Simultaneous extinction of Madagascar’s megaherbivores correlates with late Holocene human-caused landscape transformation

Reconstructing the dynamics and drivers of late Quaternary megafaunal extinctions requires direct radiometric date series that are assessed within probabilistic statistical frameworks. Extinction chronologies are poorly understood for many tropical regions, including Madagascar, which had a diverse, now-extinct Holocene large vertebrate fauna including a “megaherbivore” guild of endemic hippopotami and elephant birds. Madagascar's megaherbivores likely played vital roles in regulating ecosystem structure and nutrient cycling, but few direct dates are available for megaherbivore specimens identified to species level, with uncertainty over when and why different representatives of this guild disappeared. Here, we conduct a new investigation into Malagasy megaherbivore extinction dynamics, including 30 new AMS dates and 63 audited published dates. We use Gaussian-resampled inverse-weighted McInerny (GRIWM) analysis to estimate species-specific extinction dates for three elephant bird species (Aepyornis hildebrandti, Mullerornis modestus, Vorombe titan), eggshell representing Aepyornis or Vorombe, and two hippo species (Hippopotamus lemerlei, H. madagascariensis), and to estimate extinction dates for megaherbivore communities in different biomes. Megaherbivores persisted for millennia after first human arrival. Extinction date estimates vary significantly between biomes, with disappearance from dry deciduous forest over a millennium earlier than other biomes, possibly reflecting local variation in megaherbivore population densities or human pressures. However, megaherbivore communities including all elephant bird and hippo species persisted elsewhere across Madagascar until ∼1200-900 bp, when they collapsed suddenly. Extinctions are closely correlated in time with intensive conversion of forests to grassland at ∼1100-1000 bp, probably associated with a shift to agro-pastoralism and representing a radical change in sustainability of prehistoric human interactions with biodiversity

Development of a single droplet freezing apparatus for studying crystallisation in cocoa butter droplets

The single droplet freezing apparatus described by Pore et al. (J. Am. Oil. Chem. Soc., 86, 215-225), which allows crystallisation to be monitored in situ by X-ray diffraction, was modified to allow rapid switching of coolant gas and monitoring by video microscopy. The apparatus was used to study drops of cocoa butter undergoing simulated spray freezing at high cooling rates, e.g. 130 K/min. The transformation of an Ivory Coast cocoa butter to the Form V polymorph was significantly faster in drops (~40 h) than in static bulk samples (10 days) crystallised under isothermal conditions. Phase transformation was observed from Forms I/II → III → IV → melt → V, with Form V crystallising directly from the melt at 28.6°C. Numerical simulations of the temperature evolution within the droplet established that the drops are not isothermal, explaining why nucleation was initially observed in the lower (upstream) part of the droplet.The provision of an EPSRC studentship for AMT and project support from Nestlé PTC York is gratefully acknowledged. The apparatus was constructed by Lee Pratt, Gary Chapman, Kevin Swan and Wei-Yao Ma. Assistance with the DSC testing from Zlatko Saraçevic, video microscopy from Dr Simon Butler, and general X-ray analysis from Dr Joanna Stasiak are all gratefully acknowledged.This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.jfoodeng.2015.02.01

Growth in fossil and extant deer and implications for body size and life history evolution

© Kolb et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The attached file is the published version of the article

Genome-Wide Mapping of DNA Methylation 5mC by Methylated DNA Immunoprecipitation (MeDIP)-Sequencing Methods and Protocols

Methylated DNA immunoprecipitation is a large scale purification technique. It enables the isolation of methylated DNA fragments for subsequent locus-specific or genome-wide analysis. Here we describe an immunoprecipitation protocol using a monoclonal mouse anti 5-methyl-cytidine antibody followed by next-generation sequencing (MeDIP-Seq)

Thermal and electrical conductivity of iron at Earth's core conditions

The Earth acts as a gigantic heat engine driven by decay of radiogenic isotopes and slow cooling, which gives rise to plate tectonics, volcanoes, and mountain building. Another key product is the geomagnetic field, generated in the liquid iron core by a dynamo running on heat released by cooling and freezing to grow the solid inner core, and on chemical convection due to light elements expelled from the liquid on freezing. The power supplied to the geodynamo, measured by the heat-flux across the core-mantle boundary (CMB), places constraints on Earth's evolution. Estimates of CMB heat-flux depend on properties of iron mixtures under the extreme pressure and temperature conditions in the core, most critically on the thermal and electrical conductivities. These quantities remain poorly known because of inherent difficulties in experimentation and theory. Here we use density functional theory to compute these conductivities in liquid iron mixtures at core conditions from first principles- the first directly computed values that do not rely on estimates based on extrapolations. The mixtures of Fe, O, S, and Si are taken from earlier work and fit the seismologically-determined core density and inner-core boundary density jump. We find both conductivities to be 2-3 times higher than estimates in current use. The changes are so large that core thermal histories and power requirements must be reassessed. New estimates of adiabatic heat-flux give 15-16 TW at the CMB, higher than present estimates of CMB heat-flux based on mantle convection; the top of the core must be thermally stratified and any convection in the upper core driven by chemical convection against the adverse thermal buoyancy or lateral variations in CMB heat flow. Power for the geodynamo is greatly restricted and future models of mantle evolution must incorporate a high CMB heat-flux and explain recent formation of the inner core.Comment: 11 pages including supplementary information, two figures. Scheduled to appear in Nature, April 201

