Recognizing the importance of scale in the ecology and management of riverine fish

Processes affecting fish populations range in scale from local to global. Fish response is also scale‐dependent, with some activities varying locally while others depend on large‐scale connectivity within or between watersheds. These issues are still only partly recognized, with large‐scale research often affected by non‐independent sampling, weak inference, poor model testing or model over‐extrapolation. Available multi‐scale studies can reach different conclusions about factors affecting fishes from local studies, but results vary between examples. Potential explanations are (i) effects on fishes are context‐dependent; (ii) different species or life‐stages are limited in different ways; (iii) multi‐scale studies are too few for generalization. We advocate improved use of geostatistical tools to guide sampling or interpret the spatial extent of management problems, and we illustrate this using brown trout in Welsh streams. Our strongest recommendation is that fish ecologists recognize the importance of interactions across scales in quantifying effects on fishes so that management decisions can be better based on evidence rather than judgement or extrapolation. Copyright © 2006 John Wiley & Sons, Ltd.     

Conception assistée par ordinateur des circuits intégrés monolithiques hyperfréquences

Computer aided design of microwave monolithic integrated circuits must combine two different fields. The first domain is the simulation of microwave circuits taking into account non linear aspects development of time domain and harmonic balance simulation algorithms specialized for microwave circuits. In the second place are found, the layout algorithms which were developed for logic circuits (on Si or GaAs). The association of these two types of algorithms leads to the constitution of aCad workstation for microwave monolithic integrated circuits. Two examples of design and realization of integrated circuits with these tools are presented.     

The Esterase PfeE,the Achilles’ Heel in the Battle for Iron between Pseudomonas aeruginosa and Escherichia coli

Bacteria access iron, a key nutrient, by producing siderophores or using siderophores produced by other microorganisms. The pathogen Pseudomonas aeruginosa produces two siderophores but is also able to pirate enterobactin (ENT), the siderophore produced by Escherichia coli. ENT-Fe complexes are imported across the outer membrane of P. aeruginosa by the two outer membrane transporters PfeA and PirA. Iron is released from ENT in the P. aeruginosa periplasm by hydrolysis of ENT by the esterase PfeE. We show here that pfeE gene deletion renders P. aeruginosa unable to grow in the presence of ENT because it is unable to access iron via this siderophore. Two-species co-cultures under iron-restricted conditions show that P. aeruginosa strongly represses the growth of E. coli as long it is able to produce its own siderophores. Both strains are present in similar proportions in the culture as long as the siderophore-deficient P. aeruginosa strain is able to use ENT produced by E. coli to access iron. If pfeE is deleted, E. coli has the upper hand in the culture and P. aeruginosa growth is repressed. Overall, these data show that PfeE is the Achilles’ heel of P. aeruginosa in communities with bacteria producing ENT.     

PGRP-LB: An Inside View into the Mechanism of the Amidase Reaction

Peptidoglycan recognition proteins (PGRPs) are ubiquitous among animals and play pivotal functions in insect immunity. Non-catalytic PGRPs are involved in the activation of immune pathways by binding to the peptidoglycan (PGN), whereas amidase PGRPs are capable of cleaving the PGN into non-immunogenic compounds. Drosophila PGRP-LB belongs to the amidase PGRPs and downregulates the immune deficiency (IMD) pathway by cleaving meso-2,6-diaminopimelic (meso-DAP or DAP)-type PGN. While the recognition process is well analyzed for the non-catalytic PGRPs, little is known about the enzymatic mechanism for the amidase PGRPs, despite their essential function in immune homeostasis. Here, we analyzed the specific activity of different isoforms of Drosophila PGRP-LB towards various PGN substrates to understand their specificity and role in Drosophila immunity. We show that these isoforms have similar activity towards the different compounds. To analyze the mechanism of the amidase activity, we performed site directed mutagenesis and solved the X-ray structures of wild-type Drosophila PGRP-LB and its mutants, with one of these structures presenting a protein complexed with the tracheal cytotoxin (TCT), a muropeptide derived from the PGN. Only the Y78F mutation abolished the PGN cleavage while other mutations reduced the activity solely. Together, our findings suggest the dynamic role of the residue Y78 in the amidase mechanism by nucleophilic attack through a water molecule to the carbonyl group of the amide function destabilized by Zn²⁺.     

On the role of conserved proline residues in the structure and function of Clostridium pasteurianum 2[4Fe-4S] ferredoxin

The widespread occurrence of Pro residues adjacent to Cys ligandsin the sequences of [4Fe-4S] electron transfer proteins hasnot yet found a functional basis. The two such Pro of Clostridiumpasteurianum 2[4Fe-4S] ferredoxin have been probed by site-directedmutagenesis. Any one of them, but not both simultaneously, canbe substituted without impairing the proper folding of the protein.The reduction potentials of the ferredoxin variants fall ina narrow range of <20 mV above the potential of the nativeprotein. The biological activities with C.pasteurianum hydrogenaseand pyruvate-ferredoxin oxidoreductase do not change significantly,except when Lys replaces Pro. In these cases, the data suggestthat the two clusters of 2[4Fe-4S] ferredoxin may not alwaysbe equivalent in the interaction with the redox partners. Destabilizationof the structure has been observed as the consequence of theProl9 or Pro48 substitutions. Using 2-D NMR, this effect hasbeen associated with perturbations of both the hydrogen bondnetwork and one amino acid side chain around the [4Fe-4S] clusters.Thus, the conserved Pro found in the binding motif of [4Fe-4S]clusters in proteins strongly stabilizes the active site butdoes not play an essential role in the mechanism of electrontransfer.     

