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Proteomics

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https://www.readbyqxmd.com/read/28523650/ubiquitin-specific-peptidase-5-mediates-histidine-rich-protein-hpn-induced-cell-apoptosis-in-hepatocellular-carcinoma-through-p14-p53-signaling
#1
Yi Liu, Wei-Mao Wang, Li-Yi Zou, Li Li, Lu Feng, Ming-Zhu Pan, Min-Yi Lv, Ying Cao, Hua Wang, Hsiang-Fu Kung, Jian-Xin Pang, Wei-Ming Fu, Jin-Fang Zhang
Hpn is a small histidine-rich cytoplasmic protein from Helicobacter pylori and has been recognized as a high-risk factor for several cancers including gastric cancer, colorectal cancer, and MALT lymphoma. However, the relationship between Hpn and cancers remains elusive. In this study, we discovered that Hpn protein effectively suppressed cell growth and induced apoptosis in hepatocellular carcinoma (HCC). A two-dimensional gel electrophoresis and mass spectrometry-based comparative proteomics was performed to find the molecular targets of Hpn in HCC cells...
May 18, 2017: Proteomics
https://www.readbyqxmd.com/read/28517912/keeping-good-friends-close-the-surface-and-secreted-proteomes-of-a-probiotic-bacterium-provide-candidate-proteins-for-intestinal-attachment-and-communication-with-the-host
#2
Constance J Jeffery
Bacteria use cell surface proteins and secreted proteins to interact with host tissues. Several dozen previously published proteomics studies have identified cell surface proteins for pathogens. In this issue, Celebioglu and Svensson (Proteomics 2017, XXX, XXX-XXX) use 2-D gel electrophoresis and mass spectrometry to identify secreted and cell surface proteins of a commensual gut bacterium, Lactobacillus acidophilus NCFM. Some of the proteins are known to have functions in the cytoplasm, and their presence on the cell surface suggests they might be moonlighting proteins...
May 18, 2017: Proteomics
https://www.readbyqxmd.com/read/28516729/proteome-analysis-of-duck-tembusu-virus-dtmuv-infected-bhk-21-cells
#3
Xin Sun, Shengyu Wang, Xian Lin, Lianzhong Zhao, Dan Zhang, Chenyang Yi, Xiaomei Sun, Huanchun Chen, Meilin Jin
Duck Tembusu virus (DTMUV) is a newly emerging pathogenic flavivirus that has caused huge economic losses to the duck industry in China since 2010. Moreover, the infection has spread rapidly, posing a potential public health concern. In this study, iTRAQ approach was firstly used to quantitatively identify differentially expressed cellular proteins in DTMUV-infected BHK-21 cells which are usually employed to produce veterinary vaccines for DTMUV, as well as other flaviviruses by serial passage. We identified 192 differentially expressed cellular proteins, including 11 upregulated and 8 downregulated proteins at 24 h postinfection (hpi), as well as 25 upregulated and 151 downregulated proteins at 48 hpi, of which TLR9, DDX3X, and DDX5 may play important roles in virus propagation...
May 17, 2017: Proteomics
https://www.readbyqxmd.com/read/28513109/separation-and-identification-of-mouse-brain-tissue-microproteins-using-top-down-method-with-high-resolution-nanocapillary-liquid-chromatography-mass-spectrometry
#4
Wenxue Li, Filomena Petruzziello, Nan Zhao, Huiyuan Zhao, Xueting Ye, Xiaozhe Zhang, Gregor Rainer
Microproteins and endogenous peptides in the brain contain important substances that have critical roles in diverse biological processes, contributing to signal transduction and inter-cellular signaling. However, variability in their physical or chemical characteristics, such as molecule size, hydrophobicity and charge states, complicate the simultaneous analysis of these compounds, although this would be highly beneficial for the field of neuroscience research. Here, we present a top-down analytical method for simultaneous analysis of microproteins and endogenous peptides using high-resolution nanocapillary liquid chromatography tandem mass spectrometry...
