Articles

The Aeromonas salmonicida subsp. salmonicida exoproteome: global analysis, moonlighting proteins and putative antigens for vaccination against furunculosis

Aeromonas salmonicida subsp. salmonicida, the etiologic agent of furunculosis, is a major pathogen of fisheries worldwide. Despite the identification of several virulence factors the pathogenesis is still poorly...

Authors: Philippe Vanden Bergh, Manfred Heller, Sophie Braga-Lagache and Joachim Frey

Quantitative proteomics reveals regulatory differences in the chondrocyte secretome from human medial and lateral femoral condyles in osteoarthritic patients

Osteoarthritis (OA) is a destructive joint disease and there are no known biomarkers available for an early diagnosis. To identify potential disease biomarkers and gain further insight into the disease mechani...

Authors: Johan Stenberg, Ulla Rüetschi, Eva Skiöldebrand, Johan Kärrholm and Anders Lindahl

The Aeromonas salmonicida subsp. salmonicida exoproteome: determination of the complete repertoire of Type-Three Secretion System effectors and identification of other virulence factors

Aeromonas salmonicida subsp. salmonicida, the etiologic agent of furunculosis, is a major pathogen of fisheries worldwide. Several virulence factors have been described, but the type-three secretion system (T3SS...

Authors: Philippe Vanden Bergh, Manfred Heller, Sophie Braga-Lagache and Joachim Frey

Proteomic analysis of Fusarium oxysporum f. sp. cubense tropical race 4-inoculated response to Fusarium wilts in the banana root cells

Fusarium wilt of banana is one of the most destructive diseases in the world. This disease has caused heavy losses in major banana production areas. Except for molecular breeding methods based on plant defense...

Authors: Xingshen Li, Tingting Bai, Yunfeng Li, Xiaolei Ruan and Huaping Li

The proteome of the calcified layer organic matrix of turkey (Meleagris gallopavo) eggshell

Chicken eggshell mineralization is a prominent model for biomineralization not only because of its importance for avian reproduction but also because of the commercial interest associated with eggshell quality...

Authors: Karlheinz Mann and Matthias Mann

Potential biomarkers for adult acute myeloid leukemia minimal residual disease assessment searched by serum peptidome profiling

Post treatment minimal residual disease (MRD) determination contributes to impending relapse prediction, chemotherapy response and clinical outcomes assessment, guiding clinicians to develop reasonable and eff...

Authors: Ju Bai, Aili He, Wanggang Zhang, Chen Huang, Juan Yang, Yun Yang, Jianli Wang and Yang Zhang

Label-free mass spectrometry proteome quantification of human embryonic kidney cells following 24 hours of sialic acid overproduction

Cell surface glycoprotein sialylation is one of the most ubiquitous glycan modifications found on higher eukaryotes. The surface sialylation pattern of cells is influenced by the cellular environment but also ...

Authors: Ville I Parviainen, Sakari Joenväärä, Niina Tohmola and Risto Renkonen

Differential protein expression in perfusates from metastasized rat livers

Liver perfusates exhibit theoretical advantages regarding the discovery of disease biomarkers because they contain proteins that readily enter the blood-stream, and perfusion preserves the disease state in its...

Authors: Yang Zhang, Menglin Li, Lilong Wei, Lisi Zhu, Siqi Hu, Shuzhen Wu, Sucan Ma and Youhe Gao

Comparison of first dimension IPG and NEPHGE techniques in two-dimensional gel electrophoresis experiment with cytosolic unfolded protein response in Saccharomyces cerevisiae

Two-dimensional gel electrophoresis (2DE) is one of the most popular methods in proteomics. Currently, most 2DE experiments are performed using immobilized pH gradient (IPG) in the first dimension; however, so...

Authors: Rimantas Slibinskas, Raimundas Ražanskas, Rūta Zinkevičiūtė and Evaldas Čiplys

Erratum to: Heat stress-induced response of the proteomes of leaves from Salvia splendens vista and king

Authors: Hui Liu, Guozheng Shen, Xianping Fang, Qiaojuan Fu, Kangkang Huang, Yi Chen, Hong Yu, HengMu Zhang, Yun Zhao, Le Zhang, Liang Jin and Songlin Ruan

A note on protein expression changes in chicken breast muscle in response to time in transit before slaughtering

Aims of the research were to devise a proteome map of the chicken Pectoralis superficialis muscle, as resolved by two-dimensional gel electrophoresis, and to characterize protein expression changes in the soluble...

