Human p38α mitogen-activated protein kinase in the Asp168-Phe169-Gly170-in (DFG-in) state can bind allosteric inhibitor Doramapimod

Doramapimod (BIRB-796) is widely recognized as one of the most potent and selective type II inhibitors of human p38α mitogen-activated protein kinase (MAPK); however, the understanding of its binding mechanism remains incomplete. Previous studies indicated high affinity of the ligand to a so-called allosteric pocket revealed only in the ‘out’ state of the DFG motif (i.e. Asp168-Phe169-Gly170) when Phe169 becomes fully exposed to the solvent. The possibility of alternative binding in the DFG-in state was hypothesized, but the molecular mechanism was not known. Methods of bioinformatics, docking and long-time scale classical and accelerated molecular dynamics have been applied to study the interaction of Doramapimod with the human p38α MAPK. It was shown that Doramapimod can bind to the protein even when the Phe169 is fully buried inside the allosteric pocket and the kinase activation loop is in the DFG-in state. Orientation of the inhibitor in such a complex is significantly different from that in the known crystallographic complex formed by the kinase in the DFG-out state; however, the Doramapimod’s binding is followed by the ligand-induced conformational changes, which finally improve accommodation of the inhibitor. Molecular modelling has confirmed that Doramapimod combines the features of type I and II inhibitors of p38α MAPK, i.e. can directly and indirectly compete with the ATP binding. It can be concluded that optimization of the initial binding in the DFG-in state and the final accommodation in the DFG-out state should be both considered at designing novel efficient type II inhibitors of MAPK and homologous proteins.

Communicated by Ramaswamy H. Sarma     

非洲猪瘟病毒p35蛋白作为诊断抗原的抗原性比较

为了筛选出酶联免疫吸附测定(Enzyme linked immunosorbent assay,ELISA)反应性最佳的非洲猪瘟病毒(African swine fever virus,ASFV)诊断抗原,通过建立ELISA方法,以杆状病毒昆虫细胞表达系统表达的ASFV p30蛋白诊断抗原为参照,首次探讨原核表达系统表...     

Herbivore‐induced plant responses in Brassica oleracea prevail over effects of constitutive resistance and result in enhanced herbivore attack

1. Plant responses to herbivore attack may have community‐wide effects on the composition of the plant‐associated insect community. Thereby, plant responses to an early‐season herbivore may have profound consequences for the amount and type of future attack. 2. Here we studied the effect of early‐season herbivory by caterpillars of Pieris rapae on the composition of the insect herbivore community on domesticated Brassica oleracea plants. We compared the effect of herbivory on two cultivars that differ in the degree of susceptibility to herbivores to analyse whether induced plant responses supersede differences caused by constitutive resistance. 3. Early‐season herbivory affected the herbivore community, having contrasting effects on different herbivore species, while these effects were similar on the two cultivars. Generalist insect herbivores avoided plants that had been induced, whereas these plants were colonised preferentially by specialist herbivores belonging to both leaf‐chewing and sap‐sucking guilds. 4. Our results show that community‐wide effects of early‐season herbivory may prevail over effects of constitutive plant resistance. Induced responses triggered by prior herbivory may lead to an increase in susceptibility to the dominant specialists in the herbivorous insect community. The outcome of the balance between contrasting responses of herbivorous community members to induced plants therefore determines whether induced plant responses result in enhanced plant resistance.     

Jasmonic acid induces the production of gerbera volatiles that attract the biological control agent Phytoseiulus persimilis

Jasmonic acid (JA) is a plant hormone that is involved in the induction of plant defence in response to herbivore attack. We studied the effect of exposure of gerbera leaves to JA on indirect plant defence, i.e. attraction of natural enemies of herbivores. Treatment of gerbera leaves with JA or feeding damage by the herbivorous spider mite Tetranychus urticae, both induced the production of a complex odour blend that attracts the predatory mite Phytoseiulus persimilis. This phytoseiid predator is a very effective biological control agent of the spider mite T. urticae. Comparison of headspace composition of gerbera leaves exposed to either JA or T. urticae revealed a large degree of resemblance, but some quantitative and qualitative differences were recorded. The major chemical group in both treatments is formed by the terpenoids which quantitatively comprised up to 80% of the total odour blend. These terpenoids included (E)-4,8-dimethyl-1,3,7-nonatriene, (E)--ocimene and linalool that are known to attract P. persimilis. Aldehydes, alcohols, esters and ketones, together with nitrogenous compounds formed the remaining constituents of the odour blend. The induction of predator attractants in plants by JA may be applied in biological control programs, which is discussed in this paper.     

