A simplified approach to disulfide connectivity prediction from protein sequences

Background  

Prediction of disulfide bridges from protein sequences is useful for characterizing structural and functional properties of proteins. Several methods based on different machine learning algorithms have been applied to solve this problem and public domain prediction services exist. These methods are however still potentially subject to significant improvements both in terms of prediction accuracy and overall architectural complexity.     

NanoLC-MS/MS analysis provides new insights into the phosphorylation pattern of Cdc25B in vivo: full overlap with sites of phosphorylation by Chk1 and Cdk1/cycB kinases in vitro

NanoLC-MS/MS analysis was used to characterize the phosphorylation pattern in vivo of CDC25B3 (phosphatase splice variant 1) expressed in a human cell line and to compare it to the phosphorylation of CDC25B3 by Cdk1/cyclin B and Chk1 in vitro. Cellular CDC25B3 was purified from U2OS cells conditionally overexpressing the phosphatase. Eighteen sites were detectably phosphorylated in vivo. Nearly all existing (S/T)P sites were phosphorylated in vivo and in vitro. Eight non(S/T)P sites were phosphorylated in vivo. All these sites could be phosphorylated by kinase Chk1, which phosphorylated a total of 11 sites in vitro, with consensus sequence (R/K) X(2-3) (S/P)-non P. Nearly half of the sites identified in this study were not previously described and were not homologous to sites reported to be phosphorylated in other CDC25 species. We also show that in vivo a significant part of CDC25B molecules can be hyperphosphorylated, with up to 13 phosphates per phosphatase molecule.     

Microbial population changes during bioremediation of nitroaromatic- and nitramine-contaminated lagoon

Nitration reactions of aromatic compounds are commonly involved in military industrial processes. Military industries treated their process effluents using lagoon systems for many years. In this study, the sediment of a lagoon was investigated from a bioremediation objective. The physico-chemical characterization of the sediments showed the organic nature of the sediment (25.4% carbon with a C:N=3) highly concentrated in RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine), HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine) as well as two herbicides Dinoterb (2-tert-butyl-4,6-dinitrophenol) and Dinoseb (2-sec-butyl-4,6-dinitrophenol). Analysis of the 16S rRNA gene clone library revealed the presence of three dominant families, Geobacteriacea, Clostridiaceae and Pseudomonaceae. A bioremediation assay was carried out in anaerobic conditions in order to degrade organic compounds. In these conditions, 100% of Dinoterb and Dinoseb were degraded after 75 days of culture, while RDX and HMX were not consumed. The 16S rRNA gene clone library analysis of this incubation showed a drastic reduction of the final biodiversity composed by clones related to Enterobacteriaceae (especially Leclercia adecarboxylata) and Pseudomonaceae family. It was then suggested that Enterobacteriaceae and Pseudomonaceae were potentially involved in biodegradation of these two herbicides. To confirm this hypothesis, cultures were carried out with isolated species of Pseudomonas putida, Pseudomonas citronellolis and L. adecarboxylata in the presence of Dinoterb. The data confirmed that in the presence of glucose, these microorganisms are able to consume Dinoterb.     

Emergence of network structure due to spike-timing-dependent plasticity in recurrent neuronal networks. II. Input selectivity—symmetry breaking

Spike-timing-dependent plasticity (STDP) is believed to structure neuronal networks by slowly changing the strengths (or weights) of the synaptic connections between neurons depending upon their spiking activity, which in turn modifies the neuronal firing dynamics. In this paper, we investigate the change in synaptic weights induced by STDP in a recurrently connected network in which the input weights are plastic but the recurrent weights are fixed. The inputs are divided into two pools with identical constant firing rates and equal within-pool spike-time correlations, but with no between-pool correlations. Our analysis uses the Poisson neuron model in order to predict the evolution of the input synaptic weights and focuses on the asymptotic weight distribution that emerges due to STDP. The learning dynamics induces a symmetry breaking for the individual neurons, namely for sufficiently strong within-pool spike-time correlation each neuron specializes to one of the input pools. We show that the presence of fixed excitatory recurrent connections between neurons induces a group symmetry-breaking effect, in which neurons tend to specialize to the same input pool. Consequently STDP generates a functional structure on the input connections of the network.     

