Effect of Manganese on Lignin Degradation by Pleurotus ostreatus during Solid-State Fermentation

Lignin degradation by Pleurotus ostreatus was studied under solid-state fermentation (SSF) in chemically defined medium containing various levels of Mn. Degradation of [¹⁴C]lignin prepared from cotton branches to soluble products, as well as its mineralization to ¹⁴CO₂, was enhanced by the addition of Mn. The effect of malonate on lignin mineralization was most marked during the first 10 days of SSF, in a treatment amended with 73 μM Mn. A high concentration of Mn (4.5 mM) caused inhibition of both fungal growth and mineralization rates during the first 2 weeks of incubation. Addition of malonate reversed this effect because of chelation of Mn. Mn was found to precipitate in all treatments, with or without the addition of malonate. α-Keto-γ-methiolbutyric acid cleavage to ethylene, an indication of ^. OH production, was observed as early as 3 days of incubation in all treatments.     

Response of antioxidative enzymes to nickel and cadmium stress in hyperaccumulator plants of the genus Alyssum

The term 'phytoremediation' is used to describe the clean-up of heavy metals from contaminated soils by plants. In this study, we examined Alyssum argenteum and Alyssum maritimum for their ability to accumulate Cd²⁺. We also exemined Ni²⁺ accumulation by A. maritimum with comparison with the known Ni-hyperaccumulator A. argenteum , in a hydroponic system. Both species were tolerant to low levels of Cd²⁺, and accumulated high quantities under the experimental conditions. Only very low levels of Ni²⁺ were found in the shoot of A. maritimum , defining it as a non-hyperaccumulator. The role of the antioxidative enzyme system was investigated in relation to Ni²⁺ and Cd²⁺ stress. In both species, superoxide dismutase (SOD) activity was elevated at high Cd²⁺ concentrations, while ascorbate peroxidase (APX) activity remained unchanged and glutathione reductase (GR) activity was reduced. In the presence of Ni²⁺, A. maritimum exhibited a typical antioxidative defense mechanism, as evidenced by the elevated activities of all three enzymes tested. A. argenteum exhibited a different enzyme response pattern, with a significant reduction in SOD activity, and elevated APX and GR activities only at the highest Ni²⁺ concentration.     

Fe nutrition demand and utilization by the green alga Dunaliella bardawil

The Fe nutritional demands, requirements and mechanisms of uptake by Dunaliella bardawil as well as potential Fe sources were studied. A comparison between Fe uptake from bacterial siderophores and from synthetic ferric chelates revealed algal growth response and chlorophyll synthesis to increasing concentrations and availability at a range of 0.01 μM–5 μM, as well as differences in efficiency. Furthermore, chloroplast ultrastructure, as observed by TEM, was affected by Fe deficiency, as was chlorophyll content. Ferric reduction is involved in the Fe uptake mechanism of Fe-stressed D. bardawil. Nutrient solution with controlled levels of free Fe²⁺ as well as spectrophotometric assays were used to measure Fe³⁺ reduction. This study shows that D. bardawil utilizes Fe³⁺ via a reduction mechanism, similar to that of strategy-I higher plants. This revised version was published online in June 2006 with corrections to the Cover Date.     

Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies

Protein folding and protein binding are similar processes. In both, structural units combinatorially associate with each other. In the case of folding, we mostly handle relatively small units, building blocks or domains, that are covalently linked. In the case of multi-molecular binding, the subunits are relatively large and are associated only by non-covalent bonds. Experimentally, the difficulty in the determination of the structures of such large assemblies increases with the complex size and the number of components it contains. Computationally, the prediction of the structures of multi-molecular complexes has largely not been addressed, probably owing to the magnitude of the combinatorial complexity of the problem. Current docking algorithms mostly target prediction of pairwise interactions. Here our goal is to predict the structures of multi-unit associations, whether these are chain-connected as in protein folding, or separate disjoint molecules in the assemblies. We assume that the structures of the single units are known, either through experimental determination or modeling. Our aim is to combinatorially assemble these units to predict their structure. To address this problem we have developed CombDock. CombDock is a combinatorial docking algorithm for the structural units assembly problem. Below, we briefly describe the algorithm and present examples of its various applications to folding and to multi-molecular assemblies. To test the robustness of the algorithm, we use inaccurate models of the structural units, derived either from crystal structures of unbound molecules or from modeling of the target sequences. The algorithm has been able to predict near-native arrangements of the input structural units in almost all of the cases, suggesting that a combinatorial approach can overcome the imperfect shape complementarity caused by the inaccuracy of the models. In addition, we further show that through a combinatorial docking strategy it is possible to enhance the predictions of pairwise interactions involved in a multi-molecular assembly.     

