520 research outputs found
Tripartite ATP-Independent Periplasmic (TRAP) Transporters and Tripartite Tricarboxylate Transporters (TTT): From Uptake to Pathogenicity
The ability to efficiently scavenge nutrients in the host is essential for the viability of any pathogen. All catabolic pathways must begin with the transport of substrate from the environment through the cytoplasmic membrane, a role executed by membrane transporters. Although several classes of cytoplasmic membrane transporters are described, high-affinity uptake of substrates occurs through Solute Binding-Protein (SBP) dependent systems. Three families of SBP dependant transporters are known; the primary ATP-binding cassette (ABC) transporters, and the secondary Tripartite ATP-independent periplasmic (TRAP) transporters and Tripartite Tricarboxylate Transporters (TTT). Far less well understood than the ABC family, the TRAP transporters are found to be abundant among bacteria from marine environments, and the TTT transporters are the most abundant family of proteins in many species of ÎČ-proteobacteria. In this review, recent knowledge about these families is covered, with emphasis on their physiological and structural mechanisms, relating to several examples of relevant uptake systems in pathogenicity and colonization, using the SiaPQM sialic acid uptake system from Haemophilus influenzae and the TctCBA citrate uptake system of Salmonella typhimurium as the prototypes for the TRAP and TTT transporters, respectively. High-throughput analysis of SBPs has recently expanded considerably the range of putative substrates known for TRAP transporters, while the repertoire for the TTT family has yet to be fully explored but both types of systems most commonly transport carboxylates. Specialized spectroscopic techniques and site-directed mutagenesis have enriched our knowledge of the way TRAP binding proteins capture their substrate, while structural comparisons show conserved regions for substrate coordination in both families. Genomic and protein sequence analyses show TTT SBP genes are strikingly overrepresented in some bacteria, especially in the ÎČ-proteobacteria and some α-proteobacteria. The reasons for this are not clear but might be related to a role for these proteins in signaling rather than transport
Massive over-representation of solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family in the genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860.
Lineage-specific expansion (LSE) of protein families is a widespread phenomenon in many eukaryotic genomes, but is generally more limited in bacterial genomes. Here, we report the presence of 434 genes encoding solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family, within the 8.2âMb genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860, a gene family over-representation of unprecedented abundance in prokaryotes. Representing over 6â% of the total number of coding sequences, the SBP genes are distributed across the whole genome but are found rarely in low-GC islands, where the gene density for this family is much lower. This observation, and the much higher sequence identity between the 434 Rhodoplanes TTT SBPs compared with the average identity between homologues from different species, is indicative of a key role for LSE in the expansion. The TTT SBP genes were found in the vicinity of genes encoding membrane components of transport systems from different families, as well as regulatory proteins such as histidine-kinases and transcription factors, indicating a broad range of functions around the sensing, response and transport of organic compounds. A smaller expansion of TTT SBPs is known in some species of the ÎČ-proteobacteria Bordetella and we observed similar expansions in other ÎČ-proteobacterial lineages, including members of the genus Comamonas and the industrial biotechnology organism Cupriavidus necator, indicating that strong environmental selection can drive SBP duplication and specialisation from multiple evolutionary starting points
Identifying tree populations for conservation action through geospatial analyses
Rapid development of information and communication technologies has made it possible to easily collect georeferenced information on species and their environment, and to use it for analyzing biological diversity, its distribution and threats to it. Such analyses can importantly inform development of conservation strategies and priorities, especially across countries or species distribution ranges (Guarino et al. 2002). Data for spatial analyses on species or genetic diversity and its distribution are collected in specifically designed studies, obtained from existing records of species occurrence, or both. Observations may be complemented by species distribution modelling, where the potential occurrence of a species is predicted based on its documented geographic distribution and climate in those areas. Results on the distribution of diversity, documented or modelled, can then be compared, for example, with existing protected areas, rates of forest degradation, threats of environmental changes, or socio-economic indicators, to identify priority tree populations and tailor strategies for their conservation and sustainable use (Pautasso 2009). In this paper recent case studies on spatial biodiversity analyses across the tropics are presented, demonstrating how such analyses can help to identify most unique or most threatened populations of a tree species for conservation actions. Insights on initiating collaborative research on diversity and distributions of important Asian tree species are also discussed
