Ex vivo expansion of limbal stem cells is affected by substrate properties

Limbal epithelial stem cells play a key role in the maintenance and regulation of the corneal surface. Damage or destruction of these cells results in vascularisation and corneal opacity. Subsequent limbal stem cell transplantation requires an ex vivo expansion step and preserving cells in an undifferentiated state remains vital. In this report we seek to control the phenotype of limbal epithelial stem cells by the novel application of compressed collagen substrates. We have characterised the mechanical and surface properties of conventional collagen gels using shear rheology and scanning electron microscopy. In doing so, we provide evidence to show that compressive load can improve the stiffness of collagen substrates. In addition Western blotting and immunohistochemistry display increased cytokeratin 3 (CK3) protein expression relating to limbal epithelial cell differentiation on stiff collagen substrates. Such gels with an elastic modulus of 2900 Pa supported a significantly higher number of cells than less stiff collagen gels (3 Pa). These findings have substantial influence in the development of ocular surface constructs or experimental models particularly in the fields of stem cell research, tissue engineering and regenerative medicine.

Genome scale reconstruction of a Salmonella metabolic model comparison of similarity and differences with a commensal Escherichia coli strain

Salmonella are closely related to commensal Escherichia coli but have gained virulence factors enabling them to behave as enteric pathogens. Less well studied are the similarities and differences that exist between the metabolic properties of these organisms that may contribute toward niche adaptation of Salmonella pathogens. To address this, we have constructed a genome scale Salmonella metabolic model (iMA945). The model comprises 945 open reading frames or genes, 1964 reactions, and 1036 metabolites. There was significant overlap with genes present in E. coli MG1655 model iAF1260. In silico growth predictions were simulated using the model on different carbon, nitrogen, phosphorous, and sulfur sources. These were compared with substrate utilization data gathered from high throughput phenotyping microarrays revealing good agreement. Of the compounds tested, the majority were utilizable by both Salmonella and E. coli. Nevertheless a number of differences were identified both between Salmonella and E. coli and also within the Salmonella strains included. These differences provide valuable insight into differences between a commensal and a closely related pathogen and within different pathogenic strains opening new avenues for future explorations.

Exploring the market potential of 'local' in food systems

Local food initiatives create a niche market in many developed countries where consumer choice is being met with an expanding offering in both conventional as well as complementary retail outlets. Supermarkets in conjunction with the food service sector currently dominate food sales and consumption, and are likely to do so for the foreseeable future. However, the local food sector offers an opportunity for implementing niche marketing strategies for many businesses. Local food activities tend to be relatively independent activities and a clearer definition for “local” food would assist in consolidating this important component of the food system. Related to this, consumers would benefit from the establishment of some form of assurance system for the ‘localness’ of food. In the UK, with its well established local food market, farmers’ markets, farm shops and box schemes are currently having the largest impact in terms of total sales. Hence further research is required to confirm that support for similar business ventures in Australia would be a viable strategy for strengthening its local food systems.

Conformation and self-association of peptide amphiphiles based on the KTTKS collagen sequence

Studying peptide amphiphiles (PAs), we investigate the influence of alkyl chain length on the aggregation behavior of the collagen-derived peptide KTTKS with applications ranging from antiwrinkle cosmetic creams to potential uses in regenerative medicine. We have studied synthetic peptides amphiphiles C14− KTTKS (myristoyl Lys-Thr-Thr-Lys-Ser) and C18−KTTKS(stearoyl-Lys-Thr Thr-Lys-Ser) to investigate in detail their physicochemical properties. It is presumed that the hydrophobic chain in these self-assembling peptide amphiphiles enhances peptide permeation across the skin compared to KTTKS alone. Subsequently Cn−KTTKS should act as a prodrug and release the peptide by enzymatic cleavage. Our results should be useful in the further development of molecules with collagen-stimulating activity.

