Articles

Proteome-wide identification of arginine methylation in colorectal cancer tissues from patients

Protein arginine methylation reaction is catalyzed by protein arginine methyltransferase (PRMT) and the modification is implicated in various diseases including cancer. Currently, thousands of arginine methyla...

Authors: Yongchul Lim, Ju Yeon Lee, Su Jin Ha, Suyeun Yu, Jung Kyong Shin and Hee Cheol Kim

Production of high-quality two-dimensional gel electrophoresis profile for marine medaka samples by using Trizol-based protein extraction approaches

Marine medaka is among the most popular models of fish species for ecotoxicology and environmental research and proteomic studies are useful tools for understanding the molecular responses of medaka upon expos...

Authors: Celia Sze-Nga Kwok, Kaze King-Yip Lai, Sai-Wo Lam, Kin-Ka Chan, Steven Jing-Liang Xu and Fred Wang-Fat Lee

NEK10 interactome and depletion reveal new roles in mitochondria

Members of the family of NEK protein kinases (NIMA-related kinases) were described to have crucial roles in regulating different aspects of the cell cycle. NEK10 was reported to take part in the maintenance of...

Authors: Andressa Peres de Oliveira, Fernanda Luisa Basei, Priscila Ferreira Slepicka, Camila de Castro Ferezin, Talita D. Melo-Hanchuk, Edmarcia Elisa de Souza, Tanes I. Lima, Valquiria Tiago dos Santos, Davi Mendes, Leonardo Reis Silveira, Carlos Frederico Martins Menck and Jörg Kobarg

Protection of the transplant kidney during cold perfusion with doxycycline: proteomic analysis in a rat model

It has been previously shown that doxycycline (Doxy) protects the kidney from preservation injury by inhibition of matrix metalloproteinase. However, the precise molecular mechanism involved in this protection...

Authors: Michael A. J. Moser, Katherine Sawicka, Jolanta Sawicka, Aleksandra Franczak, Alejandro Cohen, Iwona Bil-Lula and Grzegorz Sawicki

Comprehensive analysis of the cardiac proteome in a rat model of myocardial ischemia-reperfusion using a TMT-based quantitative proteomic strategy

Traditional studies of the cardiac proteome have mainly investigated in an animal model by two-dimensional gel electrophoresis (2-DE). However, the results have not been of satisfactory quality for an understa...

Authors: Sun Ha Lim, Jongwon Lee and Mee-Jung Han

Comparative proteomic analysis of the brain and colon in three rat models of irritable bowel syndrome

Irritable bowel syndrome (IBS) has been gradually recognized as a disorder of the brain-gut interaction, but the molecular changes in the brain and colon that occur in disease development remain poorly underst...

Authors: Beihua Zhang, Hong Xue, Wei Wang, Ting Chen, Min Su, Nan Kang, Jianqin Yang, Zhaoxiang Bian, Fengyun Wang and Xudong Tang

The interactome and proteomic responses of ALKBH7 in cell lines by in-depth proteomics analysis

ALKBH7 is a mitochondrial protein, involved in programmed necrosis, fatty acid metabolism, cell cycle regulation, and prostate cancer disease. However, the exact roles of ALKBH7 and the underlying molecular me...

Authors: Shu Meng, Shaohua Zhan, Wanchen Dou and Wei Ge

Chronic kidney disease: a review of proteomic and metabolomic approaches to membranous glomerulonephritis, focal segmental glomerulosclerosis, and IgA nephropathy biomarkers

Chronic Kidney Disease (CKD) is a global health problem annually affecting millions of people around the world. It is a comprehensive syndrome, and various factors may contribute to its occurrence. In this stu...

Authors: Amir Taherkhani, Reyhaneh Farrokhi Yekta, Maede Mohseni, Massoud Saidijam and Afsaneh Arefi Oskouie

Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs

Polypterus senegalus can fully regenerate its pectoral lobed fins, including a complex endoskeleton, with remarkable precision. However, despite the enormous potential of this species for use in medical research,...

Authors: Suxiang Lu, Qian Xiong, Kang Du, Xiaoni Gan, Xuzhen Wang, Liandong Yang, Ying Wang, Feng Ge and Shunping He

Exploring the key communicator role of exosomes in cancer microenvironment through proteomics

There have been many attempts to fully understand the mechanism of cancer behavior. Yet, how cancers develop and metastasize still remain elusive. Emerging concepts of cancer biology in recent years have focus...

