Conceptual frameworks and terminology in doctoral nursing research

Aim: To define conceptual frameworks and their inherent dichotomies, and integrate them with concomitant concepts to help early nursing doctoral researchers to develop their understanding of and engage with discourse further, so that nursing can demonstrate its ability to contribute to the meta-theoretical debate of doctoral research alongside other practices and theory-based disciplines. Background: Conceptual frameworks are central to nursing doctoral studies as they map and contextualise the philosophical assumptions of the research in relation to paradigms and ontological, epistemological and methodological foundations. They shape all aspects of the research design and provide a structure for theorising. They can also be a challenge for researchers and are under-discussed in the literature. Review methods: Literature review. Discussion: The key aspects of the conceptual framework debate in terms of objectivist, subjectivist paradigms and the wider paradigm debate, including retroduction and abduction, are reviewed here together with consideration of how these apply to nursing doctoral research. Conclusion: Conceptual frameworks are pivotal to nursing doctoral research as they clarify and integrate philosophical, methodological and pragmatic aspects of doctoral thesis while helping the profession to be seen as a research-based discipline, comfortable with the language of meta-theoretical debate. Implications for research/practice: Conceptual frameworks should form the methodological foundation for all nursing doctoral research

Persistent punishment : users views of short prison sentences

Semi-structured interviews were conducted of 22 prisoners to gather information about the characteristic features of short prison sentences. Themes raised in comments included: the frequency and quality of sentences, addiction, family, and penal legitimacy. Most of the participants had extensive experience of prison, and the effects of this played out across sentences and years, accumulating and amplifying impacts. And, despite expressions of guilt and remorse, most participants saw their sentence as unjust, and mainly a reaction to offending history. We conclude by suggesting the need for research to shift focus from evaluating individual penal interventions towards more holistic and narrative accounts that cut across sentences

Identification and Overexpression of a Knotted1-Like Transcription Factor in Switchgrass (Panicum virgatum L.) for Lignocellulosic Feedstock Improvement

High biomass production and wide adaptation has made switchgrass (Panicum virgatum L.) an important candidate lignocellulosic bioenergy crop. One major limitation of this and other lignocellulosic feedstocks is the recalcitrance of complex carbohydrates to hydrolysis for conversion to biofuels. Lignin is the major contributor to recalcitrance as it limits the accessibility of cell wall carbohydrates to enzymatic breakdown into fermentable sugars. Therefore, genetic manipulation of the lignin biosynthesis pathway is one strategy to reduce recalcitrance. Here, we identified a switchgrass Knotted1 transcription factor, PvKN1, with the aim of genetically engineering switchgrass for reduced biomass recalcitrance for biofuel production. Gene expression of the endogenousPvKN1 gene was observed to be highest in young inflorescences and stems. Ectopic overexpression of PvKN1 in switchgrass altered growth, especially in early developmental stages. Transgenic lines had reduced expression of most lignin biosynthetic genes accompanied by a reduction in lignin content suggesting the involvement of PvKN1 in the broad regulation of the lignin biosynthesis pathway. Moreover, the reduced expression of the Gibberellin 20-oxidase (GA20ox) gene in tandem with the increased expression of Gibberellin 2-oxidase (GA2ox) genes in transgenic PvKN1 lines suggest that PvKN1 may exert regulatory effects via modulation of GA signaling. Furthermore, overexpression of PvKN1 altered the expression of cellulose and hemicellulose biosynthetic genes and increased sugar release efficiency in transgenic lines. Our results demonstrated that switchgrass PvKN1 is a putative ortholog of maize KN1 that is linked to plant lignification and cell wall and development traits as a major regulatory gene. Therefore, targeted overexpression of PvKN1 in bioenergy feedstocks may provide one feasible strategy for reducing biomass recalcitrance and simultaneously improving plant growth characteristics

Transgenic miR156 Switchgrass in the Field: Growth, Recalcitrance and Rust Susceptibility

