Особливості розв’язку задач параметричної ідентифікації динамічних систем в умовах інтервальної невизначеності

Розглянуто задачу параметричної ідентифікації лінійних динамічних систем методами аналізу інтервальних даних. Показано, що у випадку врахування початкових інтервальних наближень дискретних значень прогнозованої характеристики дана задача є задачею розв’язування інтервальної системи нелінійних алгебричних рівнянь. Досліджено особливості формування та властивості розв’язку таких систем.Рассмотрена задача параметрической идентификации линейных динамических систем методами анализа интервальных данных. Показано, что в случае учета начальных интервальных приближений дискретных значений прогнозированной характеристики, данная задача есть задачей решения интервальной системы нелинейных алгебраических уравнений; исследованы особенности формирования и свойства решения таких систем.The problem of parameter identification of linear dynamic systems by methods of analysis of interval data is considered. It is shown that in the case of taking into account the initial interval approximations of discrete values of the predicted characteristics, this problem is the problem of solving interval system of nonlinear algebraic equations

Absence of repellents in Ustilago maydis induces genes encoding small secreted proteins

The rep1 gene of the maize pathogen Ustilago maydis encodes a pre-pro-protein that is processed in the secretory pathway into 11 peptides. These so-called repellents form amphipathic amyloid fibrils at the surface of aerial hyphae. A SG200 strain in which the rep1 gene is inactivated (∆rep1 strain) is affected in aerial hyphae formation. We here assessed changes in global gene expression as a consequence of the inactivation of the rep1 gene. Microarray analysis revealed that only 31 genes in the ∆rep1 SG200 strain had a fold change in expression of ≥2. Twenty-two of these genes were up-regulated and half of them encode small secreted proteins (SSPs) with unknown functions. Seven of the SSP genes and two other genes that are over-expressed in the ∆rep1 SG200 strain encode proteins that can be classified as secreted cysteine-rich proteins (SCRPs). Interestingly, most of the SCRPs are predicted to form amyloids. The SCRP gene um00792 showed the highest up-regulation in the ∆rep1 strain. Using GFP as a reporter, it was shown that this gene is over-expressed in the layer of hyphae at the medium-air interface. Taken together, it is concluded that inactivation of rep1 hardly affects the expression profile of U. maydis, despite the fact that the mutant strain has a strong reduced ability to form aerial hyphae

The FlbA-regulated predicted transcription factor Fum21 of <i>Aspergillus niger</i> is involved in fumonisin production

Aspergillus niger secretes proteins throughout the colony except for the zone that forms asexual spores called conidia. Inactivation of flbA that encodes a regulator of G-protein signaling results in colonies that are unable to reproduce asexually and that secrete proteins throughout the mycelium. In addition, the ΔflbA strain shows cell lysis and has thinner cell walls. Expression analysis showed that 38 predicted transcription factor genes are differentially expressed in strain ΔflbA. Here, the most down-regulated predicted transcription factor gene, called fum21, was inactivated. Growth, conidiation, and protein secretion were not affected in strain Δfum21. Whole genome expression analysis revealed that 63 and 11 genes were down- and up-regulated in Δfum21, respectively, when compared to the wild-type strain. Notably, 24 genes predicted to be involved in secondary metabolism were down-regulated in Δfum21, including 10 out of 12 genes of the fumonisin cluster. This was accompanied by absence of fumonisin production in the deletion strain and a 25% reduction in production of pyranonigrin A. Together, these results link FlbA-mediated sporulation-inhibited secretion with mycotoxin production

Amyloids - A functional coat for microorganisms

Amyloids are filamentous protein structures ~10 nm wide and 0.1–10 µm long that share a structural motif, the cross-β structure. These fibrils are usually associated with degenerative diseases in mammals. However, recent research has shown that these proteins are also expressed on bacterial and fungal cell surfaces. Microbial amyloids are important in mediating mechanical invasion of abiotic and biotic substrates. In animal hosts, evidence indicates that these protein structures also contribute to colonization by activating host proteases that are involved in haemostasis, inflammation and remodelling of the extracellular matrix. Activation of proteases by amyloids is also implicated in modulating blood coagulation, resulting in potentially life-threatening complications.

