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See detailProteomic and genomic analysis of Chlamydomonas reinhardtii complex 1: conserved components in eukaryotes
Cardol, Pierre ULg; Vanrobaeys, F.; Devreese, B. et al

in Biochimica et Biophysica Acta-Bioenergetics (2004), 1657(Suppl. 1), 41-42

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See detailProteomic and genomic modulations induced by gamma-irradiation of human blood lymphocytes.
Turtoi, Andrei ULg; Sharan, Rajesh; Srivastava, Alok et al

in International Journal of Radiation Biology (2010), 86(10), 888-904

PURPOSE: Quantitative evaluation of early response proteins (ERPRO) and early response genes (ERG) following γ-irradiation of human lymphocytes; identification of specific proteins and genes as candidate ... [more ▼]

PURPOSE: Quantitative evaluation of early response proteins (ERPRO) and early response genes (ERG) following γ-irradiation of human lymphocytes; identification of specific proteins and genes as candidate biomarkers for the development of a novel biodosimeter. MATERIALS AND METHODS: Human peripheral blood lymphocytes were exposed to clinically relevant doses (1, 2 and 4 Gy) of γ-radiation ex-vivo. Analyses of protein and gene expression modulation were conducted 2 h post-irradiation. Global modulations were monitored using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and DNA microarray analyses of the samples originating from one human donor. On the proteome level, both phosphorylated and non-phosphorylated proteins were considered. Proteins and genes of specific interest were further targeted using Western blot (WB) and real-time quantitative polymerase chain reaction (RT-qPCR) techniques, employing samples from several human donors (n=3). RESULTS: A set of ERPRO and ERG showing significant alterations 2 h post-γ-irradiation have been identified in human lymphocytes. The most radiation responsive genes and proteins indicated alterations of cellular structure (ß-actin, talin-1 [TLN1], talin-2, zyxin-2), immune and defence reactions (major histocompatibility complex binding protein-2 [MBP2], interleukin-17E and interferon-γ), cell cycle control (cyclin-dependent kinase inhibitor-1A [CDKN1A], mouse double minute-2, annexin-A6 [ANXA6], growth arrest and DNA-damage-inducible protein-α [GADD45A], proliferating cell nuclear antigen [PCNA], dual specificity phosphatase-2 and 8 [DUSP8]) as well as detoxification processes (peroxin-1) and apoptosis (B-cell lymphoma-2 binding component-3 [BBC3]). SUMMARY: The estimations of protein concentration modulation of TLN1 and CDKN1A, phosphorylation status of ANXA6 (dose range 0-2 Gy) and MBP2 as well as the alterations in the level of gene expressions of BBC3, DUSP8, GADD45A and PCNA appears to be of potential value for future biodosimetric applications. [less ▲]

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See detailProteomic approach to investigate aphid - plant interactions
Francis, Frédéric ULg; Harmel, Nicolas; De Pauw, Edwin ULg et al

in Abstract book (2006)

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See detailProteomic approach to investigate plant – aphid interactions
Francis, Frédéric ULg; Gerkens, Pascal; De Pauw, Edwin ULg et al

Conference (2005)

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See detailProteomic changes in rat hippocampus and adrenals following short-term sleep deprivation.
Poirrier, Jean-Etienne; Guillonneau, Francois; Renaut, Jenny et al

in Proteome Science (2008), 6

ABSTRACT: BACKGROUND: To identify the biochemical changes induced by sleep deprivation at a proteomic level, we compared the hippocampal proteome of rats either after 4 hours of sleep or sleep deprivation ... [more ▼]

