Dissecting isoform selectivity of P13K inhibitors: the role of non-conserved residues in the catalytic pocket

The last few years have seen the identification of numerous small molecules that selectively inhibit specific class I isoforms of PI3K (phosphoinositide 3-kinase), yet little has been revealed about the molecular basis for the observed selectivities. Using site-directed mutagenesis, we have investigated one of the areas postulated as being critical to the observed selectivity. The residues Thr⁸⁸⁶ and Lys⁸⁹⁰ of the PI3Kγ isoform project towards the ATP-binding pocket at the entrance to the catalytic site, but are not conserved. We have made reciprocal mutations between those residues in the β isoform (Glu⁸⁵⁸ and Asp⁸⁶²) and those in the α isoform (His⁸⁵⁵ and Gln⁸⁵⁹) and evaluated the potency of a range of reported PI3K inhibitors. The results show that the potencies of β-selective inhibitors TGX221 and TGX286 are unaffected by this change. In contrast, close analogues of these compounds, particularly the α-isoform-selective compound (III), are markedly influenced by the point mutations. The collected data suggests two distinct binding poses for these inhibitor classes, one of which is associated with potent PI3Kβ activity and is not associated with the mutated residues, and a second that, in accord with earlier hypotheses, does involve this pair of non-conserved amino acids at the catalytic site entrance and contributes to the α-isoform-selectivity of the compounds studied.

Discriminating DDoS flows from flash crowds using information distance

Discriminating DDoS flooding attacks from flash crowds poses a tough challenge for the network security community. Because of the vulnerability of the original design of the Internet, attackers can easily mimic the patterns of legitimate network traffic to fly under the radar. The existing fingerprint or feature based algorithms are incapable to detect new attack strategies. In this paper, we aim to differentiate DDoS attack flows from flash crowds. We are motivated by the following fact: the attack flows are generated by the same prebuilt program (attack tools), however, flash crowds come from randomly distributed users all over the Internet. Therefore, the flow similarity among DDoS attack flows is much stronger than that among flash crowds. We employ abstract distance metrics, the Jeffrey distance, the Sibson distance, and the Hellinger distance to measure the similarity among flows to achieve our goal. We compared the three metrics and found that the Sibson distance is the most suitable one for our purpose. We apply our algorithm to the real datasets and the results indicate that the proposed algorithm can differentiate them with an accuracy around 65%.

Above- and below-ground vertebrate herbivory may each favour a different subordinate species in an aquatic plant community

At least two distinct trade-offs are thought to facilitate higher diversity in productive plant communities under herbivory. Higher investment in defence and enhanced colonization potential may both correlate with decreased competitive ability in plants. Herbivory may thus promote coexistence of plant species exhibiting divergent life history strategies. How different seasonally tied herbivore assemblages simultaneously affect plant community composition and diversity is, however, largely unknown. Two contrasting types of herbivory can be distinguished in the aquatic vegetation of the shallow lake Lauwersmeer. In summer, predominantly above-ground tissues are eaten, whereas in winter, waterfowl forage on below-ground plant propagules. In a 4-year exclosure study we experimentally separated above-ground herbivory by waterfowl and large fish in summer from below-ground herbivory by Bewick’s swans in winter. We measured the individual and combined effects of both herbivory periods on the composition of the three-species aquatic plant community. Herbivory effect sizes varied considerably from year to year. In 2 years herbivore exclusion in summer reinforced dominance of Potamogeton pectinatus with a concomitant decrease in Potamogeton pusillus, whereas no strong, unequivocal effect was observed in the other 2 years. Winter exclusion, on the other hand, had a negative effect on Zannichellia palustris, but the effect size differed considerably between years. We suggest that the colonization ability of Z. palustris may have enabled this species to be more abundant after reduction of P. pectinatus tuber densities by swans. Evenness decreased due to herbivore exclusion in summer. We conclude that seasonally tied above- and below-ground herbivory may each stimulate different components of a macrophyte community as they each favoured a different subordinate plant species.

Compensatory growth in an aquatic plant mediates exploitative competition between seasonally tied herbivores

The degree to which vertebrate herbivores exploitatively compete for the same food plant may depend on the level of compensatory plant growth. Such compensation is higher when there is reduced density-dependent competition in plants after herbivore damage. Whether there is relief from competition may largely be determined by the life-history stage of plants under herbivory. Such stage-specific compensation may apply to seasonal herbivory on the clonal aquatic plant sago pondweed (Potamogeton pectinatus L.). It winters in sediments of shallow lakes as tubers that are foraged upon by Bewick's Swans (Cygnus columbianus bewickii Yarrell), whereas aboveground biomass in summer is mostly consumed by ducks, coots, and Mute Swans. Here, tuber predation may be compensated due to diminished negative density dependence in the next growth season. However, we expected lower compensation to summer herbivory by waterfowl and fish as density of aboveground biomass in summer is closely related to photosynthetic carbon fixation. In a factorial exclosure study we simultaneously investigated (1) the effect of summer herbivory on aboveground biomass and autumn tuber biomass and (2) the effect of tuber predation in autumn on aboveground biomass and tuber biomass a year later. Summer herbivory strongly influenced belowground tuber biomass in autumn, limiting food availability to Bewick's Swans. In contrast, tuber predation in autumn by Bewick's Swans had a limited and variable effect on P. pectinatus biomass in the following growth season. Whereas relief from negative density dependence largely eliminates effects of belowground herbivory by swans, aboveground herbivory in summer limits both above- and belowground plant biomass. Hence, there was an asymmetry in exploitative competition, with herbivores in summer reducing food availability for belowground herbivores in autumn, but not the other way around.

