dehydropyrimidine (1c) radical isomers. In the case of pyridazine, 3-dehydro radical isomer (2a) is more stable than 4-dehydropyridazine (2b). Bond dissociation energy (BDE) calculations and estimation of radical stabilization energies (RSE) using isodesmic reactions revealed the stability order among the six isomeric diazine radicals as 1c < 2b < 2a < 1a < 3a < 1b. Spin densities at each radical centre and non-zero values at nitrogen centres provided information about the extent of delocalization of radical electrons, which was consistent with the relative stability order of all the isomers. The multiconfigurational CASSCF and natural bond orbital (NBO) calculations suggested the presence of direct through space interactions (between lone pairs and a radical, TS) that play a dominant role over the through bond (through intervening bonds, TB) interactions in deciding the stability order. To confirm these results, we have also estimated the proton affinities (PAs) for each nitrogen atom and compared them with their respective parent diazines, where lowering of the PA values convincingly envisaged the extent and strength of interactions between the nitrogen and radical centre. Atoms-in-molecules (AIM) analysis and estimation of hyperfine coupling constants have also been performed to verify these results. All these results showed that the through space interaction between the lone pair and the radical electron is very important for the electronic structural and stability aspects in dehydrodiazine radicals.
    Language English
    Publishing date 2018-02-07
    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/c7cp07579k
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  7. Article: Intermolecular CDC amination of remote and proximal unactivated C

    Rajamanickam, Suresh / Saraswat, Mayank / Venkataramani, Sugumar / Patel, Bhisma K

    Chemical science

    2021  Volume 12, Issue 46, Page(s) 15318–15328

    Abstract: An intermolecular radical based distal selectivity in appended alkyl chains has been developed. The selectivity is maximum when the distal carbon ... ...

    Abstract An intermolecular radical based distal selectivity in appended alkyl chains has been developed. The selectivity is maximum when the distal carbon is
    Language English
    Publishing date 2021-10-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 2559110-1
    ISSN 2041-6539 ; 2041-6520
    ISSN (online) 2041-6539
    ISSN 2041-6520
    DOI 10.1039/d1sc04365j
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Extensive heterogeneity of glycopeptides in plasma revealed by deep glycoproteomic analysis using size-exclusion chromatography.

    Saraswat, Mayank / Garapati, Kishore / Mun, Dong-Gi / Pandey, Akhilesh

    Molecular omics

    2021  Volume 17, Issue 6, Page(s) 939–947

    Abstract: Several plasma glycoproteins are clinically useful as biomarkers in a variety of diseases. Although thousands of proteins are present in plasma, >95% of the plasma proteome by mass is represented by only 22 proteins. This necessitates strategies to ... ...

    Abstract Several plasma glycoproteins are clinically useful as biomarkers in a variety of diseases. Although thousands of proteins are present in plasma, >95% of the plasma proteome by mass is represented by only 22 proteins. This necessitates strategies to deplete the abundant proteins and enrich other subsets of proteins. Although glycoproteins are abundant in plasma, in routine proteomic analyses, glycopeptides are not often investigated. Traditional methods such as lectin-based enrichment of glycopeptides followed by deglycosylation have helped understand the glycoproteome, but they lack any information about the attached glycans. Here, we apply size-exclusion chromatography (SEC) as a simple strategy to enrich intact
    MeSH term(s) Chromatography, Gel ; Chromatography, Liquid ; Glycopeptides ; Humans ; Proteomics ; Tandem Mass Spectrometry
    Chemical Substances Glycopeptides
    Language English
    Publishing date 2021-12-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2515-4184
    ISSN (online) 2515-4184
    DOI 10.1039/d1mo00132a
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  9. Article ; Online: Light-controlled shape-changing azomacrocycles exhibiting reversible modulation of pyrene fluorescence emission.

    Srivastava, Anjali / Grewal, Surbhi / Bari, Naimat K / Saraswat, Mayank / Sinha, Sharmistha / Venkataramani, Sugumar

    Organic & biomolecular chemistry

    2022  Volume 20, Issue 26, Page(s) 5284–5292

    Abstract: We report the design, synthesis, and study of light-induced shape-changing azomacrocycles. These systems have been incorporated with azobenzene photoswitches using alkoxy tethers and triazole units to afford flexibility and binding. We envision that such ...

