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Chunwei Zeng, Bo Wen, Guixue Hou, Li Lei, Zhanlong Mei, Xuekun Jia, Xiaomin Chen, Wu Zhu, Jie Li, Yehong Kuang, Weiqi Zeng, Juan Su, Siqi Liu, Cong Peng, Xiang Chen
Psoriasis is a common and chronic inflammatory skin disease that is complicated by gene-environment interactions. Although genomic, transcriptomic, and proteomic analyses have been performed to investigate the pathogenesis of psoriasis, the role of metabolites in psoriasis, particularly of lipids, remains unclear. Lipids not only comprise the bulk of the cellular membrane bilayers but also regulate a variety of biological processes such as cell proliferation, apoptosis, immunity, angiogenesis, and inflammation...
October 1, 2017: GigaScience
Esperanza Fernández, Mark O Collins, René A W Frank, Fei Zhu, Maksym V Kopanitsa, Jess Nithianantharajah, Sarah A Lemprière, David Fricker, Kathryn A Elsegood, Catherine L McLaughlin, Mike D R Croning, Colin Mclean, J Douglas Armstrong, W David Hill, Ian J Deary, Giulia Cencelli, Claudia Bagni, Menachem Fromer, Shaun M Purcell, Andrew J Pocklington, Jyoti S Choudhary, Noboru H Komiyama, Seth G N Grant
Arc is an activity-regulated neuronal protein, but little is known about its interactions, assembly into multiprotein complexes, and role in human disease and cognition. We applied an integrated proteomic and genetic strategy by targeting a tandem affinity purification (TAP) tag and Venus fluorescent protein into the endogenous Arc gene in mice. This allowed biochemical and proteomic characterization of native complexes in wild-type and knockout mice. We identified many Arc-interacting proteins, of which PSD95 was the most abundant...
October 17, 2017: Cell Reports
J Castillo, V Bernard, F A San Lucas, K Allenson, M Capello, D U Kim, P Gascoyne, F C Mulu, B M Stephens, J Huang, H Wang, A A Momin, R O Jacamo, M Katz, R Wolff, M Javle, G Varadhachary, I I Wistuba, S Hanash, A Maitra, H Alvarez
Background: Detection of circulating tumor DNA (ctDNA) can be limited due to their relative scarcity in circulation, particularly while patients are actively undergoing therapy. Exosomes provide a vehicle through which cancer-specific material can be enriched from the compendium of circulating non-neoplastic tissue-derived nucleic acids. We performed a comprehensive profiling of the pancreatic ductal adenocarcinoma (PDAC) exosomal "surfaceome" in order to identify surface proteins that will render liquid biopsies amenable to cancer-derived exosome enrichment for downstream molecular profiling...
September 25, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
Xianjun Shen, Li Yi, Xingpeng Jiang, Tingting He, Jincai Yang, Wei Xie, Po Hu, Xiaohua Hu
How to identify protein complex is an important and challenging task in proteomics. It would make great contribution to our knowledge of molecular mechanism in cell life activities. However, the inherent organization and dynamic characteristic of cell system have rarely been incorporated into the existing algorithms for detecting protein complexes because of the limitation of protein-protein interaction (PPI) data produced by high throughput techniques. The availability of time course gene expression profile enables us to uncover the dynamics of molecular networks and improve the detection of protein complexes...
2017: PloS One
Andreas Marx, Xiaohui Zhao, Joachim Lutz, Eva Höllmüller, Martin Scheffner, Florian Stengel
Ubiquitylation, the modification of proteins by ubiquitin (Ub), is one of the most prevalent and versatile post-translational modifications in eukaryotic cells. As Ub also serves as its own substrate, proteins can be modified by numerous different Ub chains, in which the individual moieties are linked via one or several of the seven lysines of Ub. Homogeneous Ub chains, in which the moieties are sequentially linked via the same residue, have been most extensively studied. Yet, due to their restricted availability, the functions of Ub chains linked via K27, K29 or K33 are poorly understood...
October 17, 2017: Angewandte Chemie
Hey-Jee Park, Nahee Bae, Hanbi Park, Dae-Wi Kim, Sang-Wook Han
Bacteria change their gene expression when exposed to different nutrient conditions. The levels of proteins do not always correlate with those of RNAs, hence proteomic analysis is required for understanding how bacteria adapt to different conditions. Herein, differentially abundant proteins from Xanthomonas oryzae pv. oryzae (Xoo), X. campestris pv. vesicatoria (Xcv), and X. axonopodis pv. glycines (Xag), which were cultured in rich media and in minimal media, were determined using label-free shotgun proteomic analysis and clusters of orthologous groups classification...