Burial depth distribution of fennel pondweed tubers (Potamogeton pectinatus) in relation to foraging by Bewick's swans

Deep burial in the sediment of tubers of fennel pondweed (Potamogeton pectinatus) has been explained in terms of avoidance by escape against consumption by Bewick's swans (Cygnus columbianus bewickii) in autumn. We therefore expected changes in foraging pressure to ultimately result in a change in the tuber distribution across sediment depth. A trade-off underlies this idea: deep tubers are less accessible to swans but must be larger to meet the higher energy demands of sprouting in spring. To test this prediction, we compared tuber burial depth over a gradient of foraging pressure both across space and across time. Tuber samples were obtained after aboveground plant senescence but before arrival of Bewick's swans. First, we compared the current tuber bank depth profile in a shallow lake with high foraging pressure, the Lauwersmeer, with that in two wetlands with moderate and low foraging pressure. Second, we compared the current tuber burial in the Lauwersmeer with that in the early 1980s when exploitation by swans had just started there. In accordance with our hypothesis, we found significantly deeper burial of tubers under high consumption risk compared to low consumption risk, both when comparing sites and comparing time periods. Since tubers in effect only survive to the next spring, the observed differences in burial depth among sites and over time cannot be a direct result of tuber losses due to consumption by swans. Rather, these observations suggest adaptive responses in tuber burial related to foraging pressure from Bewick's swans in the recent past. We thus propose that fennel pondweed exhibits flexible avoidance by escape, of a kind rarely described for plants, where both phenotypic plasticity and genotype sorting may contribute to the observed differences in tuber burial.

Aquatic plant shows flexible avoidance by escape from tuber predation by swans

Deeper burial of bulbs and tubers has been suggested as an escape against below-ground herbivory by vertebrates, but experimental evidence is lacking. As deep propagule burial can incur high costs of emergence after dormancy, burial depth may represent a trade-off between sprouting survival and herbivore avoidance. We tested whether burial depth of subterraneous tubers is a flexible trait in fennel pondweed (Potamogeton pectinatus), facing tuber predation by Bewick's swans (Cygnus columbianus bewickii) in shallow lakes in winter. In a four-year experiment involving eight exclosures, winter herbivory by swans and all vertebrate summer herbivory were excluded in a full-factorial design; we hence controlled for aboveground vertebrate herbivory in summer, possibly influencing tuber depth. Tuber depth was measured each September before swan arrival and each March before tuber sprouting. In accordance with our hypothesis, tuber depth in September decreased after excluding Bewick's swans in comparison to control plots. The summer exclosure showed an increase in tuber biomass and the number of shallow tubers, but not a significant effect on the mean burial depth of tuber mass. Our results suggest that a clonal plant like P. pectinatus can tune the tuber burial depth to predation pressure, either by phenotypic plasticity or genotype sorting, hence exhibiting flexible avoidance by escape. We suggest that a flexible propagule burial depth can be an effective herbivore avoidance strategy, which might be more widespread among tuber forming plant species than previously thought.

Enhanced physiological tremor deteriorates plantar flexor torque steadiness after bed rest

This study evaluated the effectiveness of resistance training to preserve submaximal plantar flexor (PF) torque steadiness following 60 days of bed rest (BR). Twenty-two healthy male subjects underwent either BR only (CTR, n=8), or BR plus resistance training (RT, n=14). The magnitude of torque fluctuations during steady submaximal isometric PF contractions (20%, 40%, 60% and 80% of maximum) were assessed before and after BR. Across contraction intensities, torque fluctuations (coefficient of variation, CV) increased more (P<0.05) after BR for CTR (from 0.31±0.10 to 0.92±0.63; P<0.001), than for RT (from 0.30±0.09 to 0.54±0.27; P<0.01). A shift in the spectral content of torque fluctuations towards increased rhythmic activity between 6.5 and 20Hz was observed in CTR only (P<0.05). H-reflex amplitude (H(max)/M(max) ratio) declined across groups from 0.57±0.18 before BR to 0.44±0.14 following BR (P<0.01) without correlation to CV. The present study showed that increased torque fluctuation after BR resulted from enhanced physiological tremor. Resistance training prevented the spectral shift in isometric PF torque fluctuation and offset ∼50% of the decline in performance associated with long-term BR.