May 16, 2017: Proteomics
https://www.readbyqxmd.com/read/28508553/a-targeted-proteomic-assay-for-the-measurement-of-plasma-proteoforms-related-to-human-aging-phenotypes
#5
Richard D Semba, Pingbo Zhang, Min Zhu, Elisa Fabbri, Marta Gonzalez-Freire, Ruin Moaddel, Minghui Geng-Spyropoulos, Luigi Ferrucci
Circulating polypeptides and proteins have been implicated in reversing or accelerating aging phenotypes, including growth/differentiation factor 8 (GDF8), GDF11, eotaxin, and oxytocin. These proteoforms, which are defined as the protein products arising from a single gene due to alternative splicing and post-translational modifications, have been challenging to study. Both GDF8 and GDF11 have known antagonists such as follistatin (FST), and WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing proteins 1 and 2 (WFIKKN1, WFIKKN2)...
May 16, 2017: Proteomics
https://www.readbyqxmd.com/read/28508578/proteomic-characterization-of-el4-lymphoma-derived-tumors-upon-chemotherapy-treatment-reveals-potential-roles-for-lysosomes-and-caspase-6-during-tumor-cell-death-in-vivo
#6
David A Kramer, Mohamed A Eldeeb, Melinda Wuest, John Mercer, Richard P Fahlman
The murine EL4 tumor model is an established in vivo apoptosis model for the investigation of novel cancer imaging agents and immunological treatments due to the rapid and significant response of the EL4 tumors to cyclophosphamide and etoposide combination chemotherapy. Despite the utility of this model system in cancer research little is known regarding the molecular details of the in vivo tumor cell death. Here we report the first in-depth quantitative proteomic analysis of the changes that occur in these tumors upon cyclophosphamide and etoposide treatment in vivo...
May 15, 2017: Proteomics
https://www.readbyqxmd.com/read/28508465/proteomics-show-antigen-presentation-processes-in-human-immune-cells-after-as03-h5n1-vaccination
#7
Allison C Galassie, Johannes B Goll, Parimal Samir, Travis L Jensen, Kristen L Hoek, Leigh M Howard, Tara M Allos, Xinnan Niu, Laura E Gordy, C Buddy Creech, Heather Hill, Sebastian Joyce, Kathryn M Edwards, Andrew J Link
Adjuvants enhance immunity elicited by vaccines through mechanisms that are poorly understood. Using a systems biology approach, we investigated temporal protein expression changes in five primary human immune cell populations: neutrophils, monocytes, natural killer (NK) cells, T-cells, and B-cells after administration of either an Adjuvant System 03 (AS03)-adjuvanted or unadjuvanted split-virus H5N1 influenza vaccine. Monocytes demonstrated the strongest differential signal between vaccine groups. On day 3 post-vaccination, several antigen presentation-related pathways, including MHC class I-mediated antigen processing and presentation, were enriched in monocytes and neutrophils and expression of HLA Class I proteins was increased in the AS03 group...
May 15, 2017: Proteomics
https://www.readbyqxmd.com/read/28493537/exploring-the-expression-bar-code-of-saa-variants-for-gastric-cancer-detection
#8
Deng-Chyang Wu, Kai-Yi Wang, Sophie S W Wang, Ching-Min Huang, Yi-Wei Lee, Michael Isaac Chen, Szu-An Chuang, Shu-Hua Chen, Ying-Wei Lu, Chun-Cheng Lin, Ka-Wo Lee, Wen-Hung Hsu, Kun-Pin Wu, Yu-Ju Chen
We reported an integrated platform to explore serum protein variant pattern in cancer and its utility as a new class of biomarker panel for diagnosis. On the model study of serum amyloid A (SAA), we employed nanoprobe-based affinity mass spectrometry for enrichment, identification and quantitation of SAA variants from serum of 105 gastric cancer patients in comparison with 54 gastritis patients, 54 controls, and 120 patients from other cancer. The result revealed surprisingly heterogeneous and most comprehensive SAA bar code to date, which comprises 24 SAA variants including SAA1- and SAA2-encoded products, polymorphic isoforms, N-terminal-truncated forms, and three novel SAA oxidized isotypes, in which the variant-specific peptide sequence were also confirmed by LC-MS/MS...
