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See detailProteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities
Denef, Vincent J.; Kalnejais, Linda H.; Mueller, Ryan S. et al

in Proceedings of the National Academy of Sciences of the United States of America (2010), 107(6), 2383-2390

Bacterial species concepts are controversial. More widely accepted is the need to understand how differences in gene content and sequence lead to ecological divergence. To address this relationship in ... [more ▼]

Bacterial species concepts are controversial. More widely accepted is the need to understand how differences in gene content and sequence lead to ecological divergence. To address this relationship in ecosystem context, we investigated links between genotype and ecology of two genotypic groups of Leptospirillum group II bacteria in comprehensively characterized, natural acidophilic biofilm communities. These groups share 99.7% 16S rRNA gene sequence identity and 95% average amino acid identity between their orthologs. One genotypic group predominates during early colonization, and the other group typically proliferates in later successional stages, forming distinct patches tens to hundreds of micrometers in diameter. Among early colonizing populations, we observed dominance of five genotypes that differed from each other by the extent of recombination with the late colonizing type. Our analyses suggest that the specific recombinant variant within the early colonizing group is selected for by environmental parameters such as temperature, consistent with recombination as a mechanism for ecological fine tuning. Evolutionary signatures, and strain-resolved expression patterns measured via mass spectrometry-based proteomics, indicate increased cobalamin biosynthesis, (de) methylation, and glycine cleavage in the late colonizer. This may suggest environmental changes within the biofilm during development, accompanied by redirection of compatible solutes from osmoprotectants toward metabolism. Across 27 communities, comparative proteo-genomic analyses show that differential regulation of shared genes and expression of a small subset of the similar to 15% of genes unique to each genotype are involved in niche partitioning. In summary, the results show how subtle genetic variations can lead to distinct ecological strategies. [less ▲]

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See detailProteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins.
Cappellini, Enrico; Jensen, Lars J.; Szklarczyk, Damian et al

in Journal of proteome research (2012), 11(2), 917-26

We used high-sensitivity, high-resolution tandem mass spectrometry to shotgun sequence ancient protein remains extracted from a 43 000 year old woolly mammoth ( Mammuthus primigenius ) bone preserved in ... [more ▼]

We used high-sensitivity, high-resolution tandem mass spectrometry to shotgun sequence ancient protein remains extracted from a 43 000 year old woolly mammoth ( Mammuthus primigenius ) bone preserved in the Siberian permafrost. For the first time, 126 unique protein accessions, mostly low-abundance extracellular matrix and plasma proteins, were confidently identified by solid molecular evidence. Among the best characterized was the carrier protein serum albumin, presenting two single amino acid substitutions compared to extant African ( Loxodonta africana ) and Indian ( Elephas maximus ) elephants. Strong evidence was observed of amino acid modifications due to post-mortem hydrolytic and oxidative damage. A consistent subset of this permafrost bone proteome was also identified in more recent Columbian mammoth ( Mammuthus columbi ) samples from temperate latitudes, extending the potential of the approach described beyond subpolar environments. Mass spectrometry-based ancient protein sequencing offers new perspectives for future molecular phylogenetic inference and physiological studies on samples not amenable to ancient DNA investigation. This approach therefore represents a further step into the ongoing integration of different high-throughput technologies for identification of ancient biomolecules, unleashing the field of paleoproteomics. [less ▲]

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See detailProteomic analysis of Dhh1 complexes reveals a role for Hsp40 chaperone Ydj1 in yeast P-body assembly
Cary, Greg A.; Vinh, Dani B.H.; May, Patrick UL et al

in G3 (2015)

P-bodies (PB) are ribonucleoprotein (RNP) complexes that aggregate into cytoplasmic foci when cells are exposed to stress. While the conserved mRNA decay and translational repression machineries are known ... [more ▼]

