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Journal of Proteomics

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https://www.readbyqxmd.com/read/29454112/comparative-proteomic-analysis-of-the-maize-responses-to-early-leaf-senescence-induced-by-preventing-pollination
#1
Liancheng Wu, Shunxi Wang, Lei Tian, Liuji Wu, Mingna Li, Jun Zhang, Pei Li, Weiqiang Zhang, Yanhui Chen
The aim of this study was to explore the molecular mechanisms of induced leaf senescence by preventing pollination in maize using a proteomic method combined with other physiological methods. An elite maize inbred line Yu816 were selected for evaluation of its senescence mechanism. Phenotypic and chlorophyll content analysis revealed that the onset of leaf senescence occurred earlier in non-pollinated (NONPOL) leaves than pollinated (POL) leaves. Leaf protein species of NONPOL and POL leaves were separately extracted and their proteomes were assessed using isobaric tags for relative and absolute quantitation (iTRAQ) analysis...
February 14, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29452276/application-of-targeted-mass-spectrometry-in-bottom-up-proteomics-for-systems-biology-research
#2
Nathan P Manes, Aleksandra Nita-Lazar
The enormous diversity of proteoforms produces tremendous complexity within cellular proteomes, facilitates intricate networks of molecular interactions, and constitutes a formidable analytical challenge for biomedical researchers. Currently, quantitative whole-proteome profiling often relies on non-targeted liquid chromatography-mass spectrometry (LC-MS), which samples proteoforms broadly, but can suffer from lower accuracy, sensitivity, and reproducibility compared with targeted LC-MS. Recent advances in bottom-up proteomics using targeted LC-MS have enabled previously unachievable identification and quantification of target proteins and posttranslational modifications within complex samples...
February 13, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29448056/proteomic-analysis-of-first-trimester-maternal-serum-to-identify-candidate-biomarkers-potentially-predictive-of-spontaneous-preterm-birth
#3
Arlene M D'Silva, Jon A Hyett, Jens R Coorssen
Spontaneous preterm birth (sPTB) remains a major clinical dilemma; current diagnostics and interventions have not reduced the rate of this serious healthcare burden. This study characterizes differential protein profiles and post-translational modifications (PTMs) in first trimester maternal serum using a refined top-down approach coupling two-dimensional gel electrophoresis (2DE) and mass spectrometry (MS) to directly compare subsequent term and preterm labour events and identify marked protein differences...
February 12, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29448055/proteomic-characterization-of-withaferin-a-targeted-protein-networks-for-the-treatment-of-monoclonal-myeloma-gammopathies
#4
Martin Dom, Fritz Offner, Wim Vanden Berghe, Xaveer Van Ostade
Withaferin A (WA), a natural steroid lactone from the plant Withania somnifera, is often studied because of its antitumor properties. Although many in vitro and in vivo studies have been performed, the identification of Withaferin A protein targets and its mechanism of antitumor action remain incomplete. We used quantitative chemoproteomics and differential protein expression analysis to characterize the WA antitumor effects on a multiple myeloma cell model. Identified relevant targets were further validated by Ingenuity Pathway Analysis and Western blot and indicate that WA targets protein networks that are specific for monoclonal gammopathy of undetermined significance (MGUS) and other closely related disorders, such as multiple myeloma (MM) and Waldenström macroglobulinemia (WM)...
February 12, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29448054/rage-induced-changes-in-the-proteome-of-alveolar-epithelial-cells
#5
Charles A Downs, Nicholle M Johnson, George Tsaprailis, My N Helms
The receptor for advanced glycation end-products (RAGE) is a pattern recognition receptor and member of the immunoglobulin superfamily. RAGE is constitutively expressed in the distal lung where it co-localizes with the alveolar epithelium; RAGE expression is otherwise minimal or absent, except with disease. This suggests RAGE plays a role in lung physiology and pathology. We used proteomics to identify and characterize the effects of RAGE on rat alveolar epithelial (R3/1) cells. LC-MS/MS identified 177 differentially expressed proteins and the PANTHER Classification System further segregated proteins...