    Abstract We report the design, synthesis, and study of light-induced shape-changing azomacrocycles. These systems have been incorporated with azobenzene photoswitches using alkoxy tethers and triazole units to afford flexibility and binding. We envision that such azomacrocycles are capable of reversibly binding with the guest molecule. Remarkably, we have demonstrated fully light-controlled fluorescence quenching and enhancement in the monomeric emission of pyrene (guest). Such modulations have been achieved by the photoisomerization of the azomacrocycle and, in turn, host-guest interactions. Also, the azomacrocycles tend to aggregate and can also be controlled by light or heat. We uncovered such phenomena using spectroscopic, microscopic, and isothermal titration calorimetry (ITC) studies and computations.
    MeSH term(s) Calorimetry/methods ; Pyrenes ; Spectrometry, Fluorescence/methods
    Chemical Substances Pyrenes
    Language English
    Publishing date 2022-07-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2097583-1
    ISSN 1477-0539 ; 1477-0520
    ISSN (online) 1477-0539
    ISSN 1477-0520
    DOI 10.1039/d2ob00866a
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Mass spectrometric analysis of chondroitin sulfate-linked peptides.

    Ramarajan, Madan Gopal / Saraswat, Mayank / Budhraja, Rohit / Garapati, Kishore / Raymond, Kimiyo / Pandey, Akhilesh

    Journal of proteins and proteomics

    2022  Volume 13, Issue 4, Page(s) 187–203

    Abstract: Chondroitin sulfate proteoglycans (CSPGs) are extracellular matrix components composed of linear glycosaminoglycan (GAG) side chains attached to a core protein. CSPGs play a vital role in neurodevelopment, signal transduction, cellular proliferation and ... ...

    Abstract Chondroitin sulfate proteoglycans (CSPGs) are extracellular matrix components composed of linear glycosaminoglycan (GAG) side chains attached to a core protein. CSPGs play a vital role in neurodevelopment, signal transduction, cellular proliferation and differentiation and tumor metastasis through interaction with growth factors and signaling proteins. These pleiotropic functions of proteoglycans are regulated spatiotemporally by the GAG chains attached to the core protein. There are over 70 chondroitin sulfate-linked proteoglycans reported in cells, cerebrospinal fluid and urine. A core glycan linker of 3-6 monosaccharides attached to specific serine residues can be extended by 20-200 disaccharide repeating units making intact CSPGs very large and impractical to analyze. The current paradigm of CSPG analysis involves digesting the GAG chains by chondroitinase enzymes and analyzing either the protein part, the disaccharide repeats, or both by mass spectrometry. This method, however, provides no information about the site of attachment or the composition of linker oligosaccharides and the degree of sulfation and/or phosphorylation. Further, the analysis by mass spectrometry and subsequent identification of novel CSPGs is hampered by technical challenges in their isolation, less optimal ionization and data analysis. Unknown identity of the linker oligosaccharide also makes it more difficult to identify the glycan composition using database searching approaches. Following chondroitinase digestion of long GAG chains linked to tryptic peptides, we identified intact GAG-linked peptides in clinically relevant samples including plasma, urine and dermal fibroblasts. These intact glycopeptides including their core linker glycans were identified by mass spectrometry using optimized stepped higher energy collision dissociation and electron-transfer/higher energy collision dissociation combined with hybrid database search/de novo glycan composition search. We identified 25 CSPGs including three novel CSPGs that have not been described earlier. Our findings demonstrate the utility of combining enrichment strategies and optimized high-resolution mass spectrometry analysis including alternative fragmentation methods for the characterization of CSPGs.
    Supplementary information: The online version contains supplementary material available at 10.1007/s42485-022-00092-3.
    Language English
    Publishing date 2022-10-02
    Publishing country India
    Document type Journal Article
    ZDB-ID 2890453-9
    ISSN 2524-4663 ; 0975-8151
    ISSN (online) 2524-4663
    ISSN 0975-8151
    DOI 10.1007/s42485-022-00092-3
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