October 17, 2017: Proteomics
Marilyn C Cornelis, Stefan Gustafsson, Johan Ärnlöv, Sölve Elmståhl, Stefan Söderberg, Johan Sundström, Karl Michaëlsson, Lars Lind, Erik Ingelsson
BACKGROUND: Coffee drinking has been implicated in mortality and a variety of diseases but potential mechanisms underlying these associations are unclear. Large-scale systems epidemiological approaches may offer novel insights to mechanisms underlying associations of coffee with health. OBJECTIVE: We performed an analysis of known and novel protein markers linked to cardiovascular disease and their association with habitual coffee intake in the Prospective Study of the Vasculature in Uppsala Seniors (PIVUS, n=816) and followed-up top proteins in the Uppsala Longitudinal Study of Adult Men (ULSAM, n=635) and EpiHealth (n=2418)...
October 16, 2017: Journal of Internal Medicine
Young-Min Bae, Jae-Hyun Yoon, Ji-Yeon Kim, Sun-Young Lee
AIM: In this study, the effects of addition of salt to treatment with acids (one of several organic acids and salt in various solutions including rich or minimal broth, buffer, or distilled water) on the reduction of Escherichia coli O157:H7 were investigated. The protein expression profiles corresponding to acid stress (acetic acid) with or without salt addition were studied using a comparative proteomic analysis of E. coli O157:H7. METHODS AND RESULTS: When acetic, lactic, or propionic acid was combined with 3% NaCl, mutually antagonistic effects of acid and salt on viability of E...
October 17, 2017: Journal of Applied Microbiology
Jared J Romero, Bethany E Liebig, Corey D Broeckling, Jessica E Prenni, Thomas R Hansen
Mass spectrometry (MS) approaches were used herein to identify metabolites and proteins in uterine flushings (UF) that may contribute to nourishing the conceptus. Ovine uteri collected on Day 12 of the estrous cycle (n = 5 ewes exposed to vasectomized ram) or Days 12 (n = 4), 14 (n = 5), or 16 (n = 5) of pregnancy (bred with fertile ram) were flushed using buffered saline. Metabolites were extracted using 80% methanol and profiled using ultraperformance liquid chromatography (LC) tandem mass spectrometry. The proteome was examined by digestion with trypsin, followed by the analysis of peptides with LC-MS/MS...
August 1, 2017: Biology of Reproduction
Gulustan Ozturk, Karen LeGrand, Yan Zheng, Glenn M Young
This study investigated how carbon storage regulator A (CsrA) affects expression of the Ysa and Ysc type 3 secretion (T3S) system genetic regulatory cascades that control Ysps (Yersinia secreted proteins) and Yops (Yersinia outer proteins) export, respectively. Given that most often CsrA acts as a mediator of mRNA stability, an activity that can be monitored using lacZ transcriptional fusions, we employed a collection of reporter strains to assess Ysa and Ysc gene expression. To this end, bacteria were cultivated to induce either the Ysa or the Ysc T3S system...
November 1, 2017: FEMS Microbiology Letters
Xiangfeng Zheng, Qiya Yang, Lina Zhao, Maurice Tibiru Apaliya, Xiaoyun Zhang, Hongyin Zhang
The proteomic and lysine acetylation (Kac) changes, accompanying degradation of patulin in Rhodotorula mucilaginosa were analyzed using tandem mass tagging and N6-acetyllysine affinity enrichment followed by LC-MS/MS. Proteomic results showed that expression level of short-chain reductase protein and glutathione S-transferase involved in detoxification was significantly up-regulated. In addition, the expression levels of zinc-binding oxidoreductase and quinone oxidoreductase that are involved in antioxidant process, ABC transport and MFS transport responsible for chemical transport were activated when treated with patulin...
October 18, 2017: Scientific Reports
Yuanxiang Lao, Yanyan Li, Yufang Hou, Huahai Chen, Bintao Qiu, Weiran Lin, Aihua Sun, Handong Wei, Ying Jiang, Fuchu He
Sinusoidal dedifferentiation is a complicated process induced by several factors, and exists in early stage of diverse liver diseases. The mechanism of sinusoidal dedifferentiation is poorly unknown. In this study, we established a NaAsO2-induced sinusoidal dedifferentiation mice model. Liver sinusoidal endothelial cells were isolated and isobaric tag for relative and absolute quantitation (iTRAQ) based proteomic approach was adopted to globally examine the effects of arsenic on liver sinusoidal endothelial cells (LSECs) during the progression of sinusoidal dedifferentiation...
October 18, 2017: Scientific Reports
Ajay Mishra, Benedicte Oules, Angela Oliveira Pisco, Tony Ly, Kifayathullah Liakath-Ali, Gernot Walko, Priyalakshmi Viswanathan, Matthieu Tihy, Jagdeesh Nijjher, Sara-Jane Dunn, Angus I Lamond, Fiona M Watt
Epidermal homeostasis depends on a balance between stem cell renewal and terminal differentiation. The transition between the two cell states, termed commitment, is poorly understood. Here we characterise commitment by integrating transcriptomic and proteomic data from disaggregated primary human keratinocytes held in suspension to induce differentiation. Cell detachment induces several protein phosphatases, five of which - DUSP6, PPTC7, PTPN1, PTPN13 and PPP3CA - promote differentiation by negatively regulating ERK MAPK and positively regulating AP1 transcription factors...
