Assessing the emission impacts of autonomous vehicles on metropolitan freeways

While recent studies demonstrate the societal and economic benefits of driverless vehicles, little is known about the emission impacts of autonomous vehicles (AVs) in the context of mixed traffic. This paper explores the environmental impacts of AVs along an urban freeway corridor in a metropolitan area using Vehicle Specific Power (VSP) and EMEP/EEA emission methodologies paired with VISSIM traffic model. Three different AV penetration rates were implemented for through traffic along a freeway corridor in the city of Porto (Portugal) by considering long-term market predictions (10%, 20% and 30%). Afterwards, these scenarios were compared to current situation in terms of carbon dioxide, carbon monoxide, nitrogen oxides and hydrocarbon emissions, and travel time and stop-and-go situations. The emissions and traffic performance of each scenario were evaluated on three levels: a) overall study domain; b) corridor; c) impact of AVs on conventional vehicles (CVs). AVs yielded small savings in emissions in the overall study domain for automation levels below 30% (differences in traffic performance and emissions were not statistically significant). Corridor-level analysis showed decreases of 5% in emissions can be expected with AVs technology, but it penalizes travel time up to 13% for both AV and CV, when compared to the existing situation.publishe

Sequence and structural analysis of BTB domain proteins

BACKGROUND: The BTB domain (also known as the POZ domain) is a versatile protein-protein interaction motif that participates in a wide range of cellular functions, including transcriptional regulation, cytoskeleton dynamics, ion channel assembly and gating, and targeting proteins for ubiquitination. Several BTB domain structures have been experimentally determined, revealing a highly conserved core structure. RESULTS: We surveyed the protein architecture, genomic distribution and sequence conservation of BTB domain proteins in 17 fully sequenced eukaryotes. The BTB domain is typically found as a single copy in proteins that contain only one or two other types of domain, and this defines the BTB-zinc finger (BTB-ZF), BTB-BACK-kelch (BBK), voltage-gated potassium channel T1 (T1-Kv), MATH-BTB, BTB-NPH3 and BTB-BACK-PHR (BBP) families of proteins, among others. In contrast, the Skp1 and ElonginC proteins consist almost exclusively of the core BTB fold. There are numerous lineage-specific expansions of BTB proteins, as seen by the relatively large number of BTB-ZF and BBK proteins in vertebrates, MATH-BTB proteins in Caenorhabditis elegans, and BTB-NPH3 proteins in Arabidopsis thaliana. Using the structural homology between Skp1 and the PLZF BTB homodimer, we present a model of a BTB-Cul3 SCF-like E3 ubiquitin ligase complex that shows that the BTB dimer or the T1 tetramer is compatible in this complex. CONCLUSION: Despite widely divergent sequences, the BTB fold is structurally well conserved. The fold has adapted to several different modes of self-association and interactions with non-BTB proteins

Scenario-based approach to analysis of travel time reliability with traffic simulation models

This study established a conceptual framework for capturing the probabilistic nature of travel times with the use of existing traffic simulation models. The framework features three components: scenario manager, traffic simulation models, and trajectory processor. The scenario manager captures exogenous sources of variation in travel times through external scenarios consistent with real-world roadway disruptions. The traffic simulation models then produce individual vehicle trajectories for input scenarios while further introducing randomness that stems from endogenous sources of variation. Finally, the trajectory processor constructs distributions of travel time either for each scenario or for multiple scenarios to allow users to investigate scenario-specific impact on variability in travel times and overall system reliability. Within this framework, the paper discusses methodologies for performing scenario-based reliability analysis that focuses on (a) approaches to obtaining distributions of travel times from scenario-specific outputs and (b) issues and practices associated with designing and generating input scenarios. The proposed scenario-based approach was applied to a real-world network to show detailed procedures, analysis results, and their implications

Cytological and Bioinformatical Analysis of SPE-26, a C. elegans Kelch-like Protein that Functions during the Karyosome Stage of Spermatogenesis

