Palette of possibilities: developing digital tools for displaying the uncertainty in the virtual archaeological “reconstruction” of the house V 1,7 (Casa del Torello di Bronzo) in Pompeii

This thesis has two major purposes: (1) to create a 3D virtual “reconstructive” model of the peristyle with the nymphaeum wall (room b) of the house V 1,7 (House of the Bronze Bull) in Pompeii, and (2) to prepare a probability map based on this model that will show the reliability level for each individual part. The author underlines the importance of recording paradata of the entire workflow. The aim of this study is to highlight the problems concerned with 3D virtual archaeological reconstructions – in particular, the lack of proper referencing tools and lack of reflexivity when presenting those models to the public. The basic data for this study were scans obtained in a framework of the Swedish Pompeii Project. One set of scans was imported into 3DStudio Max and the reconstruction was modelled with reference to it. After this stage, a probability map was created in order to present the plausibility of every element in the form of a color scale (green being most plausible, red being least plausible). Furthermore, the probability map was geo-referenced and visualized within ArcGIS. Once this task was realized, a database was created and linked in order to connect the different parts of the probability map with the sources used to perform the reconstruction. The project proved that 3D virtual models are useful tools in examining the spatial relations of the objects and the visual representation of the scene. The results obtained show the necessity of documenting the entire scientific process thoroughly. Furthermore, it was concluded that this subject needs to be more discussed by archaeologists, and that the scientific vocabulary concerning these implementations should be standardized

The role of Alg13 N-acetylglucosaminyl transferase in the expression of pathogenic features of Candida albicans.

Background: The pathogenic potential of Candida albicans depends on adhesion to the host cells mediated by highly glycosylated adhesins, hyphae formation and growth of biofilm. These factors require effective N-glycosylation of proteins. Here, we present consequences of up- and down- regulation of the newly identified ALG13 gene encoding N-acetylglucosaminyl transferase, a potential member of the Alg7p/Alg13p/Alg14p complex catalyzing the first two initial reactions in the N-glycosylation process. Methods: We constructed C. albicans strain alg13∆::hisG/TRp-ALG13 with one allele of ALG13 disrupted and the other under the control of a regulatable promoter, TRp. Gene expression and enzyme activity were measured using RT-qPCR and radioactive substrate. Cell wall composition was estimated by HPLC DIONEX. Protein glycosylation status was analyzed by electrophoresis of HexNAcase, a model N-glycosylated protein in C. albicans. Results: Both decreased and elevated expression of ALG13 changed expression of all members of the complex and resulted in a decreased activity of Alg7p and Alg13p and under-glycosylation of HexNAcase. The alg13 strain was also defective in hyphae formation and growth of biofilm. These defects could result from altered expression of genes encoding adhesins and from changes in the carbohydrate content of the cell wall of the mutant. General significance: This work confirms the important role of protein N-glycosylation in the pathogenic potential of C. albicans

Mg2+-Dependent Methyl Transfer by a Knotted Protein: A Molecular Dynamics Simulation and Quantum Mechanics Study

Mg2+ is required for the catalytic activity of TrmD, a bacteria-specific methyltransferase that is made up of a protein topological knot-fold, to synthesize methylated m1G37-tRNA to support life. However, neither the location of Mg2+ in the structure of TrmD nor its role in the catalytic mechanism is known. Using molecular dynamics (MD) simulations, we identify a plausible Mg2+ binding pocket within the active site of the enzyme, wherein the ion is coordinated by two aspartates and a glutamate. In this position, Mg2+ additionally interacts with the carboxylate of a methyl donor cofactor S-adenosylmethionine (SAM). The computational results are validated by experimental mutation studies, which demonstrate the importance of the Mg2+-binding residues for the catalytic activity. The presence of Mg2+ in the binding pocket induces SAM to adopt a unique bent shape required for the methyl transfer activity and causes a structural reorganization of the active site. Quantum mechanical calculations show that the methyl transfer is energetically feasible only when Mg2+ is bound in the position revealed by the MD simulations, demonstrating that its function is to align the active site residues within the topological knot-fold in a geometry optimal for catalysis. The obtained insights provide the opportunity for developing a strategy of antibacterial drug discovery based on targeting of Mg2+-binding to TrmD

Identification of bacteria and fungi inhabiting fruiting bodies of Burgundy truffle (Tuber aestivum Vittad.)