Authors: HuiSu Kim, Dong Wook Kim and Je-Yoel Cho

Unraveling proteome changes and potential regulatory proteins of bovine follicular Granulosa cells by mass spectrometry and multi-omics analysis

In previous study, we performed next-gene sequencing to investigate the differentially expressed transcripts of bovine follicular granulosa cells (GCs) at dominant follicle (DF) and subordinate follicle (SF) s...

Authors: Shuning Hou, Qingling Hao, Zhiwei Zhu, Dongmei Xu, Wenzhong Liu, Lihua Lyu and Pengfei Li

Proteomic analysis of human periodontal ligament cells under hypoxia

The periodontal ligament is essential for homeostasis of periodontal tissue. A hypoxic milieu of the periodontal tissue is generated under periodontitis or during orthodontic treatment, which affects the perio...

Authors: Qiwen Li, Tao Luo, Wenxin Lu, Xiaoxiao Yi, Zhihe Zhao and Jun Liu

Comparison of enzymatic activities and proteomic profiles of Butyrivibrio fibrisolvens grown on different carbon sources

The rumen microbiota is one of the most complex consortia of anaerobes, involving archaea, bacteria, protozoa, fungi and phages. They are very effective at utilizing plant polysaccharides, especially cellulose...

Authors: Hana Sechovcová, Lucie Kulhavá, Kateřina Fliegerová, Mária Trundová, Daniel Morais, Jakub Mrázek and Jan Kopečný

Hepatic protein Carbonylation profiles induced by lipid accumulation and oxidative stress for investigating cellular response to non-alcoholic fatty liver disease in vitro

Non-alcoholic fatty liver disease (NAFLD) is caused by excessive accumulation of fat within the liver, leading to further severe conditions such as non-alcoholic steatohepatitis (NASH). Progression of healthy ...

Authors: Peerut Chienwichai, Onrapak Reamtong, Usa Boonyuen, Trairak Pisitkun, Poorichaya Somparn, Prapin Tharnpoophasiam, Suwalee Worakhunpiset and Supachai Topanurak

Proteome modifications on tomato under extreme high light induced-stress

Abiotic stress reduces photosynthetic yield and plant growth, negatively impacting global crop production and is a major constraint faced by agriculture. However, the knowledge on the impact on plants under ex...

Authors: Débora Parrine, Bo-Sen Wu, Bilal Muhammad, Keith Rivera, Darryl Pappin, Xin Zhao and Mark Lefsrud

Key factors identified by proteomic analysis in maize (Zea mays L.) seedlings’ response to long-term exposure to different phosphate levels

Maize seedlings are constantly exposed to inorganic phosphate (Pi)-limited environments. To understand how maize cope with low Pi (LP) and high Pi (HP) conditions, physiological and global proteomic analysis o...

Authors: Yanling Sun, Chunhua Mu and Xia Liu

Calcitonin gene-related peptide promotes proliferation and inhibits apoptosis in endothelial progenitor cells via inhibiting MAPK signaling

Calcitonin gene-related peptide (CGRP) contributes to bone formation by stimulating bone marrow stromal cell (BMSC) proliferation and differentiation. However, the proliferative and apoptotic effects of CGRP o...

Authors: Jianqun Wu, Song Liu, Zhao Wang, Shenghui Ma, Huan Meng and Jijie Hu

Comparative proteomic analysis of Ulva prolifera response to high temperature stress

Ulva prolifera belongs to green macroalgae and is the dominant species of green tide. It is distributed worldwide and is therefore subject to high-temperature stress during the growth process. However, the adapta...

Authors: Meihua Fan, Xue Sun, Zhi Liao, Jianxin Wang, Yahe Li and Nianjun Xu

Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediates

The non-receptor tyrosine kinase, SRMS (Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites) is a member of the BRK family kinases (BFKs) which represents an evolution...

Authors: Raghuveera Kumar Goel, Mona Meyer, Marta Paczkowska, Jüri Reimand, Frederick Vizeacoumar, Franco Vizeacoumar, TuKiet T. Lam and Kiven Erique Lukong

Label-free quantitative mass spectrometry analysis of differential protein expression in the developing cochlear sensory epithelium

The sensory epithelium of the inner ear converts the mechanical energy of sound to electro-chemical energy recognized by the central nervous system. This process is mediated by receptor cells known as hair cel...

