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See detailExtracellular peptidase hunting for improvement of protein production in plant cells and roots
Lallemand, Jérôme ULiege; Bouché, Frédéric ULiege; Desiron, Carole et al

Poster (2015, June)

Plant-based biopharmaceuticals have gained a lot of interest in the past decade due to their reduced cost and relative safety compared to mammalian cell cultures. While the first plant-made recombinant ... [more ▼]

Plant-based biopharmaceuticals have gained a lot of interest in the past decade due to their reduced cost and relative safety compared to mammalian cell cultures. While the first plant-made recombinant proteins are now reaching the market, the production systems still need improvements to maximize their competitiveness, proteolysis being one of the main factors limiting the yields. Identifying and inhibiting in vivo endogenous proteases involved in the degradation of recombinant proteins could then lead to a significant increase in production yields. In this study, we focused on two different production systems in Arabidopsis thaliana: rhizosecretion and cell suspensions. Extracellular proteases of both systems were used in vitro to study the conditions of target protein degradation (Bovine Serum Albumine, BSA). First, proteases from both systems degrade BSA at both acidic and neutral-to-basic pH conditions. Then, serine and metallopeptidases were shown to be the main protease classes responsible for BSA degradation by rhizosecreted proteomes or extracellular cell culture media, respectively. Finally, the biochemical tests were coupled to a bioinformatics analysis of publicly available transcriptomic data, in order to reduce the number of the proteases most likely involved in BSA degradation. Using this method, only five serine proteases and two metallopeptidases remain candidates for an amiRNA-mediated in vivo inhibition. [less ▲]

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See detailExtracellular peptidase hunting for improvement of protein production in plant cells and roots
Lallemand, Jérôme ULiege; Bouché, Frédéric ULiege; Desiron, Carole et al

in Frontiers in Plant Science (2015), 6(37),

Plant-based recombinant protein production systems have gained an extensive interest over the past few years, because of their reduced cost and relative safety. Although the first products are now ... [more ▼]

Plant-based recombinant protein production systems have gained an extensive interest over the past few years, because of their reduced cost and relative safety. Although the first products are now reaching the market, progress are still needed to improve plant hosts and strategies for biopharming. Targeting recombinant proteins toward the extracellular space offers several advantages in terms of protein folding and purification, but degradation events are observed, due to endogenous peptidases. This paper focuses on the analysis of extracellular proteolytic activities in two production systems: cell cultures and root-secretion (rhizosecretion), in Arabidopsis thaliana and Nicotiana tabacum. Proteolytic activities of extracellular proteomes (secretomes) were evaluated in vitro against two substrate proteins: bovine serum albumin (BSA) and human serum immunoglobulins G (hIgGs). Both targets were found to be degraded by the secretomes, BSA being more prone to proteolysis than hIgGs. The analysis of the proteolysis pH-dependence showed that target degradation was mainly dependent upon the production system: rhizosecretomes contained more peptidase activity than extracellular medium of cell suspensions, whereas variations due to plant species were smaller. Using class-specific peptidase inhibitors, serine and metallopeptidases were found to be responsible for degradation of both substrates. An in-depth in silico analysis of genomic and transcriptomic data from Arabidopsis was then performed and led to the identification of a limited number of serine and metallo-peptidases that are consistently expressed in both production systems. These peptidases should be prime candidates for further improvement of plant hosts by targeted silencing. [less ▲]

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See detailExtracellular vesicles in blood, milk and body fluids of the female and male urogenital tract and with special regard to reproduction
Foster, Brandon; Balassa, Timea; Benen, Thomas et al

in Critical Reviews in Clinical Laboratory Sciences (2016)

Detailed reference viewed: 80 (6 ULiège)
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See detailExtracellular, penicillin-resistant DD-carboxypeptidase from Streptomyces SP [abstract]
Leyh-Bouille, Mélina; Ghuysen, Jean-Marie ULiege; Bonaly, R. et al

in Xe Congresso Internacional de Microbiologica - Resumenes - abstracts - résumés (1970)

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See detailExtracting a common high frequency signal from Northern Quebec black spruce tree-rings with a Bayesian hierarchical model
Boreux, Jean-Jacques ULiege; Naveau, P.; Guin, O. et al

in Climate of the Past (2009), 5

One basic premise of dendroclimatology is that tree rings can be viewed as climate proxies, i.e. rings are assumed to contain some hidden information about past climate. From a statistical perspective ... [more ▼]

One basic premise of dendroclimatology is that tree rings can be viewed as climate proxies, i.e. rings are assumed to contain some hidden information about past climate. From a statistical perspective, this extraction problem can be understood as the search of a hidden variable which represents the common signal within a collection of tree-ring width series. Classical average-based techniques used in dendrochronology have been applied to estimate the mean behavior of this latent variable. Still, depending on tree species, regional factors and statistical methods, a precise quantification of uncertainties associated to the hidden variable distribution is difficult to assess. To model the error propagation throughout the extraction procedure, we propose and study a Bayesian hierarchical model that focuses on extracting an inter-annual high frequency signal. Our method is applied to black spruce (Picea mariana) tree-rings recorded in Northern Quebec and compared to a classical average-based techniques used by dendrochronologists. [less ▲]

