Facile mutant identification via a single parental backcross method and application of whole genome sequencing based mapping pipelines

Forward genetic screens have identified numerous genes involved in development and metabolism, and remain a cornerstone of biological research. However, to locate a causal mutation, the practice of crossing to a polymorphic background to generate a mapping population can be problematic if the mutant phenotype is difficult to recognize in the hybrid F2 progeny, or dependent on parental specific traits. Here in a screen for leaf hyponasty mutants, we have performed a single backcross of an Ethane Methyl Sulphonate (EMS) generated hyponastic mutant to its parent. Whole genome deep sequencing of a bulked homozygous F2 population and analysis via the Next Generation EMS mutation mapping pipeline (NGM) unambiguously determined the causal mutation to be a single nucleotide polymorphisim (SNP) residing in HASTY, a previously characterized gene involved in microRNA biogenesis. We have evaluated the feasibility of this backcross approach using three additional SNP mapping pipelines; SHOREmap, the GATK pipeline, and the samtools pipeline. Although there was variance in the identification of EMS SNPs, all returned the same outcome in clearly identifying the causal mutation in HASTY. The simplicity of performing a single parental backcross and genome sequencing a small pool of segregating mutants has great promise for identifying mutations that may be difficult to map using conventional approaches.

Inferring diffusion in single live cells at the single-molecule level

The movement of molecules inside living cells is a fundamental feature of biological processes. The ability to both observe and analyse the details of molecular diffusion in vivo at the single-molecule and single-cell level can add significant insight into understanding molecular architectures of diffus- ing molecules and the nanoscale environment in which the molecules diffuse. The tool of choice for monitoring dynamic molecular localization in live cells is fluorescence microscopy, especially so combining total internal reflection fluorescence with the use of fluorescent protein (FP) reporters in offering exceptional imaging contrast for dynamic processes in the cell mem- brane under relatively physiological conditions compared with competing single-molecule techniques. There exist several different complex modes of diffusion, and discriminating these from each other is challenging at the mol- ecular level owing to underlying stochastic behaviour. Analysis is traditionally performed using mean square displacements of tracked particles; however, this generally requires more data points than is typical for single FP tracks owing to photophysical instability. Presented here is a novel approach allowing robust Bayesian ranking of diffusion processes to dis-criminate multiple complex modes probabilistically. It is a computational approach that biologists can use to understand single-molecule features in live cells.

A single copy of a virus-derived transgene encoding hairpin RNA gives immunity to barley yellow dwarf virus

Barley yellow dwarf virus-PAV (BYDV-PAV) is the most serious and widespread virus of cereals worldwide. Natural resistance genes against this luteovirus give inadequate control, and previous attempts to introduce synthetic resistance into cereals have produced variable results. In an attempt to generate barley with protection against BYDV-PAV, plants were transformed with a transgene designed to produce hairpin (hp)RNA containing BYDV-PAV sequences. From 25 independent barley lines transformed with the BYDV-PAV hpRNA construct, nine lines showed extreme resistance to the virus and the majority of these contained a single transgene. In the progeny of two independent transgenic lines, inheritance of a single transgene consistently correlated with protection against BYDV-PAV. This protection was rated as immunity because the virus could not be detected in the challenged plants by ELISA nor recovered by aphid feeding experiments. In the field, BYDV-PAV is sometimes associated with the related luteovirus Cereal yellow dwarf virus-RPV (CYDV-RPV). When the transgenic plants were challenged with BYDV-PAV and CYDV-RPV together, the plants were susceptible to CYDV-RPV but immune to BYDV-PAV. This shows that the immunity is virus-specific and not broken down by the presence of CYDV. It suggests that CYDV-RPV does not encode a silencing-suppressor gene or that its product does not protect BYDV-PAV against the plant's RNAi-like defence mechanism. Either way, our results indicate that the BYDV-PAV immunity will be robust in the field and is potentially useful in minimizing losses in cereal production worldwide.

Carrot red leaf and carrot mottle viruses : observations on the composition of the particles in single and mixed infections

Particles of carrot red leaf virus (CRLV; luteovirus group) purified from chervil (Anthriscus cerefolium) contain a single ssRNA species of mol. wt. about 1.8 x 106 and a major protein of mol. wt. about 25000. CRLV acts as a helper for aphid transmission of carrot mottle virus (CMotV; ungrouped) from mixedly infected plants. Virus preparations purified from such plants possess the infectivity of both viruses but contain particles indistinguishable from those of CRLV; some of the particles are therefore thought to consist of CMotV RNA packaged in CRLV coat protein. When RNA from such preparations was electrophoresed in agarose/polyacrylamide gels, CMotV infectivity was associated with an RNA band that migrated ahead of the CRLV RNA band and had an estimated mol. wt. of about 1.5 x 106, similar to that previously found for the infective ssRNA extracted directly from Nicotiana clevelandii leaves infected with CMotV alone. Preparations of dsRNA from CMotV-infected N. clevelandii leaves contained two species: one of mol. wt. about 3.2 x 106, presumably the replicative form of the infective ssRNA, and the other, mol. wt. about 0.9 x 106, of unknown origin and function. The infective agent in buffer extracts of CMotV-infected N. clevelandii was resistant to RNase (although the enzyme acted as a reversible inhibitor of infection at high concentrations) and is therefore not unprotected RNA. It may be protected within the approximately 52 nm enveloped structures previously reported.

