42 research outputs found
State-of-practice on as-is modelling of industrial facilities
90% of the time needed for the conversion from point clouds to 3D models of industrial facilities is spent on geometric modelling due to the sheer number of Industrial Objects (IOs) of each plant. Hence, cost reduction is only possible by automating modelling. Our previous work has successfully identified the most frequent industrial objects which are in descending order: electrical conduit, straight pipes, circular hollow sections, elbows, channels, solid bars, I-beams, angles, flanges and valves. We modelled those on a state-of-theart software, EdgeWise and then evaluated the performance of this software for pipeline and structural modelling. The modelling of pipelines is summarized in
three basic steps: (a) automated extraction of cylinders, (b) their semantic classification and (c) manual extraction and editing of pipes. The results showed that cylinders are modelled with 75 % recall and 62 % precision on average. We discovered that pipes, electrical conduit and circular hollow sections require 80 % of the Total Modelling Hours (TMH) of the 10 most frequent IOs to build the plant model. TMH was then compared to modelling hours in Revit and showed that 67 % of pipe modelling time is saved by EdgeWise. This paper is the first to evaluate state-of-the-art industrial modelling software. These findings help in better understanding the problem and serve as the foundation for researchers who are interested in solving i
Characterization of an Alkali- and Halide-Resistant Laccase Expressed in E. coli: CotA from <i>Bacillus clausii</i>
The limitations of fungal laccases at higher pH and salt concentrations have intensified the search for new extremophilic bacterial laccases. We report the cloning, expression, and characterization of the bacterial cotA from Bacillus clausii, a supposed alkalophilic ortholog of cotA from B. subtilis. Both laccases were expressed in E. coli strain BL21(DE3) and characterized fully in parallel for strict benchmarking. We report activity on ABTS, SGZ, DMP, caffeic acid, promazine, phenyl hydrazine, tannic acid, and bilirubin at variable pH. Whereas ABTS, promazine, and phenyl hydrazine activities vs. pH were similar, the activity of B. clausii cotA was shifted upwards by ~0.5-2 pH units for the simple phenolic substrates DMP, SGZ, and caffeic acid. This shift is not due to substrate affinity (K(M)) but to pH dependence of catalytic turnover: The k(cat) of B. clausii cotA was 1 s⁻¹ at pH 6 and 5 s⁻¹ at pH 8 in contrast to 6 s⁻¹ at pH 6 and 2 s⁻¹ at pH 8 for of B. subtilis cotA. Overall, k(cat)/K(M) was 10-fold higher for B. subtilis cotA at pH(opt). While both proteins were heat activated, activation increased with pH and was larger in cotA from B. clausii. NaCl inhibited activity at acidic pH, but not up to 500-700 mM NaCl in alkaline pH, a further advantage of the alkali regime in laccase applications. The B. clausii cotA had ~20 minutes half-life at 80°C, less than the ~50 minutes at 80°C for cotA from B. subtilis. While cotA from B. subtilis had optimal stability at pH~8, the cotA from B. clausii displayed higher combined salt- and alkali-resistance. This resistance is possibly caused by two substitutions (S427Q and V110E) that could repel anions to reduce anion-copper interactions at the expense of catalytic proficiency, a trade-off of potential relevance to laccase optimization
Comparative Genomic Analyses of Copper Transporters and Cuproproteomes Reveal Evolutionary Dynamics of Copper Utilization and Its Link to Oxygen
Copper is an essential trace element in many organisms and is utilized in all domains of life. It is often used as a cofactor of redox proteins, but is also a toxic metal ion. Intracellular copper must be carefully handled to prevent the formation of reactive oxygen species which pose a threat to DNA, lipids, and proteins. In this work, we examined patterns of copper utilization in prokaryotes by analyzing the occurrence of copper transporters and copper-containing proteins. Many organisms, including those that lack copper-dependent proteins, had copper exporters, likely to protect against copper ions that inadvertently enter the cell. We found that copper use is widespread among prokaryotes, but also identified several phyla that lack cuproproteins. This is in contrast to the use of other trace elements, such as selenium, which shows more scattered and reduced usage, yet larger selenoproteomes. Copper transporters had different patterns of occurrence than cuproproteins, suggesting that the pathways of copper utilization and copper detoxification are independent of each other. We present evidence that organisms living in oxygen-rich environments utilize copper, whereas the majority of anaerobic organisms do not. In addition, among copper users, cuproproteomes of aerobic organisms were larger than those of anaerobic organisms. Prokaryotic cuproproteomes were small and dominated by a single protein, cytochrome c oxidase. The data are consistent with the idea that proteins evolved to utilize copper following the oxygenation of the Earth
