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

An evaluation of viability of public private partnerships in social infrastructure procurement projects in Queensland, Australia

Public private partnerships (PPP) have been widely used as a method for public infrastructure project delivery not only locally and internationally, however the adoption of PPPs in social infrastructure procurement has still been very limited. The objective of this paper is to investigate the potential of implementation of current PPP framework in social affordable housing projects in South East Queensland. Data were collected from 22 interviewees with rich experiences in the industry. The findings of this study show that affordable housing investment have been considered by the industry practitioners as a risky business in comparison to other private rental housing investment. The main determents of the adoption of PPPs in social infrastructure project are the tenant-related factors, such as the inability of paying rent and the inability of caring the property. The study also suggests the importance of seeking strategic partnership with community-based organisation that has experiences in managing similar tenants’ profiles. Current PPP guideline is also viewed as inappropriate for the affordable housing projects, but the principle of VFM framework and risk allocation in PPPs still be applied to the affordable housing projects. This study helps to understand the viability of PPP in social housing procurement projects, and point out the importance of developing guideline for multi-stakeholder partnership and the expansion of the current VFM and PPPs guidelines.

Utilisation of seed resources by small mammals : a two-way interaction

Within the Australian wet tropics bioregion, only 900 000 hectares of once continuous rainforest habitat between Townsville and Cooktown now remains. While on the Atherton Tableland, only 4% of the rainforest that once occurred there remains today with remnant vegetation now forming a matrix of rainforest dispersed within agricultural land (sugarcane, banana, orchard crops, townships and pastoral land). Some biologists have suggested that remnants often support both faunal and floral communities that differ significantly from remaining continuous forest. Australian tropical forests possess a relatively high diversity of native small mammal species particularly rodents, which unlike larger mammalian and avian frugivores elsewhere, have been shown to be resilient to the effects of fragmentation, patch isolation and reduction in patch size. While small mammals often become the dominant mammalian frugivores, in terms of their relative abundance, the relationship that exists between habitat diversity and structure, and the impacts of small mammal foraging within fragmented habitat patches in Australia, is still poorly understood. The relationship between foraging behaviour and demography of two small mammal species, Rattus fuscipes and Melomys cervinipes, and food resources in fragmented rainforest sites, were investigated in the current study. Population densities of both species were strongly related with overall density of seed resources in all rainforest fragments. The distribution of both mammal species however, was found to be independent of the distribution of seed resources. Seed utilisation trials indicated that M.cervinipes and R.fuscipes had less impact on seed resources (extent of seed harvesting) than did other rainforest frugivores. Experimental feeding trials demonstrated that in 85% of fruit species tested, rodent feeding increased seed germination by a factor of 3.5 suggesting that in Australian tropical rainforest remnants, small mammals may play a significant role in enhancing germination of large seeded fruits. This study has emphasised the role of small mammals in tropical rainforest systems in north eastern Australia, in particular, the role that they play within isolated forest fragments where larger frugivorous species may be absent.

If it's encrypted it's secure! The viability of US state-based encryption exemptions

US state-based data breach notification laws have unveiled serious corporate and government failures regarding the security of personal information. These laws require organisations to notify persons who may be affected by an unauthorized acquisition of their personal information. Safe harbours to notification exist if personal information is encrypted. Three types of safe harbour have been identified in the literature: exemptions, rebuttable presumptions and factors. The underlying assumption of exemptions is that encrypted personal information is secure and therefore unauthorized access does not pose a risk. However, the viability of this assumption is questionable when examined against data breaches involving encrypted information and the demanding practical requirements of effective encryption management. Recent recommendations by the Australian Law Reform Commission (ALRC) would amend the Privacy Act 1988 (Cth) to implement a data breach scheme that includes a different type of safe harbour, factor based analysis. The authors examine the potential capability of the ALRC’s proposed encryption safe harbour in relation to the US experience at the state legislature level.

Expansion and chondrogenic potential of human articular chondrocytes on macroporous microcarriers

Regenerative medicine techniques are currently being investigated to replace damaged cartilage. Critical to the success of these techniques is the ability to expand the initial population of cells while minimising de-differentiation to allow for hyaline cartilage to form. Three-dimensional culture systems have been shown to enhance the differentiation of chondrocytes in comparison to two-dimensional culture systems. Additionally, bioreactor expansion on microcarriers can provide mechanical stimulation and reduce the amount of cellular manipulation during expansion. The aim of this study was to characterise the expansion of human chondrocytes on microcarriers and to determine their potential to form cartilaginous tissue in vitro. High-grade human articular cartilage was obtained from leg amputations with ethics approval. Chondrocytes were isolated by collagenase digestion and expanded in either monolayers (104 cells/cm2) or on CultiSpher-G microcarriers (104 cells/mg) for three weeks. Following expansion, monolayer cells were passaged and cells on microcarriers were either left intact or the cells were released with trypsin/EDTA. Pellets from these three groups were formed and cultured for three weeks to establish the chondrogenic differentiation potential of monolayer-expanded and microcarrier-expanded chondrocytes. Cell viability, proliferation, glycosaminoglycan (GAG) accumulation, and collagen synthesis were assessed. Histology and immunohistochemistry were also performed. Human chondrocytes remained viable and expanded on microcarriers 10.2±2.6 fold in three weeks. GAG content significantly increased with time, with the majority of GAG found in the medium. Collagen production per nanogram DNA increased marginally during expansion. Histology revealed that chondrocytes were randomly distributed on microcarrier surfaces yet most pores remained cell free. Critically, human chondrocytes expanded on microcarriers maintained their ability to redifferentiate in pellet culture, as demonstrated by Safranin-O and collagen II staining. These data confirm the feasibility of microcarriers for passage-free cultivation of human articular chondrocytes. However, cell expansion needs to be improved, perhaps through growth factor supplementation, for clinical utility. Recent data indicate that cell-laden microcarriers can be used to seed fresh microcarriers, thereby increasing the expansion factor while minimising enzymatic passage.