Modelling survival data to account for model uncertainty: a single model or model averaging?

This study considered the problem of predicting survival, based on three alternative models: a single Weibull, a mixture of Weibulls and a cure model. Instead of the common procedure of choosing a single “best” model, where “best” is defined in terms of goodness of fit to the data, a Bayesian model averaging (BMA) approach was adopted to account for model uncertainty. This was illustrated using a case study in which the aim was the description of lymphoma cancer survival with covariates given by phenotypes and gene expression. The results of this study indicate that if the sample size is sufficiently large, one of the three models emerge as having highest probability given the data, as indicated by the goodness of fit measure; the Bayesian information criterion (BIC). However, when the sample size was reduced, no single model was revealed as “best”, suggesting that a BMA approach would be appropriate. Although a BMA approach can compromise on goodness of fit to the data (when compared to the true model), it can provide robust predictions and facilitate more detailed investigation of the relationships between gene expression and patient survival. Keywords: Bayesian modelling; Bayesian model averaging; Cure model; Markov Chain Monte Carlo; Mixture model; Survival analysis; Weibull distribution

A novel energy efficient controllable stiffness joint

Achieving energy efficient legged locomotion is an important goal for the future of robot mobility. This paper presents a novel joint for legged locomotion that is energy efficient for two reasons. The first reason is the configuration of the elastic elements and actuator which we show analytically has lower energy losses than the typical arrangement. The second is that the joint stiffness, and hence stance duration, is controllable without requiring any energy from the actuator. Further, the joint stiffness can be changed significantly during the flight phase, from zero to highly rigid. Results obtained from a prototype hopper, demonstrate that the joint allows continuous and peak hopping via torque control. The results also demonstrate that the hopping frequency can be varied between 2.2Hz and 4.6Hz with associated stance duration of between 0.35 and 0.15 seconds.

Bayesian inference of traffic volumes based on Bluetooth data

The study of the relationship between macroscopic traffic parameters, such as flow, speed and travel time, is essential to the understanding of the behaviour of freeway and arterial roads. However, the temporal dynamics of these parameters are difficult to model, especially for arterial roads, where the process of traffic change is driven by a variety of variables. The introduction of the Bluetooth technology into the transportation area has proven exceptionally useful for monitoring vehicular traffic, as it allows reliable estimation of travel times and traffic demands. In this work, we propose an approach based on Bayesian networks for analyzing and predicting the complex dynamics of flow or volume, based on travel time observations from Bluetooth sensors. The spatio-temporal relationship between volume and travel time is captured through a first-order transition model, and a univariate Gaussian sensor model. The two models are trained and tested on travel time and volume data, from an arterial link, collected over a period of six days. To reduce the computational costs of the inference tasks, volume is converted into a discrete variable. The discretization process is carried out through a Self-Organizing Map. Preliminary results show that a simple Bayesian network can effectively estimate and predict the complex temporal dynamics of arterial volumes from the travel time data. Not only is the model well suited to produce posterior distributions over single past, current and future states; but it also allows computing the estimations of joint distributions, over sequences of states. Furthermore, the Bayesian network can achieve excellent prediction, even when the stream of travel time observation is partially incomplete.

Second-order elastic finite element analysis of steel structures using a single element per member

Finite element frame analysis programs targeted for design office application necessitate algorithms which can deliver reliable numerical convergence in a practical timeframe with comparable degrees of accuracy, and a highly desirable attribute is the use of a single element per member to reduce computational storage, as well as data preparation and the interpretation of the results. To this end, a higher-order finite element method including geometric non-linearity is addressed in the paper for the analysis of elastic frames for which a single element is used to model each member. The geometric non-linearity in the structure is handled using an updated Lagrangian formulation, which takes the effects of the large translations and rotations that occur at the joints into consideration by accumulating their nodal coordinates. Rigid body movements are eliminated from the local member load-displacement relationship for which the total secant stiffness is formulated for evaluating the large member deformations of an element. The influences of the axial force on the member stiffness and the changes in the member chord length are taken into account using a modified bowing function which is formulated in the total secant stiffness relationship, for which the coupling of the axial strain and flexural bowing is included. The accuracy and efficiency of the technique is verified by comparisons with a number of plane and spatial structures, whose structural response has been reported in independent studies.

