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Journal of Proteome Research

Rob Smith
Mass spectrometry is an important tool used by many scientists throughout the world. Nonetheless, feedback on the strengths and limitations of current software is often restricted to anecdote rather than formal inquiry. Over the course of 100 interviews over the state of mass spectrometry software, surprising patterns coalesced on several topics: perception of the frontier, perception of software quality, and differences between commercial and non-profit environments. Most notably, interviews suggested a substantial schism between user satisfaction with current software and developer perceptions of software quality...
March 16, 2018: Journal of Proteome Research
Ying Zhu, Qing Lei, Dan Li, Yang Zhang, Xiaogang Jiang, Zhanhong Hu, Guoqiang Xu
Protein post-translational modification by ubiquitin-fold modifier 1, UFM1, regulates many biological processes such as response to endoplasmic reticulum stress and regulation of tumor progression. Recent study has indicated that the UFM1-binding and PCI domain-containing protein 1 (UFBP1) is required for the conjugation of UFM1 to a substrate. However, other biological functions of UFBP1 have not been explored. Here, we use immunoprecipitation and label-free quantitative proteomics to identify UFBP1-interacting proteins in a mammalian cell line...
March 13, 2018: Journal of Proteome Research
Kerry R Belton, Yuan Tian, Limin Zhang, Mallappa Anitha, Philip B Smith, Gary H Perdew, Andrew D Patterson
The liver and the mammary gland have complementary metabolic roles during lactation. Substrates (e.g., glucose and amino acids) synthesized by the liver are released into the circulation and are taken up by the mammary gland for milk production (e.g., lactose and the glycerol backbone of milk triglycerides). The aryl hydrocarbon receptor (AHR) has been identified as a lactation regulator in mice, and its activation has been associated with myriad morphological, molecular, and functional defects such as stunted gland development, decreased milk production, and changes in gene expression...
March 9, 2018: Journal of Proteome Research
Fangxu Sun, Alexander A Choi, Ronghu Wu
Fatty acids (FAs) are essential components in cells and are involved in many cellular activities. Abnormal FA metabolism has been reported to be related to human diseases such as cancer and cardiovascular diseases. Identification and quantification of FAs provide insights into their functions in biological systems, but it is very challenging to analyze them due to their structures and properties. In this work, we developed a novel method by integrating tagging FAs with stable isotope labeled aminoxy tandem mass tags (aminoxyTMTs) and mass spectrometric analysis with the positive mode...
March 9, 2018: Journal of Proteome Research
Joana Carrola, Ricardo J B Pinto, Maryam Nasirpour, Carmen S R Freire, Ana M Gil, Conceição Santos, Helena Oliveira, Iola F Duarte
The expansion of biomedical and therapeutic applications of silver nanoparticles (AgNPs) raises the need to further understand their biological effects on human cells. In this work, NMR metabolomics has been applied to reveal the metabolic effects of AgNPs toward human hepatoma (HepG2) cells, which are relevant with respect to nanoparticle accumulation and detoxification. Cellular responses to widely disseminated citrate-coated AgNPs (Cit30) and to emergent biogenic AgNPs prepared using an aqueous plant extract as reducing and stabilizing agent (GS30) have been compared with a view to assess the influence of nanoparticle coating on the metabolic effects produced...
March 9, 2018: Journal of Proteome Research
Taewook Kang, Pia Jensen, Vita Solovyeva, Jonathan R Brewer, Martin R Larsen
Characterization of molecular mechanisms underlying pancreatic β-cell function in relation to glucose-stimulated insulin secretion is incomplete, especially with respect to global response in the nuclear environment. Here, we focus on the characterization of proteins in the nuclear environment of β-cells after brief, high glucose-stimulation. We compared purified nuclei derived from β-cells stimulated with 17mM glucose for 0, 2, and 5 minutes using quantitative proteomics, a time frame that most likely does not result in translation of new protein in the cell...
March 8, 2018: Journal of Proteome Research
Ning Yang, Krishna D P Anapindi, Stanislav S Rubakhin, Pingli Wei, Qing Yu, Lingjun Li, Paul J Kenny, Jonathan V Sweedler
Conserved across vertebrates, the habenular nuclei are a pair of small symmetrical structures in the epithalamus. The nuclei functionally link the forebrain and midbrain by receiving input from and projecting to several brain regions. Each habenular nucleus comprises two major asymmetrical subnuclei, the medial and lateral habenula. These subnuclei are associated with different physiological processes and disorders, such as depression, nicotine addiction, and encoding aversive stimuli or omitting expected rewarding stimuli...
