Development and application of an assay for uranyl complexation by fungal metabolites, including siderophores

An assay to detect UO2 2+ complexation was developed based on the chrome azurol S (CAS) assay for siderophores (B. Schwyn and J. B. Neilands, Anal. Biochem. 160:47-56, 1987) and was used to investigate the ability of fungal metabolites to complex actinides. In this assay the discoloration of two dyed agars (one containing a CAS-Fe3+ dye and the other containing a CAS-UO2 2+ dye) caused by ligands was quantified. The assay was tested by using the siderophore desferrioxamine B (DFO), and the results showed that there was a regular, reproducible relationship between discoloration and the amount of siderophore added. The ratio of the discoloration on the CAS-UO2 2+ agar to the discoloration on the CAS-Fe3+ agar was independent of the amount of siderophore added. A total of 113 fungi and yeasts were isolated from three soil samples taken from the Peak District National Park. The fungi were screened for the production of UO2 2+ chelators by using the CAS-based assay and were also tested specifically for hydroxamate siderophore production by using the hydroxamate siderophore auxotroph Aureobacterium flavescens JG-9. This organism is highly sensitive to the presence of hydroxamate siderophores. However, the CAS-based assay was found to be less sensitive than the A. flavescens JG-9 assay. No significant difference between the results for each site for the two tests was found. Three isolates were selected for further study and were identified as two Pencillium species and a Mucor species. Our results show that the new assay can be effectively used to screen fungi for the production of UO2 2+ chelating ligands. We suggest that hydroxamate siderophores can be produced by mucoraceous fungi

Nutritional requirements and strain heterogeneity in Ashbya gossypii

Colony radial growth rates and specific growth rates of three related Ashbya gossypii strains ATCC10895, IMI31268, MUCL29450 and an unrelated strain, CBS109.26, were measured on various carbon and nitrogen sources at pH 4.5 and pH 6.5 to elucidate physiological growth requirements and strain differences. All strains grew on yeast extract or ammonium as nitrogen sources, but not on nitrate. Substantial growth at pH 4.5 was observed only on complex medium. D-Glucose, glycerol and starch were utilised as carbon sources. Ethanol was produced during growth on glycerol. Conversion of xylose into xylitol demonstrates that the xylose reductase is active. Phenotypic differences between related strains were greater than expected. We demonstrate that A. gossypii utilizes ammonium as sole nitrogen source at pH 6.5, facilitating further physiological studies using chemically defined media in the future.The financial support of Fundacao para a Ciencia e a Tecnologia (FCT), Portugal, is acknowledged, project AshByofactory PTDC/EBB-EBI/101985/2008 and grant SFRH/BD/30229/2006 to O. Ribeiro

Studies of the growth and tropisms of aspergillus giganteus and other fungi

The tall conidiophores of Aspergillus giganteus are produced by large foot cells formed by the mycelium. They only continue to grow when exposed to light of wavelength below 530 mp. The photochemical reaction involved in the inductive process is a 'low energy' reaction, i.e. light acts as a 'triggering' mechanism. The response to light is localised in the areas of the mycelium actually exposed to the radiation. The density of tall conidiophore production, but not their height, is influenced by the concentration of glucose in the medium. The tall conidiophores have the usual type of growth curve; they reach their maximum rate of elongation when they are c. 3 mm tall. Elongation is confined to the terminal portion of the conidiophore. At low light intensities the conidiophores show regular oscillations along their length. The rate of conidiophore growth is influenced by light intensity; they do not show 'light growth reaction' of the kind found in Phycomyces sporangiophores. The conidiophores only continue to elongate in light when the relative humidity is close to 100%. There is a rapid reduction in the rate of conidiophore growth during vesicle formation; no further growth takes place after the vesicle has been formed. The optimum temperature for mycelial growth is c. 30 G, while the optimum temperature for maximum conidiophore height is 20 - 23 G.The presence in the medium of the riboflavin inhibitors, 1-lyxoflavin and mepacrine, or the p-carotene inhibitor, diphenylamine, did not inhibit the photoinductive process. The presence of gaseous carbon dioxide is not essential either during the photoinductive process or for conidiophore growth. Free oxygen is not required during the actual period of photoinduction but is required for conidiophore growth. Photoinduction in the absence of gaseous oxygen is less effective in inducing carotenogenesis than photo induction in the presence of oxygen. The conidiophores are strongly positive phototropic but do appear to be sensitive to the stimulus of gravity. There is a reversal of the normal phototropic response in ultra-violet radiation of 280 mp. and when the conidiophores are submerged in liquid paraffin