Sustainable utilization of lignocellulosic perennial grass feedstocks will be enabled by high biomass production and optimized cell wall chemistry for efficient conversion into biofuels. MicroRNAs are regulatory elements that modulate the expression of genes involved in various biological functions in plants, including growth and development. In greenhouse studies, overexpressing a microRNA (miR156) gene in switchgrass had dramatic effects on plant architecture and flowering, which appeared to be driven by transgene expression levels. Highexpressing lines were extremely dwarfed, whereas low and moderate-expressing lines had higher biomass yields, improved sugar release and delayed flowering. Four lines with moderate or low miR156 overexpression from the prior greenhouse study were selected for a field experiment to assess the relationship between miR156 expression and biomass production over three years. We also analysed important bioenergy feedstock traits such as flowering, disease resistance, cell wall chemistry and biofuel production. Phenotypes of the transgenic lines were inconsistent between the greenhouse and the field as well as among different field growing seasons. One low expressing transgenic line consistently produced more biomass (25%–56%) than the control across all three seasons, which translated to the production of 30% more biofuel per plant during the final season. The other three transgenic lines produced less biomass than the control by the final season, and the two lines with moderate expression levels also exhibited altered disease susceptibilities. Results of this study emphasize the importance of performing multiyear field studies for plants with altered regulatory transgenes that target plant growth and development

The TcEG1 beetle (Tribolium castaneum) cellulase produced in transgenic switchgrass is active at alkaline pH and auto-hydrolyzes biomass for increased cellobiose release

Background Genetically engineered biofuel crops, such as switchgrass (Panicum virgatum L.), that produce their own cell wall-digesting cellulase enzymes would reduce costs of cellulosic biofuel production. To date, non-bioenergy plant models have been used in nearly all studies assessing the synthesis and activity of plant-produced fungal and bacterial cellulases. One potential source for cellulolytic enzyme genes is herbivorous insects adapted to digest plant cell walls. Here we examine the potential of transgenic switchgrass-produced TcEG1 cellulase from Tribolium castaneum (red flour beetle). This enzyme, when overproduced in Escherichia coliand Saccharomyces cerevisiae, efficiently digests cellulose at optima of 50 °C and pH 12.0. Results TcEG1 that was produced in green transgenic switchgrass tissue had a range of endoglucanase activity of 0.16–0.05 units (µM glucose release/min/mg) at 50 °C and pH 12.0. TcEG1 activity from air-dried leaves was unchanged from that from green tissue, but when tissue was dried in a desiccant oven (46 °C), specific enzyme activity decreased by 60%. When transgenic biomass was “dropped-in” into an alkaline buffer (pH 12.0) and allowed to incubate at 50 °C, cellobiose release was increased up to 77% over non-transgenic biomass. Saccharification was increased in one transgenic event by 28%, which had a concurrent decrease in lignin content of 9%. Histological analysis revealed an increase in cell wall thickness with no change to cell area or perimeter. Transgenic plants produced more, albeit narrower, tillers with equivalent dry biomass as the control. Conclusions This work describes the first study in which an insect cellulase has been produced in transgenic plants; in this case, the dedicated bioenergy crop switchgrass. Switchgrass overexpressing the TcEG1 gene appeared to be morphologically similar to its non-transgenic control and produced equivalent dry biomass. Therefore, we propose TcEG1 transgenics could be bred with other transgenic germplasm (e.g., low-lignin lines) to yield new switchgrass with synergistically reduced recalcitrance to biofuel production. In addition, transgenes for other cell wall degrading enzymes may be stacked with TcEG1 in switchgrass to yield complementary cell wall digestion features and complete auto-hydrolysis

Enhanced characteristics of genetically modified switchgrass (Panicum virgatum L.) for high biofuel production

