scholarly journals Label-free shotgun proteomics and metabolite analysis reveal a significant metabolic shift during citrus fruit development

2011 ◽  
Vol 62 (15) ◽  
pp. 5367-5384 ◽  
Author(s):  
Ehud Katz ◽  
Kyung Hwan Boo ◽  
Ho Youn Kim ◽  
Richard A. Eigenheer ◽  
Brett S. Phinney ◽  
...  
Keyword(s):  
Fruit Development ◽  
Citrus Fruit ◽  
Shotgun Proteomics ◽  
Metabolic Shift ◽  
Label Free ◽  
Metabolite Analysis

scholarly journals Protein biocargo of citrus fruit-derived vesicles reveals heterogeneous transport and extracellular vesicles populations

2018 ◽  
Author(s):  
Gabriella Pocsfalvi ◽  
Lilla Turiák ◽  
Alfredo Ambrosone ◽  
Pasquale del Gaudio ◽  
Gina Puska ◽  
...  
Keyword(s):  
Coat Protein ◽  
Extracellular Vesicles ◽  
Intracellular Transport ◽  
Biological Activities ◽  
Citrus Fruit ◽  
Shotgun Proteomics ◽  
Biologically Active ◽  
Coat Proteins ◽  
Label Free ◽  
Shock Proteins

AbstractCellular vesicles are membrane-enclosed organelles that transport material inside and outside the cell. Plant-derived vesicles are receiving increasing attention due to their potential as nanovectors for the delivery of biologically active substances. We aimed to expand our understanding about the heterogeneity and the protein biocargo of citrus fruit juice sac cell-derived vesicles. Micro- and nanosized vesicle fractions were isolated from four citrus species,C. sinensis,C. limon,C. paradisiandC. aurantium, characterized using physicochemical methods and protein cargos were compared using label-free quantitative shotgun proteomics. In each sample approximately 600-800 proteins were identified. Orthologues of most of the top-ranking proteins have previously been reported in extracellular vesicles of mammalian origin. Patellin-3-like, clathrin heavy chain, heat shock proteins, 14-3-3 protein, glyceraldehyde-3-phosphate dehydrogenase and fructose-bisphosphate aldolase 6 were highly expressed in all citrus vesicle fractions. The presence of membrane channel aquaporin on the other hand characteristic of the nanovesicle fractions. Bioinformatics revealed more than hundred protein orthologues potentially implicated in vesicular trafficking. In particular, CCV, COPI and COPII coat proteins indicates the presence of highly heterogeneous populations of intracellular transport vesicles. Moreover, the different hydrolases and oxidoreductases transported within the citrus fruit-derived vesicles can be responsible for the various biological activities possessed by the preparations.AbbreviationsEVsextracellular vesicles;MVsmicrovesicles;NVsnanovesicles;PMplasma membrane;UCultracentrifugation;CCVclathrin coated vesicles;COPIcoat protein I;COPIIcoat protein II

scholarly journals Analysis of the Barley Malt Rootlet Proteome

2019 ◽  
Vol 21 (1) ◽  
pp. 179 ◽  
Author(s):  
Ramamurthy Mahalingam
Keyword(s):  
Animal Feed ◽  
Protein Biosynthesis ◽  
In Silico Analysis ◽  
Shotgun Proteomics ◽  
Label Free ◽  
High Coverage ◽  
Barley Malt ◽  
Naturally Occurring ◽  
Two Stages ◽  
Silico Analysis

Barley seeds are one of the main ingredients of the malting industry for brewing beer. The barley rootlets that are separated from the kilned seeds at the end of the malting process and used as animal feed are one of the byproducts of this industry. In this study, the proteome of rootlets derived from two stages of the malting process, germination and kilning, from a popular malting barley variety were analyzed. A label-free shotgun proteomics strategy was used to identify more than 800 proteins from the barley rootlets. A high coverage and high confidence Gene Ontology annotations of the barley genome was used to facilitate the functional annotation of the proteins that were identified in the rootlets. An analysis of these proteins using Kellogg Encyclopedia of Genes and Genomes (KEGG) and Plant Reactome databases indicated the enrichment of pathways associated with phytohormones, protein biosynthesis, secondary metabolism, and antioxidants. Increased levels of jasmonic acid and auxin in the rootlets further supported the in silico analysis. As a rich source of proteins and amino acids use of these by-products of the malting industry for animal feed is validated. This study also indicates rootlets as a potential source of naturally occurring phenylpropanoids and antioxidants that can be further exploited in the development of functional foods.