Authors: Enrico Zanetti, Antonio Masi, Micaela Pivato, Serena Tolin, Anna Rita Trentin, Cem Guler, Servet Yalçin and Martino Cassandro

A new type of protein chip to detect hepatocellular carcinoma-related autoimmune antibodies in the sera of hepatitis C virus-positive patients

We report here a new type of protein chip to detect antibodies in sera. This chip method was used to a prototype created to detect hepatocellular carcinoma (HCC) -related autoantibodies in the sera of hepatiti...

Authors: Junko Akada, Shuichi Kamei, Akane Ito, Moe Ito, Takao Kitagawa, Hiroko Furumoto, Yukari Kato, Michiko Tamesa, Motonari Takashima, Mutsunori Shirai, Hirofumi Yamano, Masaaki Oka, Yasuhiro Kuramitsu and Kazuyuki Nakamura

Proteomic analysis of the inhibitory effect of epigallocatechin gallate on lipid accumulation in human HepG2 cells

(−)-Epigallocatechin-3-gallate (EGCG), the most abundant catechin found in green tea, effectively reduces body weight and tissue and blood lipid accumulation. To explore the mechanism by which EGCG inhibits ce...

Authors: Zhonghua Liu, Qin Li, Jianan Huang, Qionglin Liang, Yujun Yan, Haiyan Lin, Wenjun Xiao, Yong Lin, Sheng Zhang, Bin Tan and Guoan Luo

Identification of cellular proteome using two-dimensional difference gel electrophoresis in ST cells infected with transmissible gastroenteritis coronavirus

Transmissible gastroenteritis coronavirus (TGEV) is an enteropathogenic coronavirus that causes diarrhea in pigs, which is correlated with high morbidity and mortality in suckling piglets. Information remains ...

Authors: Xin Zhang, Hong-Yan Shi, Jian-Fei Chen, Da Shi, Hong-Wu Lang, Zhong-Tian Wang and Li Feng

Identification of Enolase 1 and Thrombospondin-1 as serum biomarkers in HBV hepatic fibrosis by proteomics

Hepatic fibrosis is an inevitable process in the progression of chronic HBV infection to hepatic cirrhosis, but its detailed mechanism is still unknown. Clinic serum biomarkers of HBV hepatic cirrhosis were sc...

Authors: Bin Zhang, Zi Wang, Bin Deng, Xiaoqiong Wu, Jing Liu and Xueping Feng

Proteomic analyses of age related changes in A.BY/SnJ mouse hearts

A.BY/SnJ mice are used to study pathological alterations in the heart due to enteroviral infections. Since age is a well-known factor influencing the susceptibility of mice to infection, response to stress and...

Authors: Krishnatej Nishtala, Truong Quoc Phong, Leif Steil, Martina Sauter, Manuela Gesell Salazar, Reinhard Kandolf, Stephan B Felix, Uwe Völker, Karin Klingel and Elke Hammer

Comparative secretome analysis of four isogenic Bacillus clausii probiotic strains

The spore-bearing alkaliphilic Bacillus species constitute a large, heterogeneous group of microorganisms, important for their ability to produce enzymes, antibodies and metabolites of potential medical use. Some...

Authors: Rosa Lippolis, Rosa Anna Siciliano, Maria Fiorella Mazzeo, Anna Abbrescia, Antonio Gnoni, Anna Maria Sardanelli and Sergio Papa

Proteomic profiling for the identification of serum diagnostic biomarkers for abdominal and thoracic aortic aneurysms

Aortic aneurysm is an increasingly common vascular disorder with fatal implication. However, there is no established diagnosis other than that based on aneurysmal size. For this purpose, serum protein biomarke...

Authors: Kazumi Satoh, Tomoko Maniwa, Teiji Oda and Ken-ichi Matsumoto

Nuclear proteome response to cell wall removal in rice (Oryza sativa)

Plant cells are routinely exposed to various pathogens and environmental stresses that cause cell wall perturbations. Little is known of the mechanisms that plant cells use to sense these disturbances and tran...

Authors: Hana Mujahid, Feng Tan, Jian Zhang, Babi Ramesh Reddy Nallamilli, Ken Pendarvis and Zhaohua Peng

Heat stress-induced response of the proteomes of leaves from Salvia splendens Vista and King

Salvia splendens Ker-Gawl, most commonly used in China to add a splash of brilliant color to the surroundings during the warm season, is subject to heat stress, which can greatly affect its growth and yield.

Authors: Hui Liu, Guozheng Shen, Xianping Fang, Qiaojuan Fu, Kangkang Huang, Yi Chen, Hong Yu, Yun Zhao, Le Zhang, Liang Jin and Songlin Ruan

Azacytidine induces necrosis of multiple myeloma cells through oxidative stress

Azacytidine is an inhibitor of DNA methyltransferase and is known to be an anti-leukemic agent to induce cancer cell apoptosis. In the present study, multiple myeloma cells were treated with azacytidine at cli...

