Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

Sorghum is a food and feed cereal crop adapted to heat and drought and a staple for 500 million of the world’s poorest people. Its small diploid genome and phenotypic diversity make it an ideal C4 grass model as a complement to C3 rice. Here we present high coverage (16–45 × ) resequenced genomes of 44 sorghum lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group. We also report the first resequenced genome of S. propinquum, identifying 8 M high-quality SNPs, 1.9 M indels and specific gene loss and gain events in S. bicolor. We observe strong racial structure and a complex domestication history involving at least two distinct domestication events. These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum, providing an unmatched resource for the genetic improvement of sorghum and other grass species.

Living City 2013 Workshop

Living City 2013 Workshop, as part of a school term’s design-based curriculum connected to the KGSC/QUT Design Excellence Program and run from 11 February – 1 May, 2013, was essentially a three-day place-based urban design immersion workshop program for 25 Year 11 Visual Art and Design Students and 2 Teachers from Kelvin Grove State College (KGSC) held at both Queensland University of Technology (QUT) Gardens Point Campus and The Edge, State Library of Queensland. Mentored by 4 design professionals, 2 tertiary design academics, 2 public artists, and 12 QUT tertiary design students, the workshop explored youth-inspired public space design solutions for the active Brisbane City Council redevelopment site of Queens Wharf Road precinct. As well as the face-to-face workshops, for Living City 2013, an interactive web environment was introduced to enable students to connect with each other and program mentors throughout the course of the program. The workshop, framed within notions of ecological, economic, social and cultural sustainability, aimed to raise awareness of the layered complexity and perspectives involved in the design of shared city spaces and to encourage young people to voice their own concerns as future citizens about the shape and direction of their city. The program commenced with an introductory student briefing by stakeholders and mentors at KGSC on 11 February, an introduction to site appraisal and site visit held at QUT and Queens Wharf Road on 20 February, and a follow up site analysis session on 6 March. Day 1 Workshop on April 17 at the Edge, State Library of Queensland, as part of the Design Minds partnership (http://designminds.org.au/kelvin-grove-state-college-excellence-in-art-design/), focused on mentoring team development of a concept design for a range of selected sites. Two workshops on April 22 and 23 at QUT, to develop these designs and presentation schemes, followed this. The workshop program culminated in a visual presentation of concept design ideas and discussion with a public audience in the Ideas Gallery on The Deck, King George Square during the Brisbane City Council City Centre Master Plan Ideas Fiesta on 1 May, 2013, as referenced in the Ideas Fiesta Wrap-up Report (http://www.brisbane.qld.gov.au/planning-building/planning-guidelines-tools/city-centre-master-plan/city-centre-master-plan-ideas-fiesta). Students were introduced to design methodology, team thinking strategies, the scope of design practices and professions, presentation skills and post-secondary pathways, while participating teachers acquired content and design learning strategies transferable in many other contexts. The program was fully documented on the Living City website (http://www.livingcity.net.au/LC2013x/index.html) and has been recognised by the Brisbane City Council Youth Strategy 2014-2019 as a best practice model for making Brisbane a well-designed, subtropical city.

Exploring the boundary between the siphon and barometer in a hypobaric chamber

Siphons have been used since ancient times, but exactly how they work is still a matter of debate. In order to elucidate the modus operandi of a siphon, a 1.5 m high siphon was set up in a hypobaric chamber to explore siphon behaviour in a low-pressure environment. When the pressure in the chamber was reduced to about 0.18 atmospheres, a curious waterfall-like feature appeared downstream from the apex of the siphon. A hypothesis is presented to explain the waterfall phenomenon. When the pressure was reduced further the siphon broke into two columns - in effect becoming two back-to-back barometers. This experiment demonstrates the role of atmospheric pressure in explaining the hydrostatic characteristics of a siphon and the role of molecular cohesion in explaining the hydrodynamic aspects.