Authors: Lancia N. F. Darville and Bernd H. A. Sokolowski

Comparative iTRAQ proteomics revealed proteins associated with horn development in yak

The practice of dehorning yak raises animal safety concerns, which have been addressed by selective breeding to obtain genetically hornless yak. The POLLED locus in yak has been studied extensively; however, l...

Authors: Mingna Li, Xiaoyun Wu, Xian Guo, Pengjia Bao, Xuezhi Ding, Min Chu, Chunnian Liang and Ping Yan

Correction to: Proteomic identification and characterization of hepatic glyoxalase 1 dysregulation in non-alcoholic fatty liver disease

Following publication of the original article [1]

Authors: Christos Spanos, Elaina M. Maldonado, Ciarán P. Fisher, Petchpailin Leenutaphong, Ernesto Oviedo-Orta, David Windridge, Francisco J. Salguero, Alexandra Bermúdez-Fajardo, Mark E. Weeks, Caroline Evans, Bernard M. Corfe, Naila Rabbani, Paul J. Thornalley, Michael H. Miller, Huan Wang, John F. Dillon…

iTRAQ-Based Proteomic Analysis reveals possible target-related proteins and signal networks in human osteoblasts overexpressing FGFR2

Fibroblast growth factor receptor 2 (FGFR2) play a vital role in skeletogenesis. However, the molecular mechanisms triggered by FGFR2 in osteoblasts are still not fully understood. In this study, proteomics an...

Authors: Tianyi Cai, Baojin Wu, Xinjie Tang, Zhaoping Zhou, Junyi Yang, Ronghu Ke and Xiongzheng Mu

In-depth proteomic analyses of Haliotis laevigata (greenlip abalone) nacre and prismatic organic shell matrix

The shells of various Haliotis species have served as models of invertebrate biomineralization and physical shell properties for more than 20 years. A focus of this research has been the nacreous inner layer of t...

Authors: Karlheinz Mann, Nicolas Cerveau, Meike Gummich, Monika Fritz, Matthias Mann and Daniel J. Jackson

Correction to: Proteomic characterization of adrenal gland embryonic development reveals early initiation of steroid metabolism and reduction of the retinoic acid pathway

Upon publication of the original article [1], Marwa Eltoweissy noticed that her affiliation: “3. Department of Zoology, Faculty of Science, Alexandria University, Alexandria, Egypt” was missing. This affiliati...

Authors: Gry H. Dihazi, Gerhard A. Mueller, Abdul R. Asif, Marwa Eltoweissy, Johannes T. Wessels and Hassan Dihazi

Proteomic analysis of buccal gland secretion from fasting and feeding lampreys (Lampetra morii)

Previous studies have shown that lamprey buccal glands contain some regulators related to anticoagulation, nociception, and immune responses due to the blood sucking habit. Regrettably, the protein expression ...

Authors: Bowen Li, Meng Gou, Jianmei Han, Xiaofei Yuan, Yingying Li, Tiesong Li, Qi Jiang, Rong Xiao and Qingwei Li

ITRAQ-based quantitative proteomic analysis of processed Euphorbia lathyris L. for reducing the intestinal toxicity

Euphorbia lathyris L., a Traditional Chinese medicine (TCM), is commonly used for the treatment of hydropsy, ascites, constipation, amenorrhea, and scabies. Semen Euphorbiae Pulveratum, which is another type of E...

Authors: Yu Zhang, Yingzi Wang, Shaojing Li, Xiuting Zhang, Wenhua Li, Shengxiu Luo, Zhenyang Sun and Ruijie Nie

In vitro gentamicin exposure alters caveolae protein profile in cochlear spiral ligament pericytes

The aminoglycoside antibiotic gentamicin is an ototoxic drug and has been used experimentally to investigate cochlear damage induced by noise.

Authors: Elisa Ghelfi, Yohann Grondin, Emil J. Millet, Adam Bartos, Magda Bortoni, Clara Oliveira Gomes dos Santos, Humberto J. Trevino-Villarreal, Rosalinda Sepulveda and Rick Rogers

Effects of the complete replacement of fish oil with linseed oil on growth, fatty acid composition, and protein expression in the Chinese mitten crab (Eriocheir sinensis)

The finite marine resources make it difficult for us to obtain enough fish oil (FO) used in aquatic feeds. Another sustainable ingredients should be found to substitute FO. The effects of replacing FO with veg...