Prior to the meiotic divisions, spermatocytes undergo extended developmental processing termed meiotic prophase. As these spermatocytes transition out of meiotic prophase, they must cease transcription and prepare the chromosomes for the meiotic division. Our knowledge of the mechanisms that drive this transition remains incomplete. In this study, we analyze through cytological and bioinformatics methods a poorly understood Kelch-like protein required for Caenorhabditis elegans spermatogenesis, SPE-26. Analysis of spe-26 mutants reveals precocious meiotic spindle maturation relative to chromatin morphology beginning during the poorly-understood spermatogenesis-specific karyosome stage of late meiotic prophase. spe-26 spermatocytes also display chromosome alignment and segregation defects during the meiotic divisions. Quantitative and qualitative analysis reveal that karyosome entry occurs normally, while similar analysis reveals that spe-26 spermatocytes accumulate within the karyosome stage, suggesting SPE-26 is required for progression through and/or out of the karyosome stage. Using a newly generated antibody, immunofluorescence assays show that SPE-26 concentrates in the nucleus of karyosome stage spermatocytes, is shed to the residual body during the budding division, and is thus absent from spermatids. Next, we use various bioinformatics tools to make predictions of SPE-26 structure and function. We present the predicted secondary and tertiary structures of SPE-26, and compare sequence and structural features to its closest homologs, in addition to other well-studied Kelch-like proteins. Lastly, we predict various functional sites along the structure of SPE-26, including potential phosphorylation sites and a potential nuclear localization signal (NLS)

Structural analysis of the PATZ1 BTB domain homodimer

PATZ1 is a ubiquitously expressed transcriptional repressor belonging to the ZBTB family that is functionally expressed in T lymphocytes. PATZ1 targets the CD8 gene in lymphocyte development and interacts with the p53 protein to control genes that are important in proliferation and in the DNA-damage response. PATZ1 exerts its activity through an N-terminal BTB domain that mediates dimerization and co-repressor interactions and a C-terminal zinc-finger motif-containing domain that mediates DNA binding. Here, the crystal structures of the murine and zebrafish PATZ1 BTB domains are reported at 2.3 and 1.8 Å resolution, respectively. The structures revealed that the PATZ1 BTB domain forms a stable homodimer with a lateral surface groove, as in other ZBTB structures. Analysis of the lateral groove revealed a large acidic patch in this region, which contrasts with the previously resolved basic co-repressor binding interface of BCL6. A large 30-amino-acid glycine- and alanine-rich central loop, which is unique to mammalian PATZ1 amongst all ZBTB proteins, could not be resolved, probably owing to its flexibility. Molecular-dynamics simulations suggest a contribution of this loop to modulation of the mammalian BTB dimerization interface

Ubiquitination accomplished: E1 and E2 enzymes were not necessary

Qiu et al. (2016) show that a mono-ADP-ribosyltransferase, SdeA, from Legionella pneumophila catalyzes ADP-ribosylation of ubiquitin, allowing SdeA to modify substrate with ubiquitin in the absence of E1 and E2 enzymes

Elucidating Sequence and Structural Determinants of Carbohydrate Esterases for Complete Deacetylation of Substituted Xylans

| openaire: EC/H2020/648925/EU//BHIVEAcetylated glucuronoxylan is one of the most common types of hemicellulose in nature. The structure is formed by a β-(1→4)-linked D-xylopyranosyl (Xylp) backbone that can be substituted with an acetyl group at O-2 and O-3 positions, and α-(1→2)-linked 4-O-methylglucopyranosyluronic acid (MeGlcpA). Acetyl xylan esterases (AcXE) that target mono-or doubly acetylated Xylp are well characterized; however, the previously studied AcXE from Flavobacterium johnsoniae (FjoAcXE) was the first to remove the acetyl group from 2-O-MeGlcpA-3-O-acetyl-substituted Xylp units, yet structural characteristics of these enzymes remain unspecified. Here, six homologs of FjoAcXE were produced and three crystal structures of the enzymes were solved. Two of them are complex structures, one with bound MeGlcpA and another with acetate. All homologs were confirmed to release acetate from 2-O-MeGlcpA-3-O-acetyl-substituted xylan, and the crystal structures point to key structural elements that might serve as defining features of this unclassified carbohydrate esterase family. Enzymes comprised two domains: N-terminal CBM domain and a C-terminal SGNH domain. In FjoAcXE and all studied homologs, the sequence motif around the catalytic serine is Gly-Asn-Ser-Ile (GNSI), which differs from other SGNH hydrolases. Binding by the MeGlcpA-Xylp ligand is directed by positively charged and highly conserved residues at the interface of the CBM and SGNH domains of the enzyme.Peer reviewe