Perioperative medication management: expanding the role of the preadmission clinic pharmacist in a single centre, randomised controlled trial of collaborative prescribing

Objectives Current evidence to support non-medical prescribing is predominantly qualitative, with little evaluation of accuracy, safety and appropriateness. Our aim was to evaluate a new model of service for the Australia healthcare system, of inpatient medication prescribing by a pharmacist in an elective surgery preadmission clinic (PAC) against usual care, using an endorsed performance framework. Design Single centre, randomised controlled, two-arm trial. Setting Elective surgery PAC in a Brisbane-based tertiary hospital. Participants 400 adults scheduled for elective surgery were randomised to intervention or control. Intervention A pharmacist generated the inpatient medication chart to reflect the patient's regular medication, made a plan for medication perioperatively and prescribed venous thromboembolism (VTE) prophylaxis. In the control arm, the medication chart was generated by the Resident Medical Officers. Outcome measures Primary outcome was frequency of omissions and prescribing errors when compared against the medication history. The clinical significance of omissions was also analysed. Secondary outcome was appropriateness of VTE prophylaxis prescribing. Results There were significantly less unintended omissions of medications: 11 of 887 (1.2%) intervention orders compared with 383 of 1217 (31.5%) control (p<0.001). There were significantly less prescribing errors involving selection of drug, dose or frequency: 2 in 857 (0.2%) intervention orders compared with 51 in 807 (6.3%) control (p<0.001). Orders with at least one component of the prescription missing, incorrect or unclear occurred in 208 of 904 (23%) intervention orders and 445 of 1034 (43%) controls (p<0.001). VTE prophylaxis on admission to the ward was appropriate in 93% of intervention patients and 90% controls (p=0.29). Conclusions Medication charts in the intervention arm contained fewer clinically significant omissions, and prescribing errors, when compared with controls. There was no difference in appropriateness of VTE prophylaxis on admission between the two groups.

Alcohol ingestion impairs maximal post-exercise rates of myofibrillar protein synthesis following a single bout of concurrent training

Introduction The culture in many team sports involves consumption of large amounts of alcohol after training/competition. The effect of such a practice on recovery processes underlying protein turnover in human skeletal muscle are unknown. We determined the effect of alcohol intake on rates of myofibrillar protein synthesis (MPS) following strenuous exercise with carbohydrate (CHO) or protein ingestion. Methods In a randomized cross-over design, 8 physically active males completed three experimental trials comprising resistance exercise (8×5 reps leg extension, 80% 1 repetition maximum) followed by continuous (30 min, 63% peak power output (PPO)) and high intensity interval (10×30 s, 110% PPO) cycling. Immediately, and 4 h post-exercise, subjects consumed either 500 mL of whey protein (25 g; PRO), alcohol (1.5 g·kg body mass−1, 12±2 standard drinks) co-ingested with protein (ALC-PRO), or an energy-matched quantity of carbohydrate also with alcohol (25 g maltodextrin; ALC-CHO). Subjects also consumed a CHO meal (1.5 g CHO·kg body mass−1) 2 h post-exercise. Muscle biopsies were taken at rest, 2 and 8 h post-exercise. Results Blood alcohol concentration was elevated above baseline with ALC-CHO and ALC-PRO throughout recovery (P<0.05). Phosphorylation of mTORSer2448 2 h after exercise was higher with PRO compared to ALC-PRO and ALC-CHO (P<0.05), while p70S6K phosphorylation was higher 2 h post-exercise with ALC-PRO and PRO compared to ALC-CHO (P<0.05). Rates of MPS increased above rest for all conditions (~29–109%, P<0.05). However, compared to PRO, there was a hierarchical reduction in MPS with ALC-PRO (24%, P<0.05) and with ALC-CHO (37%, P<0.05). Conclusion We provide novel data demonstrating that alcohol consumption reduces rates of MPS following a bout of concurrent exercise, even when co-ingested with protein. We conclude that alcohol ingestion suppresses the anabolic response in skeletal muscle and may therefore impair recovery and adaptation to training and/or subsequent performance.

Facilitator for joint expert conference

Interlocutory judgment of the NSW Supreme Court in a medical negligence claim - circumstances under which a facilitator may be appointed to assist in the conduct of a joint expert conference - background - jurisdiction of the Court to appoint a facilitator - analysis of decision.