P-bodies (PB) are ribonucleoprotein (RNP) complexes that aggregate into cytoplasmic foci when cells are exposed to stress. While the conserved mRNA decay and translational repression machineries are known components of PB, how and why cells assemble RNP complexes into large foci remain unclear. Using mass spectrometry to analyze proteins immunoisolated with the core PB protein Dhh1, we show that a considerable number of proteins contain low-complexity (LC) sequences, similar to proteins highly represented in mammalian RNP granules. We also show that the Hsp40 chaperone Ydj1, which contains an LC domain and controls prion protein aggregation, is required for the formation of Dhh1-GFP foci upon glucose depletion. New classes of proteins that reproducibly coenrich with Dhh1-GFP during PB induction include proteins involved in nucleotide or amino acid metabolism, glycolysis, tRNA aminoacylation, and protein folding. Many of these proteins have been shown to form foci in response to other stresses. Finally, analysis of RNA associated with Dhh1-GFP shows enrichment of mRNA encoding the PB protein Pat1 and catalytic RNAs along with their associated mitochondrial RNA-binding proteins. Thus, global characterization of PB composition has uncovered proteins important for PB assembly and evidence suggesting an active role for RNA in PB function. [less ▲]

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See detailProteomic Characterization of Primary Mouse Hepatocytes in Collagen Monolayer and Sandwich Culture.
Orsini, Malina; Sperber, Saskia; Noor, Fozia UL et al

in Journal of cellular biochemistry (2017)

Dedifferentiation of primary hepatocytes in vitro makes their application in long-term studies difficult. Embedding hepatocytes in a sandwich of extracellular matrix is reported to delay the ... [more ▼]

Dedifferentiation of primary hepatocytes in vitro makes their application in long-term studies difficult. Embedding hepatocytes in a sandwich of extracellular matrix is reported to delay the dedifferentiation process to some extent. In this study, we compared the intracellular proteome of primary mouse hepatocytes (PMH) in conventional monolayer cultures (ML) to collagen sandwich culture (SW) after 1 day and 5 days of cultivation. Quantitative proteome analysis of PMH showed no differences between collagen SW and ML cultures after 1 day. Glycolysis and gluconeogenesis were strongly affected by long-term cultivation in both ML and SW cultures. Interestingly, culture conditions had no effect on cellular lipid metabolism. After 5 days, PMH in collagen SW and ML cultures exhibit characteristic indications of oxidative stress. However, in the SW culture the defense system against oxidative stress is significantly up-regulated to deal with this, whereas in the ML culture a down-regulation of these important enzymes takes place. Regarding the multiple effects of ROS and oxidative stress in cells, we conclude that the down-regulation of these enzymes seem to play a role in the loss of hepatic function observed in the ML cultivation. In addition, enzymes of the urea cycle were clearly down-regulated in ML culture. Proteomics confirms lack in oxidative stress defense mechanisms as the major characteristic of hepatocytes in monolayer cultures compared to sandwich cultures. J. Cell. Biochem. 9999: 1-8, 2017. (c) 2017 Wiley Periodicals, Inc. [less ▲]

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See detailProtestantismus, Kapitalismus und Konsum
Lenz, Thomas UL

Presentation (2012)

Detailed reference viewed: 17 (1 UL)
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See detailProtesting Ethnic Minorities in Europe: A Fuzzy-Set Analysis
Cebotari, Victor UL

E-print/Working paper (2010)

Detailed reference viewed: 69 (0 UL)
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See detailProteum/FL: A tool for localizing faults using mutation analysis.
Papadakis, Mike UL; Delamaro, Eduardo Márcio; Le Traon, Yves UL

in International Working Conference on Source Code Analysis and Manipulation (2013)

Detailed reference viewed: 108 (4 UL)
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See detailLe protezioni sociali ravvicinate. Sogni e incubi
Bricocoli, Massimo UL; de Leonardis, Ota

in Bianchetti, Cristina (Ed.) Territori della condivisione. Una nuova città (2014)

Detailed reference viewed: 80 (1 UL)
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See detailLes prothèses cognitives du corps humain
Derian, Maxime UL

Book published by ISTE (2018)

Les machines informatisées se retrouvent, sous diverses formes, autour de nous, dans nos poches et parfois dans notre organisme. Elles sont aujourd'hui des éléments incontournables du quotidien pour la ... [more ▼]