Sense of home, sense of place : a morpho-typological comparative study of Florida and Queensland

Cities in the 21st century have become layered and complex systems not only in terms of physical form, but also social and cultural structure. Consolidated tools to analyze the urban environment have today to be improved including a strong interdisciplinary perspective in order to understand and manage the unprecedented complexity our cities are facing. Redevelopments, new estates, internal and external migrations are all dynamics which are deeply modifying the built environment directly or indirectly also affecting local identity, culture and social structure. This paper investigates the relationship between urban form and social behaviors, with particular attention to the perception of the built environment and its use by long term residents, recent migrants as well as tourists. A comparative study is suggested between South East Queensland and Florida; this two regions share common features such as subtropical climate, similar lifestyle, leisure cities and canal estates. Neighborhoods on the Gold and Sunshine Coasts have been designed using the communities of Florida, such as Celebration or Seaside, as models. These regions share also significant migration processes, similar social problems and high crime rates, which directly affect the local economies. Comparing Florida and SEQ could provide an understanding of different strategies adopted and how urban development and lifestyle can be managed maintaining social equity and security. This study, investigates people’s perception of built form and how this affects the use of public space. The relationship between built environment and social behaviour has been previously investigated, for example by environmental psychology; the innovation proposed by this research is to study the perception of place in leisure cities at multiple levels. Locals, migrants and tourists have different understanding of the built form in the same location; this understanding affects the use of space and the attitude to visit or avoid some precincts. The research methodology integrates traditional morpho-typological investigations with qualitative methods; data are collected in the first phase through online surveys about perception of urban forms. Findings guide then the selection of neighbourhoods to be investigated in detail through questionnaires and Nolli maps, specifying morphological regions as well as recurrent building typologies. A final phase includes interviews with selected stakeholders. Major urban projects are discussed addressing how they are used and perceived by locals, migrants or tourists; the comparison between SEQ and Florida allows the identification of strategies to address migration issues in both regions with particular attention to urban form and placemaking dynamics.

Assessment of the temperature effect on childhood diarrhea using satellite imagery

A quasi-Poisson generalized linear model combined with a distributed lag non-linear model was used to quantify the main effect of temperature on emergency department visits (EDVs) for childhood diarrhea in Brisbane from 2001 to 2010. Residual of the model was checked to examine whether there was an added effect due to heat waves. The change over time in temperature-diarrhea relation was also assessed. Both low and high temperatures had significant impact on childhood diarrhea. Heat waves had an added effect on childhood diarrhea, and this effect increased with intensity and duration of heat waves. There was a decreasing trend in the main effect of heat on childhood diarrhea in Brisbane across the study period. Brisbane children appeared to have gradually adapted to mild heat, but they are still very sensitive to persistent extreme heat. Development of future heat alert systems should take the change in temperature-diarrhea relation over time into account.

Building the youth sector from the bottom up : case studies from the Queensland CPLAN Initiative 2012-2013

As part of YANQ's decentralisation across the state, YANQ have set up 10 Networks across Queensland, with Facilitators based in each of the regions. We encourage you to get in contact with your local Facilitator if you would like to have input on Workforce Development or youth policy issues. CPLANs aim to create an ongoing and sustainable structure across ten regions in Queensland to support a consistent focus on: ⋅ Policy issues relevant to young people; and ⋅ Workforce development strategies for the youth sector from a local, regional and state perspective. The ten CPLANs fall under the existing structure of YANQ and utlise and lever off the comprehensive network of youth inter-­‐agencies and networks across the state. The ten CPLANs are made up of representatives from the youth sector in each region who have an interest in contributing to policy development and workforce issues.

Nonvolatile multilevel data storage memory device from controlled ambipolar charge trapping mechanism

The capability of storing multi-bit information is one of the most important challenges in memory technologies. An ambipolar polymer which intrinsically has the ability to transport electrons and holes as a semiconducting layer provides an opportunity for the charge trapping layer to trap both electrons and holes efficiently. Here, we achieved large memory window and distinct multilevel data storage by utilizing the phenomena of ambipolar charge trapping mechanism. As fabricated flexible memory devices display five well-defined data levels with good endurance and retention properties showing potential application in printed electronics.

