Role of enzymes in growth and morphology of Neurospora crassa: cell-wall-bound enzymes and their possible role in branching

The cell wall of Neurospora crassa contains bound enzymes that can digest its structural polymers. These enzymes are not present at the same levels at all stages of growth. The levels of these autolytic enzymes vary and generally show some relationship to the process of branching. These enzymes were removed from the cell wall by β-mercaptoethanol extraction and were tested for activity against isolated cell wall fractions. Such studies, as well as autolytic studies, showed that enzymes acting on the protein portion of the cell wall (proteases) are more prominent than enzymes that act on the glucan portion (glucanases) of the cell wall. Comparative studies between the wild type and a spreading colonial mutant spco-1 showed that earlier and higher frequency of branching in spco-1 was correlated with a greater amount of these enzymes bound to the cell walls. It is concluded from these observations that autolytic enzymes acting on the protein and glucan portion of the cell walls occur as wall-bound and participate in the process of branching in Neurospora

Understanding the bulk electronic structure of Ca1-xSrxVO3

We investigate the electronic structure of Ca1-xSrxVO3 using careful state-of-the-art experiments and calculations. Photoemission spectra using synchrotron radiation reveal a hitherto unnoticed polarization dependence of the photoemission matrix elements for the surface component leading to a substantial suppression of its intensity. Bulk spectra extracted with the help of experimentally determined electron escape depth and estimated suppression of surface contributions resolve outstanding puzzles concerning the electronic structure in Ca1-xSrxVO3.Comment: 4 pages including 3 figure

Monoclonal antibodies to mycobacterial DNA gyrase A inhibit DNA supercoiling activity

DNA gyrase is an essential type II topoisomerase found in bacteria. We have previously characterized DNA gyrase from Mycobacterium tuberculosis and Mycobacterium smegmatis. In this study, several monoclonal antibodies were generated against the gyrase A subunit (GyrA) of M. smegmatis. Three, MsGyrA:C3, MsGyrA:H11 and MsGyrA:E9, were further analyzed for their interaction with the enzyme. The monoclonal antibodies showed high degree of cross-reactivity with both fast-growing and slow-growing mycobacteria. In contrast, none recognized Escherichia coli GyrA. All the three monoclonal antibodies were of IgG1 isotype falling into two distinct types with respect to epitope recognition and interaction with the enzyme. MsGyrA:C3 and MsGyrA:H11 IgG, and their respective Fab fragments, inhibited the DNA supercoiling activity catalyzed by mycobacterial DNA gyrase. The epitope for the neutralizing monoclonal antibodies appeared to involve the region towards the N-terminus (residues 351-415) of the enzyme in a conformation-dependent manner. These monoclonal antibodies would serve as valuable tools for structure-function analysis and immunocytological studies of mycobacterial DNA gyrase. In addition, they would be useful for designing peptide inhibitors against DNA gyrase

Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling

<p>Abstract</p> <p>Background</p> <p><it>Geobacter sulfurreducens </it>is a member of the <it>Geobacter </it>species, which are capable of oxidation of organic waste coupled to the reduction of heavy metals and electrode with applications in bioremediation and bioenergy generation. While the metabolism of this organism has been studied through the development of a stoichiometry based genome-scale metabolic model, the associated regulatory network has not yet been well studied. In this manuscript, we report on the implementation of a thermodynamics based metabolic flux model for <it>Geobacter sulfurreducens</it>. We use this updated model to identify reactions that are subject to regulatory control in the metabolic network of <it>G. sulfurreducens </it>using thermodynamic variability analysis.</p> <p>Findings</p> <p>As a first step, we have validated the regulatory sites and bottleneck reactions predicted by the thermodynamic flux analysis in <it>E. coli </it>by evaluating the expression ranges of the corresponding genes. We then identified ten reactions in the metabolic network of <it>G. sulfurreducens </it>that are predicted to be candidates for regulation. We then compared the free energy ranges for these reactions with the corresponding gene expression fold changes under conditions of different environmental and genetic perturbations and show that the model predictions of regulation are consistent with data. In addition, we also identify reactions that operate close to equilibrium and show that the experimentally determined exchange coefficient (a measure of reversibility) is significant for these reactions.</p> <p>Conclusions</p> <p>Application of the thermodynamic constraints resulted in identification of potential bottleneck reactions not only from the central metabolism but also from the nucleotide and amino acid subsystems, thereby showing the highly coupled nature of the thermodynamic constraints. In addition, thermodynamic variability analysis serves as a valuable tool in estimating the ranges of Δ_rG' of every reaction in the model leading to the prediction of regulatory sites in the metabolic network, thereby characterizing the regulatory network in both a model organism such as <it>E. coli </it>as well as a non model organism such as <it>G. sulfurreducens</it>.</p

A moving boundary model motivated by electric breakdown: II. Initial value problem

An interfacial approximation of the streamer stage in the evolution of sparks and lightning can be formulated as a Laplacian growth model regularized by a 'kinetic undercooling' boundary condition. Using this model we study both the linearized and the full nonlinear evolution of small perturbations of a uniformly translating circle. Within the linear approximation analytical and numerical results show that perturbations are advected to the back of the circle, where they decay. An initially analytic interface stays analytic for all finite times, but singularities from outside the physical region approach the interface for $t\to\infty$, which results in some anomalous relaxation at the back of the circle. For the nonlinear evolution numerical results indicate that the circle is the asymptotic attractor for small perturbations, but larger perturbations may lead to branching. We also present results for more general initial shapes, which demonstrate that regularization by kinetic undercooling cannot guarantee smooth interfaces globally in time.Comment: 44 pages, 18 figures, paper submitted to Physica

