Structure and assembly of immature HIV

The major structural components of HIV are synthesized as a 55-kDa polyprotein, Gag. Particle formation is driven by the self-assembly of Gag into a curved hexameric lattice, the structure of which is poorly understood. We used cryoelectron tomography and contrast-transfer-function corrected subtomogram averaging to study the structure of the assembled immature Gag lattice to approximate to 17-angstrom resolution. Gag is arranged in the immature virus as a single, continuous, but incomplete hexameric lattice whose curvature is mediated without a requirement for pentameric defects. The resolution of the structure allows positioning of individual protein domains. High-resolution crystal structures were fitted into the reconstruction to locate protein-protein interfaces involved in Gag assembly, and to identify the structural transformations associated with virus maturation. The results of this study suggest a concept for the formation of nonsymmetrical enveloped viruses of variable sizes.

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers

Background The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy. Results Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function. Conclusions We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms. Keywords: Nerita melanotragus; De novo assembly; Transcriptome; Heat shock protein; Ion torrent

Systematic Review Protocol : "Are community-based interventions effective in identifying and responding to emerging zoonotic infectious diseases?"

Review question/objective The objective of this review is to identify the effectiveness of surveillance systems and community-based interventions in identifying and responding to emerging and re-emerging zoonotic infections in Southeast Asia (SE Asia). More specifically the research questions are: 1. What is the effectiveness of community-based surveillance interventions designed to identify emerging zoonotic infectious diseases? 2. What is the effectiveness of non-pharmaceutical community-based interventions designed to prevent transmission of emerging zoonotic infectious diseases? 3. How do factors related to the emergence and management of emerging zoonotic infectious diseases impact the effectiveness of interventions designed to identify and respond to them?

Centrobin regulates the assembly of functional mitotic spindles

The proper function of the spindle is crucial to the high fidelity of chromosome segregation and is indispensable for tumor suppression in humans. Centrobin is a recently identified centrosomal protein that has a role in stabilizing the microtubule structure. Here we functionally characterize the defects in centrosome integrity and spindle assembly in Centrobin-depleted cells. Centrobin-depleted cells show a range of spindle abnormalities including unfocused poles that are not associated with centrosomes, S-shaped spindles and mini spindles. These cells undergo mitotic arrest and subsequently often die by apoptosis, as determined by live cell imaging. Co-depletion of Mad2 relieves the mitotic arrest, indicating that cells arrest due to a failure to silence the spindle checkpoint in metaphase. Consistent with this, Centrobin-depleted metaphase cells stained positive for BubR1 and BubR1 S676. Staining with a panel of centrosome markers showed a loss of centrosome anchoring to the mitotic spindle. Furthermore, these cells show less cold-stable microtubules and a shorter distance between kinetochore pairs. These results show a requirement of Centrobin in maintaining centrosome integrity, which in turn promotes anchoring of mitotic spindle to the centrosomes. Furthermore, this anchoring is required for the stability of microtubule–kinetochore attachments and biogenesis of tension-ridden and properly functioning mitotic spindle.

Collaborative extension of biodiversity monitoring protocols in the bird watching community

Citizen science projects have demonstrated the advantages of people with limited relevant prior knowledge participating in research. However, there is a difference between engaging the general public in a scientific project and entering an established expert community to conduct research. This paper describes our ongoing acoustic biodiversity monitoring collaborations with the bird watching community. We report on findings gathered over six years from participation in bird walks, observing conservation efforts, and records of personal activities of experienced birders. We offer an empirical study into extending existing protocols through in-context collaborative design involving scientists and domain experts.

Submission to the Legal Affairs and Community Safety Committee Youth Justice and Other Legislation Amendment Bill

This submission addresses the Youth Justice and Other Legislation Amendment Bill 2014 the objectives of which are to: 1. Permit repeat offenders’ identifying information to be published and open the Children’s Court for youth justice matters involving repeat offenders; 2. Create a new offence where a child commits a further offence while on bail; 3. Permit childhood findings of guilt for which no conviction was recorded to be admissible in court when sentencing a person for an adult offence; 4. Provide for the automatic transfer from detention to adult corrective services facilities of 17 year olds who have six months or more left to serve in detention; 5. Provide that, in sentencing any adult or child for an offence punishable by imprisonment, the court must not have regard to any principle, whether under statute or at law, that a sentence of imprisonment (in the case of an adult) or detention (in the case of a child) should only be imposed as a last resort; 6. Allow children who have absconded from Sentenced Youth Boot Camps to be arrested and brought before a court for resentencing without first being given a warning; and 7. Make a technical amendment to the Youth Justice Act 1992.