May 11, 2017: Proteomics
https://www.readbyqxmd.com/read/28471538/differential-accumulation-of-xanthomonas-campestris-pv-campestris-proteins-during-the-interaction-with-the-host-plant-contributions-of-an-in-vivo-system
#9
Cristiane Santos, Mariana Rocha Maximiano, Daiane G Ribeiro, Osmundo B Oliveira-Neto, André M Murad, Octávio L Franco, Angela Mehta
Xanthomonas campestris pv. campestris (Xcc) is the causal agent of black rot, a highly destructive disease that affects all brassicas. This work aimed to study the interaction Xcc-Brassica oleracea using an in vivo system in an attempt to identify proteins involved in pathogenicity. We used label-free shotgun 2D-nanoUPLC/MS(E) to analyze Xcc proteins in three conditions: in the interaction with susceptible (REK) and resistant (REU) plants and in culture medium (control condition). A model of Xcc-susceptible host interaction is proposed and shows that Xcc increases the abundance of several crucial proteins for infection and cell protection...
May 4, 2017: Proteomics
https://www.readbyqxmd.com/read/28467696/proteome-profile-of-spinneret-from-the-silkworm-bombyx-mori
#10
Xin Wang, Yi Li, Qingsong Liu, Qingyou Xia, Ping Zhao
The silkworm spinneret is an important tissue for silk fibrillogenesis and spinning. All biochemical processes during silk fibrillogenesis are correlated with silk properties. Understanding the role of spinneret in silk fibrillogenesis may help to reveal the mechanism of silk fibrillogenesis as well as improve silk quality for commercial purposes. Thus, we profiled the proteome of silkworm spinneret. A total of 1572 proteins and 232 differential abundance proteins were identified. Silk fibrillogenesis-related proteins, such as cuticle proteins, ion-transporting proteins, muscular proteins, and energy metabolic proteins, were abundant in spinneret...
May 3, 2017: Proteomics
https://www.readbyqxmd.com/read/28467633/a-method-for-rapid-and-sensitive-negative-staining-of-proteins-in-sds-page-using-2-7-dichlorofluorescein
#11
Yuan Zhang, Dongdong Yu, Jiangbo Dai, Xu Wang, Zhongxin Zhu, Yewei Huang, Jia Sun, Zhiwei Chen, Litai Jin, Yang Wang
We report here a rapid and sensitive technique for negative visualization of protein in 1-D and 2-D SDS-PAGE by using 2', 7'-Dichlorofluorescein (DCF), which appeared as transparent and colorless bands in an opaque gel matrix background. For DCF stain, down to 0.1-0.2 ng protein could be easily visualized within 7 min by only 2 steps, and the staining is 4-fold more sensitive than that of Eosin Y (EY) negative stain and glutaraldehyde (GA) silver stain, and 8-fold more sensitive than that of the commonly used Imidazole-zinc (IZ) negative stain...
May 3, 2017: Proteomics
https://www.readbyqxmd.com/read/28464451/quantitative-phosphoproteome-analysis-of-cisplatin-induced-apoptosis-in-jurkat-t-cells
#12
The Trung Tran, Margarita Strozynski, Bernd Thiede
Protein phosphorylation is one of the most important posttranslational modifications (PTMs) due to its vital role in cellular functions and signaling pathways. Protein phosphorylation is also known to be involved in the regulation of apoptosis. Previously, we have performed a SILAC-based analysis of tyrosine phosphorylated peptides of cisplatin-induced apoptotic Jurkat T cells. Here, we analyzed the global phosphorylation profile by enrichment of serine/threonine/tyrosine phosphorylated peptides using TiO2 beads...