Bacterial laccases: some recent advances and applications
Laccases belong to the large family of multi-copper oxidases (MCOs) that couple the one-electron oxidation of substrates with the four-electron reduction of molecular oxygen to water. Because of their high relative non-specific oxidation capacity particularly on phenols and aromatic amines as well as the lack of requirement for expensive organic cofactors, they have found application in a large number of biotechnological fields. The vast majority of studies and applications were performed using fungal laccases, but bacterial laccases show interesting properties such as optimal temperature above 50 °C, optimal pH at the neutral to alkaline range, thermal and chemical stability and increased salt tolerance. Additionally, bacterial systems benefit from a wide range of molecular biology tools that facilitates their engineering and achievement of high yields of protein production and set-up of cost-effective bioprocesses. In this review we will provide up-to-date information on the distribution and putative physiological role of bacterial laccases and highlight their distinctive structural and biochemical properties, discuss the key role of copper in the biochemical properties, discuss thermostability determinants and, finally, review biotechnological applications with a focus on catalytic mechanisms on phenolics and aromatic amines.info:eu-repo/semantics/publishedVersio
The Pleiotropic CymR Regulator of Staphylococcus aureus Plays an Important Role in Virulence and Stress Response
We have characterized a novel pleiotropic role for CymR, the master regulator of cysteine metabolism. We show here that CymR plays an important role both in stress response and virulence of Staphylococcus aureus. Genes involved in detoxification processes, including oxidative stress response and metal ion homeostasis, were differentially expressed in a ΔcymR mutant. Deletion of cymR resulted in increased sensitivity to hydrogen peroxide-, disulfide-, tellurite- and copper-induced stresses. Estimation of metabolite pools suggests that this heightened sensitivity could be the result of profound metabolic changes in the ΔcymR mutant, with an increase in the intracellular cysteine pool and hydrogen sulfide formation. Since resistance to oxidative stress within the host organism is important for pathogen survival, we investigated the role of CymR during the infectious process. Our results indicate that the deletion of cymR promotes survival of S. aureus inside macrophages, whereas virulence of the ΔcymR mutant is highly impaired in mice. These data indicate that CymR plays a major role in virulence and adaptation of S. aureus for survival within the host
The Regulation of Sulfur Metabolism in Mycobacterium tuberculosis
Mycobacterium tuberculosis (Mtb) has evolved into a highly successful human pathogen. It deftly subverts the bactericidal mechanisms of alveolar macrophages, ultimately inducing granuloma formation and establishing long-term residence in the host. These hallmarks of Mtb infection are facilitated by the metabolic adaptation of the pathogen to its surrounding environment and the biosynthesis of molecules that mediate its interactions with host immune cells. The sulfate assimilation pathway of Mtb produces a number of sulfur-containing metabolites with important contributions to pathogenesis and survival. This pathway is regulated by diverse environmental cues and regulatory proteins that mediate sulfur transactions in the cell. Here, we discuss the transcriptional and biochemical mechanisms of sulfur metabolism regulation in Mtb and potential small molecule regulators of the sulfate assimilation pathway that are collectively poised to aid this intracellular pathogen in its expert manipulation of the host. From this global analysis, we have identified a subset of sulfur-metabolizing enzymes that are sensitive to multiple regulatory cues and may be strong candidates for therapeutic intervention
High-Density Transcriptional Initiation Signals Underline Genomic Islands in Bacteria