Building a community of learners within the STEM higher education classroom

Building rich and authentic learning experiences in the STEM classroom, is a challenge for many educators within Higher Education. While many Higher Education Institutions have embraced the need to transform current teaching and learning practices and include a range of online tools, this has often been met with some resistance and approaches that do not always recognise the academic who are a critical component to the success of the transformational process. Over the last decade the Internet has evolved from being a tool used by a few dedicated educators to one that is being used by the majority of educators. However, what is important is how this great resource is used in teaching and learning to allow students to build knowledge. The ability for students to construct knowledge and engage in higher order thinking skills is at the heart of educational practices, and building a community of learners has the potential to support these practices, especially within STEM education. This paper explores the relationship between students and an academic teaching in a technology rich STEM learning environment and their adoption of social community and shared tools. In particular the paper reports on the critical components that make a successful community of learners and the educational tools and approaches that were successfully used to enhance the student learning experience in a STEM classroom.

Impact of community pharmacist intervention discussing patients’ beliefs to improve medication adherence

Background Adherence to evidence based medicines in patients who have experienced a myocardial infarction remains low. Individual’s beliefs towards their medicines are a strong predictor of adherence and may influence other factors that impact on adherence. Objective To investigate if community pharmacists discussing patients’ beliefs about their medicines improved medication adherence at 12 months post myocardial infarction. Setting This study included 200 patients discharged from a public teaching hospital in Queensland, Australia, following a myocardial infarction. Patients were randomised into intervention (n = 100) and control groups (n = 100) and followed for 12 months. Method All patients were interviewed between 5 to 6 weeks, at 6 and 12 months post discharge by the researcher using the repertory grid technique. This technique was used to elicit the patient’s individualised beliefs about their medicines for their myocardial infarction. In the intervention group, patients’ beliefs about their medicines were communicated by the researcher to their community pharmacist. The pharmacist used this information to tailor their discussion with the patient about their medication beliefs at designated time points (3 and 6 months post discharge). The control group was provided with usual care. Main outcome measure The difference in non-adherence measured using a medication possession ratio between the intervention and control groups at 12 months post myocardial infarction. Results There were 137 patients remaining in the study (intervention group n = 72, control group n = 65) at 12 months. In the intervention group 29 % (n = 20) of patients were non-adherent compared to 25 % (n = 16) of patients in control group. Conclusion Discussing patients’ beliefs about their medicines for their myocardial infarction did not improve medication adherence. Further research on patients beliefs should focus on targeting non-adherent patients whose reasons for their non-adherence is driven by their medication beliefs.

Community engagement for disaster resilience : flood risk management in Jakarta, Indonesia

Understanding dynamics of interactions between community groups and government agencies is crucial to improve community resilience for flood risk reduction through effective community engagement strategies. Overall, a variety of approaches are available, however they are limited in their application. Based on research of a case study in Kampung Melayu Village in Jakarta, further complexity in engaging community emerges in planning policy which requires the relocation of households living in floodplains. This complexity arises in decision-making processes due to barriers to communication. This obstacle highlights the need for a simplified approach for an effective flood risk management which will be further explored in this paper. Qualitative analyses will be undertaken following semi-structured interviews conducted with key actors within government agencies, non-governmental organisations (NGOs), and representatives of communities. The analyses involve investigation of barriers and constraints on community engagement in flood risk management, particularly relevant to collaboration mechanism, perception of risk, and technical literacy to flood risk. These analyses result in potential redirection of community consultation strategies to lead to a more effective collaboration among stakeholders in the decision-making processes. As a result, greater effectiveness in plan implementation of flood risk management potentially improves disaster resilience in the future.

Surviving the electronic panopticon: New lessons in democracy, surveillance, and community in young adult fiction

The ability of new information and communication technologies to pierce previously impenetrable physical, personal, and social boundaries has particular relevance to contemporary society and young people as there is now more information that can be collected, accessed, and distributed about individuals and groups. The ability to know about each other has become a central feature of many young people’s lives. The need to know is further complicated by other questions – Who knows? What do they know? What are the implications of this knowledge?. These questions are a consequence of society having become more mobile and networked enabling increased surveillance, tracking, and spreading of dis/information. With the acceleration of new pervasive and immersive technologies, these questions have taken on a new urgency and significance that go beyond an Orwellian Big Brother scenario. This chapter extends Foucault’s notion of the panopticon to take account of the challenges of an AmI environment of smart networked devices. By drawing on examples of recent young adult fiction, I examine some of the ways in which these texts invite their readers to reflect and speculate on the uneasy relationship between surveillance and democracy and what this means for individual rights and freedom, and a sense of place and belonging.