Morphometric stability of the corneal subbasal nerve plexus in healthy individuals a 3-year longitudinal study using corneal confocal microscopy

Purpose We examined the age-dependent alterations and longitudinal course of subbasal nerve plexus (SNP) morphology in healthy individuals. Methods Laser-scanning corneal confocal microscopy, ocular screening, and health and metabolic assessment were performed on 64 healthy participants at baseline and at 12-month intervals for 3 years. At each annual visit, eight central corneal images of the SNP were selected and analyzed using a fully-automated analysis system to quantify corneal nerve fiber length (CNFL). Two linear mixed model approaches were fitted to examine the relationship between age and CNFL, and the longitudinal changes of CNFL over three years. Results At baseline, mean age was 51.9 ± 14.7 years. The cohort was sex balanced (χ2 = 0.56, P = 0.45). Age (t = 1.6, P = 0.12) and CNFL (t = -0.50, P = 0.62) did not differ between sexes. A total of 52 participants completed the 36-month visit and 49 participants completed all visits. Age had a significant effect on CNFL (F1,33 = 5.67, P = 0.02) with a linear decrease of 0.05 mm/mm2 in CNFL per one year increase in age. No significant change in CNFL was observed over the 36-month period (F1,55 = 0.69, P = 0.41). Conclusions The CNFL showed a stable course over a 36-month period in healthy individuals, although there was a slight linear reduction in CNFL with age. The findings of this study have implications for understanding the time-course of the effect of pathology and surgical or therapeutic interventions on the morphology of the SNP, and serves to confirm the suitability of CNFL as a screening/monitoring marker for peripheral neuropathies.

Moved by spirit of Canadian nature

A travel article about a visit to Klemtu and the Great Bear Rainforest, British Columbia. A LOW-TIDE mark of rocks coated in orange seaweed borders the islands of the Great Bear Rainforest. Our seaplane stays low under the clouds. As we approach the village of Klemtu, turning into Finlayson Channel, the trees beneath us thicken against the shoreline like a concert crowd being pushed from behind. There's no gap between the dark, still sea and the front row of soaring conifers, seemingly no entry point into one of the last great wilderness areas.

The knowledge: a project by Boxcopy at Post-Museum, Singapore

‘The Knowledge’ was part of the Next Wave/Asialink project 'Invisible Structures: Australian artist collectives in Tokyo, Singapore and Yogyakarta' in January 2011. For this project, Brisbane ARI Boxcopy undertook a two-week residency at Post Musuem in Singapore. In this project, the Boxcopy artists Channon Goodwin, Joseph Breikers, Timothy P Kerr, Daniel McKewen, Raymonde Rajkowski, Tim Woodward, attempted to acquire an intimate knowledge of the city of Singapore by forming a free delivery company, The Boxcopy Publics Carriage Office of Singapore (BPCOS), which provided services around the city by foot, bike and public transport. In addition to committing to memory and documenting the streets and sites of Singapore, the BPCOS team also performed tasks such as delivering goods or messages, travel a particular route or visit a site, as requested by the people of Singapore. The project comprised this process of public interaction as well as an exhibition and website.

The glycosphingolipid P1 is an ovarian cancer-associated carbohydrate antigen involved in migration

Background The level of plasma-derived naturally circulating anti-glycan antibodies (AGA) to P1 trisaccharide has previously been shown to significantly discriminate between ovarian cancer patients and healthy women. Here we aim to identify the Ig class that causes this discrimination, to identify on cancer cells the corresponding P1 antigen recognised by circulating anti-P1 antibodies and to shed light into the possible function of this glycosphingolipid. Method An independent Australian cohort was assessed for the presence of anti-P1 IgG and IgM class antibodies using suspension array. Monoclonal and human derived anti-glycan antibodies were verified using three independent glycan-based immunoassays and flow cytometry-based inhibition assay. The P1 antigen was detected by LC-MS/MS and flow cytometry. FACS-sorted cell lines were studied on the cellular migration by colorimetric assay and real-time measurement using xCELLigence system. Results Here we show in a second independent cohort (n=155) that the discrimination of cancer patients is mediated by the IgM class of anti-P1 antibodies (P=0.0002). The presence of corresponding antigen P1 and structurally related epitopes in fresh tissue specimens and cultured cancer cells is demonstrated. We further link the antibody and antigen (P1) by showing that human naturally circulating and affinity-purified anti-P1 IgM isolated from patients ascites can bind to naturally expressed P1 on the cell surface of ovarian cancer cells. Cell-sorted IGROV1 was used to obtain two study subpopulations (P1-high, 66.1%; and P1-low, 33.3%) and observed that cells expressing high P1-levels migrate significantly faster than those with low P1-levels. Conclusions This is the first report showing that P1 antigen, known to be expressed on erythrocytes only, is also present on ovarian cancer cells. This suggests that P1 is a novel tumour-associated carbohydrate antigen recognised by the immune system in patients and may have a role in cell migration. The clinical value of our data may be both diagnostic and prognostic; patients with low anti-P1 IgM antibodies present with a more aggressive phenotype and earlier relapse.