Genomic islands (GIs), frequently associated with the pathogenicity of bacteria and having a substantial influence on bacterial evolution, are groups of “alien” elements which probably undergo special temporal–spatial regulation in the host genome. Are there particular hallmark transcriptional signals for these “exotic” regions? We here explore the potential transcriptional signals that underline the GIs beyond the conventional views on basic sequence composition, such as codon usage and GC property bias. It showed that there is a significant enrichment of the transcription start positions (TSPs) in the GI regions compared to the whole genome of Salmonella enterica and Escherichia coli. There was up to a four-fold increase for the 70% GIs, implying high-density TSPs profile can potentially differentiate the GI regions. Based on this feature, we developed a new sliding window method GIST, Genomic-island Identification by Signals of Transcription, to identify these regions. Subsequently, we compared the known GI-associated features of the GIs detected by GIST and by the existing method Islandviewer to those of the whole genome. Our method demonstrates high sensitivity in detecting GIs harboring genes with biased GI-like function, preferred subcellular localization, skewed GC property, shorter gene length and biased “non-optimal” codon usage. The special transcriptional signals discovered here may contribute to the coordinate expression regulation of foreign genes. Finally, by using GIST, we detected many interesting GIs in the 2011 German E. coli O104:H4 outbreak strain TY-2482, including the microcin H47 system and gene cluster ycgXEFZ-ymgABC that activates the production of biofilm matrix. The aforesaid findings highlight the power of GIST to predict GIs with distinct intrinsic features to the genome. The heterogeneity of cumulative TSPs profiles may not only be a better identity for “alien” regions, but also provide hints to the special evolutionary course and transcriptional regulation of GI regions
RECORDING APPROACH OF HERITAGE SITES BASED ON MERGING POINT CLOUDS FROM HIGH RESOLUTION PHOTOGRAMMETRY AND TERRESTRIAL LASER SCANNING
Different approaches and tools are required in Cultural Heritage Documentation to deal with the complexity of monuments and sites.
The documentation process has strongly changed in the last few years, always driven by technology. Accurate documentation is
closely relied to advances of technology (imaging sensors, high speed scanning, automation in recording and processing data) for
the purposes of conservation works, management, appraisal, assessment of the structural condition, archiving, publication and
research (Patias et al., 2008). We want to focus in this paper on the recording aspects of cultural heritage documentation, especially
the generation of geometric and photorealistic 3D models for accurate reconstruction and visualization purposes. The selected
approaches are based on the combination of photogrammetric dense matching and Terrestrial Laser Scanning (TLS) techniques.
Both techniques have pros and cons and recent advances have changed the way of the recording approach. The choice of the best
workflow relies on the site configuration, the performances of the sensors, and criteria as geometry, accuracy, resolution, georeferencing,
texture, and of course processing time. TLS techniques (time of flight or phase shift systems) are widely used for
recording large and complex objects and sites. Point cloud generation from images by dense stereo or multi-view matching can be
used as an alternative or as a complementary method to TLS. Compared to TLS, the photogrammetric solution is a low cost one, as
the acquisition system is limited to a high-performance digital camera and a few accessories only. Indeed, the stereo or multi-view
matching process offers a cheap, flexible and accurate solution to get 3D point clouds. Moreover, the captured images might also be
used for models texturing. Several software packages are available, whether web-based, open source or commercial. The main
advantage of this photogrammetric or computer vision based technology is to get at the same time a point cloud (the resolution
depends on the size of the pixel on the object), and therefore an accurate meshed object with its texture. After matching and
processing steps, we can use the resulting data in much the same way as a TLS point cloud, but in addition with radiometric
information for textures.
The discussion in this paper reviews recording and important processing steps as geo-referencing and data merging, the essential
assessment of the results, and examples of deliverables from projects of the Photogrammetry and Geomatics Group (INSA
Strasbourg, France)