Listening to the talk of the city: media and urban informatics in community consultation for architectural and urban design

The discipline of architecture focuses on designing the built environment in response to the needs of society, reflecting culture through materials and forms. The physical boundaries of the city have become blurred through the integration of digital media, connecting the physical environment with the digital. In the recent past the future was imagined as highly technological; Ridley Scott’s Blade Runner is set in 2019 and introduces a polluted world where supersized screens inject advertisements in the cluttered urban space. Now, in 2014 screens are central to everyday life, but in a completely different way in respect to what had been imagined. Through ubiquitous computing and social media, information is abundant. Digital technologies have changed the way people relate to urban form supporting discussion on multiple levels, allowing citizens to be more vocal than ever before. Bottom-up campaigns to oppose anticipated developments or to suggest intervention in the way cities are designed, are a common situation in several parts of the world. For some extent governments and local authorities are trying to engage with developing technologies, but a common issue is that social media cannot be controlled or filtered as can be done with more traditional consultation methods. We question how designers can use the affordances of urban informatics to obtain and navigate useful social information to inform architectural and urban design. This research investigates different approaches to engage communities in the debate on the built environment. Physical and digital discussions have been initiated to capture citizens’ opinions on the use and design of public places. Online platforms, urban screens, mobile apps and guerrilla techniques are explored in the context of Brisbane, Australia.

Community pharmacy dispensing of prescription medicine sample packs: Changing the business of medicine initiation?

Prescription medicine samples (or starter packs) are provided by pharmaceutical manufacturers to prescribing doctors as one component in the suite of marketing products used to convince them to prescribe a particular medicine [1,2]. Samples are generally newer, more expensive treatment options still covered by patent [3,4]. Safe, effective, judicious and appropriate medicine use (quality use of medicines) [5] could be enhanced by involving community pharmacists in the dispensing of starter packs. Doctors who use samples show a trend towards prescribing more expensive medicines overall [6] and also prescribe more medicines [7]. Cardiovascular health and mental health are Australian National Health Priority Areas [8] and account for approximately 30% and 17%, respectively, of annual government Pharmaceutical Benefits System (PBS) in 2006 [9]. The PBS is Australia's universal prescription subsidy scheme [9]. Antihypertensives were a major contributor to the estimated 80 000 medicine-related hospital admissions in Australia in 1999 [10] and also internationally [11,12]. The aim of this study was to pilot an alternative model for supply of free sample or starter packs of prescription medicines and ascertain if it is a viable model in daily practice.

Exploitation of the menshutkin reaction for the controlled assembly of halogen bonded architectures incorporating 1,2-diiodotetrafluorobenzene and 1,3,5-Triiodotrifluorobenzene

1,4-Diazabicyclo[2.2.2]octane (DABCO) forms well-defined co-crystals with 1,2-diiodotetrafluorobenzene (1,2-DITFB), [(1,2-DITFB)2DABCO], and 1,3,5-triiodotrifluorobenzene, [(1,3,5-TITFB)2DABCO]. Both systems exhibited lower-than-expected supramolecular connectivity, which inspired a search for polymorphs in alternative crystallization solvents. In dichloromethane solution, the Menshutkin reaction was found to occur, generating chloride anions and quaternary ammonium cations through the reaction between the solvent and DABCO. The controlled in situ production of chloride ions facilitated the crystallization of new halogen bonded networks, DABCO–CH2Cl[(1,2-DITFB)Cl] (zigzag X-bonded chains) and (DABCO–CH2Cl)3[(1,3,5-TITFB)2Cl3]·CHCl3 (2D pseudo-trigonal X-bonded nets displaying Borremean entanglement), propagating with charge-assisted C–I···Cl– halogen bonds. The method was found to be versatile, and substitution of DABCO with triethylamine (TEA) gave (TEA-CH2Cl)3[(1,2-DITFB)Cl3]·4(H2O) (mixed halogen bond hydrogen bond network with 2D supramolecular connectivity) and TEA-CH2Cl[(1,3,5-TITFB)Cl] (tightly packed planar trigonal nets). The co-crystals were typically produced in high yield and purity with relatively predictable supramolecular topology, particularly with respect to the connectivity of the iodobenzene molecules. The potential to use this synthetic methodology for crystal engineering of halogen bonded architectures is demonstrated and discussed.

The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone

Escherichia coli ST131 is now recognised as a leading contributor to urinary tract and bloodstream infections in both community and clinical settings. Here we present the complete, annotated genome of E. coli EC958, which was isolated from the urine of a patient presenting with a urinary tract infection in the Northwest region of England and represents the most well characterised ST131 strain. Sequencing was carried out using the Pacific Biosciences platform, which provided sufficient depth and read-length to produce a complete genome without the need for other technologies. The discovery of spurious contigs within the assembly that correspond to site-specific inversions in the tail fibre regions of prophages demonstrates the potential for this technology to reveal dynamic evolutionary mechanisms. E. coli EC958 belongs to the major subgroup of ST131 strains that produce the CTX-M-15 extended spectrum β-lactamase, are fluoroquinolone resistant and encode the fimH30 type 1 fimbrial adhesin. This subgroup includes the Indian strain NA114 and the North American strain JJ1886. A comparison of the genomes of EC958, JJ1886 and NA114 revealed that differences in the arrangement of genomic islands, prophages and other repetitive elements in the NA114 genome are not biologically relevant and are due to misassembly. The availability of a high quality uropathogenic E. coli ST131 genome provides a reference for understanding this multidrug resistant pathogen and will facilitate novel functional, comparative and clinical studies of the E. coli ST131 clonal lineage.