Including nonequilibrium interface kinetics in a continuum model for melting nanoscaled particles

The melting temperature of a nanoscaled particle is known to decrease as the curvature of the solid-melt interface increases. This relationship is most often modelled by a Gibbs--Thomson law, with the decrease in melting temperature proposed to be a product of the curvature of the solid-melt interface and the surface tension. Such a law must break down for sufficiently small particles, since the curvature becomes singular in the limit that the particle radius vanishes. Furthermore, the use of this law as a boundary condition for a Stefan-type continuum model is problematic because it leads to a physically unrealistic form of mathematical blow-up at a finite particle radius. By numerical simulation, we show that the inclusion of nonequilibrium interface kinetics in the Gibbs--Thomson law regularises the continuum model, so that the mathematical blow up is suppressed. As a result, the solution continues until complete melting, and the corresponding melting temperature remains finite for all time. The results of the adjusted model are consistent with experimental findings of abrupt melting of nanoscaled particles. This small-particle regime appears to be closely related to the problem of melting a superheated particle.

From selfies to climate change : the #G20 debate on Twitter

The G20 Summit that brought many of the world’s most important leaders to Brisbane last weekend was also a major Twitter event. Australian and international users expressed their concerns over the appearance of Russian warships off the Queensland coast, shared selfies from German Chancellor Angela Merkel’s impromptu visit to Brisbane’s Caxton St nightlife hub and called for action on issues ranging from Ebola to climate change...

Gold nanospikes based microsensor as a highly accurate mercury emission monitoring system

Anthropogenic elemental mercury (Hg0) emission is a serious worldwide environmental problem due to the extreme toxicity of the heavy metal to humans, plants and wildlife. Development of an accurate and cheap microsensor based online monitoring system which can be integrated as part of Hg0 removal and control processes in industry is still a major challenge. Here, we demonstrate that forming Au nanospike structures directly onto the electrodes of a quartz crystal microbalance (QCM) using a novel electrochemical route results in a self-regenerating, highly robust, stable, sensitive and selective Hg0 vapor sensor. The data from a 127 day continuous test performed in the presence of volatile organic compounds and high humidity levels, showed that the sensor with an electrodeposted sensitive layer had 260% higher response magnitude, 3.4 times lower detection limit (,22 mg/m3 or ,2.46 ppbv) and higher accuracy (98% Vs 35%) over a Au control based QCM (unmodified) when exposed to a Hg0 vapor concentration of 10.55 mg/m3 at 1016C. Statistical analysis of the long term data showed that the nano-engineered Hg0 sorption sites on the developed Au nanospikes sensitive layer play a critical role in the enhanced sensitivity and selectivity of the developed sensor towards Hg0 vapor.

Using qualitative mixed methods to study small health care organizations while maximising trustworthiness and authenticity

Background The primary health care sector delivers the majority of health care in western countries through small, community-based organizations. However, research into these healthcare organizations is limited by the time constraints and pressure facing them, and the concern by staff that research is peripheral to their work. We developed Q-RARA—Qualitative Rapid Appraisal, Rigorous Analysis—to study small, primary health care organizations in a way that is efficient, acceptable to participants and methodologically rigorous. Methods Q-RARA comprises a site visit, semi-structured interviews, structured and unstructured observations, photographs, floor plans, and social scanning data. Data were collected over the course of one day per site and the qualitative analysis was integrated and iterative. Results We found Q-RARA to be acceptable to participants and effective in collecting data on organizational function in multiple sites without disrupting the practice, while maintaining a balance between speed and trustworthiness. Conclusions The Q-RARA approach is capable of providing a richly textured, rigorous understanding of the processes of the primary care practice while also allowing researchers to develop an organizational perspective. For these reasons the approach is recommended for use in small-scale organizations both within and outside the primary health care sector.