Collaborative Dynamic 3D Scene Graphs for Automated Driving

Maps have played an indispensable role in enabling safe and automated driving. Although there have been many advances on different fronts ranging from SLAM to semantics, building an actionable hierarchical semantic representation of urban dynamic scenes from multiple agents is still a challenging problem. In this work, we present Collaborative URBan Scene Graphs (CURB-SG) that enable higher-order reasoning and efficient querying for many functions of automated driving. CURB-SG leverages panoptic LiDAR data from multiple agents to build large-scale maps using an effective graph-based collaborative SLAM approach that detects inter-agent loop closures. To semantically decompose the obtained 3D map, we build a lane graph from the paths of ego agents and their panoptic observations of other vehicles. Based on the connectivity of the lane graph, we segregate the environment into intersecting and non-intersecting road areas. Subsequently, we construct a multi-layered scene graph that includes lane information, the position of static landmarks and their assignment to certain map sections, other vehicles observed by the ego agents, and the pose graph from SLAM including 3D panoptic point clouds. We extensively evaluate CURB-SG in urban scenarios using a photorealistic simulator. We release our code at http://curb.cs.uni-freiburg.de.Comment: Refined manuscript and extended supplementar

Transcriptomic and proteomic analyses of the Aspergillus fumigatus hypoxia response using an oxygen-controlled fermenter

<p>Abstract</p> <p>Background</p> <p><it>Aspergillus fumigatus </it>is a mold responsible for the majority of cases of aspergillosis in humans. To survive in the human body, <it>A. fumigatus </it>must adapt to microenvironments that are often characterized by low nutrient and oxygen availability. Recent research suggests that the ability of <it>A. fumigatus </it>and other pathogenic fungi to adapt to hypoxia contributes to their virulence. However, molecular mechanisms of <it>A. fumigatus </it>hypoxia adaptation are poorly understood. Thus, to better understand how <it>A. fumigatus </it>adapts to hypoxic microenvironments found <it>in vivo </it>during human fungal pathogenesis, the dynamic changes of the fungal transcriptome and proteome in hypoxia were investigated over a period of 24 hours utilizing an oxygen-controlled fermenter system.</p> <p>Results</p> <p>Significant increases in transcripts associated with iron and sterol metabolism, the cell wall, the GABA shunt, and transcriptional regulators were observed in response to hypoxia. A concomitant reduction in transcripts was observed with ribosome and terpenoid backbone biosynthesis, TCA cycle, amino acid metabolism and RNA degradation. Analysis of changes in transcription factor mRNA abundance shows that hypoxia induces significant positive and negative changes that may be important for regulating the hypoxia response in this pathogenic mold. Growth in hypoxia resulted in changes in the protein levels of several glycolytic enzymes, but these changes were not always reflected by the corresponding transcriptional profiling data. However, a good correlation overall (R²= 0.2, p < 0.05) existed between the transcriptomic and proteomics datasets for all time points. The lack of correlation between some transcript levels and their subsequent protein levels suggests another regulatory layer of the hypoxia response in <it>A. fumigatus</it>.</p> <p>Conclusions</p> <p>Taken together, our data suggest a robust cellular response that is likely regulated both at the transcriptional and post-transcriptional level in response to hypoxia by the human pathogenic mold <it>A. fumigatus</it>. As with other pathogenic fungi, the induction of glycolysis and transcriptional down-regulation of the TCA cycle and oxidative phosphorylation appear to major components of the hypoxia response in this pathogenic mold. In addition, a significant induction of the transcripts involved in ergosterol biosynthesis is consistent with previous observations in the pathogenic yeasts <it>Candida albicans </it>and <it>Cryptococcus neoformans </it>indicating conservation of this response to hypoxia in pathogenic fungi. Because ergosterol biosynthesis enzymes also require iron as a co-factor, the increase in iron uptake transcripts is consistent with an increased need for iron under hypoxia. However, unlike <it>C. albicans </it>and <it>C. neoformans</it>, the GABA shunt appears to play an important role in reducing NADH levels in response to hypoxia in <it>A. fumigatus </it>and it will be intriguing to determine whether this is critical for fungal virulence. Overall, regulatory mechanisms of the <it>A. fumigatus </it>hypoxia response appear to involve both transcriptional and post-transcriptional control of transcript and protein levels and thus provide candidate genes for future analysis of their role in hypoxia adaptation and fungal virulence.</p

Proteomics of industrial fungi: trends and insights for biotechnology

Filamentous fungi are widely known for their industrial applications, namely, the production of food-processing enzymes and metabolites such as antibiotics and organic acids. In the past decade, the full genome sequencing of filamentous fungi increased the potential to predict encoded proteins enormously, namely, hydrolytic enzymes or proteins involved in the biosynthesis of metabolites of interest. The integration of genome sequence information with possible phenotypes requires, however, the knowledge of all the proteins in the cell in a system-wise manner, given by proteomics. This review summarises the progress of proteomics and its importance for the study of biotechnological processes in filamentous fungi. A major step forward in proteomics was to couple protein separation with high-resolution mass spectrometry, allowing accurate protein quantification. Despite the fact that most fungal proteomic studies have been focused on proteins from mycelial extracts, many proteins are related to processes which are compartmentalised in the fungal cell, e.g. β-lactam antibiotic production in the microbody. For the study of such processes, a targeted approach is required, e.g. by organelle proteomics. Typical workflows for sample preparation in fungal organelle proteomics are discussed, including homogenisation and sub-cellular fractionation. Finally, examples are presented of fungal organelle proteomic studies, which have enlarged the knowledge on areas of interest to biotechnology, such as protein secretion, energy production or antibiotic biosynthesis

The Ether-Cleaving Methyltransferase System of the Strict Anaerobe Acetobacterium dehalogenans: Analysis and Expression of the Encoding Genes▿

Anaerobic O-demethylases are inducible multicomponent enzymes which mediate the cleavage of the ether bond of phenyl methyl ethers and the transfer of the methyl group to tetrahydrofolate. The genes of all components (methyltransferases I and II, CP, and activating enzyme [AE]) of the vanillate- and veratrol-O-demethylases of Acetobacterium dehalogenans were sequenced and analyzed. In A. dehalogenans, the genes for methyltransferase I, CP, and methyltransferase II of both O-demethylases are clustered. The single-copy gene for AE is not included in the O-demethylase gene clusters. It was found that AE grouped with COG3894 proteins, the function of which was unknown so far. Genes encoding COG3894 proteins with 20 to 41% amino acid sequence identity with AE are present in numerous genomes of anaerobic microorganisms. Inspection of the domain structure and genetic context of these orthologs predicts that these are also reductive activases for corrinoid enzymes (RACEs), such as carbon monoxide dehydrogenase/acetyl coenzyme A synthases or anaerobic methyltransferases. The genes encoding the O-demethylase components were heterologously expressed with a C-terminal Strep-tag in Escherichia coli, and the recombinant proteins methyltransferase I, CP, and AE were characterized. Gel shift experiments showed that the AE comigrated with the CP. The formation of other protein complexes with the O-demethylase components was not observed under the conditions used. The results point to a strong interaction of the AE with the CP. This is the first report on the functional heterologous expression of acetogenic phenyl methyl ether-cleaving O-demethylases