Multiple routes to mammalian diversity

The radiation of the mammals provides a 165-million-year test case for evolutionary theories of how species occupy and then fill ecological niches. It is widely assumed that species often diverge rapidly early in their evolution, and that this is followed by a longer, drawn-out period of slower evolutionary fine-tuning as natural selection fits organisms into an increasingly occupied niche space1,2. But recent studies have hinted that the process may not be so simple3–5. Here we apply statistical methods that automatically detect temporal shifts in the rate of evolution through time to a comprehensive mammalian phylogeny6 and data set7 of body sizes of 3,185 extant species. Unexpectedly, the majority of mammal species, including two of the most speciose orders (Rodentia and Chiroptera), have no history of substantial and sustained increases in the rates of evolution. Instead, a subset of the mammals has experienced an explosive increase (between 10- and 52-fold) in the rate of evolution along the single branch leading to the common ancestor of their monophyletic group (for example Chiroptera), followed by a quick return to lower or background levels. The remaining species are a taxonomically diverse assemblage showing a significant, sustained increase or decrease in their rates of evolution. These results necessarily decouple morphological diversification from speciation and suggest that the processes that give rise to the morphological diversity of a class of animals are far more free to vary than previously considered. Niches do not seem to fill up, and diversity seems to arise whenever, wherever and at whatever rate it is advantageous.

The benefits of a compute cluster approach to high spatial resolution biodiversity richness modelling: projecting the impact of climate change on Mediterranean flora

High spatial resolution environmental data gives us a better understanding of the environmental factors affecting plant distributions at fine spatial scales. However, large environmental datasets dramatically increase compute times and output species model size stimulating the need for an alternative computing solution. Cluster computing offers such a solution, by allowing both multiple plant species Environmental Niche Models (ENMs) and individual tiles of high spatial resolution models to be computed concurrently on the same compute cluster. We apply our methodology to a case study of 4,209 species of Mediterranean flora (around 17% of species believed present in the biome). We demonstrate a 16 times speed-up of ENM computation time when 16 CPUs were used on the compute cluster. Our custom Java ‘Merge’ and ‘Downsize’ programs reduce ENM output files sizes by 94%. The median 0.98 test AUC score of species ENMs is aided by various species occurrence data filtering techniques. Finally, by calculating the percentage change of individual grid cell values, we map the projected percentages of plant species vulnerable to climate change in the Mediterranean region between 1950–2000 and 2020.

The myths of modern primitivism

RE/Search Publications’ Modern Primitives (Vale and Juno 1989) changed countless lives, bringing what had been a localized and niche set of body modification practices, aesthetics and philosophies out of San Francisco to a global audience, dominating scholarly and popular discourse around body modification subculture for more than a decade afterwards. The voice of Fakir Musafar dominates the book. This article argues that modern primitives as Musafar defines them never really existed (and never could have existed) in the terms he suggests, and goes on to address an important sub-strand within Modern Primitives almost entirely ignored by critics and commentators, who have read the book as generally representative of the body modification culture as a whole. With specific reference to contributors such as infamous tattoo artist Don Ed Hardy who do not frame their practice in ‘primitive’ terms, the article concludes with a study of an alternative account presented by Vale and Juno’s book: body modification as artistic practice.

Assessing continental-scale risks for generalist and specialist pollinating bee species under climate change

Increased risks of extinction to populations of animals and plants under changing climate have now been demonstrated for many taxa. This study assesses the extinction risks to species within an important genus of pollinating bees (Colletes: Apidae) by estimating the expected changes in the area and isolation of suitable habitat under predicted climatic condition for 2050. Suitable habitat was defined on the basis of the presence of known forage plants as well as climatic suitability. To investigate whether ecological specialisation was linked to extinction risk we compared three species which were generalist pollen foragers on several plant families with three species which specialised on pollen from a single plant species. Both specialist and generalist species showed an increased risk of extinction with shifting climate, and this was particularly high for the most specialised species (Colletes anchusae and C. wolfi). The forage generalist C. impunctatus, which is associated with Boreo-Alpine environments, is potentially threatened through significant reduction in available climatic niche space. Including the distribution of the principal or sole pollen forage plant, when modelling the distribution of monolectic or narrowly oligolectic species, did not improve the predictive accuracy of our models as the plant species were considerably more widespread than the specialised bees associated with them.

Healable supramolecular polymeric materials

This chapter details the design, synthesis and evaluation techniques required to produce healable supramolecular materials. Key developments in supramolecular polymer chemistry that laid down the design concepts necessary to produce responsive materials are summarized. Subsequently, select examples from the literature concerning the synthesis and analysis of healable materials containing hydrogen bonding, π−π stacking and metal–ligand interactions are evaluated. The last section describes the most recent efforts to produce healable gels for niche applications, including electrolytes and tissue engineering scaffolds. The chapter also describes the design criteria and production of nano-composite materials that exhibit dramatically increased strength compared to previous generations of supramolecular materials, whilst still retaining the key healing characteristics.