Emergence of network structure due to spike-timing-dependent plasticity in recurrent neuronal networks. I. Input selectivity–strengthening correlated input pathways

Spike-timing-dependent plasticity (STDP) determines the evolution of the synaptic weights according to their pre- and post-synaptic activity, which in turn changes the neuronal activity. In this paper, we extend previous studies of input selectivity induced by (STDP) for single neurons to the biologically interesting case of a neuronal network with fixed recurrent connections and plastic connections from external pools of input neurons. We use a theoretical framework based on the Poisson neuron model to analytically describe the network dynamics (firing rates and spike-time correlations) and thus the evolution of the synaptic weights. This framework incorporates the time course of the post-synaptic potentials and synaptic delays. Our analysis focuses on the asymptotic states of a network stimulated by two homogeneous pools of “steady” inputs, namely Poisson spike trains which have fixed firing rates and spike-time correlations. The (STDP) model extends rate-based learning in that it can implement, at the same time, both a stabilization of the individual neuron firing rates and a slower weight specialization depending on the input spike-time correlations. When one input pathway has stronger within-pool correlations, the resulting synaptic dynamics induced by (STDP) are shown to be similar to those arising in the case of a purely feed-forward network: the weights from the more correlated inputs are potentiated at the expense of the remaining input connections.     

Novel structural and regulatory features of rhoptry secretory kinases in Toxoplasma gondii

Serine/threonine kinases secreted from rhoptry organelles constitute important virulence factors of Toxoplasma gondii. Rhoptry kinases are highly divergent and their structures and regulatory mechanism are hitherto unknown. Here, we report the X‐ray crystal structures of two related pseudokinases named ROP2 and ROP8, which differ primarily in their substrate‐binding site. ROP kinases contain a typical bilobate kinase fold and a novel N‐terminal extension that both stabilizes the N‐lobe and provides a unique means of regulation. Although ROP2 and ROP8 were catalytically inactive, they provided a template for homology modelling of the active kinase ROP18, a major virulence determinant of T. gondii. Autophosphorylation of key residues in the N‐terminal extension resulted in ROP18 activation, which in turn phosphorylated ROP2 and ROP8. Mutagenesis and mass spectrometry experiments revealed that ROP18 was maximally activated when this phosphorylated N‐terminus relieved autoinhibition resulting from extension of aliphatic side chains into the ATP‐binding pocket. This novel means of regulation governs ROP kinases implicated in parasite virulence.     

Relationship between reversed sexual dimorphism,breeding investment and foraging ecology in a pelagic seabird,the masked booby

Reversed sexual dimorphism (RSD) may be related to different roles in breeding investment and/or foraging, but little information is available on foraging ecology. We studied the foraging behaviour and parental investment by male and female masked boobies, a species with RSD, by combining studies of foraging ecology using miniaturised activity and GPS data loggers of nest attendance, with an experimental study where flight costs were increased. Males attended the chick more often than females, but females provided more food to the chick than males. Males and females foraged during similar periods of the day, had similar prey types and sizes, diving depths, durations of foraging trips, foraging zones and ranges. Females spent a smaller proportion of the foraging trip sitting on the water and had higher diving rate than males, suggesting higher foraging effort by females. In females, trip duration correlated with mass at departure, suggesting a flexible investment through control by body mass. The experimental study showed that handicapped females and female partners of handicapped males lost mass compared to control birds, whereas there was no difference for males. These results indicate that the larger female is the main provisioner of the chick in the pair, and regulates breeding effort in relation to its own body mass, whereas males have a fixed investment. The different breeding investment between the sexes is associated with contrasting foraging strategies, but no clear niche differentiation was observed. The larger size of the females may be advantageous for provisioning the chick with large quantities of energy and for flexible breeding effort, while the smaller male invests in territory defence and nest guarding, a crucial task when breeding at high densities. In masked boobies, division of labour appears to be maximal during chick rearing—the most energy-demanding period—and may be related to evolution of RSD.     

The Atlantic elements in the Swiss flora: distribution, diversity, and conservation status

The purpose of this study was to examine the composition, distribution, ecology, and conservation status of the Atlantic elements of the Swiss flora. About 195 Atlantic and 80 Mediterranean–Atlantic vascular plant species of the European flora have been used as the basis for our analysis. The complete list of 3,143 taxa has been used as the reference for the Swiss flora. The distributions of the species are illustrated in coincidence maps based on the computer database of the Data Centre of the Swiss Flora in Geneva, Switzerland. Our study demonstrates clearly that the Atlantic flora of Europe requires a new biogeographical appraisal. The Swiss flora comprises 66 Atlantic and Mediterranean–Atlantic taxa, which are taxonomically and ecologically highly diverse. Switzerland contains 44% of all European Sub-Atlantic plants. This confirms the Sub-Atlantic geographical position of Switzerland. Only one Eu-Atlantic species growing in Switzerland, Vicia orobus, can be classified as native with certainty. This species is critically endangered and merits the highest conservation priority. Although a very alpine country, Switzerland has a relatively large number of Mediterranean–Atlantic species. The Atlantic and Mediterranean–Atlantic plants are a very threatened group in Switzerland, with wetland plants the most imperilled ecological group. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.