May 2, 2017: Proteomics
https://www.readbyqxmd.com/read/28445005/proteomic-based-investigations-on-the-mode-of-action-of-the-marine-anticancer-compound-rhizochalinin
#13
Sergey A Dyshlovoy, Katharina Otte, Simone Venz, Jessica Hauschild, Heike Junker, Tatyana N Makarieva, Stefan Balabanov, Winfried H Alsdorf, Ramin Madanchi, Friedemann Honecker, Carsten Bokemeyer, Valentin A Stonik, Gunhild von Amsberg
Rhizochalinin (Rhiz) is a novel marine natural sphingolipid-like compound which shows promising in vitro and in vivo activity in human castration-resistant prostate cancer (CRPC). In the present study, a global proteome screening approach was applied to investigate molecular targets and biological processes affected by Rhiz in CRPC. Bioinformatical analysis of the data predicted an anti-migratory effect of Rhiz on cancer cells. Validation of proteins involved in the cancer-associated processes, including cell migration and invasion, revealed down-regulation of specific isoforms of stathmin and LASP1, as well as up-regulation of Grp75, keratin 81, and precursor IL-1β by Rhiz...
April 26, 2017: Proteomics
https://www.readbyqxmd.com/read/28409884/altered-protein-expression-pattern-in-colon-tissue-of-mice-upon-supplementation-with-distinct-selenium-compounds
#14
Jette Rahn, Claudia Lennicke, Anna P Kipp, Andreas S Müller, Ludger A Wessjohann, Rudolf Lichtenfels, Barbara Seliger
The essential trace element Selenium (Se) is controversially discussed concerning its role in health and disease. Its various physiological functions are largely mediated by Se incorporation in the catalytic center of selenoproteins. To gain insights into the impact of Se deficiency and of supplementation with different Se compounds (selenite, selenate, selenomethionine) at defined concentrations (recommended, 150 μg/ kg diet; excessive, 750 μg/ kg diet) in murine colon tissues a twenty week feeding experiment was performed followed by analysis of the protein expression pattern of colon tissue specimens by 2D-DIGE and MALDI-TOF MS...
April 14, 2017: Proteomics
https://www.readbyqxmd.com/read/28397356/links-between-critical-proteins-drive-the-controllability-of-protein-interaction-networks
#15
Stefan Wuchty, Toni Boltz, Hande Küçük-McGinty
Focusing on the interactomes of Homo sapiens, Saccharomyces cerevisiae, and Escherichia coli, we investigated interactions between controlling proteins. In particular, we determined critical, intermittent, and redundant proteins based on their tendency to participate in minimum dominating sets. Independently of the organisms considered, we found that interactions that involved critical nodes had the most prominent effects on the topology of their corresponding networks. Furthermore, we observed that phosphorylation and regulatory events were considerably enriched when the corresponding transcription factors and kinases were critical proteins, while such interactions were depleted when they were redundant proteins...
April 10, 2017: Proteomics
https://www.readbyqxmd.com/read/28394504/systematic-identification-of-the-protein-substrates-of-udp-galnac-polypeptide-n-acetylgalactosaminyltransferase-t1-t2-t3-using-a-human-proteome-microarray
#16
Zhijue Xu, Xing Li, Shumin Zhou, Wenxian Xie, Jing Wang, Li Cheng, Sheng Wang, Shujuan Guo, Zhaowei Xu, Xin Cao, Menghui Zhang, Biao Yu, Hisashi Narimatsu, Sheng-Ce Tao, Yan Zhang
O-GalNAc glycosylation is the initial step of the mucin-type O-glycosylation. In humans, it is catalyzed by a family of 20 homologous UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (ppGalNAc-Ts). So far, there is very limited information on their protein substrate specificities. In this study, we developed an on-chip ppGalNAc-Ts assay which could rapidly and systematically identify the protein substrates of each ppGalNAc-T. In detail, we utilized a human proteome microarray as the protein substrates and UDP-GalNAz as the nucleotide sugar donor for click chemistry detection...