scholarly journals Proteomics in Diagnosis of Prostate Cancer/ Протеомика Во Дијагноза На Простатниот Карцином

PRILOZI ◽  
2015 ◽  
Vol 36 (1) ◽  
pp. 5-36 ◽  
Author(s):  
Katarina Davalieva ◽  
Momir Polenakovic
Keyword(s):  
Prostate Cancer ◽  
Tumor Tissue ◽  
Biomarker Discovery ◽  
Molecular Level ◽  
Specific Antigen ◽  
Shotgun Proteomics ◽  
Comparative Proteomics ◽  
Label Free ◽  
The Past ◽  
Proteomics Research

Abstract Prostate cancer (PCa) is the second most frequently diagnosed malignancy in men worldwide. The introduction of prostate specific antigen (PSA) has greatly increased the number of men diagnosed with PCa but at the same time, as a result of the low specificity, led to overdiagnosis, resulting to unnecessary biopsies and high medical cost treatments. The primary goal in PCa research today is to find a biomarker or biomarker set for clear and effecttive diagnosis of PCa as well as for distinction between aggressive and indolent cancers. Different proteomic technologies such as 2-D PAGE, 2-D DIGE, MALDI MS profiling, shotgun proteomics with label-based (ICAT, iTRAQ) and label-free (SWATH) quantification, MudPIT, CE-MS have been applied to the study of PCa in the past 15 years. Various biological samples, including tumor tissue, serum, plasma, urine, seminal plasma, prostatic secretions and prostatic-derived exosomes were analyzed with the aim of identifying diagnostic and prognostic biomarkers and developing a deeper understanding of the disease at the molecular level. This review is focused on the overall analysis of expression proteomics studies in the PCa field investigating all types of human samples in the search for diagnostics biomarkers. Emphasis is given on proteomics platforms used in biomarker discovery and characterization, explored sources for PCa biomarkers, proposed candidate biomarkers by comparative proteomics studies and the possible future clinical application of those candidate biomarkers in PCa screening and diagnosis. In addition, we review the specificity of the putative markers and existing challenges in the proteomics research of PCa.

scholarly journals Proteomic changes in the milk of water buffaloes (Bubalus bubalis) with subclinical mastitis due to intramammary infection by Staphylococcus aureus and by non-aureus staphylococci

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Salvatore Pisanu ◽  
Carla Cacciotto ◽  
Daniela Pagnozzi ◽  
Giulia Maria Grazia Puggioni ◽  
Sergio Uzzau ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Shotgun Proteomics ◽  
Subclinical Mastitis ◽  
Bubalus Bubalis ◽  
Buffalo Milk ◽  
Label Free ◽  
Western Immunoblotting ◽  
Differential Proteins ◽  
Culture Negative ◽  
Protein Dataset

Abstract Subclinical mastitis by Staphylococcus aureus (SAU) and by non-aureus staphylococci (NAS) is a major issue in the water buffalo. To understand its impact on milk, 6 quarter samples with >3,000,000 cells/mL (3 SAU-positive and 3 NAS-positive) and 6 culture-negative quarter samples with <50,000 cells/mL were investigated by shotgun proteomics and label-free quantitation. A total of 1530 proteins were identified, of which 152 were significantly changed. SAU was more impacting, with 162 vs 127 differential proteins and higher abundance changes (P < 0.0005). The 119 increased proteins had mostly structural (n = 43, 28.29%) or innate immune defence functions (n = 39, 25.66%) and included vimentin, cathelicidins, histones, S100 and neutrophil granule proteins, haptoglobin, and lysozyme. The 33 decreased proteins were mainly involved in lipid metabolism (n = 13, 59.10%) and included butyrophilin, xanthine dehydrogenase/oxidase, and lipid biosynthetic enzymes. The same biological processes were significantly affected also upon STRING analysis. Cathelicidins were the most increased family, as confirmed by western immunoblotting, with a stronger reactivity in SAU mastitis. S100A8 and haptoglobin were also validated by western immunoblotting. In conclusion, we generated a detailed buffalo milk protein dataset and defined the changes occurring in SAU and NAS mastitis, with potential for improving detection (ProteomeXchange identifier PXD012355).