Convergent structure of multitrophic communities over three continents

Ecological theory predicts that communities using the same resources should have similar structure, but evolutionary constraints on colonization and niche shifts may hamper such convergence. Multitrophic communities of wasps exploiting fig fruits, which first evolved about 75MYA, do not show long-term “inheritance” of taxonomic (lineage) composition or species diversity. However, communities on three continents have converged ecologically in the presence and relative abundance of five insect guilds that we define. Some taxa fill the same niches in each community (phylogenetic niche conservatism). However, we show that overall convergence in ecological community structure depends also on a combination of niche shifts by resident lineages and local colonizations of figs by other insect lineages. Our study explores new ground, and develops new heuristic tools, in combining ecology and phylogeny to address patterns in the complex multitrophic communities of insect on plants, which comprise a large part of terrestrial biodiversity.

Observed adaptation to climate change as initiated transition

This paper investigates whether and to what extent a wide range of actors in the UK are adapting to climate change, and whether this is evidence of a social transition. We document evidence of over 300 examples of early adopters of adaptation practice to climate change in the UK. These examples span a range of activities from small adjustments (or coping), to building adaptive capacity, to implementing actions and to creating deeper systemic change in public and private organisations in a range of sectors. We find that adaptation in the UK has been dominated by government initiatives and has principally occurred in the form of research into climate change impacts. These government initiatives have stimulated a further set of actions at other scales in public agencies, regulatory agencies and regional government (and the devolved administrations), though with little real evidence of climate change adaptation initiatives trickling down to local government level. The sectors requiring significant investment in large scale infrastructure have invested more heavily than those that do not in identifying potential impacts and adaptations. Thus we find a higher level of adaptation activity by the water supply and flood defence sectors. Sectors that are not dependent on large scale infrastructure appear to be investing far less effort and resources in preparing for climate change. We conclude that the UK government-driven top-down targeted adaptation approach has generated anticipatory action at low cost in some areas. We also conclude that these actions may have created enough niche activities to allow for diffusion of new adaptation practices in response to real or perceived climate change. These results have significant implications for how climate policy can be developed to support autonomous adaptors in the UK and other countries.

High sensitivity recording of afferent nerve activity using ultra-compliant microchannel electrodes: an acutein vivovalidation

Neuroprostheses interfaced with transected peripheral nerves are technological routes to control robotic limbs as well as convey sensory feedback to patients suffering from traumatic neural injuries or degenerative diseases. To maximize the wealth of data obtained in recordings, interfacing devices are required to have intrafascicular resolution and provide high signal-to-noise ratio (SNR) recordings. In this paper, we focus on a possible building block of a three-dimensional regenerative implant: a polydimethylsiloxane (PDMS) microchannel electrode capable of highly sensitive recordings in vivo. The PDMS 'micro-cuff' consists of a 3.5 mm long (100 µm × 70 µm cross section) microfluidic channel equipped with five evaporated Ti/Au/Ti electrodes of sub-100 nm thickness. Individual electrodes have average impedance of 640 ± 30 kΩ with a phase angle of −58 ± 1 degrees at 1 kHz and survive demanding mechanical handling such as twisting and bending. In proof-of-principle acute implantation experiments in rats, surgically teased afferent nerve strands from the L5 dorsal root were threaded through the microchannel. Tactile stimulation of the skin was reliably monitored with the three inner electrodes in the device, simultaneously recording signal amplitudes of up to 50 µV under saline immersion. The overall SNR was approximately 4. A small but consistent time lag between the signals arriving at the three electrodes was observed and yields a fibre conduction velocity of 30 m s−1. The fidelity of the recordings was verified by placing the same nerve strand in oil and recording activity with hook electrodes. Our results show that PDMS microchannel electrodes open a promising technological path to 3D regenerative interfaces.

