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Proteome Science

Carmine Mancone, Alessio Grimaldi, Giulia Refolo, Isabella Abbate, Gabriella Rozera, Dario Benelli, Gian Maria Fimia, Vincenzo Barnaba, Marco Tripodi, Mauro Piacentini, Fabiola Ciccosanti
BACKGROUND: 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 correlation. Therefore, the multi-faceted role of iron in HIV-1 infection remains enigmatic. METHODS: RT-qPCR targeting the LTR region, gag, Tat and Rev were performed to measure the levels of viral RNAs in response to iron overload. Spike-in SILAC proteomics comparing i) iron-treated, ii) HIV-1-infected and iii) HIV-1-infected/iron treated T lymphocytes was performed to define modifications in the host cell proteome...
2017: Proteome Science
Margaret L Wong, Jason Murphy, Edmund Harrington, Carrie M Gower, Rishi K Jain, Markus Schirle, Jason R Thomas
BACKGROUND: 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 have been successfully designed, no comprehensive assessment of affinity and selectivity for a series of bivalent inhibitors has been performed. Here, we present an evaluation of the structure activity relationship for bivalent kinase inhibitors targeting ABL1. METHODS: Various SNAPtag constructs bearing different specificity ligands were expressed in vitro...
2016: Proteome Science
Michael P Gotsbacher, Sungmin Cho, Ho Jeong Kwon, Peter Karuso
BACKGROUND: 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 no human binding partner is known. METHODS: In the present study we tested daptomycin in cell viability and proliferation assays against six human cell lines, describe the synthesis of biotinylated and fluorescently labeled analogues of daptomycin...
2016: Proteome Science
Kyungtae Kang, Jongmin Park, Eunha Kim
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 molecular tools. Chemical probes can provide great spatiotemporal control to elucidate biological functions of proteins as well as for interrogating biological pathways. The invention of bioorthogonal chemistry has revolutionized the field of chemical biology by providing superior chemical tools and has been widely used for investigating the dynamics and function of biomolecules in live condition...
2016: Proteome Science
Dhiraj P Murale, Seong Cheol Hong, Md Mamunul Haque, Jun-Seok Lee
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 proteins, including affinity chromatography, activity-based probes, affinity-based probes and photo-affinity labeling (PAL). PAL has become one of the most powerful strategies to study PPIs. Traditional photocrosslinkers are used in PAL, including benzophenone, aryl azide, and diazirine. Upon photoirradiation, these photocrosslinkers (Pls) generate highly reactive species that react with adjacent molecules, resulting in a direct covalent modification...
2016: Proteome Science
André Mateus, Tomi A Määttä, Mikhail M Savitski
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 hits. This has led to the development of multiple strategies for target deconvolution. Thermal proteome profiling (TPP) allows for an unbiased search of drug targets and can be applied in living cells without requiring compound labeling. TPP is based on the principle that proteins become more resistant to heat-induced unfolding when complexed with a ligand, e...
2016: Proteome Science
Lucas T Vu, Sophia M Orbach, W Keith Ray, Margaret E Cassin, Padmavathy Rajagopalan, Richard F Helm
BACKGROUND: 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 using hepatocytes and liver sinusoidal endothelial cells (LSECs) separated by a polyelectrolyte multilayer (PEM) provide a functional system while also permitting isolation of individual cell types for proteomic analyses. METHODS: To better understand the mechanisms and processes that underlie liver model function, hepatocytes were maintained as monolayers and 3D PEM-based formats in the presence or absence of primary LSECs...
2016: Proteome Science
Saul Chemonges, Rajesh Gupta, Paul C Mills, Steven R Kopp, Pawel Sadowski
BACKGROUND: 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 changes and disease states. The objective of this study was to develop a robust and comprehensive method to characterise the circulating acellular proteome in ovine serum. METHODS: Serum samples from healthy sheep were subjected to shotgun proteomic analysis using nano liquid chromatography nano electrospray ionisation tandem mass spectrometry (nanoLC-nanoESI-MS/MS) on a quadrupole time-of-flight instrument (TripleTOF® 5600+, SCIEX)...
2016: Proteome Science
Emily L O'Reilly, Richard J Burchmore, Nicholas H Sparks, P David Eckersall
BACKGROUND: 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 periods of growth that allow birds to grow optimally is important for this species. The exposure of young chicks to used litter from older flocks, containing mixed microbial populations, is a widely utilised model in poultry research. It rarely causes mortality but effects an immunogenic stimulation sufficient enough to cause reduced and uneven growth that is reflective of a challenging growing environment...
2016: Proteome Science
Zepeng Yin, Jing Ren, Lijuan Zhou, Lina Sun, Jiewan Wang, Yulong Liu, Xingshun Song
BACKGROUND: 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 sophisticated molecular network under WD. The aim of this study is to identify the effect of WD on C. humilis through physiological and global proteomics analysis and improve understanding of the WD resistance of plants. METHODS: Currently, physiological parameters were applied to investigate C...
2016: Proteome Science
Jonatan Eriksson, Simone Andersson, Roger Appelqvist, Elisabet Wieslander, Mikael Truedsson, May Bugge, Johan Malm, Magnus Dahlbäck, Bo Andersson, Thomas E Fehniger, György Marko-Varga
BACKGROUND: 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 ensures that its quality is preserved throughout its entire lifetime. We are running a 5-year longitudinal clinical study, KOL-Örestad, with the objective to identify new COPD (Chronic Obstructive Pulmonary Disease) biomarkers in blood. In the study, clinical data and blood samples are collected from both private and public health-care institutions and stored at our research center in databases and biobanks, respectively...