Les machines informatisées se retrouvent, sous diverses formes, autour de nous, dans nos poches et parfois dans notre organisme. Elles sont aujourd'hui des éléments incontournables du quotidien pour la plupart d'entre nous. Qu'il s'agisse des smartphones, d'objets connectés ou de dispositifs numériques médicaux et d'e-santé, ces outils numériques prolifèrent littéralement dans notre environnement. Ils font office de prothèses qui « augmentent » nos capacités cognitives mais également d'orthèses qui influencent bon nombre de nos comportements. La généralisation de ces machines semble même en mesure de transformer nos modes d'organisation sociale de manière conséquente. Les outils numériques qui emmaillotent sans cesse davantage le corps et l'esprit sont-ils en mesure de bouleverser notre ordre social ? Pourraient-ils littéralement entraîner demain la disparition de la société telle que nous la connaissons aujourd'hui ? Les prothèses cognitives du corps humain explore cette réflexion qui est au centre des usages des outils numériques. [less ▲]

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See detailProto-industrialisation et immigration au Luxembourg
Pauly, Michel UL

in Allegrezza, Serge e.a. (Ed.) L’immigration au Luxembourg, et après? (2007)

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See detailA protocol for generating a high-quality genome-scale metabolic reconstruction.
Thiele, Ines UL; Palsson, Bernhard O.

in Nature Protocols (2010), 5(1), 93-121

Network reconstructions are a common denominator in systems biology. Bottom-up metabolic network reconstructions have been developed over the last 10 years. These reconstructions represent structured ... [more ▼]

Network reconstructions are a common denominator in systems biology. Bottom-up metabolic network reconstructions have been developed over the last 10 years. These reconstructions represent structured knowledge bases that abstract pertinent information on the biochemical transformations taking place within specific target organisms. The conversion of a reconstruction into a mathematical format facilitates a myriad of computational biological studies, including evaluation of network content, hypothesis testing and generation, analysis of phenotypic characteristics and metabolic engineering. To date, genome-scale metabolic reconstructions for more than 30 organisms have been published and this number is expected to increase rapidly. However, these reconstructions differ in quality and coverage that may minimize their predictive potential and use as knowledge bases. Here we present a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction, as well as the common trials and tribulations. Therefore, this protocol provides a helpful manual for all stages of the reconstruction process. [less ▲]

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See detailA Protocol to Strengthen Password-Based Authentication
Vazquez Sandoval, Itzel UL; Lenzini, Gabriele UL; Stojkovski, Borce UL

in Emerging Technologies for Authorization and Authentication (2018, November)

We discuss a password-based authentication protocol that we argue to be robust against password-guessing and o -line dictionary attacks. The core idea is to hash the passwords with a seed that comes from ... [more ▼]

We discuss a password-based authentication protocol that we argue to be robust against password-guessing and o -line dictionary attacks. The core idea is to hash the passwords with a seed that comes from an OTP device, making the resulting identity token unpredictable for an adversary. We believe that the usability of this new protocol is the same as that of password-based methods with OTP, but has the advan- tage of not burdening users with having to choose strong passwords. [less ▲]

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See detailUn protocole de sauvegarde / reprise coordonné pour les applications à flot de données reconfigurables
Besseron, Xavier UL; Pigeon, Laurent; Gautier, Thierry et al

in Technique et Science Informatiques (2007)

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See detailProtocols and programs for high-throughput growth and aging phenotyping in yeast.
Jung, Paul UL; Christian, Nils UL; Kay, Daniel UL et al

in PloS one (2015), 10(3), 0119807

In microorganisms, and more particularly in yeasts, a standard phenotyping approach consists in the analysis of fitness by growth rate determination in different conditions. One growth assay that combines ... [more ▼]

In microorganisms, and more particularly in yeasts, a standard phenotyping approach consists in the analysis of fitness by growth rate determination in different conditions. One growth assay that combines high throughput with high resolution involves the generation of growth curves from 96-well plate microcultivations in thermostated and shaking plate readers. To push the throughput of this method to the next level, we have adapted it in this study to the use of 384-well plates. The values of the extracted growth parameters (lag time, doubling time and yield of biomass) correlated well between experiments carried out in 384-well plates as compared to 96-well plates or batch cultures, validating the higher-throughput approach for phenotypic screens. The method is not restricted to the use of the budding yeast Saccharomyces cerevisiae, as shown by consistent results for other species selected from the Hemiascomycete class. Furthermore, we used the 384-well plate microcultivations to develop and validate a higher-throughput assay for yeast Chronological Life Span (CLS), a parameter that is still commonly determined by a cumbersome method based on counting "Colony Forming Units". To accelerate analysis of the large datasets generated by the described growth and aging assays, we developed the freely available software tools GATHODE and CATHODE. These tools allow for semi-automatic determination of growth parameters and CLS behavior from typical plate reader output files. The described protocols and programs will increase the time- and cost-efficiency of a number of yeast-based systems genetics experiments as well as various types of screens. [less ▲]