Structural basis for the substrate recognition of aminoglycoside 7′′-phosphotransferase-Ia from Streptomyces hygroscopicus

Hygromycin B (HygB) is one of the aminoglycoside antibiotics, and it is widely used as a reagent in molecular-biology experiments. Two kinases are known to inactivate HygB through phosphorylation: aminoglycoside 7′′-phosphotransferase-Ia [APH(7′′)-Ia] from Streptomyces hygroscopicus and aminoglycoside 4-phosphotransferase-Ia [APH(4)-Ia] from Escherichia coli. They phosphorylate the hydroxyl groups at positions 7′′ and 4 of the HygB molecule, respectively. Previously, the crystal structure of APH(4)-Ia was reported as a ternary complex with HygB and 5′-adenylyl-β,γ-imidodiphosphate (AMP-PNP). To investigate the differences in the substrate-recognition mechanism between APH(7′′)-Ia and APH(4)-Ia, the crystal structure of APH(7′′)-Ia complexed with HygB is reported. The overall structure of APH(7′′)-Ia is similar to those of other aminoglycoside phosphotransferases, including APH(4)-Ia, and consists of an N-terminal lobe (N-lobe) and a C-terminal lobe (C-lobe). The latter also comprises a core and a helical domain. Accordingly, the APH(7′′)-Ia and APH(4)-Ia structures fit globally when the structures are superposed at three catalytically important conserved residues, His, Asp and Asn, in the Brenner motif, which is conserved in aminoglycoside phosphotransferases as well as in eukaryotic protein kinases. On the other hand, the phosphorylated hydroxyl groups of HygB in both structures come close to the Asp residue, and the HygB molecules in each structure lie in opposite directions. These molecules were held by the helical domain in the C-lobe, which exhibited structural differences between the two kinases. Furthermore, based on the crystal structures of APH(7′′)-Ia and APH(4)-Ia, some mutated residues in their thermostable mutants reported previously were located at the same positions in the two enzymes

Elucidating Sequence and Structural Determinants of Carbohydrate Esterases for Complete Deacetylation of Substituted Xylans

Acetylated glucuronoxylan is one of the most common types of hemicellulose in nature. The structure is formed by a β-(1→4)-linked D-xylopyranosyl (Xylp) backbone that can be substituted with an acetyl group at O-2 and O-3 positions, and α-(1→2)-linked 4-O-methylglucopyranosyluronic acid (MeGlcpA). Acetyl xylan esterases (AcXE) that target mono- or doubly acetylated Xylp are well characterized; however, the previously studied AcXE from Flavobacterium johnsoniae (FjoAcXE) was the first to remove the acetyl group from 2-O-MeGlcpA-3-O-acetyl-substituted Xylp units, yet structural characteristics of these enzymes remain unspecified. Here, six homologs of FjoAcXE were produced and three crystal structures of the enzymes were solved. Two of them are complex structures, one with bound MeGlcpA and another with acetate. All homologs were confirmed to release acetate from 2-O-MeGlcpA-3-O-acetyl-substituted xylan, and the crystal structures point to key structural elements that might serve as defining features of this unclassified carbohydrate esterase family. Enzymes comprised two domains: N-terminal CBM domain and a C-terminal SGNH domain. In FjoAcXE and all studied homologs, the sequence motif around the catalytic serine is Gly-Asn-Ser-Ile (GNSI), which differs from other SGNH hydrolases. Binding by the MeGlcpA-Xylp ligand is directed by positively charged and highly conserved residues at the interface of the CBM and SGNH domains of the enzyme