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See detailExtracting explicit and implicit causal relations from sparse, domain-specific texts
Ittoo, Ashwin ULiege; Bouma, Gosse

in Lecture Notes in Computer Science (2011)

Detailed reference viewed: 24 (1 ULiège)
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See detailExtracting high resolution records of deformation from well-imaged sections
Suppe, J; Gonzalez-Mieres, R; Hubert, Aurelia ULiege

in Abstracts with Programs - Geological Society of America (2006, October), 38(7), 132

Detailed reference viewed: 15 (4 ULiège)
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See detailExtracting Intra-Domain Topology from mrinfo Probing
Pansiot, Jean-Jacques; Mérindol, Pascal; Donnet, Benoît ULiege et al

in 11th international Conference on Passive and active Measurement (2010, April)

Activeandpassivemeasurementsfortopologydiscoveryhave known an impressive growth during the last decade. If a lot of work has been done regarding inter-domain topology discovery and modeling, only a few ... [more ▼]

Activeandpassivemeasurementsfortopologydiscoveryhave known an impressive growth during the last decade. If a lot of work has been done regarding inter-domain topology discovery and modeling, only a few papers raise the question of how to extract intra-domain topologies from measurements results. In this paper, based on a large dataset collected with mrinfo, a multicast tool that silently discovers all interfaces of a router, we provide a mechanism for retrieving intra-domain topologies. The main challenge is to assign an AS number to a border router whose IP addresses are not mapped to the same AS. Our algorithm is based on probabilistic and empirical IP allocation rules. The goal of our pool of rules is to converge to a consistent router to AS mapping. We show that our router-to-AS algorithm results in a mapping in more than 99% of the cases. Furthermore, with mrinfo, point-to-point links between routers can be distinguished from multiple links attached to a switch, providing an accurate view of the collected topologies. Finally, we provide a set of large intra-domain topologies in various formats. [less ▲]

Detailed reference viewed: 17 (2 ULiège)
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See detailExtracting Meronymy Relationships from Domain-Specific, Textual Corporate Databases
Ittoo, Ashwin ULiege; Bouma, Gosse; Maruster, Laura et al

in Lecture Notes in Computer Science (2010)

Detailed reference viewed: 41 (0 ULiège)
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See detailExtracting oscillating components from nonstationary time series: A wavelet-induced method
Deliège, Adrien ULiege; Nicolay, Samuel ULiege

in Physical Review. E : Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics (2017), 96

This paper consists in the description and application of a method called wavelet-induced mode extraction (WIME) in the context of time-frequency analysis. WIME aims to extract the oscillating components ... [more ▼]

This paper consists in the description and application of a method called wavelet-induced mode extraction (WIME) in the context of time-frequency analysis. WIME aims to extract the oscillating components that build amplitude modulated-frequency modulated signals. The essence of this technique relies on the successive extractions of the dominant ridges of wavelet-based time-frequency representations of the signal under consideration. Our tests on simulated examples indicate strong decomposition and reconstruction skills, trouble-free handling of crossing trajectories in the time-frequency plane, sharp performances in frequency detection in the case of mode-mixing problems, and a natural tolerance to noise. These results are compared with those obtained with empirical mode decomposition. We also show that WIME still gives meaningful results with real-life data, namely, the Oceanic Niño Index. [less ▲]

Detailed reference viewed: 93 (32 ULiège)
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See detailExtracting residues from stone tools for optical analysis: towards an experiment-based protocol
Cnuts, Dries ULiege; Rots, Veerle ULiege

in Archaeological and Anthropological sciences (2017)

The identification of residues is traditionally based on the distinctive morphologies of the residue fragments by means of light microscopy. Most residue fragments are amorphous, in the sense that they ... [more ▼]

The identification of residues is traditionally based on the distinctive morphologies of the residue fragments by means of light microscopy. Most residue fragments are amorphous, in the sense that they lack distinguishing shapes or easily visible structures under reflected light microscopy. Amorphous residues can only be identified by using transmitted light microscopy, which requires the extraction of residues from the tool’s surface. Residues are usually extracted with a pipette or an ultrasonic bath in combination with distilled water. However, a number of researchers avoid residue extraction because it is unclear whether current extraction techniques are representative for the use-related residue that adheres to a flaked stone tool. In this paper, we aim at resolving these methodological uncertainties by critically evaluating current extraction methodologies. Attention is focused on the variation in residue types, their causes of deposition and their adhesion and on the most successful technique for extracting a range of residue types from the stone tool surface. Based on an experimental reference sample in flint, we argue that a stepwise extraction protocol is most successful in providing rep- resentative residue extractions and in preventing damage, destruction or loss of residue. [less ▲]

Detailed reference viewed: 34 (1 ULiège)
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See detailExtraction abrégée de la racine carrée
Catalan, Eugène ULiege

in Nouvelles Annales de Mathématiques : Journal des Candidats aux Ecoles Polytechnique et Normale (1858), 17

Detailed reference viewed: 21 (2 ULiège)
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See detailExtraction and characterisation of a dietary fibre concentrate from date pulp
Roiseux, O.; Blecker, Christophe ULiege; Besbes, S. et al

Poster (2006, June)

Detailed reference viewed: 18 (2 ULiège)