Error, Bias, and Long-Branch Attraction in Data for Two Chloroplast Photosystem Genes in Seed Plants

Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brady

The role of relational capabilities in developing the capacity for supply chain innovation

The purpose of this paper is to gain a better understanding of the types of relational capabilities supply chain participants develop to enable ongoing supply chain innovation capacity building that produces improved business outcomes. This is exploratory research using qualitative data gathered by using five interviews, with the Australian road freight industry as the context. Two key relational capabilities and the improvement of four key business outcomes were identified as being present in the interaction of freight transport service providers with members of their supply chain. The data also demonstrates that by entering into competence building relationships with customers and suppliers firms can build capabilities that will increase their capacity for supply chain innovation. Even in short term arm’s length relationships firms can acquire improved skills behaviours and practices that enhance their operation effectiveness and the efficiency of the supply chain relationships.

Construction supply chain development interim report

The supply chain in the construction industry is less well developed than in manufacturing. This project proposes to bring world class international business profile benchmarking to assist in the development of small and medium sized (SME) subcontractors. This approach has been widely used in Europe and has enabled significant sectoral supply chain development. The construction SME supply chain is a critical component in the delivery of all construction projects. Furthermore, it undermines the sustainability of the individual enterprise and puts construction projects and jobs at risk. Government procurement agencies view this as construction industry capacity building. In the developed and developing worlds, SME sector firms routinely make up over 95% of companies. The construction industry supply chain is dominated by such firms. Supply chain development and capacity building have been largely neglected in the construction sector, despite rhetoric about the importance of the SME sector to the economy This project seeks to investigate the potential to apply the International Business Profile Benchmarking instrument with the construction industry. The project recognises that there are many facets to the quest for continuous improvement in the construction industry and in wider workplace in general. This first interim report reviews the international literature relating to construction industry performance measurement and performance improvement. A summary of the findings follow. ‘Best value’ is dealt with in a separate interim report.

Construction supply chain economic policy implementation for sectoral change : moving beyond the rhetoric

Construction sector policy makers have the opportunity to create improvements and develop economic, social and environmental sustainability through supply chain economics. The idea of the supply chain concept to improve firm behaviour and industry performance is not new. However there has been limited application and little or no measurement to monitor successful implementation. Often purchasing policies have been developed with sound strategic procurement principles but even these have had limited penetration in to the processes and practices of infrastructure agencies. The research reported in this paper documents an action research study currently being undertaken in the Australian construction sector which aims to explore supply chain economic policy implementation for sectoral change by two government agencies. The theory which informs this study is the emerging area of construction supply chain economics. There are five stages to the project including; demand analysis, chain analysis, government agency organizational audit, supplier strategy and strategic alignment. The overall objective is towards the development of a Supplier Group Strategy Map for two public sector agencies. Two construction subsectors are examined in detail; construction and demolition waste and precast concrete. Both of these subsectors are critical to the economic and environmental sustainability performance of the construction sector and the community as a whole in the particular jurisdictions. The local and state government agencies who are at the core of the case studies rely individually on the performance of these sectors. The study is set within the context of a sound state purchasing policy that has however, had limited application by the two agencies. Partial results of the study are presented and early findings indicate that the standard risk versus expenditure procurement model does not capture the complexities of project, owner and government risk considerations. A new model is proposed in this paper, which incorporates the added dimension of time. The research results have numerous stakeholders; they will hold particular value for those interested in regional construction sector economics, government agencies who develop and implement policy and who have a large construction purchasing imprint and the players involved in the two subsectors. Even though this is a study in Australia it has widespread applicability as previous research indicates that procurement reform is of international significance and policy implementation is problematic.

Investigating the role of ICT in improving productivity in construction supply chains in Australian construction industry.

The Australian construction industry is a fragmented and profoundly competitive industry with high levels of subcontracting resulting in complex supply chain formations. Traditional methods and forms of communication are being proven as inefficient and losing their charm while participants face heavy volumes of communications that often occurs on a daily basis between trading partners in a supply chain on projects. Information Communication Technologies (ICT), due to their robustness and the ability to quickly disseminate data/information, have the capacity to address highlighted communication issues in a structured and an efficient manner. Timesavings produced by these can be directly translated in terms of productivity gain. This paper presents perceptions of subcontractors working in the construction industry in Melbourne Australia on the use of ICT obtained through an exploratory study.