October 18, 2017: ELife
Fernanda G Kugeratski, Michel Batista, Carla Vanessa de Paula Lima, Lisa J Neilson, Elizabeth Sousa da Cunha, Lyris M F de Godoy, Sara Zanivan, Marco Aurelio Krieger, Fabricio K Marchini
The pathogenic protozoan T. brucei alternates into distinct developmental stages in the mammalian and insect hosts. The mitogen-activated protein kinase (MAPK) signaling pathways transduce extracellular stimuli into a range of cellular responses, which ultimately lead to the adaptation to the external environment. Here, we combined a loss of function approach with stable isotope labelling with amino acids in cell culture (SILAC)-based mass spectrometry (MS) to investigate the role of the mitogen-activated kinase kinase 5 (MKK5) in T...
October 18, 2017: Journal of Proteome Research
Guðjón Ólafsson, Peter H Thorpe
Artificially tethering two proteins or protein fragments together is a powerful method to query molecular mechanisms. However, this approach typically relies upon a prior understanding of which two proteins, when fused, are most likely to provide a specific function and is therefore not readily amenable to large-scale screening. Here, we describe the Synthetic Physical Interaction (SPI) method to create proteome-wide forced protein associations in the budding yeast Saccharomyces cerevisiae. This method allows thousands of protein-protein associations to be screened for those that affect either normal growth or sensitivity to drugs or specific conditions...
2018: Methods in Molecular Biology
Laura Hui-Ru Tan, Angela Jin-Rong Tan, Yu-Ying Ng, John Jia-En Chua, Wee-Siong Chew, Sneha Muralidharan, Federico Torta, Bamaprasad Dutta, Siu Kwan Sze, Deron R Herr, Wei-Yi Ong
Sphingomyelinases are a family of enzymes that hydrolyze sphingomyelin to generate phosphocholine and ceramide. The brain distribution and function of neutral sphingomyelinase 2 (nSMase2) were elucidated in this study. nSMase2 mRNA expression was greatest in the striatum, followed by the prefrontal cortex, hippocampus, cerebellum, thalamus, brainstem, and olfactory bulb. The striatum had the highest level of nSMase2 protein expression, followed by the prefrontal cortex, thalamus, hippocampus, brainstem, and cerebellum...
October 17, 2017: Molecular Neurobiology
Yifan Zhai, Zhiming Zhang, Huanhuan Gao, Hao Chen, Meng Sun, Wenqing Zhang, Yi Yu, Li Zheng
Diapause is a physiological adaptation that allows an organism to survive adverse environmental conditions. Diapause occurs at a specific developmental stage in each species. There are few reports regarding the molecular regulatory mechanism of nymphal diapause in Laodelphax striatellus, which is an important graminaceous crop pest. Our previous studies identified the conditions for nymphal diapause in this species. Here, we combined RNA sequencing transcriptomics and quantitative proteomic analyses to identify nymphal diapause-related genes and proteins...
October 17, 2017: Scientific Reports
Lei Li, Steven M Jay, Yan Wang, Shu-Wei Wu, Zhengguo Xiao
An effective cytotoxic T lymphocyte (CTL) response against intracellular pathogens is generally accomplished by immense CTL expansion and activation, which can destroy infected cells. Vigorous immune responses can lead to activation of bystander CD8(+) T cells, but the contribution from antigen-specific CTLs is not well understood. We found that CTLs secrete extracellular vesicles following antigen stimulation. These CTL-derived vesicles contain CTL proteins and exhibit markers and size profiles consistent with exosomes...
October 17, 2017: Scientific Reports
Jae Hun Jung, Yong Woo Ji, Ho Sik Hwang, Jae Won Oh, Hyun Chang Kim, Hyung Keun Lee, Kwang Pyo Kim
To understand the pathophysiology of dry eye disease (DED), it is necessary to characterize proteins in the ocular surface fluids, including tear fluid (TF) and lacrimal fluid (LF). There have been several reports of TF proteomes, but few proteomic studies have examined LF secreted from the lacrimal gland (LG). Therefore, we characterized the proteins constituting TF and LF by liquid chromatography mass spectrometry. TF and LF were collected from patients with non-Sjögren syndrome DED and from healthy subjects...
October 17, 2017: Scientific Reports
Marcella Bonanomi, Valentina Roffia, Antonella De Palma, Alessio Lombardi, Francesco Antonio Aprile, Cristina Visentin, Paolo Tortora, Pierluigi Mauri, Maria Elena Regonesi
The protein ataxin-3 carries a polyglutamine stretch close to the C-terminus that triggers a neurodegenerative disease in humans when its length exceeds a critical threshold. A role as a transcriptional regulator but also as a ubiquitin hydrolase has been proposed for this protein. Here, we report that, when expressed in the yeast Pichia pastoris, full-length ataxin-3 enabled almost normal growth at 37 °C, well above the physiological optimum of 30 °C. The N-terminal Josephin domain (JD) was also effective but significantly less, whereas catalytically inactive JD was completely ineffective...
October 17, 2017: Scientific Reports
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