April 10, 2017: Proteomics
https://www.readbyqxmd.com/read/28394474/proteomic-identification-of-rainbow-trout-blood-plasma-proteins-and-their-relationship-to-seminal-plasma-proteins
#17
Joanna Nynca, G J Arnold, T Fröhlich, A Ciereszko
The characterization of fish blood proteomes is important for comparative studies of seminal and blood proteins as well as for the analysis of fish immune mechanisms and pathways. In this study LC-MS/MS and 2D DIGE were applied to compare rainbow trout seminal (SP) and blood plasma (BP) proteomes. The 54 differentially abundant proteins identified in SP are involved in a variety of signalling pathways, including protein ubiquitination, liver X receptor/retinoid X receptor (LXR/RXR) and farnesoid X receptor (FXR)/RXR activation, cell cycle and acute phase signalling...
April 10, 2017: Proteomics
https://www.readbyqxmd.com/read/28393466/improving-basic-and-membrane-protein-ms-detection-of-the-culture-filtrate-proteins-from-mycobacterium-tuberculosis-h37rv-by-biomimetic-affinity-pre-fractionation
#18
Guorong Ma, Fuqiang Zhou, Lina Gao, Zhanqiang Sun, Li Deng, Shulin Zhang, Rongxiu Li
The culture filtrate proteins (CFPs) from Mycobacterium tuberculosis (MTB) have been shown to induce protective immune responses in human and animal models, making them a promising source of candidate targets for tuberculosis drugs, vaccines and diagnostics. The constituents of the MTB CFP proteome are complex and vary with growth conditions. To effectively profile CFPs, gel-based pre-fractionation is usually performed before MS analysis. In this study, we describe a novel pre-fractionation approach by which the proteome is divided into seven partially overlapping fractions by biomimetic affinity chromatography (BiAC) using a six-column cascade...
April 9, 2017: Proteomics
https://www.readbyqxmd.com/read/28393464/exo-and-surface-proteomes-of-the-probiotic-bacterium-lactobacillus-acidophilus-ncfm
#19
Hasan Ufuk Celebioglu, Birte Svensson
Lactobacillus acidophilus NCFM is a well-known probiotic bacterium extensively studied for its beneficial health effects. Exoproteome (proteins exported into culture medium) and surface proteome (proteins attached to S-layer) of this probiotic were identified by using 2DE followed by MALDI TOF MS to find proteins potentially involved in bacteria-host interactions. The exo- and surface proteomes included 43 and 39 different proteins from 72 and 49 successfully identified spots, respectively. Twenty-two proteins were shared between the two proteomes; both contained the major surface layer protein that participates in host interaction as well as several well-known and putative moonlighting proteins...
April 9, 2017: Proteomics
https://www.readbyqxmd.com/read/28390171/class-paired-fuzzy-subnets-a-paired-variant-of-the-rank-based-network-analysis-family-for-feature-selection-based-on-protein-complexes
#20
Wilson Wen Bin Goh, Limsoon Wong
Identifying reproducible yet relevant protein features in proteomics data is a major challenge. Analysis at the level of protein complexes can resolve this issue and we have developed a suite of feature-selection methods collectively referred to as Rank-Based Network Analysis (RBNA). RBNAs differ in their individual statistical test setup but are similar in the sense that they deploy rank-defined weights amongst proteins per sample. This procedure is known as gene fuzzy scoring. Currently, no RBNA exists for paired-sample scenarios where both control and test tissues originate from the same source (e...
April 8, 2017: Proteomics
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