Alternative Ways to Become a Juvenile or a Definitive Phenotype (and on Some Persisting Linguistic Offenses)

Lack of knowledge of early and juvenile development often makes it difficult to decide when a fish becomes a juvenile or, for that matter, a definitive phenotype. According to the established life-history model, a fish develops naturally in a saltatory manner, its entire life consisting of a sequence of stabilized self-organizing steps, separated by distinct less stabilized thresholds. Changes are usually introduced during thresholds. In principle, there are two ways to reach the juvenile period: by indirect or by direct development. Indirectly developing fishes have a distinct larva period that ends in a cataclysmic or mild remodeling process, called metamorphosis, from which the fishes emerge as juveniles. During metamorphosis, most temporary organs and structures of the embryos and larvae are replaced by definitive organs and structures that are also possessed by the adults. In contrast, directly developing fishes have no larvae. Their embryos develop directly into juveniles and do not need major remodeling. Consequently, the beginning of their juvenile period is morphologically and functionally less distinct than in indirect development. The life-history model helps to find criteria that identify the natural boundaries between the different periods in the life of a fish, among them, the beginning of the juvenile period. Looking at it from a different angle, when ontogeny progresses from small eggs with little yolk, larvae are required as the necessary providers of additional nutrients (feeding entities similar to amphibian tadpoles or butterfly caterpillars) in order to accumulate materials for the metamorphosis into the definitive phenotypes. Directly developing fishes start with large demersal eggs provided with an adequate volume of high density yolk and so require no or little external nutrients to develop into the definitive phenotype. These large eggs are released and develop in concentrated clutches. It therefore becomes possible and highly effective to guard them in nests or bear them in external pouches, gill chambers or the buccal cavity. Viviparity is the next natural step. Now the maternal investment into large yolks can be supplemented or replaced by direct food supply to the developing embryos like, for example, the secretion of uterine histotrophe or nutrient transfer via placental analogues. When the young of guarders and bearers start exogenous feeding, they are much larger or better developed than larvae of nonguarders and the larva period in the former is reduced to a vestige or eliminated entirely. In the latter case, the juvenile period begins with the first exogenous feeding. Such precocial fishes are more specialized and able to survive better in competitive environments. In contrast, altricial forms retain or revert to a life-history style with indirect development and high fecundity when dispersal is advantageous or essential. Fishes become juveniles when the definitive phenotype is formed in most structures, either indirectly from a larva via metamorphosis or directly from the embryo.     

Growth and architecture of small honey mesquites under jackrabbit browsing: overcoming the disadvantage of being eaten

Browsing is an important mortality factor in seedlings and small plants. However, the induced changes in the architecture of plant survivors may influence subsequent browsing, opening the possibility of compensating for the damage done. How jackrabbit (Lepus californicus) browsing affects the growth and architecture of small individuals of honey mesquite, Prosopis glandulosa var. torreyana, a tree/shrub that produces spines at every node, was explored. Naturally established mesquites of unknown age were selected in one site, and 2-year-old mesquites were transplanted in another site. In both cases, half of them were exposed to jackrabbits and the other half were excluded as controls. After 4 years, shoot production (height, length and number of derived shoots) and plant growth (height and cover) increased 1.4-2.5-fold in naturally established controls relative to exposed plants, depending on the measured variable. In the transplant experiment, the increases were 2.8-7.1-fold in controls relative to exposed plants 2 years after initiation of the experiment. The net loss of biomass in treatment vs. control plants in these experiments suggests a negative response to browsing which has been defined as under-compensation. Alternative architectures in honey mesquites were evident at the end of the exclusion experiments: controls had long branches and an extended crown cover, while exposed plants had short branches and a compact crown cover. Results indicated that mesquites were able to grow under browser pressure by packing many stems in a compact matrix armed with spines and producing one or more shoots tall and wide enough to escape from jackrabbits.     