Authors: Enbing Tian, Haiping Tang, Renhua Xu, Chongdong Liu, Haiteng Deng and Qingtao Wang

Impact of pyrrolidine-bispyrrole DNA minor groove binding agents and chirality on global proteomic profile in Escherichia Coli

There is great interest in the design of small molecules that selectively target minor grooves of duplex DNA for controlling specific gene expression implicated in a disease. The design of chiral small molecul...

Authors: Ya-ting Yang, Chun-Yu Lin, Jingyueh Jeng and Chi-Wi Ong

In-depth mass spectrometric mapping of the human vitreous proteome

Mapping of proteins involved in normal eye functions is a prerequisite to identify pathological changes during eye disease processes. We therefore analysed the proteome of human vitreous by applying in-depth p...

Authors: Sebastian Aretz, Tim U Krohne, Kerstin Kammerer, Uwe Warnken, Agnes Hotz-Wagenblatt, Marion Bergmann, Boris V Stanzel, Tore Kempf, Frank G Holz, Martina Schnölzer and Jürgen Kopitz

Interactions by 2D Gel Electrophoresis Overlap (iGEO): a novel high fidelity approach to identify constituents of protein complexes

Here we describe a novel approach used to identify the constituents of protein complexes with high fidelity, using the integrin-associated scaffolding protein PINCH as a test case. PINCH is comprised of five L...

Authors: Masaaki Yoshigi, Stephen M Pronovost and Julie L Kadrmas

Comparative proteome analysis of Tumor necrosis factor α-stimulated human Vascular Smooth Muscle Cells in response to melittin

Bee venom has been used to relieve pain and to treat inflammatory diseases, including rheumatoid arthritis, in humans. To better understand the mechanisms of the anti-inflammatory and anti-atherosclerosis effe...

Authors: Hyun-Ji Cho, Jeong-Han Kang, Kwan-Kyu Park, Jung-Yoon Choe, Yoon-Yub Park, Yong-Suk Moon, Il-Kyung Chung, Hyeun-Wook Chang, Cheorl-Ho Kim, Yung Hyun Choi, Wun-Jae Kim, Sung-Kwon Moon and Young-Chae Chang

A SELDI mass spectrometry study of experimental autoimmune encephalomyelitis: sample preparation, reproducibility, and differential protein expression patterns

Experimental autoimmune encephalomyelitis (EAE) is an autoimmune, inflammatory disease of the central nervous system that is widely used as a model of multiple sclerosis (MS). Mitochondrial dysfunction appears...

Authors: Sausan Azzam, Laurie Broadwater, Shuo Li, Ernest J Freeman, Jennifer McDonough and Roger B Gregory

Members of the high mobility group B protein family are dynamically expressed in embryonic neural stem cells

Neural Stem Cells (NSCs) are a distinct group of cells present in the embryonic and adult mammalian central nervous system (CNS) that are able to differentiate into neurons, astrocytes and oligodendrocytes. As...

Authors: Ariel B Abraham, Robert Bronstein, Emily I Chen, Antonius Koller, Lorenza Ronfani, Mirjana Maletic-Savatic and Stella E Tsirka

Whole gel processing procedure for GeLC-MS/MS based proteomics

SDS-PAGE followed by in-gel digestion (IGD) is a popular workflow in mass spectrometry-based proteomics. In GeLC-MS/MS, a protein lysate of a biological sample is separated by SDS-PAGE and each gel lane is sli...

Authors: Sander R Piersma, Marc O Warmoes, Meike de Wit, Inge de Reus, Jaco C Knol and Connie R Jiménez

Retraction Note: clinical and technical phosphoproteomic research

Authors: Elena López, Isabel López, Antonio Ferreira and Julia Sequí

Proteomics approach combined with biochemical attributes to elucidate compatible and incompatible plant-virus interactions between Vigna mungo and Mungbean Yellow Mosaic India Virus

Vigna mungo, a tropical leguminous plant, highly susceptible to yellow mosaic disease caused by Mungbean Yellow Mosaic India Virus (MYMIV) resulting in high yield penalty. The molecular events occurring during c...

Authors: Subrata Kundu, Dipjyoti Chakraborty, Anirban Kundu and Amita Pal

Plasma proteome changes associated with refractory anemia and refractory anemia with ringed sideroblasts in patients with myelodysplastic syndrome

Refractory anemia and refractory anemia with ringed sideroblasts are two myelodysplastic syndrome (MDS) subgroups linked with anemia. MDS is a group of heterogeneous oncohematological bone marrow disorders cha...

