Manipulation of Single DNA Molecules through Nano-fludic Devices: Simulation and Theory

Nanofludic platforms such as solid-state nanopores and nanochannels enable the manipulation of DNA molecules and have the potential to be a low-cost and high-efficiency DNA sequencing device. DNA nanopore translocation is a process where DNA moves from one chamber to another through a nanopore. To get into the pore, the molecule entropy decreases and free energy increases. In order to thread the DNA throughout the pore, an electric bias is applied to overcome the entropic energy barrier. The occupation of DNA impedes the ion transport and creates a blockage current of which the amplitude and duration provide the information on the DNA sequence since different bases (or base pairs) can be discriminated through different magnitude of blockage. Mining DNA sequence from the electric current profile requires an accurate knowledge of the passage time of a given base along the molecule. Our model assumes that the translocation process at high fields proceeds too fast for the chain to relax, and thus the distribution of translocation times of a given monomer are controlled by the initial conformation of the chain (the distribution of its loops). The model predicts the translocation time distribution is determined by the distribution of initial conformation as well as by the thermal fluctuations to the conformation during the translocation process. Narrow nanochannels require high threshold electric fields to achieve DNA translocation, leading to short dwell times of DNA in these channels. Nano-funnels integrated with nano-channels reduce the free energy barrier and lower the threshold electric field required for DNA translocation. A focused electric field within the funnel increases the electric force on the DNA, compresses the molecule, and increases the osmotic pressure at the nano-channel entrance which facilitates the entry at lower electric fields. Besides controlling the speed of the molecule's movement, appropriately designed nano-funnels such as parabolic shaped ones can also function as tweezers that allow the trapping and stable control of the position of the DNA molecule. A combination of a series of nano-funnels devices enable a wider range of location and speed manipulation and can assist genome mapping and sequencing when equipped with base detector.Doctor of Philosoph

Enhanced nanochannel translocation and localization of genomic DNA molecules using three-dimensional nanofunnels

The ability to precisely control the transport of single DNA molecules through a nanoscale channel is critical to DNA sequencing and mapping technologies that are currently under development. Here we show how the electrokinetically driven introduction of DNA molecules into a nanochannel is facilitated by incorporating a three-dimensional nanofunnel at the nanochannel entrance. Individual DNA molecules are imaged as they attempt to overcome the entropic barrier to nanochannel entry through nanofunnels with various shapes. Theoretical modeling of this behavior reveals the pushing and pulling forces that result in up to a 30-fold reduction in the threshold electric field needed to initiate nanochannel entry. In some cases, DNA molecules are stably trapped and axially positioned within a nanofunnel at sub-threshold electric field strengths, suggesting the utility of nanofunnels as force spectroscopy tools. These applications illustrate the benefit of finely tuning nanoscale conduit geometries, which can be designed using the theoretical model developed here.Forcing a DNA molecule into a nanoscale channel requires overcoming the free energy barrier associated with confinement. Here, the authors show that DNA injected through a funnel-shaped entrance more efficiently enters the nanochannel, thanks to facilitating forces generated by the nanofunnel geometry

Study on particle plugging in propagating fractures based on CFD-DEM

In the drilling and completion process of fractured formations, wellbore stability is a key factor affecting the safety of drilling and completing engineering. Previous studies have demonstrated that propping moderately and plugging fractures with soluble particles can improve formation fracture pressure. When it comes to particle transport in 3D rough propagation fractures, the interactions between particle-fracture-fluid need to be considered. Meanwhile, size-exclusion, particle bridging/strain effects all influence particle transport behavior and ultimately particle plugging effectiveness. However, adequate literature review shows that fracture plugging, and fracture propagation have not been considered together. In this study, a coupled CFD-DEM method was put forward to simulate the particle plugging process of propagating fracture, and the effects of positive pressure difference, fracture roughness, particle concentration, and particle shape on the plugging mechanism were examined. It is concluded through the study that: 1) Positive pressure difference too large will lead to excessive fracture aperture, making the particles unable to form effective plugging in the middle of the fracture; positive pressure difference too small will lead to fracture aperture too small, making particles unable to enter into and plug the fracture. 2) No matter how the concentration, particle size and friction coefficient change, they mainly affect the thickness of the plugging layer, while the front end of the particle is still dominated by single-particle bridging, and double-particles bridging and multiple-particles bridging are hardly ever seen. For the wellbore strengthening approaches, such as stress cages, fracture tip sealing, etc., specific analysis should be carried out according to the occurrence of extended fractures. For example, for fractures with low roughness, the particles rarely form effective tight plugging in the middle of the fracture, so it is more suitable for fracture tip sealing; For the fracture with high roughness, if the positive pressure difference is controlled properly to ensure reasonable fracture extension, the particle plugging effect will be good, and the stress cage method is recommended for borehole strengthening