ABSTRACT: BACKGROUND: To identify the biochemical changes induced by sleep deprivation at a proteomic level, we compared the hippocampal proteome of rats either after 4 hours of sleep or sleep deprivation obtained by gentle handling. Because sleep deprivation might induce some stress, we also analyzed proteomic changes in rat adrenals in the same conditions. After sleep deprivation, proteins from both tissues were extracted and subjected to 2D-DIGE analysis followed by protein identification through mass spectrometry and database search. RESULTS: In the hippocampus, 87 spots showed significant variation between sleep and sleep deprivation, with more proteins showing higher abundance in the latter case. Of these, 16 proteins were present in sufficient amount for a sequencing attempt and among the 12 identified proteins, inferred affected cellular functions include cell metabolism, energy pathways, transport and vesicle trafficking, cytoskeleton and protein processing. Although we did not observe classical, macroscopic effect of stress in sleep-deprived rats, 47 protein spots showed significant variation in adrenal tissue between sleep and sleep deprivation, with more proteins showing higher abundance following sleep. Of these, 16 proteins were also present in sufficient amount for a sequencing attempt and among the 13 identified proteins, the most relevant cellular function that was affected was cell metabolism. CONCLUSION: At a proteomic level, short term sleep deprivation is characterized by a higher expression of some proteins in the hippocampus and a lower abundance of other proteins in the adrenals (compared to normal sleep control). Altogether, this could indicate a general activation of a number of cellular mechanisms involved in the maintenance of wakefulness and in increased energy expenditure during sleep deprivation. These findings are relevant to suggested functions of sleep like energy repletion and the restoration of molecular stocks or a more global homeostasis of synaptic processes. [less ▲]

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See detailProteomic characterization of a Chlamydomonas reinhardtii mutant lacking the mitochondrial alternative oxidase
Mathy, Grégory ULg

Conference (2009, September 27)

Conférence réalisée sur la carractérisation d'un mutant AOX- chez l'algue unicellulaire Chlamydomonas reinhardtii

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See detailProteomic characterization of bovine herpesvirus 4 extracellular virions.
Lété, Céline ULg; Palmeira, Leonor ULg; Leroy, Baptiste et al

in Journal of Virology (2012), 86(21), 11567-80

Gammaherpesviruses are important pathogens in human and animal populations. During early events of infection, these viruses manipulate preexisting host cell signaling pathways to allow successful ... [more ▼]

Gammaherpesviruses are important pathogens in human and animal populations. During early events of infection, these viruses manipulate preexisting host cell signaling pathways to allow successful infection. The different proteins that compose viral particles are therefore likely to have critical functions not only in viral structures and in entry into target cell but also in evasion of the host's antiviral response. In this study, we analyzed the protein composition of bovine herpesvirus 4 (BoHV-4), a close relative of the human Kaposi's sarcoma-associated herpesvirus. Using mass spectrometry-based approaches, we identified 37 viral proteins associated with extracellular virions, among which 24 were resistant to proteinase K treatment of intact virions. Analysis of proteins associated with purified capsid-tegument preparations allowed us to define protein localization. In parallel, in order to identify some previously undefined open reading frames, we mapped peptides detected in whole virion lysates onto the six frames of the BoHV-4 genome to generate a proteogenomic map of BoHV-4 virions. Furthermore, we detected important glycosylation of three envelope proteins: gB, gH, and gp180. Finally, we identified 38 host proteins associated with BoHV-4 virions; 15 of these proteins were resistant to proteinase K treatment of intact virions. Many of these have important functions in different cellular pathways involved in virus infection. This study extends our knowledge of gammaherpesvirus virions composition and provides new insights for understanding the life cycle of these viruses. [less ▲]

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See detailProteomic characterization of murid herpesvirus 4 extracellular virions.
Vidick, Sarah ULg; Leroy, Baptiste; Gonon Rodrigues Palmeira, Leonor ULg et al

in PloS one (2013), 8(12), 83842

Gammaherpesvirinae, such as the human Epstein-Barr virus (EBV) and the Kaposi's sarcoma associated herpesvirus (KSHV) are highly prevalent pathogens that have been associated with several neoplastic ... [more ▼]