Authors: Banghong Wei, Zhigang Yang, Yongxu Cheng, Jianyi Wang and Junyu Zhou

Profiling the interactome of protein kinase C ζ by proteomics and bioinformatics

Protein kinase C ζ (PKCζ), an isoform of the atypical protein kinase C, is a pivotal regulator in cancer. However, the molecular and cellular mechanisms whereby PKCζ regulates tumorigenesis and metastasis are ...

Authors: Chunyu Hou, Yuan Li, Huiqin Liu, Mengjiao Dang, Guoxuan Qin, Ning Zhang and Ruibing Chen

Proteomic identification and characterization of hepatic glyoxalase 1 dysregulation in non-alcoholic fatty liver disease

Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease worldwide. However, its molecular pathogenesis is incompletely characterized and clinical biomarkers remain scarce. The aims of these ...

Authors: Christos Spanos, Elaina M. Maldonado, Ciarán P. Fisher, Petchpailin Leenutaphong, Ernesto Oviedo-Orta, David Windridge, Francisco J. Salguero, Alexandra Bermúdez-Fajardo, Mark E. Weeks, Caroline Evans, Bernard M. Corfe, Naila Rabbani, Paul J. Thornalley, Michael H. Miller, Huan Wang, John F. Dillon…

Effect of ovarian cancer ascites on SKOV-3 cells proteome: new proteins associated with aggressive phenotype in epithelial ovarian cancer

Epithelial ovarian cancer is the second most lethal gynecological cancer worldwide. Ascites can be found in all clinical stages, however in advanced disease stages IIIC and IV it is more frequent and could be ...

Authors: Alfredo Toledo-Leyva, Julio César Villegas-Pineda, Sergio Encarnación-Guevara, Dolores Gallardo-Rincón and Patricia Talamás-Rohana

Proteomic identification of moesin upon exposure to acrolein

Acrolein (allyl Aldehyde) as one of smoke irritant exacerbates chronic airway diseases and increased in sputum of patients with asthma and chronic obstructive lung disease. But underlying mechanism remains unr...

Authors: Pureun-Haneul Lee, Byeong-Gon Kim, Sun-Hye Lee, George D. Leikauf and An-Soo Jang

Chemical proteomics, an integrated research engine for exploring drug-target-phenotype interactions

Authors: Ho Jeong Kwon and Peter Karuso

Comparative proteomic analysis between nitrogen supplemented and starved conditions in Magnaporthe oryzae

Fungi are constantly exposed to nitrogen limiting environments, and thus the efficient regulation of nitrogen metabolism is essential for their survival, growth, development and pathogenicity. To understand ho...

Authors: Yeonyee Oh, Suzanne L. Robertson, Jennifer Parker, David C. Muddiman and Ralph A. Dean

Proteomic analysis of early salt stress responsive proteins in alfalfa roots and shoots

Alfalfa (Medicago sativa) is the most extensively cultivated forage legume in the world, and salinity stress is the most problematic environmental factors limiting alfalfa production. To evaluate alfalfa tissue v...

Authors: Junbo Xiong, Yan Sun, Qingchuan Yang, Hong Tian, Heshan Zhang, Yang Liu and Mingxin Chen

Iron overload down-regulates the expression of the HIV-1 Rev cofactor eIF5A in infected T lymphocytes

Changes in iron metabolism frequently accompany HIV-1 infection. However, while many clinical and in vitro studies report iron overload exacerbates the development of infection, many others have found no corre...

Authors: Carmine Mancone, Alessio Grimaldi, Giulia Refolo, Isabella Abbate, Gabriella Rozera, Dario Benelli, Gian Maria Fimia, Vincenzo Barnaba, Marco Tripodi, Mauro Piacentini and Fabiola Ciccosanti

Examining the influence of specificity ligands and ATP-competitive ligands on the overall effectiveness of bivalent kinase inhibitors

Identifying selective kinase inhibitors remains a major challenge. The design of bivalent inhibitors provides a rational strategy for accessing potent and selective inhibitors. While bivalent kinase inhibitors...

Authors: Margaret L. Wong, Jason Murphy, Edmund Harrington, Carrie M. Gower, Rishi K. Jain, Markus Schirle and Jason R. Thomas

Daptomycin, a last-resort antibiotic, binds ribosomal protein S19 in humans

Daptomycin is a recently introduced, last-resort antibiotic that displays a unique mode of action against Gram-positive bacteria that is not fully understood. Several bacterial targets have been proposed but n...

Authors: Michael P. Gotsbacher, Sungmin Cho, Ho Jeong Kwon and Peter Karuso

Tetrazine ligation for chemical proteomics

Determining small molecule—target protein interaction is essential for the chemical proteomics. One of the most important keys to explore biological system in chemical proteomics field is finding first-class m...