Heavy truck suspension optimization based on modified skyhook damping control

This paper presents a multi-objective optimization strategy for heavy truck suspension systems based on modified skyhook damping (MSD) control, which improves ride comfort and road-friendliness simultaneously. A four-axle heavy truck-road coupling system model was established using functional virtual prototype technology; the model was then validated through a ride comfort test. As the mechanical properties and time lag of dampers were taken into account, MSD control of active and semi-active dampers was implemented using Matlab/Simulink. Through co-simulations with Adams and Matlab, the effects of passive, semi-active MSD control, and active MSD control were analyzed and compared; thus, control parameters which afforded the best integrated performance were chosen. Simulation results indicated that MSD control improves a truck’s ride comfort and roadfriendliness, while the semi-active MSD control damper obtains road-friendliness comparable to the active MSD control damper.

A study on matching and multi-objective fuzzy control strategy of heavy truck suspension system

Matching method of heavy truck-rear air suspensions is discussed, and a fuzzy control strategy which improves both ride comfort and road friendliness of truck by adjusting damping coefficients of the suspension system is found. In the first place, a Dongfeng EQ1141G7DJ heavy truck’s ten DOF whole vehicle-road model was set up based on Matlab/Simulink and vehicle dynamics. Then appropriate passive air suspensions were chosen to replace the original rear leaf springs of the truck according to truck-suspension matching criterions, consequently, the stiffness of front leaf springs were adjusted too. Then the semi-active fuzzy controllers were designed for further enhancement of the truck’s ride comfort and the road friendliness. After the application of semi-active fuzzy control strategy through simulation, is was indicated that both ride comfort and road friendliness could be enhanced effectively under various road conditions. The strategy proposed may provide theory basis for design and development of truck suspension system in China.

Multilineage differentiation potential of bone and cartilage cells derived from explant culture

To date, mesenchymal stem cells (MSCs) from various tissues have been reported, but the yield and differentiation potential of different tissue-derived MSCs is still not clear. This study was undertaken in an attempt to investigate the multilineage stem cell potential of bone and cartilage explant cultures in comparison with bone marrow derived mesenchymal stem cells (BMSCs). The results showed that the surface antigen expression of tissue-derived cells was consistent with that of mesenchymal stem cells, such as lacking the haematopoietic and common leukocyte markers (CD34, CD45) while expressing markers related to adhesion (CD29, CD166) and stem cells (CD90, CD105). The tissue-derived cells were able to differentiate into osteoblast, chondrocyte and adipocyte lineage pathways when stimulated in the appropriate differentiating conditions. However, compared with BMSCs, tissue-derived cells showed less capacity for multilineage differentiation when the level of differentiation was assessed in monolayer culture by analysing the expression of tissue-specific genes by reverse transcription polymerase chain reaction (RT-PCR) and histology. In high density pellet cultures, tissue-derived cells were able to differentiate into chondrocytes, expressing chondrocyte markers such as proteoglycans, type II collagen and aggrecan. Taken together, these results indicate that cells derived from tissue explant cultures reserved certain degree of differentiation properties of MSCs in vitro.

Determining heavy vehicle suspension health from vibratory wheel loads

A low-cost test bed was made from a modified heavy vehicle (HV) brake tester. By rotating a test HV’s wheel on an eccentric roller, a known vibration was imparted to the wheel under test. A control case for dampers in good condition was compared with two test cases of ineffective shock absorbers. Measurement of the forces at the bearings of the roller provided an indication of the HV wheel-forces. Where the level of serviceability of the shock absorbers varied, differences in wheel load provided a quality indicator corresponding to a change of damper characteristic. Conclusions regarding the levels of damper maintenance beyond which HV suspensions cause road damage and dynamic wheel forces at the threshold of tyre wear at which HV shock absorbers are normally replaced are presented.