Gammaherpesvirinae, such as the human Epstein-Barr virus (EBV) and the Kaposi's sarcoma associated herpesvirus (KSHV) are highly prevalent pathogens that have been associated with several neoplastic diseases. As EBV and KSHV are host-range specific and replicate poorly in vitro, animal counterparts such as Murid herpesvirus-4 (MuHV-4) have been widely used as models. In this study, we used MuHV-4 in order to improve the knowledge about proteins that compose gammaherpesviruses virions. To this end, MuHV-4 extracellular virions were isolated and structural proteins were identified using liquid chromatography tandem mass spectrometry-based proteomic approaches. These analyses allowed the identification of 31 structural proteins encoded by the MuHV-4 genome which were classified as capsid (8), envelope (9), tegument (13) and unclassified (1) structural proteins. In addition, we estimated the relative abundance of the identified proteins in MuHV-4 virions by using exponentially modified protein abundance index analyses. In parallel, several host proteins were found in purified MuHV-4 virions including Annexin A2. Although Annexin A2 has previously been detected in different virions from various families, its role in the virion remains controversial. Interestingly, despite its relatively high abundance in virions, Annexin A2 was not essential for the growth of MuHV-4 in vitro. Altogether, these results extend previous work aimed at determining the composition of gammaherpesvirus virions and provide novel insights for understanding MuHV-4 biology. [less ▲]

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See detailProteomic comparison of high and low responders to eccentric exercise
Hody, Stéphanie ULg; Croisier, Jean-Louis ULg; Leprince, Pierre ULg et al

in Meeusen, R.; Duchateau, J.; Roelands, B. (Eds.) et al Book of Abstracts of the 17th annual Congress of the ECSS (2012, July)

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See detailProteomic comparison of High and Low responders to eccentric exercise
Hody, Stéphanie ULg; Croisier, Jean-Louis ULg; Leprince, Pierre ULg et al

in Abstract book du Colloque de la Société Belge des Neurosciences (2009, May)

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See detailProteomic evolution of s.cerevisiae during chronological aging
Blomme, Arnaud ULg; Mac Cord, Allan ULg; Sluse, Francis ULg et al

Poster (2010, July 19)

Opposite to the replicative aging, which refers to the exponential decline in the capacity of a single cell to divide, chronological aging of the yeast Saccharomyces cerevisiae refers to the time period a ... [more ▼]

Opposite to the replicative aging, which refers to the exponential decline in the capacity of a single cell to divide, chronological aging of the yeast Saccharomyces cerevisiae refers to the time period a yeast cell can survive in a non-dividing state. In 2006, Allen and co-workers reported that yeast cells evolve into two cell types during stationary phase: a high density population defined as quiescent cells (Q) and a low density population defined as non-quiescent (NQ) cells. These two populations mainly differ by their viability, measured as the ability to form colonies when platted on Petri dishes, and can be separated by differential centrifugation on density gradient. In this work, we used the quantitative proteomics technique of 2DDIGE (two Dimensional Differential In-Gel Electrophoresis) to compare the evolution of the yeast cellular soluble proteome during chronological aging. We also checked the impact of the carbon source on stationary-phase cell differentiation. As the ratio of Q/NQ cells is decreasing with time, we have selected three distinct periods: 0 day (32h after outset of yeast culture on glucose, 100% of Q cells), 7 days (50% of Q cells) and 14 days (100% of NQ cells) to realize 3 proteomics comparisons (fig 1). [less ▲]

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See detailProteomic Investigation of Aphid Honeydew Reveals an Unexpected Diversity of Proteins
Sabri, Ahmed; Vandermoten, Sophie ULg; Leroy, Pascal et al

in PLoS ONE (2013), 8(9),

Aphids feed on the phloem sap of plants, and are the most common honeydew-producing insects. While aphid honeydew is primarily considered to comprise sugars and amino acids, its protein diversity has yet ... [more ▼]

Aphids feed on the phloem sap of plants, and are the most common honeydew-producing insects. While aphid honeydew is primarily considered to comprise sugars and amino acids, its protein diversity has yet to be documented. Here, we report on the investigation of the honeydew proteome from the pea aphid Acyrthosiphon pisum. Using a two-Dimensional <br />Differential in-Gel Electrophoresis (2D-Dige) approach, more than 140 spots were isolated, demonstrating that aphid honeydew also represents a diverse source of proteins. About 66% of the isolated spots were identified through mass spectrometry analysis, revealing that the protein diversity of aphid honeydew originates from several organisms (i.e. the host aphid and its microbiota, including endosymbiotic bacteria and gut flora). Interestingly, our experiments also allowed to identify some proteins like chaperonin, GroEL and Dnak chaperones, elongation factor Tu (EF-Tu), and flagellin that might act as mediators in the plant-aphid interaction. In addition to providing the first aphid honeydew proteome analysis, we propose to reconsider the importance of this substance, mainly acknowledged to be a waste product, from the aphid <br />ecology perspective. [less ▲]

