Single-particle reconstruction can be used to perform three-dimensional (3D) imaging of homogeneous populations of nano-sized objects, in particular viruses and proteins. Here, it is demonstrated that it can also be used to obtain 3D reconstructions of heterogeneous populations of inorganic nanoparticles. An automated acquisition scheme in a scanning transmission electron microscope is used to collect images of thousands of nanoparticles. Particle images are subsequently semi-automatically clustered in terms of their properties and separate 3D reconstructions are performed from selected particle image clusters. The result is a 3D dataset that is representative of the full population. The study demonstrates a methodology that allows 3D imaging and analysis of inorganic nanoparticles in a fully automated manner that is truly representative of large particle populations.

This study is motivated by the need to develop stochastic parameterisations for representing the effects of mesoscale oceanic eddies in non-eddy-resolving and eddy-permitting ocean circulation models. A necessary logical step on the way to such parameterisations is the understanding of flow responses to spatially stationary and localised, time-dependent ‘plunger’ forcings intended to represent transient eddy flux divergences. Specifically, this study develops an understanding of the plunger-induced convergence of potential vorticity (PV) fluxes using the linearised single-layer shallow-water model. Time-periodic solutions are obtained and the ‘footprint’, defined as the time-mean, quasi-linear PV flux convergence, quantifies the cumulative PV redistribution induced by the plunger. Using the footprint, the equivalent eddy flux (EEF) is defined such that it succinctly quantifies the extent of the PV redistribution, and its dependencies on the forcing latitude and the background flow are examined in detail. For a uniform background flow the EEF is positive for all forcing latitudes, corresponding to net-poleward PV flux convergence, as expected by current theory of $\unicode[STIX]{x1D6FD}$-plane Rossby waves. The EEF also has a robust dependence on the direction and magnitude of a uniform background flow, which is a useful quality for the EEF to provide a basis for a parameterisation of eddy PV fluxes. We also examine the PV redistribution due to forcing on top of a Gaussian jet background flow and find that forcing proximity to the jet core is the primary factor in determining whether the jet is sharpened or broadened.

We have applied mechanical exfoliation for the preparation of ultra-thin samples of the phyllosilicate mineral biotite. We demonstrate that the 'scotch tape' approach, which was made famous as an early method for production of single-atom-thick graphene, can be used for production of sheet-silicate specimens that are sufficiently thin to allow high-resolution transmission electron microscope (HRTEM) imaging to be achieved successfully while also being free from the specimen preparation artefacts that are often caused by ion-beam milling techniques. Exfoliation of the biotite parallel to the (001) planes has produced layers as thin as two structural TOT units thick (∼2 nm). The minimal specimen thickness enabled not only HRTEM imaging but also the application of subsequent exit wavefunction restoration to reveal the pristine biotite lattice. Exit wavefunction restoration recovers the full complex electron wave from a focal series of HRTEM images, removing the effects of coherent lens aberrations. This combination of methods therefore produces images in which the observed features are readily interpreted to obtain atomic resolution structural information.

Synthesis of Ni and Zn substituted nano-greigite, Fe3S4, is achieved from single source diethyldithiocarbamato precursor compounds, producing particles typically 50–100 nm in diameter with plate-like pseudohexagonal morphologies. Up to 12 wt.% Ni is incorporated into the greigite structure, and there is evidence that Zn is also incorporated but Co is not substituted into the lattice. The Fe L3 X-ray absorption spectra for these materials have a narrow single peak at 707.7 eV and the resulting main X-ray magnetic circular dichroism (XMCD) has the same sign at 708.75 eV. All XMCD spectra also have a broad positive feature at 711 eV, a characteristic of covalent mixing. The greigite XMCD spectra contrast with the three clearly defined XMCD site specific peaks found in the ferrite spinel, magnetite. The Fe L2,3X-ray absorption spectra and XMCD spectra of the greigite reflect and reveal the high conductivity of greigite and the very strong covalency of the Fe–S bonding. The electron hopping between Fe3+ and Fe2+ on octahedral sites results in an intermediate oxidation state of the Fe in the Oh site of Fe2.5+ producing an effective formula of [Fe3+ ↑]A-site[2Fe2.5+ ↓]B-siteS42–]. The Ni L2,3 X-ray absorption spectra and XMCD reveal substitution on the Oh site with a strongly covalent character and an oxidation state <Ni1.5+ in a representative formula [Fe3+ ↑]A[[(2 – x)Fe2.5+ ↓][Nix1.5+]]BS42–.