Authors: Kyungtae Kang, Jongmin Park and Eunha Kim

Photo-affinity labeling (PAL) in chemical proteomics: a handy tool to investigate protein-protein interactions (PPIs)

Protein-protein interactions (PPIs) trigger a wide range of biological signaling pathways that are crucial for biomedical research and drug discovery. Various techniques have been used to study specific protei...

Authors: Dhiraj P. Murale, Seong Cheol Hong, Md. Mamunul Haque and Jun-Seok Lee

Thermal proteome profiling: unbiased assessment of protein state through heat-induced stability changes

In recent years, phenotypic-based screens have become increasingly popular in drug discovery. A major challenge of this approach is that it does not provide information about the mechanism of action of the hit...

Authors: André Mateus, Tomi A. Määttä and Mikhail M. Savitski

The hepatocyte proteome in organotypic rat liver models and the influence of the local microenvironment

Liver models that closely mimic the in vivo microenvironment are useful for understanding liver functions, capabilities, and intercellular communication processes. Three-dimensional (3D) liver models assembled...

Authors: Lucas T. Vu, Sophia M. Orbach, W. Keith Ray, Margaret E. Cassin, Padmavathy Rajagopalan and Richard F. Helm

Characterisation of the circulating acellular proteome of healthy sheep using LC-MS/MS-based proteomics analysis of serum

Unlike humans, there is currently no publicly available reference mass spectrometry-based circulating acellular proteome data for sheep, limiting the analysis and interpretation of a range of physiological cha...

Authors: Saul Chemonges, Rajesh Gupta, Paul C. Mills, Steven R. Kopp and Pawel Sadowski

The effect of microbial challenge on the intestinal proteome of broiler chickens

In poultry production intestinal health and function is paramount to achieving efficient feed utilisation and growth. Uncovering the localised molecular mechanisms that occur during the early and important per...

Authors: Emily L. O’Reilly, Richard J. Burchmore, Nicholas H. Sparks and P. David Eckersall

Water deficit mechanisms in perennial shrubs Cerasus humilis leaves revealed by physiological and proteomic analyses

Drought (Water deficit, WD) poses a serious threat to extensively economic losses of trees throughout the world. Chinese dwarf cherry (Cerasus humilis) is a good perennial plant for studying the physiological and...

Authors: Zepeng Yin, Jing Ren, Lijuan Zhou, Lina Sun, Jiewan Wang, Yulong Liu and Xingshun Song

Merging clinical chemistry biomarker data with a COPD database - building a clinical infrastructure for proteomic studies

Data from biological samples and medical evaluations plays an essential part in clinical decision making. This data is equally important in clinical studies and it is critical to have an infrastructure that en...

Authors: Jonatan Eriksson, Simone Andersson, Roger Appelqvist, Elisabet Wieslander, Mikael Truedsson, May Bugge, Johan Malm, Magnus Dahlbäck, Bo Andersson, Thomas E. Fehniger and György Marko-Varga

Proteomic profiling of HBV infected liver biopsies with different fibrotic stages

Hepatitis B virus (HBV) is a global health problem, and infected patients if left untreated may develop cirrhosis and eventually hepatocellular carcinoma. This study aims to enlighten pathways associated with ...

Authors: Seyma Katrinli, Kamil Ozdil, Abdurrahman Sahin, Oguzhan Ozturk, Gozde Kir, Ahmet Tarik Baykal, Emel Akgun, Omer Sinan Sarac, Mehmet Sokmen, H. Levent Doğanay and Gizem Dinler Doğanay

Disulfide proteomics of rice cultured cells in response to OsRacl and probenazole-related immune signaling pathway in rice

Reactive oxygen species (ROS) production is an early event in the immune response of plants. ROS production affects the redox-based modification of cysteine residues in redox proteins, which contribute to prot...

Authors: Kazuko Morino, Mayumi Kimizu and Masayuki Fujiwara

Proteomic analysis of microparticles isolated from malaria positive blood samples

Malaria continues to be a great public health concern due to the significant mortality and morbidity associated with the disease especially in developing countries. Microparticles (MPs), also called plasma mem...

Authors: Samuel Antwi-Baffour, Jonathan Kofi Adjei, Francis Agyemang-Yeboah, Max Annani-Akollor, Ransford Kyeremeh, George Awuku Asare and Ben Gyan