Morphological Instabilities in a growing Yeast Colony: Experiment and Theory

We study the growth of colonies of the yeast Pichia membranaefaciens on agarose film. The growth conditions are controlled in a setup where nutrients are supplied through an agarose film suspended over a solution of nutrients. As the thickness of the agarose film is varied, the morphology of the front of the colony changes. The growth of the front is modeled by coupling it to a diffusive field of inhibitory metabolites. Qualitative agreement with experiments suggests that such a coupling is responsible for the observed instability of the front.Comment: RevTex, 4 pages and 3 figure

Regulation of polarised growth in fungi

Polarised growth in fungi occurs through the delivery of secretory vesicles along tracks formed by cytoskeletal elements to specific sites on the cell surface where they dock with a multiprotein structure called the exocyst before fusing with the plasmamembrane. The budding yeast, Saccharomyces cerevisiae has provided a useful model to investigate the mechanisms involved and their control. Cortical markers, provided by bud site selection pathways during budding, the septin ring during cytokinesis or the stimulation of the pheromone response receptors during mating, act through upstream signalling pathways to localise Cdc24, the GEF for the rho family GTPase, Cdc42. Cdc42 in its GTP-bound activates a multiprotein protein complex called the polarisome which nucleates actin cables along which the secretory vesicles are transported to the cell surface. Hyphae can elongate at a rate orders of magnitude faster than the extension of a yeast bud, so understanding hyphal growth will require substantial modification of the yeast paradigm. The rapid rate of hyphal growth is driven by a structure called the Spitzenkörper, located just behind the growing tip and which is rich in secretory vesicles. It is thought that secretory vesicles are delivered to the apical region where they accumulate in the Spitzenkörper. The Spitzenkörper then acts as vesicle supply centre in which vesicles exit the Spitzenkörper in all directions, but because of its proximity, the tip receives a greater concentration of vesicles per unit area than subapical regions. There are no obvious equivalents to the bud site selection pathway to provide a spatial landmark for polarised growth in hyphae. However, an emerging model is the way that the site of polarised growth in the fission yeast, Schizosaccharomyces pombe, is marked by delivery of the kelch repeat protein, Tea1, along microtubules. The relationship of the Spitzenkörper to the polarisome and the mechanisms that promote its formation are key questions that form the focus of current research

Zeros of slice functions and polynomials over dual quaternions

This work studies the zeros of slice functions over the algebra of dual quaternions and it comprises applications to the problem of factorizing motion polynomials. The class of slice functions over an alternative $*$-algebra $A$ was defined by Ghiloni and Perotti in 2011, extending the class of slice regular functions introduced by Gentili and Struppa in 2006. Both classes strictly include the polynomials over $A$. We focus on the case when $A$ is the algebra of dual quaternions $\mathbb{DH}$. The specific properties of this algebra allow a full characterization of the zero sets, which is not available over general alternative $*$-algebras. This characterization sheds some light on the study of motion polynomials over $\mathbb{DH}$, introduced by Heged\"us, Schicho, and Schr\"ocker in 2013 for their relevance in mechanism science.Comment: 37 pages, to appear in Trans. Amer. Math. So

Spatial organisation of ecologically relevant high order flow properties and implications for river habitat assessment