February 12, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29438852/transcriptome-analysis-to-assess-the-cholestatic-hepatotoxicity-induced-by-polygoni-multiflori-radix-up-regulation-of-key-enzymes-of-cholesterol-and-bile-acid-biosynthesis
#6
Li-Long Jiang, Dong-Sheng Zhao, Ya-Xi Fan, Qiong Yu, Yi-Sheng Lai, Ping Li, Hui-Jun Li
Polygoni Multiflori Radix (PMR) has been commonly used as a tonic in China for centuries. However, PMR-associated hepatotoxicity is becoming a safety issue. Cholestasis often occurs in PMR-induced hepatotoxicity in clinical medicine, but the exact mechanism is not completely understood. An RNA-Seq method was employed, in the present study, to explore the molecular mechanism of cholestatic liver injury induced by PMR, characterized by the hepatic transcriptional response in rats exposed to 1 and 20 g/kg PMR for 90 days...
February 10, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29438851/redox-responses-are-preserved-across-muscle-fibres-with-differential-susceptibility-to-aging
#7
Neil T Smith, Ana Soriano-Arroquia, Katarzyna Goljanek-Whysall, Malcolm J Jackson, Brian McDonagh
Age-related loss of muscle mass and function is associated with increased frailty and loss of independence. The mechanisms underlying the susceptibility of different muscle types to age-related atrophy are not fully understood. Reactive oxygen species (ROS) are recognised as important signalling molecules in healthy muscle and redox sensitive proteins can respond to intracellular changes in ROS concentrations modifying reactive thiol groups on Cysteine (Cys) residues. Conserved Cys residues tend to occur in functionally important locations and can have a direct impact on protein function through modifications at the active site or determining protein conformation...
February 10, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29438850/secreted-protein-extract-analyses-present-the-plant-pathogen-alternaria-alternata-as-a-suitable-industrial-enzyme-toolbox
#8
L García-Calvo, R V Ullán, M Fernández-Aguado, A M García-Lino, R Balaña-Fouce, C Barreiro
Lignocellulosic plant biomass is the most abundant carbon source in the planet, which makes it a potential substrate for biorefinery. It consists of polysaccharides and other molecules with applications in pharmaceutical, food and feed, cosmetics, paper and textile industries. The exploitation of these resources requires the hydrolysis of the plant cell wall, which is a complex process. Aiming to discover novel fungal natural isolates with lignocellulolytic capacities, a screening for feruloyl esterase activity was performed in samples taken from different metal surfaces...
February 10, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29432917/polyphenol-extracts-from-dried-sugarcane-inhibit-inflammatory-mediators-in-an-in-vitro-colon-cancer-model
#9
Daniel Bucio-Noble, Liisa Kautto, Christoph Krisp, Malcolm S Ball, Mark P Molloy
Sugarcane is an important crop grown in tropical regions for sugar, and for ethanol production. Sugarcane is also a source of phytochemicals but its nutraceutical potential has been under-explored. We show that ethanol extracts of whole dried sugarcane (WDS) recovers a rich content of polyphenols, flavonoids and antioxidant activity that act on inflammatory mediator proteins. To investigate the mechanisms of this activity, we stimulated SW480 colon cancer cells with lipopolysaccharide, exposed cells to WDS and quantitated changes to the proteome and phosphoproteome using label-free mass spectrometry...
February 10, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29432918/exploration-of-the-platelet-proteome-in-patients-with-early-stage-cancer
#10
Siamack Sabrkhany, Marijke J E Kuijpers, Jaco C Knol, Steven W M Olde Damink, Anne-Marie C Dingemans, Henk M Verheul, Sander R Piersma, Thang V Pham, Arjan W Griffioen, Mirjam G A Oude Egbrink, Connie R Jimenez
Platelets play an important role in tumor growth and, at the same time, platelet characteristics are affected by cancer presence. Therefore, we investigated whether the platelet proteome harbors differentially expressed proteins associated with early-stage cancer. For this proof-of-concept study, patients with early-stage lung (n = 8) or head of pancreas cancer (n = 4) were included, as were healthy sex- and age-matched controls for both subgroups. Blood samples were collected from controls and from patients before surgery...
