BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping

Physical and linkage mapping underpin efforts to sequence and characterize the genomes of eukaryotic organisms by providing a skeleton framework for whole genome assembly. Hitherto, linkage and physical “contig” maps were generated independently prior to merging. Here, we develop a new and easy method, BAC HAPPY MAPPING (BAP mapping), that utilizes BAC library pools as a HAPPY mapping panel together with an Mbp-sized DNA panel to integrate the linkage and physical mapping efforts into one pipeline. Using Arabidopsis thaliana as an exemplar, a set of 40 Sequence Tagged Site (STS) markers spanning ~10% of chromosome 4 were simultaneously assembled onto a BAP map compiled using both a series of BAC pools each comprising 0.7x genome coverage and dilute (0.7x genome) samples of sheared genomic DNA. The resultant BAP map overcomes the need for polymorphic loci to separate genetic loci by recombination and allows physical mapping in segments of suppressed recombination that are difficult to analyze using traditional mapping techniques. Even virtual “BAC-HAPPY-mapping” to convert BAC landing data into BAC linkage contigs is possible.Giang T. H. Vu, Paul H. Dear, Peter D. S. Caligari and Mike J. Wilkinso

Uniaxial compression of single crystal and polycrystalline tantalum

A series of compression experiments characterising the elastic-plastic response of single crystal and polycrystalline tantalum from quasi-static to intermediate strain-rates (10^−3 – 10^3 s−1) over a range of temperatures (233–438 K) are reported in this paper. The single crystal experiments show significant differences in the response of the three principle crystal orientations of tantalum in terms of yield, work hardening and ultimate deformed shapes. Modelling is undertaken using a dislocation mechanics based crystal plasticity finite element model giving insight into the underlying microscopic processes that govern the macroscopic response. The simulations show the importance of the dislocation mobility relations and laws governing the evolution of the mobile dislocation density for capturing the correct behaviours. The inclusion of the twinning/anti-twinning asymmetry is found to influence [100] orientation most strongly, and is shown to be critical for matching the relative yield strengths. In general the simulations are able to adequately match experimental trends although some specific details such as exact strain hardening evolution are not reproduced suggesting a more complex hardening model is required. 3D finite element simulations approximating the tests are also undertaken and are able to predict the final deformed sample shapes well once the twinning/anti-twinning asymmetry is included (particularly for the [100] orientation). The polycrystalline data in both as-received and cold rolled conditions shows the initial yield strength is highest and work hardening rate is lowest for the cold-rolled material due to the increase in mobile dislocation density caused by the prior work. The general behavioural trends with temperature and strain-rate of the polycrystalline materials are reproduced in the single crystal data however the specific form of stress versus strain curves are significantly different. This is discussed in terms of the similar active slip systems in polycrystalline material to high symmetry single crystals but with the significant added effect of grain boundary interactions

A provisional database for the silicon content of foods in the United Kingdom

Si may play an important role in bone formation and connective tissue metabolism. Although biological interest in this element has recently increased, limited literature exists on the Si content of foods. To further our knowledge and understanding of the relationship between dietary Si and human health, a reliable food composition database, relevant for the UK population, is required. A total of 207 foods and beverages, commonly consumed in the UK, were analysed for Si content. Composite samples were analysed using inductively coupled plasma&ndash;optical emission spectrometry following microwave-assisted digestion with nitric acid and H2O2. The highest concentrations of Si were found in cereals and cereal products, especially less refined cereals and oat-based products. Fruit and vegetables were highly variable sources of Si with substantial amounts present in Kenyan beans, French beans, runner beans, spinach, dried fruit, bananas and red lentils, but undetectable amounts in tomatoes, oranges and onions. Of the beverages, beer, a macerated whole-grain cereal product, contained the greatest level of Si, whilst drinking water was a variable source with some mineral waters relatively high in Si. The present study provides a provisional database for the Si content of UK foods, which will allow the estimation of dietary intakes of Si in the UK population and investigation into the role of dietary Si in human health.<br /

Dynamics of oligomer populations formed during the aggregation of Alzheimer's Aβ42 peptide

Oligomeric species populated during the aggregation of the Aβ42 peptide have been identified as potent cytotoxins linked to Alzheimer’s disease, but the fundamental molecular pathways that control their dynamics have yet to be elucidated. By developing a general approach that combines theory, experiment and simulation, we reveal, in molecular detail, the mechanisms of Aβ42 oligomer dynamics during amyloid fibril formation. Even though all mature amyloid fibrils must originate as oligomers, we found that most Aβ42 oligomers dissociate into their monomeric precursors without forming new fibrils. Only a minority of oligomers converts into fibrillar structures. Moreover, the heterogeneous ensemble of oligomeric species interconverts on timescales comparable to those of aggregation. Our results identify fundamentally new steps that could be targeted by therapeutic interventions designed to combat protein misfolding diseases

Selecting Grassland Species for Saline Environments

In Australia, around 5.7 million hectares of agricultural land are currently affected by dryland salinity or at risk from shallow water tables and this figure is expected to increase over the next 50 years (LWRA, 2001). Most improved grassland species cannot tolerate the combined effects of salt and waterlogging and, therefore, the productivity of sown grasslands in salt-affected areas is low. However, there is potential to overcome the lack of suitably adapted fodder species by introducing new, salt and waterlogging-tolerant species and by diversifying the gene pool of proven species. Potential species include exotic, naturalised and native Australian grass, legumes, herb and shrub species that are halophytes and non-halophytes. A collaborative national project in southern Australia commenced in 2004 with the objective of evaluating a range of forage species for saline environments

Size constancy in bat biosonar?