Background Lignocellulosic biomass is one of the most promising renewable and clean energy resources to reduce greenhouse gas emissions and dependence on fossil fuels. However, the resistance to accessibility of sugars embedded in plant cell walls (so-called recalcitrance) is a major barrier to economically viable cellulosic ethanol production. A recent report from the US National Academy of Sciences indicated that, “absent technological breakthroughs”, it was unlikely that the US would meet the congressionally mandated renewable fuel standard of 35 billion gallons of ethanol-equivalent biofuels plus 1 billion gallons of biodiesel by 2022. We here describe the properties of switchgrass (Panicum virgatum) biomass that has been genetically engineered to increase the cellulosic ethanol yield by more than 2-fold. Results We have increased the cellulosic ethanol yield from switchgrass by 2.6-fold through overexpression of the transcription factor PvMYB4. This strategy reduces carbon deposition into lignin and phenolic fermentation inhibitors while maintaining the availability of potentially fermentable soluble sugars and pectic polysaccharides. Detailed biomass characterization analyses revealed that the levels and nature of phenolic acids embedded in the cell-wall, the lignin content and polymer size, lignin internal linkage levels, linkages between lignin and xylans/pectins, and levels of wall-bound fucose are all altered in PvMYB4-OX lines. Genetically engineered PvMYB4-OX switchgrass therefore provides a novel system for further understanding cell wall recalcitrance. Conclusions Our results have demonstrated that overexpression of PvMYB4, a general transcriptional repressor of the phenylpropanoid/lignin biosynthesis pathway, can lead to very high yield ethanol production through dramatic reduction of recalcitrance. MYB4-OX switchgrass is an excellent model system for understanding recalcitrance, and provides new germplasm for developing switchgrass cultivars as biomass feedstocks for biofuel production. Keywords: Switchgrass; Bioenergy; Biofuel; Feedstock; Cellulosic ethanol; PvMYB4; Transcription factor; Cell wall; Recalcitrance; Lignin; Hemicellulose; Pecti

New perspectives on the ecology of early domestic fowl: an interdisciplinary approach.

Introduced into Europe during the Bronze- and Iron Ages as an exotic, non-native species, very little is currently understood about the origins and spread of early domestic fowl, Gallus gallus domesticus. Ecological niche modelling of extant Red Junglefowl, Gallus gallus, presents a unique opportunity to examine historical ecological implications associated with its descendant, the chicken, in early stages of domestication. We model the environmental conditions associated with Red Junglefowl populations both in south-east Asia, where the bird originates, and populations transported further afield as a consequence of human interaction. This allows us to establish the full extent of the ecological tolerance of the ancestor bird. We show that potential for suitable sets of environmental conditions for Red Junglefowl in Europe ranges from poor to limited, based on both current climate and when projecting to mid-Holocene (ca. 4000BC) climate simulations. This suggests that human intervention played a vital contribution during early domestication to ensure the future widespread success of the chicken. These conclusions offer new insights into the archaeological evidence. We identify areas in the native range as the probable location of first domestication, and not China as has been suggested. We suggest that a dispersal route into Europe via the Mediterranean offers the best ecological potential to aid survival for a recently domesticated version of this species. Identifying the environmental tolerances of Red Junglefowl may also aid future conservation of this species, now highly endangered in its true wild form

Downregulation of a UDP-Arabinomutase Gene in Switchgrass (Panicum virgatum L.) Results in Increased Cell Wall Lignin While Reducing Arabinose-Glycans