Single wall carbon nanotubes (SWCNTs) and liquid-phase exfoliated multilayer graphene (MLG) material thin films were assembled at a polarizable organic/water interface. A simple, spontaneous route to functionalize/decorate the interfacial assembly of MLG and SWCNTs with noble metal nanoparticles, at the interface between two immiscible electrolyte solutions (ITIES), is reported. The formation of MLG- or SWCNT-based metal nanocomposites was confirmed using various microscopic (scanning electron, transmission electron, and atomic force microscopy) and several spectroscopic (energy dispersive x-ray and Raman spectroscopy) techniques. Increasing the interfacial deposition time of the metal nanoparticles on the assembled low-dimensional carbon material increased the amount of the metal particles/structures, resulting in greater coverage of the MLG or SWCNTs with metal nanoparticles. This low-cost and convenient solution chemistry based impregnation method can serve as a means to prepare nanoscale carbonaceous material-based metal nanocomposites for their potential exploitation as electro-active materials, e.g., new generation catalysts or electrode materials.

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013.

Milk is a source of bioactive molecules with wide-ranging functions. Among these, the immune properties have been the best characterised. In recent years, it has become apparent that besides the immunoglobulins, milk also contains a range of minor immune-related proteins that collectively form a significant first line of defence against pathogens, acting both within the mammary gland itself as well as in the digestive tract of the suckling neonate. We have used proteomics technologies to characterise the repertoire of host-defence-related milk proteins in detail, revealing more than 100 distinct gene products in milk, of which at least 15 are known host-defence-related proteins. Those having intrinsic antimicrobial activity likely function as effector proteins of the local mucosal immune defence (e.g. defensins, cathelicidins and the calgranulins). Here, we focus on the activities and biological roles of the cathelicidins and mammary serum amyloid A. The function of the immune-related milk proteins that do not have intrinsic antimicrobial activity is also discussed, notably lipopolysaccharide-binding protein, RNase4, RNase5/angiogenin and cartilage-glycoprotein 39 kDa. Evidence is shown that at least some of these facilitate recognition of microbes, resulting in the activation of innate immune signalling pathways in cells associated with the mammary and/or gut mucosal surface. Finally, the contribution of the bacteria in milk to its functionality is discussed. These investigations are elucidating how an effective first line of defence is achieved in the bovine mammary gland and how milk contributes to optimal digestive function in the suckling calf. This study will contribute to a better understanding of the health benefits of milk, as well as to the development of high-value ingredients from milk.

Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.

Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.

Nineteen wheat cultivars, released from 1934 to 2000, were grown at two organic and two non-organic sites in each of 3 years (2004–05, 2005–06 and 2006–07). Assessments included grain yield, grain protein concentration, protein yield, disease incidence and green leaf area (GLA). The superiority of each cultivar (the sum of the squares of the differences between its mean in each environment and the mean of the best cultivar there, divided by twice the number of environments; CS) was calculated for yield, grain protein concentration and protein yield, and ranked in each environment. The yield and grain protein concentration CS were more closely correlated with cultivar release date at the non-organic sites than at organic sites. This difference may be attributed to higher yield levels with larger differences among cultivars at the non-organic sites, rather than to improved stability (i.e. similar ranks) across sites. The significant difference in the correlation of protein yield CS and cultivar age between organic and non-organic sites would support evidence that the ability to take up mineral nitrogen (N) compared to soil N has been a component of the selection conditions of more modern cultivars (released after 1989). This is supported by assessment of GLA, where more modern cultivars in the non-organic systems had greater late-season GLA, a trend that was not identified in organic conditions. This effect could explain the poor correlation between age and protein yield CS in organic compared to non-organic conditions where modern cultivars are selected to benefit from later nitrogen (N) availability which includes the spring nitrogen applications tailored to coincide with peak crop demand. Under organic management, N release is largely based on the breakdown of fertility-building crops incorporated (ploughed-in) in the previous autumn. The release of nutrients from these residues is dependent on the soil conditions, which includes temperature and microbial populations, in addition to the potential leaching effect of high winter rainfall in the UK. In organic cereal crops, early resource capture is a major advantage for maximizing the utilization of nutrients from residue breakdown. It is concluded that selection of cultivars under conditions of high agrochemical inputs selects for cultivars that yield well under maximal conditions in terms of nutrient availability and pest, disease and weed control. The selection conditions for breeding have a tendency to select cultivars which perform relatively better in non-organic compared to organic systems.

By 1973 the last populations of the Bush Elephant (Loxondonta africana africana) in the Republic of Rwanda comprised two small groups of ca 70 animals each. Both were surrounded by expanding human settlement which caused rising conflict between Elephants and Man. Eventually the elephants' removal became imperative. Adults (103) and unweaned immatures (3) were therefore shot.

Extended abstract of a paper presented at Microscopy and Microanalysis 2009 in Richmond, Virginia, USA, July 26 – July 30, 2009