February 9, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29427760/interaction-proteomics-by-using-in-cell-nmr-spectroscopy
#11
Leonard Breindel, David S Burz, Alexander Shekhtman
A synopsis of in-cell NMR spectroscopic approaches to study interaction proteomics in prokaryotic and eukaryotic cells is presented. We describe the use of in-cell NMR spectroscopy to resolve high resolution protein structures, discuss methodologies for determining and analyzing high and low affinity protein-target structural interactions, including intrinsically disordered proteins, and detail important functional interactions that result from these interactions. SIGNIFICANCE: The ultimate goal of structural and biochemical research is to understand how macromolecular interactions give rise to and regulate biological activity in living cells...
February 7, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29427759/quantitative-analysis-of-core-fucosylation-of-serum-proteins-in-liver-diseases-by-lc-ms-mrm
#12
Junfeng Ma, Miloslav Sanda, Renhuizi Wei, Lihua Zhang, Radoslav Goldman
Aberrant core fucosylation of proteins has been linked to liver diseases. In this study, we carried out multiple reaction monitoring (MRM) quantification of core fucosylated N-glycopeptides of serum proteins partially deglycosylated by a combination of endoglycosidases (endoF1, endoF2, and endoF3). To minimize variability associated with the preparatory steps, the analysis was performed without enrichment of glycopeptides or fractionation of serum besides the nanoRP chromatography. Specifically, we quantified core fucosylation of 22 N-glycopeptides derived from 17 proteins together with protein abundance of these glycoproteins in a cohort of 45 participants (15 disease-free control, 15 fibrosis and 15 cirrhosis patients) using a multiplex nanoUPLC-MS-MRM workflow...
February 7, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29425737/the-lysine-acetylome-of-the-nematocidal-bacterium-bacillus-nematocida-and-impact-of-nematode-on-the-acetylome
#13
Xin-Li Sun, Yun-He Yang, Li Zhu, Fang-Yu Liu, Jian-Ping Xu, Xiao-Wei Huang, Ming-He Mo, Tong Liu, Ke-Qin Zhang
Bacillus nematocida B16 (B16) is a pathogenic bacterium that is nematotoxic to plant-parasitic nematodes. In this study, we performed a quantitative lysine acetylome analysis on B16 to understand the potential roles of protein lysine acetylation on this host-pathogen interaction. Altogether, we identified 529 acetylation sites in 349 proteins, quantified 411 sites in 288 proteins, determined that the acetylation levels of 18 sites were up-regulated and those of 19 sites were down-regulated during pathogenesis...
February 6, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29425736/targeted-proteomics-analyses-of-phosphorylation-dependent-signalling-networks
#14
Sara L Banerjee, Ugo Dionne, Jean-Philippe Lambert, Nicolas Bisson
Protein phosphorylation often regulates interactions between components of signalling networks. Its tight regulation by opposing actions of kinases and phosphatases contribute to making this modification key in controlling the dynamic architecture of phosphorylation-dependent networks. The introduction in cell signalling research of long-standing targeted proteomics approaches such as selected reaction monitoring (SRM) combined with the development of state-of-the-art methods such as parallel reaction monitoring (PRM) and data-independent analysis (DIA), have allowed delineating temporal quantitative profiles of interactions networks...
February 6, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29425735/revealing-the-interaction-mode-of-the-highly-flexible-sorghum-bicolor-hsp70-hsp90-organizing-protein-hop-a-conserved-carboxylate-clamp-confers-high-affinity-binding-to-hsp90
#15
Regina Adão, Letícia M Zanphorlin, Tatiani B Lima, Dev Sriranganadane, Käthe M Dahlström, Glaucia M S Pinheiro, Fabio C Gozzo, Leandro R S Barbosa, Carlos H I Ramos
Proteostasis is dependent on the Hsp70/Hsp90 system (the two chaperones and their co-chaperones). Of these, Hop (Hsp70/Hsp90 organizing protein), also known as Sti1, forms an important scaffold to simultaneously binding to both Hsp70 and Hsp90. Hop/Sti1 has been implicated in several disease states, for instance cancer and transmissible spongiform encephalopathies. Therefore, human and yeast homologous have been better studied and information on plant homologous is still limited, even though plants are continuously exposed to environmental stress...