Tuber species may be regarded as complex microhabitats hosting diverse microorganisms inside their fruiting bodies. Here, we investigated the structure of microbial communities inhabiting the gleba of wild growing (in stands) T. aestivum, using Illumina sequencing and culture-based methods. The two methods used in combination allowed to extract more information on complex microbiota of Tuber aestivum gleba. Analysis of the V3–V4 region of 16S rDNA identified nine phyla of bacteria present in the gleba of T. aestivum ascomata, mostly Proteobacteria from the family Bradyrhizobiaceae. Our results ideally match the earlier data for other Tuber species where the family Bradyrhizobiaceae was the most represented. The ITS1 region of fungal rDNA represented six alien fungal species belonging to three phyla. To complement the metagenomic analysis, cultivable fungi and bacteria were obtained from the gleba of the same T. aestivum fruiting bodies. The identified fungi mostly belong to the phylum Basidiomycota and same to Ascomycota. Analysis of cultivable bacteria revealed that all the specimens were colonized by different strains of Bacillus. Fungal community inhabiting T. aestivum fruiting bodies was never shown before

The Origin of the Wigner Energy

Surfaces of experimental masses of even-even and odd-odd nuclei exhibit a sharp slope discontinuity at N=Z. This cusp (Wigner energy), reflecting an additional binding in nuclei with neutrons and protons occupying the same shell model orbitals, is usually attributed to neutron-proton pairing correlations. A method is developed to extract the Wigner term from experimental data. Both empirical arguments and shell-model calculations suggest that the Wigner term can be traced back to the isospin T=0 part of nuclear interaction. Our calculations reveal the rather complex mechanism responsible for the nuclear binding around the N=Z line. In particular, we find that the Wigner term cannot be solely explained in terms of correlations between the neutron-proton J=1, T=0 (deuteron-like) pairs.Comment: 10 RevTeX pages, 3 Postscript figures include

Increased activity of the sterol branch of the mevalonate pathway elevates glycosylation of secretory proteins and improves antifungal properties of Trichoderma atroviride.

Some Trichoderma spp. have an ability to inhibit proliferation of fungal plant pathogens in the soil. Numerous compounds with a proven antifungal activity are synthesized via the terpene pathway. Here, we stimulated the activity of the mevalonate pathway in T. atroviride P1 by expressing the Saccharomyces cerevisiae ERG20 gene coding for farnesyl pyrophosphate (FPP) synthase, a key enzyme of this pathway. ERG20-expressing Trichoderma strains showed higher activities of FPP synthase and squalene synthase, the principal recipient of FPP in the mevalonate pathway. We also observed activation of dolichyl phosphate mannose (DPM) synthase, an enzyme in protein glycosylation, and significantly increased O- and N-glycosylation of secreted proteins. The hyper-glycosylation of secretory hydrolases could explain their increased activity observed in the ERG20 transformants. Analysis of the antifungal properties of the new strains revealed that the hydrolases secreted by the transformants inhibited growth of a plant pathogen, Pythium ultimum more efficiently compared to the control strain. Consequently, the biocontrol activity of the transgenic strains, determined as their ability to protect bean seeds and seedlings against harmful action of P. ultimum, was also improved substantially

Candida albicans; exploring glycosylation pathway in the search of targets for antimicrobial agents and yeast to hyphae transition