March 8, 2018: Journal of Proteome Research
Paul R Evans, Kyle J Gerber, Eric B Dammer, Duc M Duong, Devrishi Goswami, Daniel J Lustberg, Juan Zou, Jenny J Yang, Serena M Dudek, Patrick R Griffin, Nicholas T Seyfried, John R Hepler
Regulator of G Protein Signaling 14 (RGS14) is a complex scaffolding protein that integrates G protein and MAPK signaling pathways. In the adult mouse brain, RGS14 is predominantly expressed in hippocampal CA2 neurons where it naturally inhibits synaptic plasticity and hippocampus-dependent learning and memory. However, the signaling proteins that RGS14 natively engages to regulate plasticity are unknown. Here, we show that RGS14 exists in a high molecular weight protein complex in brain. To identify RGS14 neuronal interacting partners, endogenous RGS14 immunoprecipitated from mouse brain was subjected to mass spectrometry and proteomic analysis...
March 8, 2018: Journal of Proteome Research
Kathryn Volkening, Brian Keller, Cheryl Leysta-Lantz, Michael J Strong
Tar DNA binding protein of 43kDa (TDP-43) is a dual function RNA/DNA binding protein with varied cellular functions. In degenerating motor neurons in ALS, TDP-43 relocalizes from the nucleus to the cytosol where it is sequestered into inclusions. It is likely that the pathogenic role of TDP-43 in ALS can involve either a gain or a loss of function, depending on the nature of its RNA or protein interactor. However, while TDP-43 binding partners have been identified in a range of model systems and from the human brain, interactors from human spinal cord tissue have not...
March 7, 2018: Journal of Proteome Research
Kasey L DeAtley, Michelle L Colgrave, Angela Canovas, Gene Wijffels, Ryan L Ashley, Gail A Silver, Gonzalo Rincon, Juan F Medrano, Alma Islas-Trejo, Marina R S Fortes, Antonio Reverter, Laercio Porto-Neto, Sigrid A Lehnert, Milton G Thomas
Puberty in cattle is regulated by an endocrine axis which includes a complex milieu of neuropeptides in the hypothalamus and pituitary gland. The neuropeptidome of hypothalamic-pituitary tissue of pre- (PRE) and post-pubertal (POST) Bos indicus-influenced heifers was characterized, followed by quantitative analysis of 51 fertility-related neuropeptides in these tissues. Comparison of peptide abundances with gene expression levels allowed assessment of post-transcriptional peptide processing. Based on classical cleavage, 233 mature neuropeptides from 35 precursor proteins were detected in hypothalamus and pituitary gland tissues of three PRE and three POST Brangus heifers...
March 7, 2018: Journal of Proteome Research
Cheng Huang, Caitlin Lewis, Natalie A Borg, Meritxell Canals, Henry Diep, Grant Drummond, Robert J Goode, Ralf B Schittenhelm, Antony Vinh, Mingyu Zhu, Barbara Kemp-Harper, Oded Kleifeld, Martin J Stone
Macrophages, which accumulate in tissues during inflammation, may be polarized towards pro-inflammatory (M1) or tissue reparative (M2) phenotypes. The balance between these phenotypes can have a substantial influence on the outcome of inflammatory diseases such as atherosclerosis. Improved biomarkers of M1 and M2 macrophages would be beneficial for research, diagnosis and monitoring the effects of trial therapeutics in such diseases. To identify novel biomarkers, we have characterized the global proteomes of THP-1 macrophages polarized to M1 and M2 states, in comparison with unpolarized (M0) macrophages...
March 6, 2018: Journal of Proteome Research
Bing Han, Ning Yang, Hai Pu, Tai Wang
Cell polarity is essential for generating diverse cell functions. The underlying mechanisms of how a cell establishes, maintains and changes its polarity are poorly understood. Recently, sterol-rich membrane microdomains are found to be associated with these processes. However, both its exact characteristics and importance are still unclear. Here we show microdomains change dynamically in developing and germinating rice pollen with selective enrichment in the aperture and the tip of newly-born pollen tubes by use of the sterol-specific probe filipin...
March 6, 2018: Journal of Proteome Research
Kun-Hsing Yu, Tsung-Lu Lee, Chi-Shiang Wang, Yu-Ju Chen, Christopher Ré, Samuel C Kou, Jung-Hsien Chiang, Isaac S Kohane, Michael Snyder
There are more than 3.7 million published articles on the biological functions or disease implications of proteins, constituting an important resource of proteomics knowledge. However, it is difficult to summarize the millions of proteomics findings in the literature manually and quantify their relevance to the biology and diseases of interest. In this study, we developed a fully-automated bioinformatics framework to identify and prioritize proteins associated with any biological entity. We used the 22 targeted areas of the Biology/Disease-driven (B/D)-Human Proteome Project (HPP) as examples, prioritized the relevant proteins through their Protein Universal Reference Publication-Originated Search Engine (PURPOSE) scores, validated the relevance of the score by comparing the protein prioritization results with a curated database, computed the scores of proteins across the topics of B/D-HPP, and characterized the top proteins in the common model organisms...