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See detailProteomic kinetic analysis of blister fluid and serum in a patient with drug-induced toxic epidermal necrolysis. A comparison with skin immunohistochemistry.
Paquet, Philippe; Meuwis, Marie-Alice ULg; Mazzucchelli, Gabriel ULg et al

in Current Drug Safety (2012), 7(5), 339-51

Drug-induced toxic epidermal necrolysis (TEN) is a rare but potentially lethal bullous disease whose complex pathomechanisms remain uncertain. The aim of the study was an exploratory attempt to assess TEN ... [more ▼]

Drug-induced toxic epidermal necrolysis (TEN) is a rare but potentially lethal bullous disease whose complex pathomechanisms remain uncertain. The aim of the study was an exploratory attempt to assess TEN pathobiology using a combination of immunohistochemistry and proteomics. Skin blister fluid (BF) and serum were collected in a patient in the early TEN stage at day (D) +4 of evolution and three days later (D +7). Intravenous cyclosporine A (CsA) treatment was initiated since D +4. Immunohistochemistry was performed on skin blister biopsies. In addition, proteomic analyses compared the BF protein content before and at the issue of the 3-day CsA treatment. Proteins were selected according to their prominent differential abundance in BF between D+4 and D+7, when influenced by lesional skin cells, but not in serum. Among 300 proteins, four were considered. Glutathione transferase pi was related to oxidative stress in TEN epidermis. The monocyte differentiation antigen CD14 and myeloperoxidase indicated macrophage activation. The proinflammatory S100-A8 protein probably originated from activated keratinocytes and/or macrophages. These proteomic findings were in line with immunohistochemistry and supported the prominent involvement of keratinocytes and macrophages in TEN pathomechanism. As opposed to CD14, other proteins were mainly present in BF at D+7, confirming that CsA expressed little effect, if any, on the activity of keratinocytes and macrophages in the present TEN patient. Of note, the present exploratory study using proteomic analyses in a single TEN case supports a pathogenic hypothesis without establishing any firm conclusion. [less ▲]

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See detailProteomic mass spectra classification using decision tree based ensemble methods.
Geurts, Pierre ULg; Fillet, Marianne ULg; De Seny, Dominique ULg et al

in Bioinformatics (2005), 21(14), 3138-45

MOTIVATION: Modern mass spectrometry allows the determination of proteomic fingerprints of body fluids like serum, saliva or urine. These measurements can be used in many medical applications in order to ... [more ▼]

MOTIVATION: Modern mass spectrometry allows the determination of proteomic fingerprints of body fluids like serum, saliva or urine. These measurements can be used in many medical applications in order to diagnose the current state or predict the evolution of a disease. Recent developments in machine learning allow one to exploit such datasets, characterized by small numbers of very high-dimensional samples. RESULTS: We propose a systematic approach based on decision tree ensemble methods, which is used to automatically determine proteomic biomarkers and predictive models. The approach is validated on two datasets of surface-enhanced laser desorption/ionization time of flight measurements, for the diagnosis of rheumatoid arthritis and inflammatory bowel diseases. The results suggest that the methodology can handle a broad class of similar problems. [less ▲]

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See detailProteomic study of cold-repressed proteins in the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125
Piette, Florence; D'Amico, Salvino; Leprince, Pierre ULg et al

Poster (2010)

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See detailProteomic study of lumbar spinal cord after quadricipital eccentric exercise
Lacrosse, Zoé ULg; Hody, Stéphanie ULg; Leprince, Pierre ULg et al

Poster (2013, September 12)

Eccentric muscle contractions are characterized by an increase of muscle tension as it lengthens (slowering movements). Unaccustomed or intense eccentric exercise causes “Delayed-Onset Muscle Soreness” ... [more ▼]