Diffusion of hydrophobin proteins in solution and interactions with a graphite surface

<p>Abstract</p> <p>Background</p> <p>Hydrophobins are small proteins produced by filamentous fungi that have a variety of biological functions including coating of spores and surface adhesion. To accomplish these functions, they rely on unique interface-binding properties. Using atomic-detail implicit solvent rigid-body Brownian dynamics simulations, we studied the diffusion of HFBI, a class II hydrophobin from <it>Trichoderma reesei</it>, in aqueous solution in the presence and absence of a graphite surface.</p> <p>Results</p> <p>In the simulations, HFBI exists in solution as a mixture of monomers in equilibrium with different types of oligomers. The oligomerization state depends on the conformation of HFBI. When a Highly Ordered Pyrolytic Graphite (HOPG) layer is present in the simulated system, HFBI tends to interact with the HOPG layer through a hydrophobic patch on the protein.</p> <p>Conclusions</p> <p>From the simulations of HFBI solutions, we identify a tetrameric encounter complex stabilized by non-polar interactions between the aliphatic residues in the hydrophobic patch on HFBI. After the formation of the encounter complex, a local structural rearrangement at the protein interfaces is required to obtain the tetrameric arrangement seen in HFBI crystals. Simulations performed with the graphite surface show that, due to a combination of a geometric hindrance and the interaction of the aliphatic sidechains with the graphite layer, HFBI proteins tend to accumulate close to the hydrophobic surface.</p

The effects of ditch dams on water‐level dynamics in tropical peatlands

A significant proportion of tropical peatlands has been drained for agricultural purposes, resulting in severe degradation. Hydrological restoration, which usually involves blocking ditches, is therefore a priority. Nevertheless, the influence of ditch blocking on tropical peatland hydrological functioning is still poorly understood. We studied water-level dynamics using a combination of automated and manual dipwells, and also meteorological data during dry and wet seasons over 6 months at three locations in Sebangau National Park, Kalimantan, Indonesia. The locations were a forested peatland (Forested), a drained peatland with ditch dams (Blocked), and a drained peatland without ditch dams (Drained). In the dry season, water tables at all sites were deeper than the Indonesian regulatory requirement of 40 cm from the peat surface. In the dry season, the ditches were dry and water did not flow to them. The dry season water-table drawdown rates — solely due to evapotranspiration — were 9.3 mm day−1 at Forested, 9.6 mm day−1 at Blocked, but 12.7 mm day−1 at Drained. In the wet season, the proportion of time during which water tables in the wells were deeper than the 40 cm limit ranged between 16% and 87% at Forested, 0% at Blocked, and between 0% and 38% at Drained. In the wet season, water flowed from the peatland to ditches at Blocked and Drained. The interquartile range of hydraulic gradients between the lowest ditch outlet and the farthest well from ditches at Blocked was 3.7 × 10−4 to 7.8 × 10−4 m m−1, but 1.9 × 10−3 to 2.6 × 10−3 m m−1 at Drained. Given the results from Forested, a water-table depth limit policy based on field data may be required, to reflect natural seasonal dynamics in tropical peatlands. Revised spatial designs of dams or bunds are also required, to ensure effective water-table management as part of tropical peatland restoration

Predicting species dominance shifts across elevation gradients in mountain forests in Greece under a warmer and drier climate

The Mediterranean Basin is expected to face warmer and drier conditions in the future, following projected increases in temperature and declines in precipitation. The aim of this study is to explore how forests dominated by Abies borisii-regis, Abies cephalonica, Fagus sylvatica, Pinus nigra and Quercus frainetto will respond under such conditions. We combined an individual-based model (GREFOS), with a novel tree ring data set in order to constrain tree diameter growth and to account for inter- and intraspecific growth variability. We used wood density data to infer tree longevity, taking into account inter- and intraspecific variability. The model was applied at three 500-m-wide elevation gradients at Taygetos in Peloponnese, at Agrafa on Southern Pindos and at Valia Kalda on Northern Pindos in Greece. Simulations adequately represented species distribution and abundance across the elevation gradients under current climate. We subsequently used the model to estimate species and functional trait shifts under warmer and drier future conditions based on the IPCC A1B scenario. In all three sites, a retreat of less drought-tolerant species and an upward shift of more drought-tolerant species were simulated. These shifts were also associated with changes in two key functional traits, in particular maximum radial growth rate and wood density. Drought-tolerant species presented an increase in their average maximal growth and decrease in their average wood density, in contrast to less drought-tolerant species