Supply chain sustainability: a relationship management approach

Purpose: In this research we examined, by means of case studies, the mechanisms by which relationships can be managed and by which communication and cooperation can be enhanced in sustainable supply chains. The research was predicated on the contention that the development of a sustainable supply chain depends, in part, on the transfer of knowledge and capabilities from the larger players in the supply chain. Design/Methodology/Approach: The research adopted a triangulated approach in which quantitative data were collected by questionnaire, interviews were conducted to explore and enrich the quantitative data and case studies were undertaken in order to illustrate and validate the findings. Handy‟s (1985) view of organisational culture, Allen & Meyer‟s (1990) concepts of organisational commitment and Van de Ven & Ferry‟s (1980) measures of organisational structuring have been combined into a model to test and explain how collaborative mechanisms can affect supply chain sustainability. Findings: It has been shown that the degree of match and mismatch between organisational culture and structure has an impact on staff‟s commitment level. A sustainable supply chain depends on convergence – that is the match between organisational structuring, organisation culture and organisation commitment. Research Limitations/implications: The study is a proof of concept and three case studies have been used to illustrate the nature of the model developed. Further testing and refinement of the model in practice should be the next step in this research. Practical implications: The concept of relationship management needs to filter down to all levels in the supply chain if participants are to retain commitment and buy-in to the relationship. A sustainable supply chain requires proactive relationship management and the development of an appropriate organisational culture, and trust. By legitimising individuals‟ expectations of the type of culture which is appropriate to their company and empowering employees to address mismatches that may occur a situation can be created whereby the collaborating organisations develop their competences symbiotically and so facilitate a sustainable supply chain. Originality/value: The culture/commitment/structure model developed from three separate strands of management thought has proved to be a powerful tool for analysing collaboration in supply chains and explaining how and why some supply chains are sustainable, and others are not.

Investigating relationships between relationship quality, customer loyalty and cooperation : an empirical study of convenience stores' franchise chain systems in Taiwan

Franchising has been widely accepted as an effective way to conduct and expand businesses. However, a franchise system is not a guarantee of success in the market. A successful franchise system should rely on a close and strong franchising relationship. Franchising is an important relationship management business. Franchising arrangements normally last for a number of years, so the franchisor and franchisee in the arrangement relationship are usually motivated to cooperate with each other. In addition, highly loyal franchisees may be obtained through a successful long-term franchising relationship. Over the last few decades, there has been a tremendous wave of interest in franchising relationships. However, little research has been conducted to determine the reasons for long-term franchising relationships. As a result, this study focuses on the important elements that might lead to a successful long-term franchising relationship. This study attempts to examine empirically three essential constructs (relationship quality, cooperation and customer loyalty), which might lead to successful long-term franchising relationships between franchisees and franchisors among the convenience stores in Taiwan. Mailed questionnaires were utilised to collect the research data. A total of 500 surveys were mailed randomly to the manager/supervisor of convenience stores’ franchisees among the four main franchisors (7-ELEVEN, Family, Hi-Life and OK) in Taiwan. The final sample size is 120, yielding a response rate of 24 per cent. The results show that relationship quality positively influences the cooperative relationships between franchisors and franchisees. Relationship quality is also positively correlated with franchisees’ loyalty. Additionally, the results indicate that the cooperative relationships between franchisors and franchisees are significantly associated with franchisees’ loyalty.

A re-examination of the Ghrelin and Ghrelin receptor genes

The last few years have seen dramatic advances in genomics, including the discovery of a large number of non-coding and antisense transcripts. This has revolutionised our understanding of multifaceted transcript structures found within gene loci and their roles in the regulation of development, neurogenesis and other complex processes. The recent and continuing surge of knowledge has prompted researchers to reassess and further dissect gene loci. The ghrelin gene (GHRL) gives rise to preproghrelin, which in turn produces ghrelin, a 28 amino acid peptide hormone that acts via the ghrelin receptor (growth hormone secretagogue receptor/GHSR 1a). Ghrelin has many important physiological and pathophysiological roles, including the stimulation of growth hormone (GH) release, appetite regulation, and cancer development. A truncated receptor splice variant, GHSR 1b, does not bind ghrelin, but dimerises with GHSR 1a, and may act as a dominant negative receptor. The gene products of ghrelin and its receptor are frequently overexpressed in human cancer While it is well known that the ghrelin axis (ghrelin and its receptor) plays a range of important functional roles, little is known about the molecular structure and regulation of the ghrelin gene (GHRL) and ghrelin receptor gene (GHSR). This thesis reports the re-annotation of the ghrelin gene, discovery of alternative 5’ exons and transcription start sites, as well as the description of a number of novel splice variants, including isoforms with a putative signal peptide. We also describe the discovery and characterisation of a ghrelin antisense gene (GHRLOS), and the discovery and expression of a ghrelin receptor (growth hormone secretagogue receptor/GHSR) antisense gene (GHSR-OS). We have identified numerous ghrelin-derived transcripts, including variants with extended 5' untranslated regions and putative secreted obestatin and C-ghrelin transcripts. These transcripts initiate from novel first exons, exon -1, exon 0 and a 5' extended 1, with multiple transcription start sites. We used comparative genomics to identify, and RT-PCR to experimentally verify, that the proximal exon 0 and 5' extended exon 1 are transcribed in the mouse ghrelin gene, which suggests the mouse and human proximal first exon architecture is conserved. We have identified numerous novel antisense transcripts in the ghrelin locus. A candidate non-coding endogenous natural antisense gene (GHRLOS) was cloned and demonstrates very low expression levels in the stomach and high levels in the thymus, testis and brain - all major tissues of non-coding RNA expression. Next, we examined if transcription occurs in the antisense orientation to the ghrelin receptor gene, GHSR. A novel gene (GHSR-OS) on the opposite strand of intron 1 of the GHSR gene was identified and characterised using strand-specific RT-PCR and rapid amplification of cDNA ends (RACE). GHSR-OS is differentially expressed and a candidate non-coding RNA gene. In summary, this study has characterised the ghrelin and ghrelin receptor loci and demonstrated natural antisense transcripts to ghrelin and its receptor. Our preliminary work shows that the ghrelin axis generates a broad and complex transcriptional repertoire. This study provides the basis for detailed functional studies of the the ghrelin and GHSR loci and future studies will be needed to further unravel the function, diagnostic and therapeutic potential of the ghrelin axis.

