Development of a 3D tissue engineered skeletal muscle and bone pre-clinical co-culture platform

Pre-clinical studies are a necessary step in the process of material and drug testing. For this, high-throughput monolayer cell cultures are conducted followed by in vivo animal experiments. However, animal use is ethically questionable and in many cases yields misleading results. In vitro three dimensional (3D) tissue engineered (TE) structures have been shown to better represent in vivo tissue morphology and biochemical pathways than monolayer cultures and are less ethically questionable than animal models. Therefore, an in vitro biomimetic musculoskeletal junction (MSKjct) is required as a more relevant pre-clinical testbed. This thesis describes the steps taken to co-culture 3D TE skeletal muscle and bone models as a material testbed and towards an in vitro MSKjct. [Continues.

The Jahn-Teller active fluoroperovskites ACrF3A\mathrm{CrF_3} A=Na+,K+A=\mathrm{Na^+},\mathrm{K^+}: thermo- and magneto optical correlations as function of the AA-site

Chromium (II) fluoroperovskites $A\mathrm{CrF_3}(A\mathrm{=Na^+,K^+})$ are strongly correlated Jahn-Teller active materials at low temperatures. In this paper, we examine the role that the $A$-site ion plays in this family of fluoroperovskites using both experimental methods (XRD, optical absorption spectroscopy and magnetic fields) and DFT simulations. Temperature-dependent optical absorption experiments show that the spin-allowed transitions $E_2$ and $E_3$ only merge completely for $A$= Na at 2 K. Field-dependent optical absorption measurements at 2 K show that the oscillating strength of the spin-allowed transitions in $\mathrm{NaCrF_3}$ increases with increasing applied field. Direct magneto-structural correlations which suppress the spin-flip transitions are observed for ${\rm KCrF_3}$ below its Ne\'el temperature. In ${\rm NaCrF_3}$ the spin-flip transitions vanish abruptly below 9 K revealing magneto-optical correlations not linked to crystal structure changes. This suggests that as the long range ordering is reduced local JT effects in the individual ${\rm CrF_6^{4-}}$ octahedra take control of the observed behavior. Our results show clear deviation from the pattern found for the isoelectronic $A_x{\rm MnF}_{3+x}$ system. The size of the $A$-site cation is shown to be central in dictating the physical properties and phase transitions in $A{\rm CrF}_3$, opening up the possibility of varying the composition to create novel states of matter with tuneable properties

Agent based modelling : initial assessment for use on soil bioaccessibility

This report describes the testing of Agent Based Modelling implementations in three different software packages: Repast-simphony, NetLogo and Insight-maker. These software have been evaluated against their capability to simulate the exposure of people as agents moving across Arsenic contaminated soils. Two of the three tested software (Repast-simphony and NetLogo) are recommended for assessment on more complex problems. An outline work plan is presented for future work

Heavy metal bioavailability and bioaccessibility in soil

This chapter considers the use of a variety of approaches to assess either the bioavailability or the bioaccessibility of metals in soil. The bioavailability of metals from soils is considered with respect to a series of single-extraction methods, including the use of ethylenediaminetetraacetic acid (EDTA), acetic acid, diethylenetriaminepentaacetic acid (DTPA), ammonium nitrate, calcium chloride and sodium nitrate. Then, a procedure for the recovery of metals using a three-stage sequential extraction protocol is described. Two alternate approaches for assessing the environmental health risk to humans by undertaking in vitro gastrointestinal extraction (also known as the physiologically based extraction test, PBET) are considered. Finally, two acid digestion protocols that allow the pseudo-total metal content of samples to be assessed are provided. In all cases details of how the different approaches can be performed are provided, including the specific reagents required (and their preparation), details of the different extraction and acid digestion protocols to be followed and suitable analytical details to allow the measurement of metals by inductively coupled plasma mass spectrometry (ICP-MS) with/without a collision/reaction cell. A detailed Notes section provides experimental details to guide the reader through some of the practical aspects of the procedures. Finally, some experimental results are provided as evidence of the suitability of the approaches described including single-extraction data, using EDTA and acetic acid, for metals in CRM BCR 700. In addition, in vitro gastrointestinal extraction data are provided for metals in CRM SRM 1570A (spinach leaves). The influence of time on the intestinal fluid phase on the recovery of metals in CRM SRM 1570A (spinach leaves) and CRM INCT-TL-1 (tea leaves) is investigated, as well as the repeatability in terms of recovery of metals from soil over a 3-week period by in vitro gastrointestinal extraction