PhDThe turbulent properties of flow in rivers are of fundamental importance to aquatic organisms yet are rarely quantified during routine river habitat assessment surveys or the design of restoration schemes due to their complex nature. This thesis uses a detailed review of the literature to highlight the various ways in which plants and animals modify the flow field, how this can deliver beneficial effects; and how turbulence can also generate threats to growth and survival. The thesis then presents the results from detailed field assessments of turbulence properties undertaken on low, intermediate and high gradient rivers to advance scientific understanding of the hydrodynamics of rivers and inform effective habitat assessment and restoration. A reach-scale comparison across sites reveals spatial variations in the relationships between turbulent parameters, emphasising the need for direct measurement of turbulence properties, while a geomorphic unit scale assessment suggests that variations in turbulence at the scale of individual roughness elements, and/or within the same broad groupings of geomorphic units (e.g. different types of pools) can have an important influence on hydraulic habitat. The importance of small-scale flow obstructions is further emphasised through analysis of the temporal dynamics of turbulence properties with changes in flow stage and vegetation growth. The highest magnitude temporal changes in turbulence properties were associated with individual boulders and vegetation patches respectively, indicating flow intensification around these sub-geomorphic unit scale features. Experimental research combining flow measurement with underwater videography reveals that more sophisticated turbulence parameters provide a better explanation of fish behaviour and habitat use under field conditions, further supporting direct measurement of turbulent properties where possible. The new insights into interactions between geomorphology, hydraulics and aquatic organisms generated by this work offer opportunities for refining habitat assessment and restoration design protocols to better integrate the important role of turbulence in generating suitable physical habitat for aquatic organisms.SMART (Science for the MAnagement of Rivers and their Tidal systems) Joint Doctorate Erasmus Mundus programme funded by the European Union

The peroxin PEX14 of Neurospora crassa is essential for the biogenesis of both glyoxysomes and Woronin bodies

In the filamentous fungus Neurospora crassa, glyoxysomes and Woronin bodies coexist in the same cell. Because several glyoxysomal matrix proteins and also HEX1, the dominant protein of Woronin bodies, possess typical peroxisomal targeting signals, the question arises as to how protein targeting to these distinct yet related types of microbodies is achieved. Here we analyzed the function of the Neurospora ortholog of PEX14, an essential component of the peroxisomal import machinery. PEX14 interacted with both targeting signal receptors and was localized to glyoxysomes but was virtually absent from Woronin bodies. Nonetheless, a pex14 Delta mutant not only failed to grow on fatty acids because of a defect in glyoxysomal beta-oxidation but also suffered from cytoplasmic bleeding, indicative of a defect in Woronin body-dependent septal pore plugging. Inspection of pex14 Delta mutant hyphae by fluorescence and electron microscopy indeed revealed the absence of Woronin bodies. When these cells were subjected to subcellular fractionation, HEX1 was completely mislocalized to the cytosol. Expression of GFP-HEX1 in wild-type mycelia caused the staining of Woronin bodies and also of glyoxysomes in a targeting signal-dependent manner. Our data support the view that Woronin bodies emerge from glyoxysomes through import of HEX1 and subsequent fission

Elastic Feature Consolidation for Cold Start Exemplar-Free Incremental Learning

Exemplar-Free Class Incremental Learning (EFCIL) aims to learn from a sequence of tasks without having access to previous task data. In this paper, we consider the challenging Cold Start scenario in which insufficient data is available in the first task to learn a high-quality backbone. This is especially challenging for EFCIL since it requires high plasticity, which results in feature drift which is difficult to compensate for in the exemplar-free setting. To address this problem, we propose a simple and effective approach that consolidates feature representations by regularizing drift in directions highly relevant to previous tasks and employs prototypes to reduce task-recency bias. Our method, called Elastic Feature Consolidation (EFC), exploits a tractable second-order approximation of feature drift based on an Empirical Feature Matrix (EFM). The EFM induces a pseudo-metric in feature space which we use to regularize feature drift in important directions and to update Gaussian prototypes used in a novel asymmetric cross entropy loss which effectively balances prototype rehearsal with data from new tasks. Experimental results on CIFAR-100, Tiny-ImageNet, ImageNet-Subset and ImageNet-1K demonstrate that Elastic Feature Consolidation is better able to learn new tasks by maintaining model plasticity and significantly outperform the state-of-the-art.Comment: Accepted at Twelfth International Conference on Learning Representations (ICLR 2024