The manipulation of apoptosis-related genes to generate resistance to Fusarium wilt and water stress in banana

Bananas are susceptible to a diverse range of biotic and abiotic stresses, many of which cause serious production constraints worldwide. One of the most destructive banana diseases is Fusarium wilt caused by the soil-borne fungus, Fusarium oxysporum f. sp. cubense (Foc). No effective control strategy currently exists for this disease which threatens global banana production. Although disease resistance exists in some wild bananas, attempts to introduce resistance into commercially acceptable bananas by conventional breeding have been hampered by low fertility, long generation times and association of poor agronomical traits with resistance genes. With the advent of reliable banana transformation protocols, molecular breeding is now regarded as a viable alternative strategy to generate disease-resistant banana plants. Recently, a novel strategy involving the expression of anti-apoptosis genes in plants was shown to result in resistance against several necrotrophic fungi. Further, the transgenic plants showed increased resistance to a range of abiotic stresses. In this thesis, the use of anti-apoptosis genes to generate transgenic banana plants with resistance to Fusarium wilt was investigated. Since water stress is an important abiotic constraint to banana production, the resistance of the transgenic plants to water stress was also examined. Embryogenic cell suspensions (ECS) of two commercially important banana cultivars, Grand Naine (GN) and Lady Finger (LF), were transformed using Agrobacterium with the anti-apoptosis genes, Bcl-xL, Bcl-xL G138A, Ced-9 and Bcl- 2 3’ UTR. An interesting, and potentially important, outcome was that the use of anti-apoptosis genes resulted in up to a 50-fold increase in Agrobacterium-mediated transformation efficiency of both LF and GN cells over vector controls. Regenerated plants were subjected to a complete molecular characterisation in order to detect the presence of the transgene (PCR), transcript (RT-PCR) and gene product (Western blot) and to determine the gene copy number (Southern blot). A total of 36 independently-transformed GN lines (8 x Bcl-xL, 5 x Bcl-xL G138A, 15 x Ced-9 and 8 x Bcl-2 3’ UTR) and 41 independently-transformed LF lines (8 x Bcl-xL, 7 x BclxL G138A, 13 x Ced-9 and 13 x Bcl-2 3’ UTR) were identified. The 41 transgenic LF lines were multiplied and clones from each line were acclimatised and grown under glasshouse conditions for 8 weeks to allow monitoring for phenotypic abnormalities. Plants derived from 3 x Bcl-xL, 2 x Ced-9 and 5 x Bcl-2 3’ UTR lines displayed a variety of aberrant phenotypes. However, all but one of these abnormalities were off-types commonly observed in tissue-cultured, non-transgenic banana plants and were therefore unlikely to be transgene-related. Prior to determining the resistance of the transgenic plants to Foc race 1, the apoptotic effects of the fungus on both wild-type and Bcl-2 3’ UTR-transgenic LF banana cells were investigated using rapid in vitro root assays. The results from these assays showed that apoptotic-like cell death was elicited in wild-type banana root cells as early as 6 hours post-exposure to fungal spores. In contrast, these effects were attenuated in the root cells of Bcl-2 3’ UTR-transgenic lines that were exposed to fungal spores. Thirty eight of the 41 transgenic LF lines were subsequently assessed for resistance to Foc race 1 in small-plant glasshouse bioassays. To overcome inconsistencies in rating the internal (vascular discolouration) disease symptoms, a MatLab-based computer program was developed to accurately and reliably assess the level of vascular discolouration in banana corms. Of the transgenic LF banana lines challenged with Foc race 1, 2 x Bcl-xL, 3 x Ced-9, 2 x Bcl-2 3’ UTR and 1 x Bcl-xL G138A-transgenic line were found to show significantly less external and internal symptoms than wild-type LF banana plants used as susceptible controls at 12 weeks post-inoculation. Of these lines, Bcl-2 3’ UTR-transgenic line #6 appeared most resistant, displaying very mild symptoms similar to the wild-type Cavendish banana plants that were included as resistant controls. This line remained resistant for up to 23 weeks post-inoculation. Since anti-apoptosis genes have been shown to confer resistance to various abiotic stresses in other crops, the ability of these genes to confer resistance against water stress in banana was also investigated. Clonal plants derived from each of the 38 transgenic LF banana plants were subjected to water stress for a total of 32 days. Several different lines of transgenic plants transformed with either Bcl-xL, Bcl-xL G138A, Ced-9 or Bcl-2 3’ UTR showed a delay in visual water stress symptoms compared with the wild-type control plants. These plants all began producing new growth from the pseudostem following daily rewatering for one month. In an attempt to determine whether the protective effect of anti-apoptosis genes in transgenic banana plants was linked with reactive oxygen species (ROS)-associated programmed cell death (PCD), the effect of the chloroplast-targeting, ROS-inducing herbicide, Paraquat, on wild-type and transgenic LF was investigated. When leaf discs from wild-type LF banana plants were exposed to 10 ìM Paraquat, complete decolourisation occurred after 48 hours which was confirmed to be associated with cell death and ROS production by trypan blue and 3,3-diaminobenzidine (DAB) staining, respectively. When leaf discs from the transgenic lines were exposed to Paraquat, those derived from some lines showed a delay in decolourisation, suggesting only a weak protective effect from the transgenes. Finally, the protective effect of anti-apoptosis genes against juglone, a ROS-inducing phytotoxin produced by the causal agent of black Sigatoka, Mycosphaerella fijiensis, was investigated. When leaf discs from wild-type LF banana plants were exposed to 25 ppm juglone, complete decolourisation occurred after 48 hours which was again confirmed to be associated with cell death and ROS production by trypan blue and DAB staining, respectively. Further, TdT-mediated dUTP nick-end labelling (TUNEL) assays on these discs suggested that the cell death was apoptotic. When leaf discs from the transgenic lines were exposed to juglone, discs from some lines showed a clear delay in decolourisation, suggesting a protective effect. Whether these plants are resistant to black Sigatoka is unknown and will require future glasshouse and field trials. The work presented in this thesis provides the first report of the use of anti-apoptosis genes as a strategy to confer resistance to Fusarium wilt and water stress in a nongraminaceous monocot, banana. Such a strategy may be exploited to generate resistance to necrotrophic pathogens and abiotic stresses in other economically important crop plants.