Angiostatic effects of K252a, a Trk inhibitor, in murine brain capillary endothelial cells

Nerve growth factor (NGF) supports the survival and differentiation of sympathetic and sensory neurons and is also mitogenic for a variety of tumors. K252a, an antagonist of NGF receptor TrkA, was previously used as a pharmacological tool to study NGF actions and as a lead compound for developing anti-tumor drugs. Since recently, NGF was characterized as an angiogenic factor, we sought to investigate the angiostatic properties of K252a on endothelial cells (ECs). For this purpose, we used a murine brain microcapillary ECs model in which we found autocrine release of NGF in the culture medium and activation of TrkA receptor-induced downstream signaling molecules Erk1/2, Akt, and PLCγ. In this model, we demonstrated the angiostatic property of K252a based on its ability to affect several important angiogenic steps. K252a, but not its cell membrane impermeable analogue K252b at 100 nM: (i) inhibited the proliferation of the ECs by 45 ± 9%; (ii) reduced by 70 ± 4% the migration of the ECs measured in a wound-closure model; (iii) reduced by 29 ± 9% the formation of tube-like structures of the ECs cultured on Matrigel; (iv) stimulated by 100 ± 25% the collagen deposition by the ECs, a process responsible for the increased endothelial barrier functions expressed by 22 ± 5% reduction of paracellular permeability and by 17 ± 3% elevation of transendothelial electrical resistance. These data suggest that NGF/TrkA may represent a target for the development of novel, K252a-derived multikinase inhibitors drugs with anti-tumor and angiostatic dual activities.     

The effect of growth conditions and genetic background on laccase production by the fungusPleurotus ostreatus

The measurement of growth rate of three isolates—P14, P15 and P19 (obtained after regeneration of protoplasts of the control strain) with significantly higher (P14, P19) or lower (P15) activity of laccase than the control strain (P. ostreatus florida F6) revealed similar patterns for P14 and P19; P15 had a higher growth rate and the highest rate was observed in the control strain. The rate of mineralization of¹⁴C-lignin on SSF (perlite) by strains F6 and P15 was almost the same and it was higher than that of P14 and P19 strains. The enzyme pattern of the individual isolates, studied by gel electrophoresis and activity staining of laccase, did not show any difference in isozyme patterns of the isolates, but there were differences in the level of gene expression. Presented at the 4th Mini-Symposium on Biosorption and Microbial Degradation, Prague, Czech Republic, November 26–29, 1996.     

Multidimensional Mapping Method Using an Arrayed Sensing System for Cross-Reactivity Screening

When measuring chemical information in biological fluids, challenges of cross-reactivity arise, especially in sensing applications where no biological recognition elements exist. An understanding of the cross-reactions involved in these complex matrices is necessary to guide the design of appropriate sensing systems. This work presents a methodology for investigating cross-reactions in complex fluids. First, a systematic screening of matrix components is demonstrated in buffer-based solutions. Second, to account for the effect of the simultaneous presence of these species in complex samples, the responses of buffer-based simulated mixtures of these species were characterized using an arrayed sensing system. We demonstrate that the sensor array, consisting of electrochemical sensors with varying input parameters, generated differential responses that provide synergistic information of sample. By mapping the sensing array response onto multidimensional heat maps, characteristic signatures were compared across sensors in the array and across different matrices. Lastly, the arrayed sensing system was applied to complex biological samples to discern and match characteristic signatures between the simulated mixtures and the complex sample responses. As an example, this methodology was applied to screen interfering species relevant to the application of schizophrenia management. Specifically, blood serum measurement of antipsychotic clozapine and antioxidant species can provide useful information regarding therapeutic efficacy and psychiatric symptoms. This work proposes an investigational tool that can guide multi-analyte sensor design, chemometric modeling and biomarker discovery.     

On the Estimation of Time Dependent Lift of a European Starling (Sturnus vulgaris) during Flapping Flight

We study the role of unsteady lift in the context of flapping wing bird flight. Both aerodynamicists and biologists have attempted to address this subject, yet it seems that the contribution of unsteady lift still holds many open questions. The current study deals with the estimation of unsteady aerodynamic forces on a freely flying bird through analysis of wingbeat kinematics and near wake flow measurements using time resolved particle image velocimetry. The aerodynamic forces are obtained through two approaches, the unsteady thin airfoil theory and using the momentum equation for viscous flows. The unsteady lift is comprised of circulatory and non-circulatory components. Both approaches are presented over the duration of wingbeat cycles. Using long-time sampling data, several wingbeat cycles have been analyzed in order to cover both the downstroke and upstroke phases. It appears that the unsteady lift varies over the wingbeat cycle emphasizing its contribution to the total lift and its role in power estimations. It is suggested that the circulatory lift component cannot assumed to be negligible and should be considered when estimating lift or power of birds in flapping motion.     

Colonization of cucumber seeds by bacteria during germination

Detailed analysis revealed fundamental differences between bacterial association with cucumber (Cucumis sativus) seeds and seedlings roots. Seed colonization by bacteria seems to result from passive encounter between bacteria, conveyed by imbibed soil solution, and the germinating seed. In accordance, the seed-associated bacterial community composition directly reflected that of the germination medium and was characterized by low dominance. Transition from seed to root was marked by a shift in bacterial community composition and in an increase in dominance values. Furthermore, settlement of bacteria on roots was tightly controlled by the specific properties of each root segment. Size and richness of the seed-associated bacterial community were clearly determinate by the community in the germination medium. In contrast, for fully developed and active roots, the medium effect on these parameters was negligible. Perturbation of the seed environment by a pathogen (Pythium aphanidermatum) had major consequences on the seed bacterial community. However, those were mostly related to direct pathogen-bacteria rather than seed-bacteria interactions. In conclusion, simple, even passive processes may determine the initial stage of plant-microbe association during seed germination, prior to extension of the primary root. Therefore, seed germination is a unique phase in the plant life cycle, with respect to its interaction with the below-ground microbiome.