Authors: Pavel Májek, Zuzana Riedelová-Reicheltová, Jiří Suttnar, Klára Pečánková, Jaroslav Čermák and Jan E Dyr

Profiling and annotation of human kidney glomerulus proteome

The comprehensive analysis of human kidney glomerulus we previously performed using highly purified glomeruli, provided a dataset of 6,686 unique proteins representing 2,966 distinct genes. This dataset, howev...

Authors: Zenyui Cui, Yutaka Yoshida, Bo Xu, Ying Zhang, Masaaki Nameta, Sameh Magdeldin, Tomoo Makiguchi, Toshikazu Ikoma, Hidehiko Fujinaka, Eishin Yaoita and Tadashi Yamamoto

Proteomic analysis of elite soybean Jidou17 and its parents using iTRAQ-based quantitative approaches

Derived from Hobbit as the female parent and Zao5241 as the male parent, the elite soybean cultivar Jidou17 is significantly higher yielding and shows enhanced qualities and stronger resistance to non-biologic...

Authors: Jun Qin, Feng Gu, Duan Liu, Changcheng Yin, Shuangjin Zhao, Hao Chen, Jianan Zhang, Chunyan Yang, Xu Zhan and Mengchen Zhang

The 3T3-L1 adipocyte glycogen proteome

Glycogen is a branched polysaccharide of glucose residues, consisting of α-1-4 glycosidic linkages with α-1-6 branches that together form multi-layered particles ranging in size from 30 nm to 300 nm. Glycogen ...

Authors: David Stapleton, Chad Nelson, Krishna Parsawar, Marcelo Flores-Opazo, Donald McClain and Glendon Parker

Pre-analytical stability of the plasma proteomes based on the storage temperature

This study examined the effect of storage temperature on the protein profile of human plasma. Plasma samples were stored for 13 days at -80°C, -20°C, +4°C and room temperature (20-25°C) prior to proteomic anal...

Authors: Sara Pasella, Angela Baralla, Elisabetta Canu, Sara Pinna, James Vaupel, Marta Deiana, Claudio Franceschi, Giovannella Baggio, Angelo Zinellu, Salvatore Sotgia, Giuseppe Castaldo, Ciriaco Carru and Luca Deiana

Monitoring post mortem changes in porcine muscle through 2-D DIGE proteome analysis of Longissimus muscle exudate

Meat quality is a complex trait influenced by a range of factors with post mortem biochemical processes highly influential in defining ultimate quality. High resolution two-dimensional DIfference Gel Electrophore...

Authors: Alessio Di Luca, Giuliano Elia, Anne Maria Mullen and Ruth M Hamill

Comparative proteomic analysis of the effect of temperature and fertilizer on gliadin and glutenin accumulation in the developing endosperm and flour from Triticum aestivum L. cv. Butte 86

Flour quality is largely determined by the gluten proteins, a complex mixture of proteins consisting of high molecular weight-glutenin subunits (HMW-GS), low molecular weight-glutenin subunits (LMW-GS), and α-...

Authors: William J Hurkman, Charlene K Tanaka, William H Vensel, Roger Thilmony and Susan B Altenbach

Proteins from Tuber magnatum Pico fruiting bodies naturally grown in different areas of Italy

A number of Tuber species are ecologically important. The fruiting bodies of some of these also have value as a cooking ingredient due to the fact that they possess exceptional flavor and aromatic properties. In ...

Authors: Federico Vita, Valentina Lucarotti, Emanuele Alpi, Raffaella Balestrini, Antonietta Mello, Angela Bachi, Massimo Alessio and Amedeo Alpi

Identification of differentially expressed proteins of Arthrospira (Spirulina) plantensis-YZ under salt-stress conditions by proteomics and qRT-PCR analysis

Arthrospira (Spirulina) platensis as a representative species of cyanobacteria has been recognized and used worldwide as a source of protein in the food, which possesses some unusual and valuable physiological c...

Authors: Huili Wang, Yanmei Yang, Wei Chen, Li Ding, Peizhen Li, Xiaokai Zhao, Xuedong Wang, Aiying Li and Qiyu Bao

On protein abundance distributions in complex mixtures

Mass spectrometry, an analytical technique that measures the mass-to-charge ratio of ionized atoms or molecules, dates back more than 100 years, and has both qualitative and quantitative uses for determining c...