Microbial cell wall is mostly synthesized by the glycosylated proteins with the distinct enzymatic activity. In this review we have concentrated on the description of the certain steps of glycosylation and their effect on the cell wall integrity and yeast to hyphae transition, the process enhancing the pathogenic properties of C.albicans. The glycoproteins play an invaluable role in C. albicans virulence and they modulate adhesive, invasive, morphogenetic and immune stimulating properties of the pathogen as well as its susceptibility to the antifungal agents. Therefore, understanding of C. albicans glycobiology might let us expand the arsenal in the war against fungal enemies. The early stages of N-, O-glycans and GPI-anchor synthesis requires dolichol - the lipid carrier of sugar residues. Diminished supply of dolichol causes series of defects in C. albicans cells, among which aberrant protein glycosylation is the most evident. Furthermore, the relations between the cell wall composition and integrity, resistance to some antifungal and cell wall disturbing agents and dolichol dependent glycosylation are observed. Moreover relevance of these reactions for the morphological differentiation of C.albicans is described

Molecular characterization of central cytoplasmic loop in Aspergillus nidulans AstA transporter

AstA (alternative sulfate transporter) belongs to a large, but poorly characterized, Dal5 family of allantoate permeases of the Major Facilitator Superfamily. The astA gene has been cloned from an IAM 2006 Japanese strain of Aspergillus nidulans by complementation of a sulfate permease-deficient mutant. In this study we show that conserved lysine residues in Central Cytoplasmic Loop (CCL) of the AstA protein may participate in anion selectivity, and control kinetic properties of the AstA transporter. A three-dimensional model containing four clustered lysine residues was created, showing a novel substrate-interacting structure in Major Facilitator Superfamily transporters. The assimilation constant (Kτ) of wild type AstA protein is 85 μM, while Vmax/mg of DW of AstA is twice that of the main sulfate transporter SB per mg of dry weight (DW) of mycelium (1.53 vs. 0.85 nmol/min, respectively). Amino acid substitutions in CCL did not abolish sulfate uptake, but affected its kinetic parameters. Mutants affected in the lysine residues forming the postulated sulfate-interacting pocket in AstA were able to grow and uptake sulfate, indicating that CCL is not crucial for sulfate transportation. However, these mutants exhibited altered values of Kτ and Vmax, suggesting that CCL is involved in control of the transporter activity

Yil102c-A is a Functional Homologue of the DPMII Subunit of Dolichyl Phosphate Mannose Synthase in Saccharomyces cerevisiae

: In a wide range of organisms, dolichyl phosphate mannose (DPM) synthase is a complex of tree proteins Dpm1, Dpm2, and Dpm3. However, in the yeast Saccharomyces cerevisiae, it is believed to be a single Dpm1 protein. The function of Dpm3 is performed in S. cerevisiae by the C-terminal transmembrane domain of the catalytic subunit Dpm1. Until present, the regulatory Dpm2 protein has not been found in S. cerevisiae. In this study, we show that, in fact, the Yil102c-A protein interacts directly with Dpm1 in S. cerevisiae and influences its DPM synthase activity. Deletion of the YIL102c-A gene is lethal, and this phenotype is reversed by the dpm2 gene from Trichoderma reesei. Functional analysis of Yil102c-A revealed that it also interacts with glucosylphosphatidylinositol-N-acetylglucosaminyl transferase (GPI-GnT), similar to DPM2 in human cells. Taken together, these results show that Yil102c-A is a functional homolog of DPMII from T. reesei and DPM2 from humans

Nuclear structure far from stability

Modern nuclear structure theory is rapidly evolving towards regions of exotic short-lived nuclei far from stability, nuclear astrophysics applications, and bridging the gap between low-energy QCD and the phenomenology of finite nuclei. The principal objective is to build a consistent microscopic theoretical framework that will provide a unified description of bulk properties, nuclear excitations and reactions. Stringent constraints on the microscopic approach to nuclear dynamics, effective nuclear interactions, and nuclear energy density functionals, are obtained from studies of the structure and stability of exotic nuclei with extreme isospin values, as well as extended asymmetric nucleonic matter. Recent theoretical advances in the description of structure phenomena in exotic nuclei far from stability are reviewed.Comment: 18 pp, plenary talk, International Nuclear Physics Conference (INPC 2004), Goeteborg, Sweden, June 27 - July 2, 200