Energy-balance models of the solar corona

Solar coronal observations have shown that the corona has a highly complex structure which presumably owes its existence to the magnetic field. Models in thermal and hydrostatic equilibrium are here calculated in order to try and explain many of these observations. Coronal holes occur where open field lines reach out into space. The model of McWhirter, et al. (1975) for the inner corona in such a configuration is generalised to allow different types and magnitudes of heating as well as different area divergences and flows. It is found that hot, fast upflows cannot always exist in thermal equilibrium. The choice of boundary conditions can appreciably alter the results, and so different choices are compared. Most of the corona, especially in active regions, appears to consist of coronal loops. Subtle relations for energy balance models of such loops are found to exist between the physical parameters of a loop's length, base density, and heat input. No solution exists at coronal temperatures in certain cases, which may explain the observations of very cool loops. The effect of a loop's geometry and field line divergence on the structure is found. Results predicted from scaling laws are compared, and the uniqueness of the solution for a loop with a fixed mass is studied. The error in the predicted emission measure through assuming uniform pressure is shown to be considerable. The life-time of a loop can often be many days, suggesting the existence of a thermally stable state. A global stability analysis is performed, and it is found that a loop's stability may depend critically upon its length. Thermally isolated loops, which are the most unstable type, can be thermally stable, provided their pressure falls off sufficiently rapidly with height (due to hydrostatic equilibrium)

Determination of the nature of the Cu coordination complexes formed in the presence of NO and NH3 within SSZ-13

Ammonia-selective catalytic reduction (NH3-SCR) using Cu zeolites is a well-established strategy for the abatement of NOx gases. Recent studies have demonstrated that Cu is particularly active when exchanged into the SSZ-13 zeolite, and its location in either the 6r or 8r renders it an excellent model system for fundamental studies. In this work, we examine the interaction of NH3-SCR relevant gases (NO and NH3) with the Cu2+ centers within the SSZ-13 structure, coupling powder diffraction (PD), X-ray absorption spectroscopy (XAFS), and density functional theory (DFT). This combined approach revealed that, upon calcination, cooling and gas exposure Cu ions tend to locate in the 8r window. After NO introduction, Cu-ions are seen to coordinate to two framework oxygens and one NO molecule, resulting in a bent Cu-nitrosyl complex with a Cu-N-O bond angle of similar to 150 degrees. Whilst Cu seems to be partially reduced/changed in coordination state, NO is partially oxidized. On exposure to NH3 while the PD data suggest the Cu2+ ion occupies a similar position, simulation and XAFS pointed toward the formation of a Jahn-Teller distorted hexaamine complex [Cu(NH3)(6)](2+) in the center of the cha cage. These results have important implications in terms of uptake and storage of these reactive gases and potentially for the mechanisms involved in the NH3-SCR process

AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap

Honey bee, Apis mellifera, drones are typically haploid, developing from an unfertilized egg, inheriting only their queen’s alleles and none from the many drones she mated with. Thus the ordered combination or ‘phase’ of alleles is known, making drones a valuable haplotype resource. We collated whole-genome sequence data for 1,407 drones, including 45 newly sequenced Scottish drones, collectively representing 19 countries, 8 subspecies and various hybrids. Following alignment to Amel_HAv3.1, variant calling and quality filtering, we retained 17.4 M high quality variants across 1,328 samples with a genotyping rate of 98.7%. We demonstrate the utility of this haplotype resource, AmelHap, for genotype imputation, returning >95% concordance when up to 61% of data is missing in haploids and up to 12% of data is missing in diploids. AmelHap will serve as a useful resource for the community for imputation from low-depth sequencing or SNP chip data, accurate phasing of diploids for association studies, and as a comprehensive reference panel for population genetic and evolutionary analyses.For the purpose of open access, the author has applied a Creative Commons Attribution (CC BY) licence to any Author Accepted Manuscript version arising from this submission. This work was supported by a grant from the CB Dennis British Beekeepers’ Research Trust awarded to MB and DW, and through strategic investment funding to the Roslin Institute from the Biotechnology and Biological Sciences Research Council (BBS/E/D/30002276). MP was supported by a Basque Government grant (IT1233-19)