Molecular architecture of the human sinus node: insights into the function of the cardiac pacemaker.

BACKGROUND: Although we know much about the molecular makeup of the sinus node (SN) in small mammals, little is known about it in humans. The aims of the present study were to investigate the expression of ion channels in the human SN and to use the data to predict electrical activity. METHODS AND RESULTS: Quantitative polymerase chain reaction, in situ hybridization, and immunofluorescence were used to analyze 6 human tissue samples. Messenger RNA (mRNA) for 120 ion channels (and some related proteins) was measured in the SN, a novel paranodal area, and the right atrium (RA). The results showed, for example, that in the SN compared with the RA, there was a lower expression of Na(v)1.5, K(v)4.3, K(v)1.5, ERG, K(ir)2.1, K(ir)6.2, RyR2, SERCA2a, Cx40, and Cx43 mRNAs but a higher expression of Ca(v)1.3, Ca(v)3.1, HCN1, and HCN4 mRNAs. The expression pattern of many ion channels in the paranodal area was intermediate between that of the SN and RA; however, compared with the SN and RA, the paranodal area showed greater expression of K(v)4.2, K(ir)6.1, TASK1, SK2, and MiRP2. Expression of ion channel proteins was in agreement with expression of the corresponding mRNAs. The levels of mRNA in the SN, as a percentage of those in the RA, were used to estimate conductances of key ionic currents as a percentage of those in a mathematical model of human atrial action potential. The resulting SN model successfully produced pacemaking. CONCLUSIONS: Ion channels show a complex and heterogeneous pattern of expression in the SN, paranodal area, and RA in humans, and the expression pattern is appropriate to explain pacemaking.