scholarly journals Characterization of the MDSC Proteome Associated with Metastatic Murine Mammary Tumors Using Label-Free Mass Spectrometry and Shotgun Proteomics

PLoS ONE ◽  
2011 ◽  
Vol 6 (8) ◽  
pp. e22446 ◽  
Author(s):  
Angela M. Boutté ◽  
W. Hayes McDonald ◽  
Yu Shyr ◽  
Li Yang ◽  
P. Charles Lin
Keyword(s):  
Mass Spectrometry ◽  
Shotgun Proteomics ◽  
Mammary Tumors ◽  
Label Free

scholarly journals Staphylococcus aureus Induces Hypoxia and Cellular Damage in Porcine Dermal Explants

2015 ◽  
Vol 83 (6) ◽  
pp. 2531-2541 ◽  
Author(s):  
Abdul G. Lone ◽  
Erhan Atci ◽  
Ryan Renslow ◽  
Haluk Beyenal ◽  
Susan Noh ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Cell Death ◽  
Effective Diffusion ◽  
Oxygen Demand ◽  
Shotgun Proteomics ◽  
Cellular Damage ◽  
Label Free ◽  
Content Type ◽  
Dermal Tissue ◽  
The Difference

We developed a porcine dermal explant model to determine the extent to whichStaphylococcus aureusbiofilm communities deplete oxygen, change pH, and produce damage in underlying tissue. Microelectrode measurements demonstrated that dissolved oxygen (DO) in biofilm-free dermal tissue was 4.45 ± 1.17 mg/liter, while DO levels for biofilm-infected tissue declined sharply from the surface, with no measurable oxygen detectable in the underlying dermal tissue. Magnetic resonance imaging demonstrated that biofilm-free dermal tissue had a significantly lower relative effective diffusion coefficient (0.26 ± 0.09 to 0.30 ± 0.12) than biofilm-infected dermal tissue (0.40 ± 0.12 to 0.48 ± 0.12;P< 0.0001). Thus, the difference in DO level was attributable to biofilm-induced oxygen demand rather than changes in oxygen diffusivity. Microelectrode measures showed that pH within biofilm-infected explants was more alkaline than in biofilm-free explants (8.0 ± 0.17 versus 7.5 ± 0.15, respectively;P< 0.002). Cellular and nuclear details were lost in the infected explants, consistent with cell death. Quantitative label-free shotgun proteomics demonstrated that both proapoptotic programmed cell death protein 5 and antiapoptotic macrophage migration inhibitory factor accumulated in the infected-explant spent medium, compared with uninfected-explant spent media (1,351-fold and 58-fold, respectively), consistent with the cooccurrence of apoptosis and necrosis in the explants. Biofilm-origin proteins reflected an extracellular matrix-adapted lifestyle ofS. aureus. S. aureusbiofilms deplete oxygen, increase pH, and induce cell death, all factors that contribute to impede wound healing.

Flavonol synthase gene expression during citrus fruit development

2002 ◽  
Vol 114 (2) ◽  
pp. 251-258 ◽  
Author(s):  
Takaya Moriguchi ◽  
Masayuki Kita ◽  
Kazunori Ogawa ◽  
Yasuhiko Tomono ◽  
Tomoko Endo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruit Development ◽  
Citrus Fruit ◽  
Flavonol Synthase
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