Authors: JA Koziol, NM Griffin, F Long, Y Li, M Latterich and JE Schnitzer

Comparative proteomic analysis implicates eEF2 as a novel target of PI3Kγ in the MDA-MB-231 metastatic breast cancer cell line

Cancer cell migration is fundamentally required for breast tumour invasion and metastasis. The insulin-like growth factor 1 tyrosine kinase receptor (IGF-1R) and the chemokine G-protein coupled receptor, CXCR4...

Authors: Meizhi Niu, Manuela Klingler-Hoffmann, Julie A Brazzatti, Briony Forbes, Chareeporn Akekawatchai, Peter Hoffmann and Shaun R McColl

Major soluble proteome changes in Deinococcus deserti over the earliest stages following gamma-ray irradiation

Deinococcus deserti VCD115 has been isolated from Sahara surface sand. This radiotolerant bacterium represents an experimental model of choice to understand adaptation to harsh conditions encountered in hot arid...

Authors: Alain Dedieu, Elodie Sahinovic, Philippe Guérin, Laurence Blanchard, Sylvain Fochesato, Bruno Meunier, Arjan de Groot and Jean Armengaud

Comparisons of protein profiles of beech bark disease resistant and susceptible American beech (Fagus grandifolia)

Beech bark disease is an insect-fungus complex that damages and often kills American beech trees and has major ecological and economic impacts on forests of the northeastern United States and southeastern Cana...

Authors: Mary E Mason, Jennifer L Koch, Marek Krasowski and Judy Loo

Unrestrictive identification of post-translational modifications in the urine proteome without enrichment

Research on the human urine proteome may lay the foundation for the discovery of relevant disease biomarkers. Post-translational modifications (PTMs) have important effects on the functions of protein biomarke...

Authors: Liu Liu, Xuejiao Liu, Wei Sun, Mingxi Li and Youhe Gao

Proteomic analysis of S-nitrosylation induced by 1-methyl-4-phenylpyridinium (MPP⁺)

Nitric oxide (NO) mediates its function through the direct modification of various cellular targets. S-nitrosylation is a post-translational modification of cysteine residues by NO that regulates protein funct...

Authors: Akira T Komatsubara, Tomoya Asano, Hiroki Tsumoto, Kazuharu Shimizu, Takumi Nishiuchi, Masanori Yoshizumi and Kentaro Ozawa

Wounding, insect chewing and phloem sap feeding differentially alter the leaf proteome of potato, Solanum tuberosum L.

Various factors shape the response of plants to herbivorous insects, including wounding patterns, specific chemical effectors and feeding habits of the attacking herbivore. Here we performed a comparative prot...

Authors: Marc-Olivier Duceppe, Conrad Cloutier and Dominique Michaud

Improved spatial learning and memory by perilla diet is correlated with immunoreactivities to neurofilament and α-synuclein in hilus of dentate gyrus

Perilla (Perilla frutescens) oil is very rich in α-linolenic acid, an omega-3 fatty acid. As it is widely reported that omega-3 fatty acid supplementation improves cognitive function in children and adults, feedi...

Authors: Jinwoo Lee, Sunmin Park, Ju-Young Lee, Yeong Keun Yeo, Jong Sang Kim and Jinkyu Lim

An antibody microarray analysis of serum cytokines in neurodegenerative Parkinsonian syndromes

Microarray technology may offer a new opportunity to gain insight into disease-specific global protein expression profiles. The present study was performed to apply a serum antibody microarray to screen for di...

Authors: Philipp Mahlknecht, Sylvia Stemberger, Fabienne Sprenger, Johannes Rainer, Eva Hametner, Rudolf Kirchmair, Christoph Grabmer, Christoph Scherfler, Gregor K Wenning, Klaus Seppi, Werner Poewe and Markus Reindl

An individual urinary proteome analysis in normal human beings to define the minimal sample number to represent the normal urinary proteome

The urinary proteome has been widely used for biomarker discovery. A urinary proteome database from normal humans can provide a background for discovery proteomics and candidate proteins/peptides for targeted ...

Authors: Xuejiao Liu, Chen Shao, Lilong Wei, Jindan Duan, Shuzhen Wu, Xuewang Li, Mingxi Li and Wei Sun

Label-free quantitative proteomics of CD133-positive liver cancer stem cells

CD133-positive liver cancer stem cells, which are characterized by their resistance to conventional chemotherapy and their tumor initiation ability at limited dilutions, have been recognized as a critical targ...

Authors: Sheng-Ta Tsai, Chih-Chiang Tsou, Wan-Yu Mao, Wei-Chao Chang, Hsin-Ying Han, Wen-Lian Hsu, Chung-Leung Li, Chia-Ning Shen and Chung-Hsuan Chen