Association of psychological distress, smoking and genetic risk with the incidence of lung cancer: a large prospective population-based cohort study

BackgroundEmerging evidence suggests a potential link between psychological distress (anxiety and depression) and lung cancer risk, however, it is unclear whether other factors such as tobacco smoking and genetic susceptibility modify the association.MethodsWe included 405,892 UK Biobank participants free of cancer at baseline. Psychological distress was measured using the Patient Health Questionnaire-4 (PHQ-4). A polygenic risk score (PRS) was calculated using 18 lung cancer-associated genetic loci. Multivariable Cox regression models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs).ResultsDuring a median follow-up of 7.13 years, 1754 lung cancer cases were documented. The higher score of psychological distress was associated with an increased risk of lung cancer (HRper 1-SD= 1.07, 95% CI: 1.02-1.11) after adjustment for smoking and other confounders. Mediation analysis revealed that 16.8% (95% CI: 13.0%-20.6%) of the distress-lung cancer association was mediated by smoking. Compared with never smokers with no distress, participants with heavy smoking and high distress had the highest risk of lung cancer (HR=18.57, 95% CI: 14.51-23.76). Both multiplicative and additive interactions were observed between smoking and psychological distress in lung cancer. Furthermore, the greatest relative increase in risk was observed among those with high genetic risk and high distress (HR=1.87, 95%CI: 1.50-2.33), and there was a significant additive interaction between the PRS and psychological distress.ConclusionOur results indicate that psychological distress was associated with an elevated risk of incident lung cancer, and such relation was modified by tobacco smoking and genetic susceptibility

The origin and maintenance of diversity in British Euphrasia (Orobanchaceae)

Plant species exhibit extensive diversity due to various evolutionary processes such as speciation, polyploidisation, hybridisation, and shifts in mating system, which can rapidly generate novelty. The maintenance of this diversity subsequently depends on both biotic and abiotic factors that may lead to population expansion or extinction. The taxonomically complex genus Euphrasia in Britain and Ireland, with its great diversity in ploidy, mating systems, and ecology, serves as an ideal system to address fundamental questions about the origins and maintenance of plant diversity. The overarching aim of this thesis is to elucidate the evolutionary mechanisms driving diversity in this rapid radiation at both inter- and intra-species levels. First, we use genotyping-by-sequencing and spatially-aware clustering methods to investigate genetic structure across 378 populations spanning 18 British Euphrasia species, including diploids and tetraploids with varying mating systems (Chapter 2). The rest of the thesis performs more focused comparisons of the distinct selfing species E. micrantha and the mixed-mating species E. arctica. This includes a phylogeographic analysis using chloroplast and nuclear ribosomal DNA (Chapter 3), and an assessment of the impact of mating systems on genetic structure using nuclear SNP data (Chapter 4). Finally, a common garden experiment investigates ecological adaptation by measuring plant performance in different soil pH and host conditions (Chapter 5). The population genetic study reveals permeable species boundaries, with genetic clustering largely by geography rather than species identity. Notably, only northern Scottish populations of E. micrantha show clear genome-wide divergence from other species. Incongruence between plastid and nuclear ribosomal genomes within E. micrantha reveals different evolutionary histories. While cpDNA indicates postglacial expansion with distinct East and West dispersal in Scotland, nrDNA suggests ongoing hybridisation with other species, signifying local hybridisation. Nuclear SNP data show high inbreeding coefficients and many runs of homozygosity in both E. micrantha and E. arctica, showing of the profound genomic consequences of self-fertilisation in Euphrasia. However, occasional outcrossing may rescue the long-term loss of diversity and result in evolutionary novelty. From an ecological perspective, the common garden study found that soil pH significantly influenced the performance of Euphrasia species. Notably, E. micrantha displayed a narrower pH tolerance compared to E. arctica, highlighting the importance of edaphic specialisation, which may play a role in Euphrasia speciation. These findings offer insights into the complex evolutionary pressures shaping Euphrasia’s diversity and highlight the need to study how the interactions between selfing, hybridisation, polyploidy and edaphic specialisation impact speciation in other plant lineages