Designing a road traffic model for the cross-sectoral analysis of future national infrastructure

This paper presents a UK national road traffic model developed as part of the ITRC MISTRAL - a large interdisciplinary project of the Infrastructure Transitions Research Consortium (ITRC). The proposed model includes passenger and freight vehicle flows on major UK roads and predicts future demand in the form of an inter-zonal origin-destination matrix, using and elasticity-based simulation approach. An important part of the model is the network assignment step during which predicted flows are assigned to the road network. This allows for the assessment of road capacity utilisation and facilitates the identification of "pinch points" where future infrastructure investments might be targeted. Several policy interventions are studied in the paper, including road expansion with additional lanes, new road development and vehicle electrification. The model also explicitly considers cross-sectoral interdependencies with other infrastructure networks, primarily with the energy sector where the transport sector is the largest consumer, the digital communications sector, water supply and waste management. In future extensions, the model will also be able to estimate the environmental footprint and assess the risk and resilience of the transport network. This model has the potential to inform policy makers about the long-term performance of UK road infrastructure, considering a range of possible future scenarios for population growth, technological innovation and climate change

Geochemical assessment of the degree of isolation of edge-of-aquifer groundwater along a fringe of the southern High Plains Aquifer, USA

© 2019, The Author(s). The edge of regional aquifers can be complex hydrodynamic systems with unique flow dynamics, water quality, and continuity relationships with the main aquifer system. A site near the southwestern margin of the High Plains Aquifer (USA) was investigated to characterize the local hydrogeology and its relationship with the regional aquifer system. Measurements of tritium, ion concentrations, oxygen and hydrogen isotopes, and hydraulic heads documented (1) a discontinuous saturated zone, (2) no inflow to the study area from the regional aquifer, (3) focused recharge beneath playas with limited local mixing between pockets of saturation, (4) outflow orthogonal to the regional aquifer flow direction, (5) localized multi-year reversals in flow direction following high precipitation events, and (6) a magnified influence of the paleo-erosional surface of the basement rock (Dockum Group) on groundwater isolation and flow direction. In isolated areas, groundwater can be trapped on decadal time scales by depressions in the Dockum, or by recharge events that periodically reverse groundwater gradients

The implications of ambitious decarbonisation of heat and road transport for Britain’s net zero carbon energy systems

Decarbonisation of heating and road transport are regarded as necessary but very challenging steps on the pathway to net zero carbon emissions. Assessing the most efficient routes to decarbonise these sectors requires an integrated view of energy and road transport systems. Here we describe how a national gas and electricity transmission network model was extended to represent multiple local energy systems and coupled with a national energy demand and road transport model. The integrated models were applied to assess a range of technologies and policies for heating and transport where the UK’s 2050 net zero carbon emissions target is met. Overall, annual primary energy use is projected to reduce by between 25% and 50% by 2050 compared to 2015, due to ambitious efficiency improvements within homes and vehicles. However, both annual and peak electricity demands in 2050 are more than double compared with 2015. Managed electric vehicle charging could save 14TWh/year in gas-fired power generation at peak times, and associated emissions, whilst vehicle-to-grid services could provide 10GW of electricity supply during peak hours. Together, managed vehicle charging, and vehicle-to-grid supplies could result in a 16% reduction in total annual energy costs. The provision of fast public charging facilities could reduce peak electricity demand by 17GW and save an estimated £650 million annually. Although using hydrogen for heating and transport spreads the hydrogen network costs between homeowners and motorists, it is still estimated to be more costly overall compared to an all-electric scenario. Bio-energy electricity generation plants with carbon capture and storage are required to drive overall energy system emissions to net zero, utilisation of which is lowest when heating is electrified, and road transport consists of a mix of electric and hydrogen fuel-cell vehicles. The analysis demonstrates the need for an integrated systems approach to energy and transport policies and for coordination between national and local governments