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See detailProtocols and Stability Analysis for Energy Harvesting TDMA Systems with/without Relaying
Ottersten, Björn UL; Krikidis, Ioannis; Zheng, Gan UL

in IEEE Global Telecommunications Conference (GLOBECOM) (2013, December)

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See detailPROTOGIM: a novel tool to search motifs and domains in hypothetical proteins of protozoan genomes.
Cestari, Igor S.; Haver, Nicolaas J.; Barbosa Da Silva, Adriano UL et al

in Parasitology research (2006), 98(4), 375-7

Whole sequencing of protozoan trypanosomatid genomes revealed the presence of several predicted unknown genes coding for hypothetical proteins. Pairwise, alignment-based, computational methods available ... [more ▼]

Whole sequencing of protozoan trypanosomatid genomes revealed the presence of several predicted unknown genes coding for hypothetical proteins. Pairwise, alignment-based, computational methods available online are unable to identify the function of these sequences. To detect clues to identify the function of hypothetical proteins, a user-friendly, bioinformatic tool named PROTOzoan Gene Identification Motifs (PROTOGIM, available on http://www.biowebdb.org/protogim ) was developed, which allows the user to search functional patterns of hypothetical proteins through the screening of regular expression in the sequences. The analysis of 1,194 trypanosomatid hypothetical proteins through PROTOGIM resulted in an identification of motifs and domains in 98% of the cases, demonstrating the reliability and accuracy of the employed method. The added value of this tool is the possibility to modify or insert new regular expressions to perform an analysis against either one or several sequences at the same time. An in silico strategy along with biochemical and molecular characterizations creates new possibilities to find the functions of hypothetical proteins at the postgenome era. [less ▲]

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See detailProtons selectively induce lasting excitation and sensitization to mechanical stumulation of nociceptors in rat skin, in vitro
Steen, Kai h; Reeh, Peter-Werner; Anton, Fernand UL et al

in Journal of Neuroscience (1992), 12(1), 86-95

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See detailPrototype Incorporated Emotional Neural Network (PI-EmNN)
Oyedotun, Oyebade UL; Khashman, Adnan

in IEEE Transactions on Neural Networks and Learning Systems (2017)

Artificial neural networks (ANNs) aim to simulate the biological neural activities. Interestingly, many ‘engineering’ prospects in ANN have relied on motivations from cognition and psychology studies. So ... [more ▼]

Artificial neural networks (ANNs) aim to simulate the biological neural activities. Interestingly, many ‘engineering’ prospects in ANN have relied on motivations from cognition and psychology studies. So far, two important learning theories that have been subject of active research are the prototype and adaptive learning theories. The learning rules employed for ANNs can be related to adaptive learning theory, where several examples of the different classes in a task are supplied to the network for adjusting internal parameters. Conversely, prototype learning theory uses prototypes (representative examples); usually, one prototype per class of the different classes contained in the task. These prototypes are supplied for systematic matching with new examples so that class association can be achieved. In this paper, we propose and implement a novel neural network algorithm based on modifying the emotional neural network (EmNN) model to unify the prototype and adaptive learning theories. We refer to our new model as “PI-EmNN” (Prototype-Incorporated Emotional Neural Network). Furthermore, we apply the proposed model to two real-life challenging tasks, namely; static hand gesture recognition and face recognition, and compare the result to those obtained using the popular back propagation neural network (BPNN), emotional back propagation neural network (EmNN), deep networks and an exemplar classification model, k-nearest neighbor (k-NN). [less ▲]

Detailed reference viewed: 90 (17 UL)