Overexpression of coconut AINTEGUMENTA-like gene, CnANT, promotes in vitro regeneration in transgenic Arabidopsis

Knowledge of the molecular biological changes underlying the process of embryogenesis is important for the improvement of somatic embryogenesis of coconut. Among the transcription factors that control the transition from vegetative to embryogenic growth, members of APETALA2/Ethylene-responsive element binding protein domain family play an important role in promoting embryo development. Significant insights into the role of AP2 genes have been obtained by the ectopic expression of AP2 sub family genes in transgenic Arabidopsis. A homolog of the AINTEGUMENTA-like gene that encodes the two AP2 domains and the linker region was identified in the coconut genome. Phylogenetic analysis showed that this gene, CnANT, encodes a protein that branched with BABY BOOM/PLETHORA clade in the AINTEGUMENTA-like major clade and was similar to the oil palm EgAP2-1 protein. According to real time RT-PCR results, higher expression of CnANT was observed in more mature zygotic embryos. Also, high CnANT expression was recorded in embryogenic callus compared to other stages of somatic embryogenesis. We examined the effect of ectopic CnANT expression on the development and regenerative capacity of transgenic Arabidopsis. Overexpression of CnANT in Arabidopsis induced hormone free regeneration of explants. Furthermore, ectopic expression of CnANT enhanced regeneration in vitro and suggested a role for this gene in cell proliferation during in vitro culture.

New age estimates for the Palaeolithic assemblages and Pleistocene succession of Casablanca, Morocco

Marine and aeolian Quaternary sediments from Casablanca, Morocco were dated using the optically stimulated luminescence (OSL) signal of quartz grains. These sediments form part of an extensive succession spanning the Pleistocene, and contain a rich faunal and archaeological record, including an Acheulian lithic assemblage from before the Brunhes–Matayama boundary, and a Homo erectus jaw from younger cave deposits. Sediment samples from the sites of Reddad Ben Ali, Oulad J’mel, Sidi Abderhamane and Thomas Quarries have been dated, in order to assess the upper limits of OSL. The revision of previously measured mammalian tooth enamel electron spin resonance (ESR) dates from the Grotte des Rhinocéros, Oulad Hamida Quarry 1, incorporating updated environmental dose rate measurements and attenuation calculations, also provide chronological constraint for the archaeological material preserved at Thomas Quarries. Several OSL age estimates extend back to around 500,000 years, with a single sample providing an OSL age close to 1 Ma in magnetically reversed sediments. These luminescence dates are some of the oldest determined, and their reliability is assessed using both internal criteria based on stratigraphic consistency, and external lithostratigraphic, morphostratigraphic and independent chronological constraints. For most samples, good internal agreement is observed using single aliquot regenerative-dose OSL measurements, while multiple aliquot additive-dose measurements generally have poorer resolution and consistency. Novel slow-component and component-resolved OSL approaches applied to four samples provide significantly enhanced dating precision, and an examination of the degree of signal zeroing at deposition. A comparison of the OSL age estimates with the updated ESR dates and one U-series date demonstrate that this method has great potential for providing reliable age estimates for sediments of this antiquity. We consider the cause of some slight age inversion observed at Thomas Quarries, and provide recommendations for further luminescence dating within this succession.

Bioactive films produced from self-assembling peptide amphiphiles as versatile substrates for tuning cell adhesion and tissue architecture in serum-free conditions

The development of versatile bioactive surfaces able to emulate in vivo conditions is of enormous importance to the future of cell and tissue therapy. Tuning cell behaviour on two-dimensional surfaces so that the cells perform as if they were in a natural three-dimensional tissue represents a significant challenge, but one that must be met if the early promise of cell and tissue therapy is to be fully realised. Due to the inherent complexities involved in the manufacture of biomimetic three-dimensional substrates, the scaling up of engineered tissue-based therapies may be simpler if based upon proven two-dimensional culture systems. In this work, we developed new coating materials composed of the self-assembling peptide amphiphiles (PAs) C16G3RGD (RGD) and C16G3RGDS (RGDS) shown to control cell adhesion and tissue architecture while avoiding the use of serum. When mixed with the C16ETTES diluent PA at 13 : 87 (mol mol-1) ratio at 1.25 times 10-3 M, the bioactive {PAs} were shown to support optimal adhesion, maximal proliferation, and prolonged viability of human corneal stromal fibroblasts ({hCSFs)}, while improving the cell phenotype. These {PAs} also provided stable adhesive coatings on highly-hydrophobic surfaces composed of striated polytetrafluoroethylene ({PTFE)}, significantly enhancing proliferation of aligned cells and increasing the complexity of the produced tissue. The thickness and structure of this highly-organised tissue were similar to those observed in vivo, comprising aligned newly-deposited extracellular matrix. As such, the developed coatings can constitute a versatile biomaterial for applications in cell biology, tissue engineering, and regenerative medicine requiring serum-free conditions.