Background: Switchgrass (Panicum virgatum L.) is a C4 perennial prairie grass and a dedicated feedstock for lignocellulosic biofuels. Saccharification and biofuel yields are inhibited by the plant cell wall’s natural recalcitrance against enzymatic degradation. Plant hemicellulose polysaccharides such as arabinoxylans structurally support and cross-link other cell wall polymers. Grasses predominately have Type II cell walls that are abundant in arabinoxylan, which comprise nearly 25% of aboveground biomass. A primary component of arabinoxylan synthesis is uridine diphosphate (UDP) linked to arabinofuranose (Araf). A family of UDP-arabinopyranose mutase (UAM)/reversible glycosylated polypeptides catalyze the interconversion between UDP-arabinopyranose (UDP-Arap) and UDP-Araf. Results: The expression of a switchgrass arabinoxylan biosynthesis pathway gene, PvUAM1, was decreased via RNAi to investigate its role in cell wall recalcitrance in the feedstock. PvUAM1 encodes a switchgrass homolog of UDP-arabinose mutase, which converts UDP-Arap to UDP-Araf. Southern blot analysis revealed each transgenic line contained between one to at least seven T-DNA insertions, resulting in some cases, a 95% reduction of native PvUAM1 transcript in stem internodes. Transgenic plants had increased pigmentation in vascular tissues at nodes, but were otherwise similar in morphology to the non-transgenic control. Cell wall-associated arabinose was decreased in leaves and stems by over 50%, but there was an increase in cellulose. In addition, there was a commensurate change in arabinose side chain extension. Cell wall lignin composition was altered with a concurrent increase in lignin content and transcript abundance of lignin biosynthetic genes in mature tillers. Enzymatic saccharification efficiency was unchanged in the transgenic plants relative to the control. Conclusion: Plants with attenuated PvUAM1 transcript had increased cellulose and lignin in cell walls. A decrease in cell wall-associated arabinose was expected, which was likely caused by fewer Araf residues in the arabinoxylan. The decrease in arabinoxylan may cause a compensation response to maintain cell wall integrity by increasing cellulose and lignin biosynthesis. In cases in which increased lignin is desired, e.g., feedstocks for carbon fiber production, downregulated UAM1 coupled with altered expression of other arabinoxylan biosynthesis genes might result in even higher production of lignin in biomass

Developing a nature recovery network using systematic conservation planning

Conservation area networks in most countries are fragmented and inadequate. To tackle this in England, government policies are encouraging stakeholders to create local-level nature recovery networks. Here, we describe work led by a wildlife organization that used the systematic conservation planning approach to identify a nature recovery network for three English counties and select focal areas within it where they will focus their work. The network was based on identifying core zones to maintain current biodiversity and recovery zones for habitat restoration, meeting area-based targets for 50 priority habitat, landscape, landcover, and ecosystem service types. It included the existing designated sites for conservation, which cover 6.05% of the study site, and identified an additional 11.6% of land as core zones and 18% as recovery zones, reflecting the organization's call for 30% of England to be conserved and connected by 2030. We found that systematic conservation planning worked well in this context, identifying a connected, adequate, representative, and efficient network and producing transparent and repeatable results. The analysis also highlighted the pressing need for government agencies to provide national-level guidance and datasets for setting targets and including species data in spatial planning, creating a national framework to inform local action

Ethanol and High-Value Terpene Co-Production from Lignocellulosic Biomass of Cymbopogon flexuosus and Cymbopogon martinii

Cymbopogon flexuosus, lemongrass, and C. martinii, palmarosa, are perennial grasses grown to produce essential oils for the fragrance industry. The objectives of this study were (1) to evaluate biomass and oil yields as a function of nitrogen and sulfur fertilization, and (2) to characterize their utility for lignocellulosic ethanol compared to Panicum virgatum (switchgrass). Mean biomass yields were 12.83 Mg lemongrass ha⁻¹ and 15.11 Mg palmarosa ha⁻¹ during the second harvest year resulting in theoretical biofuel yields of 2541 and 2569 L ethanol ha⁻¹ respectively compared to reported 1749–3691 L ethanol ha⁻¹ for switchgrass. Pretreated lemongrass yielded 198 mL ethanol (g biomass)⁻¹ and pretreated palmarosa yielded 170 mL ethanol (g biomass)⁻¹. Additionally, lemongrass yielded 85.7 kg essential oil ha⁻¹ and palmarosa yielded 67.0 kg ha⁻¹ with an estimated value of USD $857 and$1005 ha⁻¹. These data suggest that dual-use crops such as lemongrass and palmarosa may increase the economic viability of lignocellulosic biofuels