Integration host factor: putting a twist on protein-DNA recognition

Integration host factor (IHF) is a DNA-bending protein that recognizes its cognate sites through indirect readout. Previous studies have shown that binding of wild-type (WT)-IHF is disrupted by a T to A mutation at the center position of a conserved TTR motif in its binding site, and that substitution of betaGlu44 with Ala prevented IHF from discriminating between A and T at this position. We have determined the crystal structures and relative binding affinities for all combinations of WT-IHF and IHF-betaGlu44Ala bound to the WT and mutant DNAs. Comparison of these structures reveals that DNA twist plays a major role in DNA recognition by IHF, and that this geometric parameter is dependent on the dinucleotide step and not on the bound IHF variant.     

Mutualistic relationships between phytoplankton and bacteria caused by carbon excretion from phytoplankton

For the competition system of phytoplankton and bacteria through inorganic phosphorus, our mathematical model showed that mutualistic relationships between them could occur due to production and consumption of extracellular organic carbon by phytoplankton and bacteria. In our model, phytoplankton are limited in their growth by light and phosphorus, and bacteria are limited in their growth by phosphorus and carbon released from phytoplankton. We adopted permanence as a criterion of the coexistence in mathematical analysis, and led necessary conditions of permanence in the model. Under these coexistence conditions, we estimated the strength of total effects of interactions between phytoplankton and bacteria at the steady state by press perturbation method. The results of this estimation indicated the mutualistic interactions between phytoplankton and bacteria. This suggests that mutualistic situation could occur due to the introduction of carbon flow from phytoplankton to bacteria, even if phytoplankton and bacteria compete with each other through common resource, inorganic phosphorus.     

Deer browsing reduces leaf damage by herbivorous insects through an induced response of the host plant

We aimed to demonstrate an indirect relationship between a mammalian herbivore (sika deer) and herbivorous insects on the induced responses of a shared host plant, Viburnum dilatatum. Field studies were conducted at three sites (i.e. two islands and one mainland) and within a deer exclusion area. One island, Kinkazan (Kz) Island, harbored a high density of deer while the other sites (controls) had no deer or very low densities of deer. The deer exclusion area had been established approximately 10years earlier on Kz. We collected leaves above the browsing line of the deer and measured leaf hardness and tannin concentration. Leaf damage by insects was used as a measure of insect abundance. Leaves collected at Kz were harder than those from one of the control sites and from inside the deer exclusion area, while no difference was detected among the other controls and inside the exclusion area. In contrast, the tannin concentration of leaves from Kz was lower than in leaves from the control site. Leaf damage by herbivorous insects was lower in Kz than the other study sites. In addition, hole-type leaf damage tended to be higher inside, rather than outside, the exclusion area. These results suggest the possibility that deer browsing increased leaf hardness, which exerted an indirect negative effect on the herbivorous insects utilizing the common host plant. To our knowledge, this is the first study to provide evidence of indirect negative effects between mammalian herbivores and herbivorous insects sharing a host plant.     

Mechanisms of successional dynamics: Consumers and the rise and fall of species dominance

Insight into potential mechanisms of succession following disturbance to an ecological community can be gained by considering processes that contribute to the rise (colonization, interactions with established species) and demise (differential mortality) of specific stages within the successional sequence. Most successional theories focus on the rise to dominance, assuming demise is the result of competition, but other factors can cause differential mortality among species, including physical disturbance, senescence, and consumers. In rocky intertidal communities on the coast of Washington state, USA, gaps in mussel beds exhibit a succession from predator-susceptible to predator-resistant species following disturbance, suggesting that differential consumption by mobile species may play an important role in the demise of early succession species and the eventual dominance of the mussel Mytilus californianus. Experimental manipulation of a dominant species earlier in succession, the blue mussel Mytilus trossulus, demonstrated that this species inhibits the invasion of M. californianus in the absence of predators. Experimental manipulation of predatory snails (Nucella emarginata and Nucella canaliculata), which feed heavily on M. trossulus but not M. californianus, greatly increased the rate at which M. californianus invaded gaps. These results and those of other studies indicate that consumers frequently have important effects on the dynamics of succession in benthic marine systems, and might also play a role in other settings.