Effect of dietary n−3 and n−6 polyunsaturated fatty acids on lipid-metabolizing enzymes in obese rat liver

This study was designed to examine whether n−3 and n−6 polyunsaturated fatty acids at a very low dietary level (about 0.2%) would alter liver activities in respect to fatty acid oxidation. Obese Zucker rats were used because of their low level of fatty acid oxidation, which would make increases easier to detect. Zucker rats were fed diets containing different oil mixtures (5%, w/w) with the same ratio of n−6/n−3 fatty acids supplied either as fish oil or arachidonic acid concentrate. Decreased hepatic triacylglycerol levels were observed only with the diet containing fish oil. In mitochondrial outer membranes, which support carnitine palmitoyltransferase I activity, cholesterol content was similar for all diets, while the percentage of 22∶6n−3 and 20∶4n−6 in phospholipids was enhanced about by 6 and 3% with the diets containing fish oil and arachidonic acid, respectively. With the fish oil diet, the only difference found in activities related to fatty acid oxidation was the lower sensitivity of carnitine palmitoyltransferase I to malonyl-CoA inhibition. With the diet containing arachidonic acid, peroxisomal fatty acid oxidation and carnitine palmitoyltransferase I activity were markedly depressed. Compared with the control diet, the diets enriched in fish oil and in arachidonic acid gave rise to a higher specific activity of aryl-ester hydrolase in microsomal fractions. We suggest that slight changes in composition of n−3 or n−6 polyunsaturated fatty acids in mitochondrial outer membranes may alter carnitine palmitoyltransferase I activity.     

Towards identifying the roll motion parameters of a motorcycle simulator

This study aimed at identifying the roll motion parameters of a motorcycle simulator prototype. Experienced motorcyclists tuned the angular physical movement of the mock-up and that of the visual scene to achieve an optimal riding experience during curves. The participants exceeded the rolling angles that would be required in real-world riding, while avoiding leaning the mock-up beyond 10°. In addition, they were more influenced by the speed of the virtual motorcycle than by road curvature, especially in a wide field of view. Heterogeneity was found in the roll applied to the visual scene. The overall patterns suggest that at least when washout is not applied to remove the side forces that in real-world riding are compensated by a centrifugal force, greater roll of the visual at the expense of the mock-up is mandatory to avoid performance biases that might be enhanced due to fear of falling off the simulator. Future roll motion models must take into consideration factors such as riding postures, which might not only influence the forces operating on the rider-motorcycle system, but also how motorcyclists perceive the visual world.     

The ChaLearn gesture dataset (CGD 2011)

This paper describes the data used in the ChaLearn gesture challenges that took place in 2011/2012, whose results were discussed at the CVPR 2012 and ICPR 2012 conferences. The task can be described as: user-dependent, small vocabulary, fixed camera, one-shot-learning. The data include 54,000 hand and arm gestures recorded with an RGB-D \(\hbox {Kinect}^\mathrm{TM}\) camera. The data are organized into batches of 100 gestures pertaining to a small gesture vocabulary of 8–12 gestures, recorded by the same user. Short continuous sequences of 1–5 randomly selected gestures are recorded. We provide man-made annotations (temporal segmentation into individual gestures, alignment of RGB and depth images, and body part location) and a library of function to preprocess and automatically annotate data. We also provide a subset of batches in which the user’s horizontal position is randomly shifted or scaled. We report on the results of the challenge and distribute sample code to facilitate developing new solutions. The data, datacollection software and the gesture vocabularies are downloadable from http://gesture.chalearn.org. We set up a forum for researchers working on these data http://groups.google.com/group/gesturechallenge.     

Détermination de constantes cinétiques du craquage catalytique par la modélisation du test de microactivité (MAT)

The microactivity test (MAT) for cracking catalyst test works with an approximately plug flow isothermal reactor. The yields at the outlet of such a reactor is numerically computed in the case of lumped kinetic with large molecular expansion and rapid catalyst deactivation expressed versus poison concentration. The poison (coke in cracking reaction) is considered as a product formed by several reaction routes. The results are applied to catalytic cracking kinetic with a four lump model (feedstock, gasoline, gas, coke). The comparison between experimental and computed yields, permits the adjustment of kinetic constants with a set of experimental results obtained from a laboratory scale reactor derived from the MAT. The simulation of concentration profile in the reactor permits a better understanding of the reaction courses.     

Thermal crosslinking of collagen immobilized on poly(acrylic acid) grafted poly(ethylene terephthalate) films

Graft polymerization of acrylic acid onto plasma‐treated poly(ethylene terephthalate) (PET) films was used to prepare surfaces suitable for collagen immobilization by dip‐coating. Such surfaces could be used as matrices for smooth muscle cell cultures in tissue engineering. Contact angle measurements showed that plasma‐treated and grafted PET films undergo considerable surface reorganization during storage under ambient conditions. However, after collagen immobilization the contact angle remained relatively stable. The amount of collagen initially attached to the film surface increased with increasing poly(acrylic acid) graft density, but subsequent washing in water led to significant collagen loss. This loss could nevertheless be substantially reduced by thermal crosslinking of the collagen in the range 110–130 °C. Atomic force microscopy (AFM) observations suggested that the washed crosslinked collagen has a very similar structure to that of the un‐crosslinked collagen. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 85: 1874–1880, 2002