eFLINT: a domain-specific language for executable norm specifications
Software systems that share potentially sensitive data are subjected to laws, regulations, policies and/or contracts. The monitoring, control and enforcement processes applied to these systems are currently to a large extent manual, which we rather automate by embedding the processes as dedicated and adaptable software services in order to improve efficiency and effectiveness. This approach requires such regulatory services to be closely aligned with a formal description of th
The Next Generation of Human-Drone Partnerships: Co-Designing an Emergency Response System
The use of semi-autonomous Unmanned Aerial Vehicles (UAV) to support
emergency response scenarios, such as fire surveillance and search and rescue,
offers the potential for huge societal benefits. However, designing an
effective solution in this complex domain represents a "wicked design" problem,
requiring a careful balance between trade-offs associated with drone autonomy
versus human control, mission functionality versus safety, and the diverse
needs of different stakeholders. This paper focuses on designing for
situational awareness (SA) using a scenario-driven, participatory design
process. We developed SA cards describing six common design-problems, known as
SA demons, and three new demons of importance to our domain. We then used these
SA cards to equip domain experts with SA knowledge so that they could more
fully engage in the design process. We designed a potentially reusable solution
for achieving SA in multi-stakeholder, multi-UAV, emergency response
applications.Comment: 10 Pages, 5 Figures, 2 Tables. This article is publishing in CHI202
Baseline and innate immune response characterization of a Zfp30 knockout mouse strain
Airway neutrophilia is correlated with disease severity in a number of chronic and acute pulmonary diseases, and dysregulation of neutrophil chemotaxis can lead to host tissue damage. The gene Zfp30 was previously identified as a candidate regulator of neutrophil recruitment to the lungs and secretion of CXCL1, a potent neutrophil chemokine, in a genome-wide mapping study using the Collaborative Cross. ZFP30 is a putative transcriptional repressor with a KRAB domain capable of inducing heterochromatin formation. Using a CRISPR-mediated knockout mouse model, we investigated the role that Zfp30 plays in recruitment of neutrophils to the lung using models of allergic airway disease and acute lung injury. We found that the Zfp30 null allele did not affect CXCL1 secretion or neutrophil recruitment to the lungs in response to various innate immune stimuli. Intriguingly, despite the lack of neutrophil phenotype, we found there was a significant reduction in the proportion of live Zfp30 homozygous female mutant mice produced from heterozygous matings. This deviation from the expected Mendelian ratios implicates Zfp30 in fertility or embryonic development. Overall, our results indicate that Zfp30 is an essential gene but does not influence neutrophilic inflammation in this particular knockout model
Evidence of Color Coherence Effects in W+jets Events from ppbar Collisions at sqrt(s) = 1.8 TeV
We report the results of a study of color coherence effects in ppbar
collisions based on data collected by the D0 detector during the 1994-1995 run
of the Fermilab Tevatron Collider, at a center of mass energy sqrt(s) = 1.8
TeV. Initial-to-final state color interference effects are studied by examining
particle distribution patterns in events with a W boson and at least one jet.
The data are compared to Monte Carlo simulations with different color coherence
implementations and to an analytic modified-leading-logarithm perturbative
calculation based on the local parton-hadron duality hypothesis.Comment: 13 pages, 6 figures. Submitted to Physics Letters
Measurement of the B0-anti-B0-Oscillation Frequency with Inclusive Dilepton Events
The - oscillation frequency has been measured with a sample of
23 million \B\bar B pairs collected with the BABAR detector at the PEP-II
asymmetric B Factory at SLAC. In this sample, we select events in which both B
mesons decay semileptonically and use the charge of the leptons to identify the
flavor of each B meson. A simultaneous fit to the decay time difference
distributions for opposite- and same-sign dilepton events gives ps.Comment: 7 pages, 1 figure, submitted to Physical Review Letter
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