Eccentric muscle contractions are characterized by an increase of muscle tension as it lengthens (slowering movements). Unaccustomed or intense eccentric exercise causes “Delayed-Onset Muscle Soreness” (DOMS). DOMS include muscle pain that appears 24 to 72 hours after exercise, but also stiffness, edema and muscle proteins release in plasma as a hallmark of muscle fibers injuries. The only systematic intervention that brings a muscle protection against DOMS is to realize submaximal eccentric contractions with a progressively increased intensity. The mechanism of this protection, called the “Repeated Bout Effect” (RBE), is not understood. However, it is likely explained by cellular, mechanical and neural theories [Scand.J.Med.&Sci.Sports, 13, 88, 2003]. The objective of this study is to better understand which neural signal is released in the muscle synapse and which brings protection by RBE. Male adult mice (C57BL6) were randomly divided into downhill running (DHR), uphill running (UHR) and untrained control (CONT) groups (n=4/group). DHR group is characterized by eccentric contractions of the quadriceps while UHR is concerned by concentric contractions. Running groups performed a warm-up of ten minutes followed by an interval exercise on an inclined treadmill at a velocity of 20cm/s. The latter consisted of running 18 bouts of 5 minutes interspersed with a 2 minutes rest. Lumbar spinal cord was dissected 24h after the race. Nuclear and cytoplasmic proteins were separately extracted and subjected to a 2D-DIGE analysis coupled with mass spectrometry. We do not observe any cytoplasmic protein modification while in the nuclear extract, seven spots were more abundant in eccentric group and four in concentric group in comparison with control group. The mass spectrometry of these proteins reveals that they are implicated in axoplasmic transport. At 24 hours, too few proteins modifications were detected in lumbar spinal cord, maybe as a consequence of a too short period between race and euthanasia. Implication of axoplasmic transport comforts our starting hypothesis that nervous system is able to protect muscle during the RBE by a synthesis and then a synaptic release of molecules modifying the muscle physiology. [less ▲]

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See detailProteomic study of lumbar spinal cord after quadricipital eccentric exercise
Lacrosse, Zoé ULg; Lacrosse, Zoé ULg; Hody, Stéphanie ULg et al

in 17th EURON PhD meeting (2013, September)

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See detailProteomic study of plant-aphid interactions: between defense and adaptations.
Francis, Frédéric ULg; Gerkens, P.; De Pauw, Edwin ULg et al

in Comparative Biochemistry and Physiology. Part A, Physiology (2005), 141

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See detailProteomics for prediction and characterization of response to infliximab in Crohn's disease: a pilot study.
Meuwis, Marie-Alice ULg; Fillet, Marianne ULg; Lutteri, Laurence ULg et al

in Clinical Biochemistry (2008), 41(12), 960-7

OBJECTIVES: Infliximab is the first anti-TNFalpha accepted by the Food and Drug Administration for use in inflammatory bowel disease treatment. Few clinical, biological and genetic factors tend to predict ... [more ▼]

OBJECTIVES: Infliximab is the first anti-TNFalpha accepted by the Food and Drug Administration for use in inflammatory bowel disease treatment. Few clinical, biological and genetic factors tend to predict response in Crohn's disease (CD) patient subcategories, none widely predicting response to infliximab. DESIGN AND METHODS: Twenty CD patients showing clinical response or non response to infliximab were used for serum proteomic profiling on Surface Enhanced Lazer Desorption Ionisation-Time of Flight-Mass Spectrometry (SELDI-TOF-MS), each before and after treatment. Univariate and multivariate data analysis were performed for prediction and characterization of response to infliximab. RESULTS: We obtained a model of classification predicting response to treatment and selected relevant potential biomarkers, among which platelet aggregation factor 4 (PF4). We quantified PF4, sCD40L and IL-6 by ELISA for correlation studies. CONCLUSIONS: This first proteomic pilot study on response to infliximab in CD suggests association between platelet metabolism and response to infliximab and requires validation studies on a larger cohort of patients. [less ▲]

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