Genomic complexity of the variable region-containing chitin-binding proteins in amphioxus

<p>Abstract</p> <p>Background</p> <p>The variable region-containing chitin-binding proteins (VCBPs) are found in protochordates and consist of two tandem immunoglobulin variable (V)-type domains and a chitin-binding domain. We previously have shown that these polymorphic genes, which primarily are expressed in the gut, exhibit characteristics of immune genes. In this report, we describe VCBP genomic organization and characterize adjacent and intervening genetic features which may influence both their polymorphism and complex transcriptional repertoire.</p> <p>Results</p> <p>VCBP genes 1, 2, 4, and 5 are encoded in a single contiguous gene-rich chromosomal region and VCBP3 is encoded in a separate locus. The VCBPs exhibit extensive haplotype variation, including copy number variation (CNV), indel polymorphism and a markedly elevated variation in repeat type and density. In at least one haplotype, inverted repeats occur more frequently than elsewhere in the genome. Multi-animal cDNA screening, as well as transcriptional profilingusing a novel transfection system, suggests that haplotype-specific transcriptional variants may contribute to VCBP genetic diversity.</p> <p>Conclusion</p> <p>The availability of the <it>Branchiostoma floridae </it>genome (Joint Genome Institute, Brafl1), along with BAC and PAC screening and sequencing described here, reveal that the relatively limited number of VCBP genes present in the amphioxus genome exhibit exceptionally high haplotype variation. These VCBP haplotypes contribute a diverse pool of allelic variants, which includes gene copy number variation, pseudogenes, and other polymorphisms, while contributing secondary effects on gene transcription as well.</p

A multi-dimensional view of transport-related social exclusion: A comparative study of Greater Perth and Sydney

Transport-related social exclusion is a complex issue. It can be studied from a variety of angles, be influenced by a number of factors, and affect diverse population groups. This study investigates transport-related social exclusion from a multi-dimensional view. Transport inequity was measured based on different development stages of a region using the Lorenz Curve and Gini index, and compared socio-economic characteristics, such as housing affordability, employment self-sufficiency, urban sprawl, and transport-mode share at different degrees of spatial aggregation. Two hierarchical spatial aggregation levels are used: (1) Sydney – Perth; (2) Inner – Middle – Outer sectors. Spatial gaps of transport-related social exclusion are identified for both cities and a number of policy implications are considered to provide suggestions to improve transport-related social inclusion in both cities

Charge Transfer-Mediated Dramatic Enhancement of Raman Scattering upon Molecular Point Contact Formation

Charge-transfer enhancement of Raman scattering plays a crucial role in current-carrying molecular junctions. However, the microscopic mechanism of light scattering in such nonequilibrium systems is still imperfectly understood. Here, using low-temperature tip-enhanced Raman spectroscopy (TERS), we investigate how Raman scattering evolves as a function of the gap distance in the single C60-molecule junction consisting of an Ag tip and various metal surfaces. Precise gap-distance control allows the examination of two distinct transport regimes, namely tunneling regime and molecular point contact (MPC). Simultaneous measurement of TERS and the electric current in scanning tunneling microscopy shows that the MPC formation results in dramatic Raman enhancement that enables one to observe the vibrations undetectable in the tunneling regime. This enhancement is found to commonly occur not only for coinage but also transition metal substrates. We suggest that the characteristic enhancement upon the MPC formation is rationalized by charge-transfer excitation

A Composite Resilience Index for Road Transport Networks

This paper is concerned with the development of a composite index for the resilience of road transport networks under disruptive events. The index employs three resilience characteristics, namely redundancy, vulnerability and mobility. Two different approaches, i.e. equal weighting and principal component analysis, are adopted to conduct the aggregation. In addition, the impact of the availability of real-time travel information for travellers on the three resilience characteristics and the composite resilience index is described. The application of the index on a synthetic road transport network of Delft city (Netherlands) shows that it responds well to traffic load changes and supply variations. The composite resilience index could be of use in various ways including supporting decision makers in understanding the dynamic nature of resilience under different disruptive events, highlighting weaknesses in the network and in assisting future planning to mitigate the impacts of disruptive events

Meta-analysis derived atopic dermatitis (MADAD) transcriptome defines a robust AD signature highlighting the involvement of atherosclerosis and lipid metabolism pathways

BACKGROUND: Atopic dermatitis (AD) is a common inflammatory skin disease with limited treatment options. Several microarray experiments have been conducted on lesional/LS and non-lesional/NL AD skin to develop a genomic disease phenotype. Although these experiments have shed light on disease pathology, inter-study comparisons reveal large differences in resulting sets of differentially expressed genes (DEGs), limiting the utility of direct comparisons across studies. METHODS: We carried out a meta-analysis combining 4 published AD datasets to define a robust disease profile, termed meta-analysis derived AD (MADAD) transcriptome. RESULTS: This transcriptome enriches key AD pathways more than the individual studies, and associates AD with novel pathways, such as atherosclerosis signaling (IL-37, selectin E/SELE). We identified wide lipid abnormalities and, for the first time in vivo, correlated Th2 immune activation with downregulation of key epidermal lipids (FA2H, FAR2, ELOVL3), emphasizing the role of cytokines on the barrier disruption in AD. Key AD “classifier genes” discriminate lesional from nonlesional skin, and may evaluate therapeutic responses. CONCLUSIONS: Our meta-analysis provides novel and powerful insights into AD disease pathology, and reinforces the concept of AD as a systemic disease. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12920-015-0133-x) contains supplementary material, which is available to authorized users

Tax treatment of employer commuting support: an international review

Correctly pricing transport behaviour to take account of the ‘external’ costs such as congestion and emissions imposed on society by excessive car use has long been a tenet of effective transportation demand management. But while policy‐makers have striven to increase public transport subsidies, raise petrol taxes and introduce road‐user charging schemes to price the real costs of car travel properly, in most cases correcting the wider influences of the personal tax regime has begun only relatively recently. This paper is based on work undertaken for the Department of the Environment, Transport and the Regions, and the Inland Revenue of the UK government, which is currently working on addressing this very issue. In addition to reporting the British situation, the paper also uses a series of case studies to outline how this same process has been approached in the USA, Ireland, Germany, the Netherlands, Switzerland and Norway, and how successful they have been thus far with respect to transportation demand management objectives. It then draws conclusions about which direction policy‐makers should be aiming for in the future

Assessment of energy efficiency and sustainability scenarios in the transport system

Background Energy Policy is one of the main drivers of Transport Policy. A number of strategies to reduce current energy consumption trends in the transport sector have been designed over the last decades. They include fuel taxes, more efficient technologies and changing travel behavior through demand regulation. But energy market has a high degree of uncertainty and the effectiveness of those policy options should be assessed. Methods A scenario based assessment methodology has been developed in the frame of the EU project STEPS. It provides an integrated view of Energy efficiency, environment, social and competitiveness impacts of the different strategies. It has been applied at European level and to five specific Regions. Concluding remarks The results are quite site specific dependent. However they show that regulation measures appear to be more effective than new technology investments. Higher energy prices could produce on their turn a deterioration of competitiveness and a threat for social goals