2016: Proteome Science
Seyma Katrinli, Kamil Ozdil, Abdurrahman Sahin, Oguzhan Ozturk, Gozde Kir, Ahmet Tarik Baykal, Emel Akgun, Omer Sinan Sarac, Mehmet Sokmen, H Levent Doğanay, Gizem Dinler Doğanay
BACKGROUND: 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 HBV related liver fibrosis for delineation of potential new therapeutic targets and biomarkers. METHODS: Tissue samples from 47 HBV infected patients with different fibrotic stages (F1 to F6) were enrolled for 2D-DIGE proteomic screening. Differentially expressed proteins were identified by mass spectrometry and verified by western blotting...
2016: Proteome Science
Kazuko Morino, Mayumi Kimizu, Masayuki Fujiwara
BACKGROUND: 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 protein functions such as enzymatic activity, protein-protein interactions, oligomerization, and intracellular localization. Thus, the sensitivity of cysteine residues to changes in the cellular redox status is critical to the immune response of plants. METHODS: We used disulfide proteomics to identify immune response-related redox proteins...
2016: Proteome Science
Samuel Antwi-Baffour, Jonathan Kofi Adjei, Francis Agyemang-Yeboah, Max Annani-Akollor, Ransford Kyeremeh, George Awuku Asare, Ben Gyan
BACKGROUND: 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 membrane derived extracellular vesicles (PMEVs) are subcellular structures that are generated when they bud off the plasma membrane. They can be found in healthy individuals but the numbers tend to increase in pathological conditions including malaria. Although, various studies have been carried out on the protein content of specific cellular derived MPs, there seems to be paucity of information on the protein content of circulating MPs in malaria and their association with the various signs and symptoms of the disease...
2016: Proteome Science
N C Rath, R Liyanage, S K Makkar, J O Lay
BACKGROUND: Eggshells which consist largely of calcareous outer shell and shell membranes, constitute a significant part of poultry hatchery waste. The shell membranes (ESM) not only contain proteins that originate from egg whites but also from the developing embryos and different contaminants of microbial and environmental origins. As feed supplements, during post hatch growth, the hatchery egg shell membranes (HESM) have shown potential for imparting resistance of chickens to endotoxin stress and exert positive health effects...
2016: Proteome Science
Weibo Ren, Xiangyang Hou, Yuqing Wang, Warwick Badgery, Xiliang Li, Yong Ding, Huiqin Guo, Zinian Wu, Ningning Hu, Lingqi Kong, Chun Chang, Chao Jiang, Jize Zhang
BACKGROUND: The degradation of the steppe of Inner Mongolia, due to overgrazing, has resulted in ecosystem damage as well as extensive reductions in sheep production. The growth performance of sheep is greatly reduced because of overgrazing, which triggers massive economic losses every year. The liver is an essential organ that has very important roles in multiple functions, such as nutrient metabolism, immunity and others, which are closely related to animal growth. However, to our knowledge, no detailed studies have evaluated hepatic metabolism adaption in sheep due to overgrazing...
2016: Proteome Science
Lina Zhang, Aalt D J van Dijk, Kasper Hettinga
BACKGROUND: Milk is the most important food for growth and development of the neonate, because of its nutrient composition and presence of many bioactive proteins. Differences between human and bovine milk in low abundant proteins have not been extensively studied. To better understand the differences between human and bovine milk, the qualitative and quantitative differences in the milk proteome as well as their changes over lactation were compared using both label-free and labelled proteomics techniques...
2016: Proteome Science
Jize Zhang, Yang Gao, Qingping Lu, Renna Sa, Hongfu Zhang
BACKGROUND: Non-starch polysaccharide enzymes (NSPEs) have long been used in monogastric animal feed production to degrade non-starch polysaccharides (NSPs) to oligosaccharides in order to promote growth performance and gastrointestinal (GI) tract health. However, the precise molecular mechanism of NSPEs in the improvement of the mammalian small intestine remains unknown. METHODS: In this study, isobaric tags were applied to investigate alterations of the small intestinal mucosa proteome of growing pigs after 50 days of supplementation with 0...
2016: Proteome Science
Tyman E Stanford, Christopher J Bagley, Patty J Solomon
BACKGROUND: Proteomic matrix-assisted laser desorption/ionisation (MALDI) linear time-of-flight (TOF) mass spectrometry (MS) may be used to produce protein profiles from biological samples with the aim of discovering biomarkers for disease. However, the raw protein profiles suffer from several sources of bias or systematic variation which need to be removed via pre-processing before meaningful downstream analysis of the data can be undertaken. Baseline subtraction, an early pre-processing step that removes the non-peptide signal from the spectra, is complicated by the following: (i) each spectrum has, on average, wider peaks for peptides with higher mass-to-charge ratios (m/z), and (ii) the time-consuming and error-prone trial-and-error process for optimising the baseline subtraction input arguments...
2016: Proteome Science
Fang Chen, Carl Spiessens, Thomas D'Hooghe, Karen Peeraer, Sebastien Carpentier
BACKGROUND: Human follicular fluid (FF) is a unique biological fluid in which the oocyte develops in vivo, and presents an optimal source for non-invasive biochemical predictors. Oocyte quality directly influences the embryo development and hence, may be used as a predictor of embryo quality. Peptide profiling of FF and its potential use as a biomarker for oocyte quality has never been reported. METHODS: This study screened FF for peptide biomarkers that predict the outcome of in vitro fertilization (IVF)...
2016: Proteome Science
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