February 6, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29408543/precision-medicine-in-cow-milk-allergy-proteomics-perspectives-from-allergens-to-patients
#16
Enza D' Auria, Chiara Mameli, Cristian Piras, Lucia Cococcioni, Andrea Urbani, Gian Vincenzo Zuccotti, Paola Roncada
Cow's milk allergy (CMA) is one of the most common food allergies, especially during childhood. CMA is an immunological mediated adverse reaction to one or more cow's milk proteins, which are normally harmless to a non-allergic individual, as the result of a failure of oral tolerance. To make a correct diagnosis of CMA and a proper treatment are critical in clinical practice. Application of proteomics along with new bio-informatics tools in the field of food allergy is one of the hot topics presented in recent years...
February 3, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29408313/tmt-based-quantitative-proteomics-analysis-reveals-the-response-of-camellia-sinensis-to-fluoride
#17
Yanli Liu, Dan Cao, Linlong Ma, Xiaofang Jin, Pingfang Yang, Fei Ye, Panpan Liu, Ziming Gong, Chaoling Wei
The tea plant is a fluoride hyperaccumulator, and fluoride accumulation in its leaves is closely related to human health. To dissect molecular mechanisms underlying fluoride accumulation/detoxification, the leaves of tea seedlings exposed to different fluoride treatments for 30 days were sampled for physiological and proteomics analyses. The results showed that fluoride had no adverse effects on the growth of tea seedlings in spite of high content fluoride accumulation in their leaves. Through TMT coupled with UPLC MS/MS, 189 differentially accumulated proteins were quantified, of which 41 and 148 were localized in the cell wall and cellular compartments respectively...
February 2, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29410240/the-use-of-omics-profiling-to-improve-outcomes-of-bone-regeneration-and-osseointegration-how-far-are-we-from-personalized-medicine-in-dentistry
#18
E Calciolari, N Donos
Increased life expectancy and broader restorative dental treatment alternatives for missing teeth have resulted in an increasing request of bone regeneration/augmentation procedures not only in healthy patients, but also in elderly and medically compromised ones. This is also combined with a growing demand for short implant loading protocols and for optimal aesthetic results. In order to meet these new dental needs, personalized treatment strategies tailored on each individual's characteristics and healing profile are warranted...
February 1, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29408692/proteomic-analysis-of-the-sarcolemma-enriched-fraction-from-dystrophic-mdx-4cv-skeletal-muscle
#19
Sandra Murphy, Margit Zweyer, Michael Henry, Paula Meleady, Rustam R Mundegar, Dieter Swandulla, Kay Ohlendieck
The highly progressive neuromuscular disorder dystrophinopathy is triggered by primary abnormalities in the Dmd gene, which causes cytoskeletal instability and loss of sarcolemmal integrity. Comparative organellar proteomics was employed to identify sarcolemma-associated proteins with an altered concentration in dystrophic muscle tissue from the mdx-4cv mouse model of dystrophinopathy. A lectin agglutination method was used to prepare a sarcolemma-enriched fraction and resulted in the identification of 190 significantly changed protein species...
February 1, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29398619/patient-derived-xenografts-pdx-for-personalized-treatment-of-pancreatic-cancer-emerging-allies-in-the-war-on-a-devastating-cancer
#20
Evangelia Sereti, Theodosia Karagianellou, Ioanna Kotsoni, Dimitrios Magouliotis, Konstantinos Kamposioras, Engin Ulukaya, Nikos Sakellaridis, Dimitrios Zacharoulis, Konstantinos Dimas
The prognosis of pancreatic ductal adenocarcinoma (PDAC), the eighth most lethal cancer for men and ninth for women worldwide, remains dismal. The increasing rates of deaths by PDAC indicate that the overall management of the disease in 21st century is still insufficient. Thus it is obvious that there is an unmet need to improve management of PDAC by finding new biomarkers to screen high risk patients, confirm diagnosis, and predict response to treatment as well more efficacious and safer treatments. Patient Derived Xenografts (PDX) have been developed as a new promising tool in an effort to mirror genetics, tumor heterogeneity and cancer microenvironment of the primary tumor...
February 1, 2018: Journal of Proteomics
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