A moving boundary problem motivated by electric breakdown: I. Spectrum of linear perturbations

An interfacial approximation of the streamer stage in the evolution of sparks and lightning can be written as a Laplacian growth model regularized by a `kinetic undercooling' boundary condition. We study the linear stability of uniformly translating circles that solve the problem in two dimensions. In a space of smooth perturbations of the circular shape, the stability operator is found to have a pure point spectrum. Except for the zero eigenvalue for infinitesimal translations, all eigenvalues are shown to have negative real part. Therefore perturbations decay exponentially in time. We calculate the spectrum through a combination of asymptotic and series evaluation. In the limit of vanishing regularization parameter, all eigenvalues are found to approach zero in a singular fashion, and this asymptotic behavior is worked out in detail. A consideration of the eigenfunctions indicates that a strong intermediate growth may occur for generic initial perturbations. Both the linear and the nonlinear initial value problem are considered in a second paper.Comment: 37 pages, 6 figures, revised for Physica

Appraisal of the Marine Fisheries of Kerala

Kerala, the southwestern part of the peninsular India, has a narrow stretch of land with a long surf-beaten coast on the western side and a lush green mountain range on the eastern side. The coastline is 590 km long, which is almost one-tenth of the Indian coastline. Marine fishing, using artisanal tackles like boat-seines, shore-seines and Chinese dip nets, is an age-old tradition of the state. Mechanisation was started in late fifties by the Indo-Norwegian Project, at first in the Quilon area. The early sixties too saw an important technological development, namely the shift from cotton to nylon nets. By mid-sixties, individual entrepreneures entered the scene, paving way for a fast development of trawl fishery in the coastal waters. Commercial purse-seining started during late seventies, and the process of large-scale motorisation of country crafts began in early eighties

Emerging pharmacotherapy of tinnitus

Tinnitus, the perception of sound in the absence of an auditory stimulus, is perceived by about 1 in 10 adults, and for at least 1 in 100, tinnitus severely affects their quality of life. Because tinnitus is frequently associated with irritability, agitation, stress, insomnia, anxiety and depression, the social and economic burdens of tinnitus can be enormous. No curative treatments are available. However, tinnitus symptoms can be alleviated to some extent. The most widespread management therapies consist of auditory stimulation and cognitive behavioral treatment, aiming at improving habituation and coping strategies. Available clinical trials vary in methodological rigor and have been performed for a considerable number of different drugs. None of the investigated drugs have demonstrated providing replicable long-term reduction of tinnitus impact in the majority of patients in excess of placebo effects. Accordingly, there are no FDA or European Medicines Agency approved drugs for the treatment of tinnitus. However, in spite of the lack of evidence, a large variety of different compounds are prescribed off-label. Therefore, more effective pharmacotherapies for this huge and still growing market are desperately needed and even a drug that produces only a small but significant effect would have an enormous therapeutic impact. This review describes current and emerging pharmacotherapies with current difficulties and limitations. In addition, it provides an estimate of the tinnitus market. Finally, it describes recent advances in the tinnitus field which may help overcome obstacles faced in the pharmacological treatment of tinnitus. These include incomplete knowledge of tinnitus pathophysiology, lack of well-established animal models, heterogeneity of different forms of tinnitus, difficulties in tinnitus assessment and outcome measurement and variability in clinical trial methodology. © 2009 Informa UK Ltd.Fil: Langguth, Berthold. Universitat Regensburg; AlemaniaFil: Salvi, Richard. State University of New York; Estados UnidosFil: Elgoyhen, Ana Belen. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentin

Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum

Halobacterium salinarum is a bioenergetically flexible, halophilic microorganism that can generate energy by respiration, photosynthesis, and the fermentation of arginine. In a previous study, using a genome-scale metabolic model, we have shown that the archaeon unexpectedly degrades essential amino acids under aerobic conditions, a behavior that can lead to the termination of growth earlier than necessary. Here, we further integratively investigate energy generation, nutrient utilization, and biomass production using an extended methodology that accounts for dynamically changing transport patterns, including those that arise from interactions among the supplied metabolites. Moreover, we widen the scope of our analysis to include phototrophic conditions to explore the interplay between different bioenergetic modes. Surprisingly, we found that cells also degrade essential amino acids even during phototropy, when energy should already be abundant. We also found that under both conditions considerable amounts of nutrients that were taken up were neither incorporated into the biomass nor used as respiratory substrates, implying the considerable production and accumulation of several metabolites in the medium. Some of these are likely the products of forms of overflow metabolism. In addition, our results also show that arginine fermentation, contrary to what is typically assumed, occurs simultaneously with respiration and photosynthesis and can contribute energy in levels that are comparable to the primary bioenergetic modes, if not more. These findings portray a picture that the organism takes an approach toward growth that favors the here and now, even at the cost of longer-term concerns. We believe that the seemingly "greedy" behavior exhibited actually consists of adaptations by the organism to its natural environments, where nutrients are not only irregularly available but may altogether be absent for extended periods that may span several years. Such a setting probably predisposed the cells to grow as much as possible when the conditions become favorable