March 5, 2018: Journal of Proteome Research
Alexander Gardner, Harold G Parkes, Guy H Carpenter, Po-Wah So
Metabolic profiling by1 H-NMR spectroscopy is an under-utilised technology in salivary research although preliminary studies have identified promising results in multiple fields (diagnostics, nutrition, sports physiology). Translation of preliminary findings into validated, clinically approved knowledge is hindered by variability in protocol for the collection, storage, preparation and analysis of saliva. This study aims to evaluate the effects of differing sample pre-treatments on the1 H-NMR metabolic profile of saliva...
March 2, 2018: Journal of Proteome Research
Manyun Dai, Huiying Hua, Hante Lin, Gangming Xu, Xiaowei Hu, Fei Li, Frank J Gonzalez, Aiming Liu, Julin Yang
Alpha-naphthylisothiocyanate (ANIT) is an experimental agent used to induce intrahepatic cholestasis. The Ppara-null mouse line is widely employed to explore the physiological and pathological roles of PPARα. However, little is known about how PPARα influences the hepatotoxicity of ANIT. In the present study, wild-type and Ppara-null mice were orally treated with ANIT to induce cholestasis. The serum metabolome of wild-type mice segregated from that of the Ppara-null mice, driven by changes of bile acid (BA) metabolites...
March 2, 2018: Journal of Proteome Research
Mingrui An, Jianhui Zhu, Jing Wu, Kyle C Cuneo, David M Lubman
Circulating microvesicles are able to mediate long-distance cell-cell communications. It is essential to understand how microvesicles from pancreatic cancer act on other cells in the body. In this work, serum-derived microvesicles were isolated from 10 patients with locally advanced pancreatic cancer and healthy controls. Using Cell Transwell and WST-1 reagents, we found that microvesicles from pancreatic cancer accelerated migration and proliferation of PANC-1 cells. Meanwhile, the proliferation of these cancer microvesicles treated cells (CMTCs) was affected less by 10 µM of gemcitabine relative to healthy microvesicles treated cells (HMTCs)...
March 1, 2018: Journal of Proteome Research
Minoo Bagheri, Farshad Farzadfar, Lu Qi, Mir Saeed Yekaninejad, Maryam Chamari, Oana A Zeleznik, Zahra Kalantar, Zarin Ebrahimi, Ali Sheidaie, Berthold Koletzko, Olaf Uhl, Abolghasem Djazayery
BACKGROUND: A particular sub-group of obese adults, considered as metabolically healthy obese (MHO), have a reduced risk of metabolic complications. However, the molecular basis contributing to this healthy phenotype remains unclear. OBJECTIVE: To identify obesity-related metabolite patterns differed between MHO and metabolically unhealthy obese (MUHO) groups and examine whether these patterns are associated with the development of cardiometabolic disorders in a sample of Iranian adult population aged 18-50 years...
March 1, 2018: Journal of Proteome Research
Yang Zhou, Cheng Hu, Xinjie Zhao, Ping Luo, Jingyi Lu, Qing Li, Miao Chen, Dandan Yan, Xin Lu, Hongwei Kong, Weiping Jia, Guowang Xu
Sulfonylureas are one of the commonly used drugs in type 2 diabetes mellitus (T2DM) but with considerable incidence of monotherapy failure. However, the mechanism of patients' drug response is unclear, and suitability evaluation biomarkers are in urgent need for precision medicine. In this study, a pseudotargeted gas chromatography-mass spectrometry method was employed to investigate the serum metabolic profiling of 66 significant responders and 24 nonsignificant responders at baseline and 16 weeks after gliclazide modified-release (MR) monotherapy...
February 28, 2018: Journal of Proteome Research
Adelaida Esteban-Fernandez, Clara Ibañez, Carolina Simó, Begoña Bartolome, M Victoria Moreno-Arribas
Moderate red wine consumption has been widely described to exert several benefits in human health. This is mainly due to its unique content of bioactive polyphenols, which suffer several modifications along their pass through digestive system, including microbial transformation in the colon and phase II metabolism, to be finally excreted in urine and feces. In order to determine the impact of moderate wine consumption in the overall urinary metabolome of healthy volunteers (n=41), samples from a red wine interventional study (250 mL/day, 28 days) were investigated...
February 27, 2018: Journal of Proteome Research
Sylvester M Greer, Marshall Bern, Christopher Becker, Jennifer S Brodbelt
To extend proteome coverage obtained from bottom-up mass spectrometry approaches, three complementary ion activation methods, higher energy collision dissociation (HCD), ultraviolet photodissociation (UVPD), and negative mode UVPD (NUVPD), are used to interrogate the tryptic peptides in a human hepatocyte lysate using a high performance Orbitrap mass spectrometer. The utility of combining results from multiple activation techniques (HCD+UVPD+NUVPD) is analyzed for total depth and breadth of proteome coverage...
February 26, 2018: Journal of Proteome Research
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