JURNAL AGROTEKNOLOGI
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Developing atom probe tomography of phyllosilicates in preparation for extra-terrestrial sample return
No full textHydrous phyllosilicate minerals, including the serpentine subgroup, are likely to be major constituents of material that will be bought back to Earth by missions to Mars and to primitive asteroids Ryugu and Bennu. Small quantities (< 60 g) of micrometre-sized, internally heterogeneous material will be available for study, requiring minimally destructive techniques. Many conventional methods are unsuitable for phyllosilicates as they are typically finely crystalline and electron beam-sensitive resulting in amorphisation and dehydration. New tools will be required for nanoscale characterisation of these precious extra-terrestrial samples. Here we test the effectiveness of atom probe tomography (APT) for this purpose. Using lizardite from the Ronda peridotite, Spain, as a terrestrial analogue, we outline an effective analytical protocol to extract nanoscale chemical and structural measurements of phyllosilicates. The potential of APT is demonstrated by the unexpected finding that the Ronda lizardite contains SiO-rich nanophases, consistent with opaline silica that formed as a by-product of the serpentinisation of olivine. Our new APT approach unlocks previously unobservable nanominerals and nanostructures within phyllosilicates owing to resolution limitations of more established imaging techniques. APT will provide unique insights into the processes and products of water/rock interaction on Earth, Mars and primitive asteroids
Adaptive response of a metal–organic framework through reversible disorder–disorder transitions
No full textThe ultrahigh porosity and varied functionalities of porous metal–organic frameworks make them excellent candidates for applications that range widely from gas storage and separation to catalysis and sensing. An interesting feature of some frameworks is the ability to open their pores to a specific guest, enabling highly selective separation. A prerequisite for this is bistability of the host structure, which enables the framework to breathe, that is, to switch between two stability minima in response to its environment. Here we describe a porous framework DUT-8(Ni)—which consists of nickel paddle wheel clusters and carboxylate linkers—that adopts a configurationally degenerate family of disordered states in the presence of specific guests. This disorder originates from the nonlinear linkers arranging the clusters in closed loops of different local symmetries that in turn propagate as complex tilings. Solvent exchange stimulates the formation of distinct disordered frameworks, as demonstrated by high-resolution transmission electron microscopy and diffraction techniques. Guest exchange was shown to stimulate repeatable switching transitions between distinct disorder states
In vitro study of human immune responses to hyaluronic acid hydrogels, recombinant spidroins and human neural progenitor cells of relevance to spinal cord injury repair
No full textScaffolds of recombinant spider silk protein (spidroin) and hyaluronic acid (HA) hydrogel hold promise in combination with cell therapy for spinal cord injury. However, little is known concerning the human immune response to these biomaterials and grafted human neural stem/progenitor cells (hNPCs). Here, we analyzed short- and long-term in vitro activation of immune cells in human peripheral blood mononuclear cells (hPBMCs) cultured with/without recombinant spidroins, HA hydrogels, and/or allogeneic hNPCs to assess potential host–donor interactions. Viability, proliferation and phenotype of hPBMCs were analyzed using NucleoCounter and flow cytometry. hPBMC viability was confirmed after exposure to the different biomaterials. Short-term (15 h) co-cultures of hPBMCs with spidroins, but not with HA hydrogel, resulted in a significant increase in the proportion of activated CD69+ CD4+ T cells, CD8+ T cells, B cells and NK cells, which likely was caused by residual endotoxins from the Escherichia coli expression system. The observed spidroin-induced hPBMC activation was not altered by hNPCs. It is resource-effective to evaluate human compatibility of novel biomaterials early in development of the production process to, when necessary, make alterations to minimize rejection risk. Here, we present a method to evaluate biomaterials and hPBMC compatibility in conjunction with allogeneic human cells
Targeting the bacterial SOS response for new antimicrobial agents: drug targets, molecular mechanisms and inhibitors
No full textAntimicrobial resistance is a pressing threat to global health, with multidrug-resistant pathogens becoming increasingly prevalent. The bacterial SOS pathway functions in response to DNA damage that occurs during infection, initiating several pro-survival and resistance mechanisms, such as DNA repair and hypermutation. This makes SOS pathway components potential targets that may combat drug-resistant pathogens and decrease resistance emergence. This review discusses the mechanism of the SOS pathway; the structure and function of potential targets AddAB, RecBCD, RecA and LexA; and efforts to develop selective small-molecule inhibitors of these proteins. These inhibitors may serve as valuable tools for target validation and provide the foundations for desperately needed novel antibacterial therapeutics
Incorporating human mobility data improves forecasts of Dengue fever in Thailand
No full textOver 390 million people worldwide are infected with dengue fever each year. In the absence of an effective vaccine for general use, national control programs must rely on hospital readiness and targeted vector control to prepare for epidemics, so accurate forecasting remains an important goal. Many dengue forecasting approaches have used environmental data linked to mosquito ecology to predict when epidemics will occur, but these have had mixed results. Conversely, human mobility, an important driver in the spatial spread of infection, is often ignored. Here we compare time-series forecasts of dengue fever in Thailand, integrating epidemiological data with mobility models generated from mobile phone data. We show that geographically-distant provinces strongly connected by human travel have more highly correlated dengue incidence than weakly connected provinces of the same distance, and that incorporating mobility data improves traditional time-series forecasting approaches. Notably, no single model or class of model always outperformed others. We propose an adaptive, mosaic forecasting approach for early warning systems
The impact of mobility network properties on predicted epidemic dynamics in Dhaka and Bangkok