Laser Microdissection of the Alveolar Duct Enables Single-Cell Genomic Analysis

Complex tissues such as the lung are composed of structural hierarchies such as alveoli, alveolar ducts, and lobules. Some structural units, such as the alveolar duct, appear to participate in tissue repair as well as the development of bronchioalveolar carcinoma. Here, we demonstrate an approach to conduct laser microdissection of the lung alveolar duct for single-cell PCR analysis. Our approach involved three steps. (1) The initial preparation used mechanical sectioning of the lung tissue with sufficient thickness to encompass the structure of interest. In the case of the alveolar duct, the precision-cut lung slices were 200 μm thick; the slices were processed using near-physiologic conditions to preserve the state of viable cells. (2) The lung slices were examined by transmission light microscopy to target the alveolar duct. The air-filled lung was sufficiently accessible by light microscopy that counterstains or fluorescent labels were unnecessary to identify the alveolar duct. (3) The enzymatic and microfluidic isolation of single cells allowed for the harvest of as few as several thousand cells for PCR analysis. Microfluidics based arrays were used to measure the expression of selected marker genes in individual cells to characterize different cell populations. Preliminary work suggests the unique value of this approach to understand the intra- and intercellular interactions within the regenerating alveolar duct

Real-time single-molecule imaging reveals a direct interaction between UvrC and UvrB on DNA tightropes

Nucleotide excision DNA repair is mechanistically conserved across all kingdoms of life. In prokaryotes, this multi-enzyme process requires six proteins: UvrA?D, DNA polymerase I and DNA ligase. To examine how UvrC locates the UvrB? DNA pre-incision complex at a site of damage, we have labeled UvrB and UvrC with different colored quantum dots and quantitatively observed their interactions with DNA tightropes under a variety of solution conditions using oblique angle fluorescence imaging. Alone, UvrC predominantly interacts statically with DNA at low salt. Surprisingly, however, UvrC and UvrB together in solution bind to form the previously unseen UvrBC complex on duplex DNA. This UvrBC complex is highly motile and engages in unbiased one-dimensional diffusion. To test whether UvrB makes direct contact with the DNA in the UvrBC?DNA complex, we investigated three UvrB mutants: Y96A, a b-hairpin deletion and D338N. These mutants affected the motile properties of the UvrBC complex, indicating that UvrB is in intimate contact with the DNA when bound to UvrC. Given the in vivo excess of UvrB and the abundance of UvrBC in our experiments, this newly identified complex is likely to be the predominant form of UvrC in the cell. © 2013 The Author(s)

Digital PCR provides sensitive and absolute calibration for high throughput sequencing

<p>Abstract</p> <p>Background</p> <p>Next-generation DNA sequencing on the 454, Solexa, and SOLiD platforms requires absolute calibration of the number of molecules to be sequenced. This requirement has two unfavorable consequences. First, large amounts of sample-typically micrograms-are needed for library preparation, thereby limiting the scope of samples which can be sequenced. For many applications, including metagenomics and the sequencing of ancient, forensic, and clinical samples, the quantity of input DNA can be critically limiting. Second, each library requires a titration sequencing run, thereby increasing the cost and lowering the throughput of sequencing.</p> <p>Results</p> <p>We demonstrate the use of digital PCR to accurately quantify 454 and Solexa sequencing libraries, enabling the preparation of sequencing libraries from nanogram quantities of input material while eliminating costly and time-consuming titration runs of the sequencer. We successfully sequenced low-nanogram scale bacterial and mammalian DNA samples on the 454 FLX and Solexa DNA sequencing platforms. This study is the first to definitively demonstrate the successful sequencing of picogram quantities of input DNA on the 454 platform, reducing the sample requirement more than 1000-fold without pre-amplification and the associated bias and reduction in library depth.</p> <p>Conclusion</p> <p>The digital PCR assay allows absolute quantification of sequencing libraries, eliminates uncertainties associated with the construction and application of standard curves to PCR-based quantification, and with a coefficient of variation close to 10%, is sufficiently precise to enable direct sequencing without titration runs.</p

Real-time single-molecule observation of rolling-circle DNA replication

We present a simple technique for visualizing replication of individual DNA molecules in real time. By attaching a rolling-circle substrate to a TIRF microscope-mounted flow chamber, we are able to monitor the progression of single-DNA synthesis events and accurately measure rates and processivities of single T7 and Escherichia coli replisomes as they replicate DNA. This method allows for rapid and precise characterization of the kinetics of DNA synthesis and the effects of replication inhibitors