Differences between in vitro viability and differentiation and in vivo bone-forming efficacy of human mesenchymal stem cells cultured on PCL-TCP scaffolds

Human mesenchymal stem cells (hMSCs) possess great therapeutic potential for the treatment of bone disease and fracture non-union. Too often however, in vitro evidence alone of the interaction between hMSCs and the biomaterial of choice is used as justification for continued development of the material into the clinic. Clearly for hMSC-based regenerative medicine to be successful for the treatment of orthopaedic trauma, it is crucial to transplant hMSCs with a suitable carrier that facilitates their survival, optimal proliferation and osteogenic differentiation in vitro and in vivo. This motivated us to evaluate the use of polycaprolactone-20% tricalcium phosphate (PCL-TCP) scaffolds produced by fused deposition modeling for the delivery of hMSCs. When hMSCs were cultured on the PCL-TCP scaffolds and imaged by a combination of phase contrast, scanning electron and confocal laser microscopy, we observed five distinct stages of colonization over a 21-day period that were characterized by cell attachment, spreading, cellular bridging, the formation of a dense cellular mass and the accumulation of a mineralized extracellular matrix when induced with osteogenic stimulants. Having established that PCL-TCP scaffolds are able to support hMSC proliferation and osteogenic differentiation, we next tested the in vivo efficacy of hMSC-loaded PCL-TCP scaffolds in nude rat critical-sized femoral defects. We found that fluorescently labeled hMSCs survived in the defect site for up to 3 weeks post-transplantation. However, only 50% of the femoral defects treated with hMSCs responded favorably as determined by new bone volume. As such, we show that verification of hMSC viability and differentiation in vitro is not sufficient to predict the efficacy of transplanted stem cells to consistently promote bone formation in orthotopic defects in vivo.

Seed Transmission of Broad Bean Stain Virus in the Wild Legume Vicia Palestina Boiss

Abstract Seed-transmissibility of brood bean stain virus (BBSV) was investigated in a number of wild legume species. Genninating axes of seeds coliected from BBSV -infected plants were tested by the enzyme-linked immunosorbent assay (ELISA). The virus was found to be seedtransmitted in Vida pal«stina.

Pseudoseeds : investigating long-distance, ocean seed dispersal with wireless sensors

Recent theoretical research has shown that ocean currents and wind interact to disperse seeds over long distances among isolated landmasses. Dispersal of seeds among isolated oceanic islands, by birds, oceans and man, is a well-known phenomenon, and many widespread island plants have traits that facilitate this process. Crucially, however, there have been no mechanistic vector-based models of long-distance dispersal for seeds among isolated oceanic islands based on empirical data. Here, we propose a plan to develop seed analogues, or pseudoseeds, fitted with wireless sensor technology that will enable high-fidelity tracking as they disperse across the ocean. The pseudoseeds will be precisely designed to mimic actual seed buoyancy and morphology enabling realistic and accurate, vector-based dispersal models of ocean seed dispersal over vast geographic scales.

Computer planning of stereotactic iodine-125 seed brachytherapy for recurrent malignant gliomas

At St Thomas' Hospital, we have developed a computer program on a Titan graphics supercomputer to plan the stereotactic implantation of iodine-125 seeds for the palliative treatment of recurrent malignant gliomas. Use of the Gill-Thomas-Cosman relocatable frame allows planning and surgery to be carried out at different hospitals on different days. Stereotactic computed tomography (CT) and positron emission tomography (PET) scans are performed and the images transferred to the planning computer. The head, tumour and frame fiducials are outlined on the relevant images, and a three-dimensional model generated. Structures which could interfere with the surgery or radiotherapy, such as major vessels, shunt tubing etc., can also be outlined and included in the display. Catheter target and entry points are set using a three-dimensional cursor controlled by a set of dials attached to the computer. The program calculates and displays the radiation dose distribution within the target volume for various catheter and seed arrangements. The CT co-ordinates of the fiducial rods are used to convert catheter co-ordinates from CT space to frame space and to calculate the catheter insertion angles and depths. The surgically implanted catheters are after-loaded the next day and the seeds left in place for between 4 and 6 days, giving a nominal dose of 50 Gy to the edge of the target volume. 25 patients have been treated so far.

The utilization of waste date seed as bio-oil and activated carbon by pyrolysis process

The renovation of biomass waste in the form of date seed waste into activated carbon and biofuel by fixed bed pyrolysis reactor has been focused in this study to obtain gaseous, liquid, and solid products. The date seed in particle form is pyrolysed in an externally heated fixed bed reactor with nitrogen as the carrier gas. The reactor is heated from 400◦C to 600◦C. A maximum liquid yield of 50wt.% and char of 30wt.% are obtained at a reactor bed temperature of 500◦C with a running time of 120 minutes. The oil is found to possess favorable flash point and reasonable density and viscosity. The higher calorific value is found to be 28.636 MJ/kg which is significantly higher than other biomass derived. Decolonization of 85–97% is recorded for the textile effluent and 75–90% for the tannery effluent, in all cases decreasing with temperature increase. Good adsorption capacity of the prepared activated carbon in case of diluted textile and tannery effluent was found.