Forming a joint venture project team for multi-discipline engineering services in Australia

Joint venture design teams are formed to combine resources and expertise in order to secure multi-discipline engineering design services on major projects. Bringing together resources from two ordinarily competing companies to form one joint team is however challenging as each parent company brings to the project its own organisational culture, processes and team attitudes. This study examined the factors that impact on forming a successful joint venture project team. Three critical areas were identified from an extensive literature review; Joint Venture Arrangements, Parent Companies and Forming the Team; and a survey was conducted with professionals who have worked in joint venture project teams in the Australian building industry in order to identify factors that affected successful joint venture team formation, and the common lessons learnt. This study reinforced the importance of three key criteria - trust, commitment and compatibility - for partner alignment. The results also identified four key lessons learnt which included; selecting the right resources, enabling a collaborative working environment by way of project office, implementing an independent Joint Venture Manager, and allocating work which is best for project with fees reflecting risk where risk is disproportionate.

From single crystal surfaces to single atoms : investigating active sites in electrocatalysis

Electrocatalytic processes will undoubtedly be at the heart of energising future transportation and technology with the added importance of being able to create the necessary fuels required to do so in an environmentally friendly and cost effective manner. For this to be successful two almost mutually exclusive surface properties need to be reconciled, namely producing highly active/reactive surface sites that exhibit long term stability. This article reviews the various approaches which have been undertaken to study the elusive nature of these active sites on metal surfaces which are considered as adatoms or clusters of adatoms with low coordination number. This includes the pioneering studies at extended well defined stepped single crystal surfaces using cyclic voltammetry up to the highly sophisticated in situ electrochemical imaging techniques used to study chemically synthesised nanomaterials. By combining the information attained from single crystal surfaces, individual nanoparticles of defined size and shape, density functional theory calculations and new concepts such as mesoporous multimetallic thin films and single atom electrocatalysts new insights into the design and fabrication of materials with highly active but stable active sites can be achieved. The area of electrocatalysis is therefore not only a fascinating and exciting field in terms of realistic technological and economical benefits but also from the fundamental understanding that can be acquired by studying such an array of interesting materials.

Prevention of surgical site infection in total joint arthroplasty : an international tertiary care center survery

Background Prevention strategies are critical to reduce infection rates in total joint arthroplasty (TJA), but evidence-based consensus guidelines on prevention of surgical site infection (SSI) remain heterogeneous and do not necessarily represent this particular patient population. Questions/Purposes What infection prevention measures are recommended by consensus evidence-based guidelines for prevention of periprosthetic joint infection? How do these recommendations compare to expert consensus on infection prevention strategies from orthopedic surgeons from the largest international tertiary referral centers for TJA? Patients and Methods A review of consensus guidelines was undertaken as described by Merollini et al. Four clinical guidelines met inclusion criteria: Centers for Disease Control and Prevention's, British Orthopedic Association, National Institute of Clinical Excellence's, and National Health and Medical Research Council's (NHMRC). Twenty-eight recommendations from these guidelines were used to create an evidence-based survey of infection prevention strategies that was administered to 28 orthopedic surgeons from members of the International Society of Orthopedic Centers. The results between existing consensus guidelines and expert opinion were then compared. Results Recommended strategies in the guidelines such as prophylactic antibiotics, preoperative skin preparation of patients and staff, and sterile surgical attire were considered critically or significantly important by the surveyed surgeons. Additional strategies such as ultraclean air/laminar flow, antibiotic cement, wound irrigation, and preoperative blood glucose control were also considered highly important by surveyed surgeons, but were not recommended or not uniformly addressed in existing guidelines on SSI prevention. Conclusion Current evidence-based guidelines are incomplete and evidence should be updated specifically to address patient needs undergoing TJA.

Effects of joint thickness, adhesion and web shells to the face shell bedded concrete masonry loaded in compression

The Australian masonry standard allows either prism tests or correction factors based on the block height and mortar thickness to evaluate masonry compressive strength. The correction factor helps the taller units with conventional 10 mm mortar being not disadvantaged due to size effect. In recent times, 2-4 mm thick, high-adhesive mortars and H blocks with only the mid-web shell are used in masonry construction. H blocks and thinner and higher adhesive mortars have renewed interest of the compression behaviour of hollow concrete masonry and hence is revisited in this paper. This paper presents an experimental study carried out to examine the effects of the thickness of mortar joints, the type of mortar adhesives and the presence of web shells in the hollow concrete masonry prisms under axial compression. A non-contact digital image correlation technique was used to measure the deformation of the prisms and was found adequate for the determination of strain fi eld of the loaded face shells subjected to axial compression. It is found that the absence of end web shells lowers the compressive strength and stiffness of the prisms and the thinner and higher adhesive mortars increase the compressive strength and stiffness, while lowering the Poisson's ratio. © Institution of Engineers Australia, 2013.