Perception and encoding of object size is an important feature of sensory systems. In the visual system object size is encoded by the visual angle (visual aperture) on the retina, but the aperture depends on the distance of the object. As object distance is not unambiguously encoded in the visual system, higher computational mechanisms are needed. This phenomenon is termed "size constancy". It is assumed to reflect an automatic re-scaling of visual aperture with perceived object distance. Recently, it was found that in echolocating bats, the 'sonar aperture', i.e., the range of angles from which sound is reflected from an object back to the bat, is unambiguously perceived and neurally encoded. Moreover, it is well known that object distance is accurately perceived and explicitly encoded in bat sonar. Here, we addressed size constancy in bat biosonar, recruiting virtual-object techniques. Bats of the species Phyllostomus discolor learned to discriminate two simple virtual objects that only differed in sonar aperture. Upon successful discrimination, test trials were randomly interspersed using virtual objects that differed in both aperture and distance. It was tested whether the bats spontaneously assigned absolute width information to these objects by combining distance and aperture. The results showed that while the isolated perceptual cues encoding object width, aperture, and distance were all perceptually well resolved by the bats, the animals did not assign absolute width information to the test objects. This lack of sonar size constancy may result from the bats relying on different modalities to extract size information at different distances. Alternatively, it is conceivable that familiarity with a behaviorally relevant, conspicuous object is required for sonar size constancy, as it has been argued for visual size constancy. Based on the current data, it appears that size constancy is not necessarily an essential feature of sonar perception in bats

Risk factors of direct heat-related hospital admissions during the 2009 heatwave in Adelaide, Australia: a matched case-control study

Objective: The extreme heatwave of 2009 in South Australia dramatically increased morbidity, with a 14-fold increase in direct heat-related hospitalisation in metropolitan Adelaide. Our study aimed to identify risk factors for the excess morbidity. Design: A matched case–control study of risk factors was conducted. Setting: Patients and matched community controls were interviewed to gather data on demographics, living environment, social support, health status and behaviour changes during the heatwave. Participants: Cases were all hospital admissions with heat-related diagnoses during the 5-day heatwave in 2009. Controls were randomly selected from communities. Outcome measures: Descriptive analyses, simple and multiple conditional logistic regressions were performed. Adjusted ORs (AORs) were estimated. Results: In total, 143 hospital patients and 143 matched community controls were interviewed, with a mean age of 73 years (SD 21), 96% European ethnicity, 63% retired, 36% with high school or higher education, and 8% institutional living. The regression model indicated that compared with the controls, cases were more likely to have heart disease (AOR=13.56, 95% CI 1.27 to 144.86) and dementia (AOR=26.43, 95% CI 1.99 to 350.73). The protective factors included higher education level (AOR=0.48, 95% CI 0.23 to 0.99), having air-conditioner in the bedroom (AOR=0.12, 95% CI 0.02 to 0.74), having an emergency button (AOR=0.09, 95% CI 0.01 to 0.96), using refreshment (AOR=0.10, 95% CI 0.01 to 0.84), and having more social activities (AOR=0.11, 95% CI 0.02 to 0.57). Conclusions: Pre-existing heart disease and dementia significantly increase the risk of direct heat-related hospitalisations during heatwaves. The presence of an air-conditioner in the bedroom, more social activities, a higher education level, use of emergency buttons and refreshments reduce the risk during heatwaves.Y. Zhang, M. Nitschke, A. Krackowizer, K. Dear, D. Pisaniello, P. Weinstein, G. Tucker, S. Shakib, P. B

Mutation at the Evi1 locus in Junbo mice causes susceptibility to otitis media

Otitis media ( OM), inflammation of the middle ear, remains the most common cause of hearing impairment in children. It is also the most common cause of surgery in children in the developed world. There is evidence from studies of the human population and mouse models that there is a significant genetic component predisposing to OM, yet nothing is known about the underlying genetic pathways involved in humans. We identified an N-ethyl-N-nitrosourea-induced dominant mouse mutant Junbo with hearing loss due to chronic suppurative OM and otorrhea. This develops from acute OM that arises spontaneously in the postnatal period, with the age of onset and early severity dependent on the microbiological status of the mice and their air quality. We have identified the causal mutation, a missense change in the C-terminal zinc finger region of the transcription factor Evi1. This protein is expressed in middle ear basal epithelial cells, fibroblasts, and neutrophil leukocytes at postnatal day 13 and 21 when inflammatory changes are underway. The identification and characterization of the Junbo mutant elaborates a novel role for Evi1 in mammalian disease and implicates a new pathway in genetic predisposition to OM

Evaluation of the Workplace Environment in the UK, and the Impact on Users’ Levels of Stimulation

The purpose of this study is to evaluate a number of recently completed workplaces in the UK. The first aim is to assess the impact of various aspects of the workplace environment on users’ levels of stimulation. The body of previous research undertaken into the workplace environment, identified the aspects to be investigated. Samples of employees from the sixteen businesses were surveyed to determine their perceptions of the workplaces. The results were entered into a regression analysis, and the most significant predictors of perceived stimulation identified. The data also revealed a dramatic reduction in staff arousal levels from mornings to afternoons. Thus, there is a second aim to determine whether changes to significant aspects of the workplace environment during the day can counteract the reduction in users’ stimulation. Two further workplaces were studied to enable changes to be made over a 12-week period. A sample of employees completed questionnaires, and semi-structured interviews revealed the reasons behind the results. It was found that provision of artwork, personal control of temperature and ventilation and regular breaks were the most significant contributions to increasing stimulation after lunch; while user choice of layout, and design and décor of workspaces and break areas, were the most significant aspects at design stage