No full textProperties of city-level commuting networks are expected to influence epidemic potential of cities and modify the speed and spatial trajectory of epidemics when they occur. In this study, we use aggregated mobile phone user data to reconstruct commuter mobility networks for Bangkok (Thailand) and Dhaka (Bangladesh), two megacities in Asia with populations of 16 and 21 million people, respectively. We model the dynamics of directly-transmitted infections (such as SARS-CoV-2) propagating on these commuting networks, and find that differences in network structure between the two cities drive divergent predicted epidemic trajectories: the commuting network in Bangkok is composed of geographically-contiguous modular communities and epidemic dispersal is correlated with geographic distance between locations, whereas the network in Dhaka has less distinct geographic structure and epidemic dispersal is less constrained by geographic distance. We also find that the predicted dynamics of epidemics vary depending on the local topology of the network around the origin of the outbreak. Measuring commuter mobility, and understanding how commuting networks shape epidemic dynamics at the city level, can support surveillance and preparedness efforts in large cities at risk for emerging or imported epidemics
Characterizing atmospheres of transiting Earth-like exoplanets orbiting M Dwarfs with James Webb space telescope
No full textA number of transiting, potentially habitable Earth-sized exoplanets have recently been detected around several nearby M dwarf stars. These worlds represent important targets for atmospheric characterization for the upcoming NASA James Webb Space Telescope (JWST). Given that available time for exoplanet characterization will be limited, it is critically important to first understand the capabilities and limitations of JWST when attempting to detect atmospheric constituents for potentially Earth-like worlds orbiting cool stars. Here, we explore coupled climate-chemistry atmospheric models for Earth-like planets orbiting a grid of M dwarf hosts. Using a newly-developed and validated JWST instrument model—the JWST Exoplanet Transit Simulator—we investigate the detectability of key biosignature and habitability indicator gaseous species for a variety of relevant instruments and observing modes. Spectrally resolved detection scenarios as well as cases where the spectral impact of a given species is integrated across the entire range of an instrument/mode are considered and serve to highlight the importance of considering information gained over an entire observable spectral range. Our results indicate that detectability of gases at individual wavelengths is overly challenging for JWST but integrating the spectral impact of a species across the entire wavelength range of an instrument/mode significantly improves requisite detection times. When considering the entire spectral coverage of an instrument/mode, detections of methane, carbon dioxide, oxygen and water at signal-to-noise ratio 5 could be achieved with observations of several tens of transits (or less) for cloud-free Earth-like worlds orbiting mid-to late-type M dwarfs at system distances of up to 10–15 pc. When compared to previous results, requisite exposure times for gas species detection depend on approaches to quantifying the spectral impact of the species as well as underlying photochemical model assumptions. Thus, constraints on atmospheric abundances, even if just upper limits, by JWST have the potential to further our understanding of terrestrial atmospheric chemistry
Persistent homology in two-dimensional atomic networks
No full textThe topology of two-dimensional network materials is investigated by persistent homology analysis. The constraint of two dimensions allows for a direct comparison of key persistent homology
metrics (persistence diagrams, cycles, Betti numbers) with more traditional metrics such as the
ring-size distributions. Two different types of networks are employed in which the topology is manipulated systematically. In the first, comparatively rigid networks are generated for a triangle-raft
model, which are representative of materials such as silica bilayers. In the second, more flexible networks are generated using a bond-switching algorithm, which are representative of materials such as
graphene. Bands are identified in the persistence diagrams by reference to the length-scales associated with distorted polygons. The triangle-raft models with the largest ordering allow specific bands
Bn (n = 1, 2, 3,. . .) to be allocated to configurations of atoms separated by n bonds. The persistence
diagrams for the more disordered network models also display bands albeit less pronounced. The
persistent homology method thereby provides information on n-body correlations that is not accessible from structure factors or radial distribution functions. An analysis of the persistent cycles gives
the primitive ring statistics, provided the level of disorder is not too large. The method also gives
information on the regularity of rings that is unavailable from a ring-statistics analysis. The utility
of the persistent homology method is demonstrated by its application to experimentally-obtained
configurations of silica bilayers and graphene
Measurements by x-ray diffraction of the temperature dependence of lattice parameter and crystallite size for isostatically‑pressed graphite
No full textSynthetic polygranular graphites of various grades and manufacturing routes are used in nuclear reactors for power generation, and may be used in potential fourth generation and other advanced reactor designs that will operate at higher temperature. Attention is given in this paper to isostatically-moulded synthetic polygranular graphites with porosities in the range 8% to 18%. The lattice parameters a and c for the hexagonal graphite have been measured over the temperature range from room temperature to 800°C by x-ray diffraction. The variation with temperature of the crystal lattice parameters, coherence length (crystallite size) and microstrain are discussed with reference to the microstructure and the relative strength of the bonds in-plane and normal to the graphene layers
Energy transition: modelling the impact on natural gas
No full textIn the debate about the impact of the Energy Transition on the current global energy system it is becoming increasingly clear that there are multiple pathways, technologies and outcomes that can help the world to decarbonize. The two scenarios prepared by the OIES are designed to limit the global temperature rise to well below 2 °C, one scenario which is favourable to natural gas and one which is less favourable. The favourable scenario has gas demand slightly higher than current levels in 2050, but with significant levels of abatement and carbon capture, while the unfavourable scenario has gas demand in 2050 at some 60% of today’s levels, but still with significant levels of abatement. The need to switch from coal to gas in the Asian markets leads to rapid growth in LNG trade in the 2020s, sustained at least through 2040. In the unfavourable case LNG trade declines rapidly in the 2030s, giving rise to potential stranded assets. Both scenarios involve natural gas to a much greater degree than the IEA’s Net Zero pathway but are still consistent with limiting the global temperature rise. We do not suggest that this is “the” answer, but it does offer an alternative view of the future which may be considered more achievable given current infrastructure in place and the important role that gas can clearly play in many regions as an agent of decarbonisation