Synergistic Antibacterial Effects of Metallic Nanoparticle Combinations

© The Author(s) 2019.Metallic nanoparticles have unique antimicrobial properties that make them suitable for use within medical and pharmaceutical devices to prevent the spread of infection in healthcare. The use of nanoparticles in healthcare is on the increase with silver being used in many devices. However, not all metallic nanoparticles can target and kill all disease-causing bacteria. To overcome this, a combination of several different metallic nanoparticles were used in this study to compare effects of multiple metallic nanoparticles when in combination than when used singly, as single elemental nanoparticles (SENPs), against two common hospital acquired pathogens (Staphylococcus aureus and Pseudomonas. aeruginosa). Flow cytometry LIVE/DEAD assay was used to determine rates of cell death within a bacterial population when exposed to the nanoparticles. Results were analysed using linear models to compare effectiveness of three different metallic nanoparticles, tungsten carbide (WC), silver (Ag) and copper (Cu), in combination and separately. Results show that when the nanoparticles are placed in combination (NPCs), antimicrobial effects significantly increase than when compared with SENPs (P < 0.01). This study demonstrates that certain metallic nanoparticles can be used in combination to improve the antimicrobial efficiency in destroying morphologically distinct pathogens within the healthcare and pharmaceutical industry.Peer reviewe

Developing an award program for children's settings to support healthy eating and physical activity and reduce the risk of overweight and obesity

<p>Abstract</p> <p>Background</p> <p>This paper aimed to identify the best way to engage, motivate and support early childhood services (ECS) and primary schools (PS) to create policy and practise changes to promote healthy eating and physical activity. This information would be used to develop a suitable program to implement within these children's settings to reduce the risk of childhood overweight and obesity.</p> <p>Methods</p> <p>The Medical Research Council's (UK) framework for the design and evaluation of complex interventions was used to guide the development of the healthy eating and physical activity program suitable for ECS and PS. Within this framework a range of evaluation methods, including stakeholder planning, in-depth interviews with ECS and PS staff and acceptability and feasibility trials in one local government area, were used to ascertain the best way to engage and support positive changes in these children's settings.</p> <p>Results</p> <p>Both ECS and PS identified that they had a role to play to improve children's healthy eating and physical activity. ECS identified their role in promoting healthy eating and physical activity as important for children's health, and instilling healthy habits for life. PS felt that these were health issues, rather than educational issues; however, schools saw the link between healthy eating and physical activity and student learning outcomes. These settings identified that a program that provides a simple guide that recognises good practise in these settings, such as an award scheme using a health promoting schools approach, as a feasible and acceptable way for them to support children's healthy eating and physical activity.</p> <p>Conclusion</p> <p>Through the process of design and evaluation a program - <it>Kids - 'Go for your life'</it>, was developed to promote and support children's healthy eating and physical activity and reduce the risk of childhood overweight and obesity. <it>Kids - 'Go for your life' </it>used an award program, based on a health promoting schools approach, which was demonstrated to be a suitable model to engage ECS and PS and was acceptable and feasible to create policy and practise changes to support healthy eating and physical activity for children.</p

Middle Pleistocene vertebrate fossils from the Nefud Desert, Saudi Arabia: Implications for biogeography and palaeoecology

The current paucity of Pleistocene vertebrate records from the Arabian Peninsula - a landmass of over 3 million km2 - is a significant gap in our knowledge of the Quaternary. Such data are critical lines of contextual evidence for considering animal and hominin dispersals between Africa and Eurasia generally, and hominin palaeoecology in the Pleistocene landscapes of the Arabian interior specifically. Here, we describe an important contribution to the record and report stratigraphically-constrained fossils of mammals, birds and reptiles from recent excavations at Ti’s al Ghadah in the southwestern Nefud Desert. Combined U-series and ESR analyses of Oryx sp. teeth indicate that the assemblage is Middle Pleistocene in age and dates to ca. 500 ka. The identified fauna is a biogeographical admixture that consists of likely endemics and taxa of African and Eurasian affinity and includes extinct and extant (or related Pleistocene forms of) mammals (Palaeoloxodon cf. recki, Panthera cf. gombaszogenis, Equus hemionus, cf. Crocuta crocuta, Vulpes sp., Canis anthus, Oryx sp.), the first Pleistocene records of birds from the Arabian Peninsula (Struthio sp., Neophron percnopterus, Milvus cf. migrans, Tachybaptus sp. Anas sp., Pterocles orientalis, Motacilla cf. alba) and reptiles (Varanidae/Uromastyx sp.). We infer that the assemblage reflects mortality in populations of herbivorous animals and their predators and scavengers that were attracted to freshwater and plant resources in the inter-dune basin. At present, there is no evidence to suggest hominin agency in the accumulation of the bone assemblages. The inferred ecological characteristics of the taxa recovered indicate the presence, at least periodically, of substantial water-bodies and open grassland habitats

Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome

Transposable elements (TEs) have no longer been totally considered as “junk DNA” for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C(chromosomeconformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r=0.9, P<2.2×1016; IMR90 fibroblasts: r = 0.94, P < 2.2 × 1016) and also have a significant positive correlation withsomeremote functional DNA elements like enhancers and promoters (Enhancer: hESC: r=0.997, P=2.3×10−4; IMR90: r=0.934, P=2×10−2; Promoter: hESC: r = 0.995, P = 3.8 × 10−4; IMR90: r = 0.996, P = 3.2 × 10−4). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes