Sequence capture and next-generation resequencing of multiple tagged nucleic acid samples for mutation screening of urea cycle disorders

Molecular genetic testing is commonly used to confirm clinical diagnoses of inherited urea cycle disorders (UCDs); however, conventional mutation screenings encompassing only the coding regions of genes may not detect disease-causing mutations occurring in regulatory elements and introns. Microarray-based target enrichment and next-generation sequencing now allow more-comprehensive genetic screening. We applied this approach to UCDs and combined it with the use of DNA bar codes for more cost-effective, parallel analyses of multiple samples.

Next generation e-learning platform: virtual laboratory simulations

Bioscience subjects require a significant amount of training in laboratory techniques to produce highly skilled science graduates. Many techniques which are currently used in diagnostic, research and industrial laboratories require expensive equipment for single users; examples of which include next generation sequencing, quantitative PCR, mass spectrometry and other analytical techniques. The cost of the machines, reagents and limited access frequently preclude undergraduate students from using such cutting edge techniques. In addition to cost and availability, the time taken for analytical runs on equipment such as High Performance Liquid Chromatography (HPLC) does not necessarily fit with the limitations of timetabling. Understanding the theory underlying these techniques without the accompanying practical classes can be unexciting for students. One alternative from wet laboratory provision is to use virtual simulations of such practical which enable students to see the machines and interact with them to generate data. The Faculty of Science and Technology at the University of Westminster has provided all second and third year undergraduate students with iPads so that these students all have access to a mobile device to assist with learning. We have purchased licences from Labster to access a range of virtual laboratory simulations. These virtual laboratories are fully equipped and require student responses to multiple answer questions in order to progress through the experiment. In a pilot study to look at the feasibility of the Labster virtual laboratory simulations with the iPad devices; second year Biological Science students (n=36) worked through the Labster HPLC simulation on iPads. The virtual HPLC simulation enabled students to optimise the conditions for the separation of drugs. Answers to Multiple choice questions were necessary to progress through the simulation, these focussed on the underlying principles of the HPLC technique. Following the virtual laboratory simulation students went to a real HPLC in the analytical suite in order to separate of asprin, caffeine and paracetamol. In a survey 100% of students (n=36) in this cohort agreed that the Labster virtual simulation had helped them to understand HPLC. In free text responses one student commented that "The terminology is very clear and I enjoyed using Labster very much”. One member of staff commented that “there was a very good knowledge interaction with the virtual practical”.

The development of 20 microsatellite loci for the Australian marine mollusk, Donax deltoides, through next generation DNA sequencing

 Next Generation DNA sequencing was used to develop a suite of microsatellite markers for the marine mollusk, Donax deltoides. A total of 20 polymorphic loci were identified and 12 characterized using 30 individuals from a single population (Venus Bay) in south eastern Australia. We observed moderate to high genetic variation across most loci (mean number of alleles per locus = 7.3; mean heterozygosity = 0.633) with only a single locus (Ddel32) displaying significant deviation from Hardy–Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, however two loci were found to be influenced by null alleles. The 10 viable markers characterized in the present study provide a valuable resource for future population genetic assessments and fisheries management of D. deltoides in Australia.

Activity of cabazitaxel in castration-resistant prostate cancer progressing after docetaxel and next-generation endocrine agents

Background Cabazitaxel, abiraterone, and enzalutamide are survival-prolonging treatments in men with castration-resistant prostate cancer (CRPC) progressing following docetaxel chemotherapy. The sequential activity of these agents has not been studied and treatment sequencing remains a key dilemma for clinicians. Objective To describe the antitumour activity of cabazitaxel after docetaxel and next-generation endocrine agents. Design, setting, and participants We report on a cohort of 59 men with progressing CRPC treated with cabazitaxel, 37 of whom had received prior abiraterone and 9 of whom had received prior enzalutamide. Outcome measurements and statistical analysis Changes in prostate-specific antigen (PSA) level were used to determine activity on abiraterone, enzalutamide, and cabazitaxel treatment. Radiologic tumour regressions according to Response Evaluation Criteria in Solid Tumors (RECIST) and symptomatic benefit were evaluated for cabazitaxel therapy. Results and limitations The post-endocrine-therapy patients received abiraterone (n = 32), sequential abiraterone and enzalutamide (n = 5) or enzalutamide (n = 4). These patients received a median of 7 mo of abiraterone and 11 mo of enzalutamide. A median of six cabazitaxel cycles (range: 1-10 cycles) were delivered, with ≥50% PSA declines in 16 of 41 (39%) patients, soft tissue radiologic responses in 3 of 22 (14%) evaluable patients, and symptomatic benefit in 9 of 37 evaluable patients (24%). Median overall survival and progression-free survival were 15.8 and 4.6 mo, respectively. Antitumor activity on cabazitaxel was less favourable in the abiraterone- and enzalutamide-naïve cohort (n = 18), likely reflecting biologic differences in this cohort. These data were obtained from a retrospective analysis. Conclusions This is the first report of cabazitaxel activity in CRPC progressing after treatment with docetaxel and abiraterone or enzalutamide. We demonstrate significant cabazitaxel activity in this setting. Patient summary We looked at the antitumour activity of the chemotherapy drug cabazitaxel in men previously treated with docetaxel chemotherapy and the hormonal drugs abiraterone and enzalutamide. Cabazitaxel appeared active when given after abiraterone and enzalutamide. We can reassure men that cabazitaxel can be used after these novel endocrine treatments. © 2013 European Association of Urology.

Utilization of Probabilistic Models in Short Read Assembly from Second-Generation Sequencing

With the advent of cheaper and faster DNA sequencing technologies, assembly methods have greatly changed. Instead of outputting reads that are thousands of base pairs long, new sequencers parallelize the task by producing read lengths between 35 and 400 base pairs. Reconstructing an organism’s genome from these millions of reads is a computationally expensive task. Our algorithm solves this problem by organizing and indexing the reads using n-grams, which are short, fixed-length DNA sequences of length n. These n-grams are used to efficiently locate putative read joins, thereby eliminating the need to perform an exhaustive search over all possible read pairs. Our goal was develop a novel n-gram method for the assembly of genomes from next-generation sequencers. Specifically, a probabilistic, iterative approach was utilized to determine the most likely reads to join through development of a new metric that models the probability of any two arbitrary reads being joined together. Tests were run using simulated short read data based on randomly created genomes ranging in lengths from 10,000 to 100,000 nucleotides with 16 to 20x coverage. We were able to successfully re-assemble entire genomes up to 100,000 nucleotides in length.

Plant-pathogen interactions: toward development of next-generation disease-resistant plants

Briskly evolving phytopathogens are dire threats to our food supplies and threaten global food security. From the recent advances made toward high-throughput sequencing technologies, understanding of pathogenesis and effector biology, and plant innate immunity, translation of these means into new control tools is being introduced to develop durable disease resistance. Effectoromics as a powerful genetic tool for uncovering effector-target genes, both susceptibility genes and executor resistance genes in effector-assisted breeding, open up new avenues to improve resistance. TALENs (Transcription Activator-Like Effector Nucleases), engineered nucleases and CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats)/Cas9 systems are breakthrough and powerful techniques for genome editing, providing efficient mechanisms for targeted crop protection strategies in disease resistance programs. In this review, major advances in plant disease management to confer durable disease resistance and novel strategies for boosting plant innate immunity are highlighted.

Creative Commons : the next generation : Creative Commons licence use five years on

Since its launch in 2001, the Creative Commons open content licensing initiative has received both praise and censure. While some have touted it as a major step towards removing the burdens copyright law imposes on creativity and innovation in the digital age, others have argued that it robs artists of their rightful income. This paper aims to provide a brief overview and analysis of the practical application of the Creative Commons licences five years after their launch. It looks at how the Creative Commons licences are being used and who is using them, and attempts to identify likely motivations for doing so. By identifying trends in how this licence use has changed over time, it also attempts to rebut arguments that Creative Commons is a movement of academics and hobbyists, and has no value for traditional organisations or working artists.

Next Generation ‘Filmmaking’: New Markets, New Methods and New Business Models

Digital production and distribution technologies may create new opportunities for filmmaking in Australia. A culture of new approaches to filmmaking is emerging driven by ‘next generation filmmakers’ who are willing to consider new business models: from online web series to short films produced for mobile phones. At the same time cultural representation itself is transforming within an interactive, social media driven environment. Yet there is very little research into next generation filmmaking. The aim of this paper is to scope and discuss three key aspects of next generation filmmaking, namely: digital trends in film distribution and marketing; processes and strategies of ‘next generation’ filmmakers; and case studies of viable next generation business models and filmmaking practices. We conclude with a brief examination of the implications for media and cultural policy which suggests the future possibility of a rapprochement between creative industries discourse and cultural policy.

Signal authentication and integrity schemes for next generation global navigation satellite systems

This paper describes a number of techniques for GNSS navigation message authentication. A detailed analysis of the security facilitated by navigation message authentication is given. The analysis takes into consideration the risk of critical applications that rely on GPS including transportation, finance and telecommunication networks. We propose a number of cryptographic authentication schemes for navigation data authentication. These authentication schemes provide authenticity and integrity of the navigation data to the receiver. Through software simulation, the performance of the schemes is quantified. The use of software simulation enables the collection of authentication performance data of different data channels, and the impact of various schemes on the infrastructure and receiver. Navigation message authentication schemes have been simulated at the proposed data rates of Galileo and GPS services, for which the resulting performance data is presented. This paper concludes by making recommendations for optimal implementation of navigation message authentication for Galileo and next generation GPS systems.

Sustaining the next generation of teacher-researchers to work for social justice

This chapter explores a research project involving teachers working with some of the most disadvantaged young people in South Australia, children growing up in poverty, in families struggling with homelessness and ill-health, in the outer southern suburbs. Additionally, there were particular children were struggling with intellectual, emotional and social difficulties which were extreme enough for them not be included in a mainstream class. The research project made two crucial interrelated moves to support teachers to tackle this tough work. First, the project had an explicit social justice agenda. We were not simply researching literacy outcomes, but literacy pedagogies for the students teachers were most worried about. And we wanted to understand how the material conditions of students’ everyday lifeworlds impacted on the working conditions of teachers’ schoolworlds. We sought to open up a discursive space where teachers could talk about poverty, violence, racism and classism in ways that would take them beyond despair and into new imaginings and positive action. Second, the project was designed to start from the urgent questions of early career teachers and to draw on the accumulated practice wisdom of their chosen mentors. Hence we designed not only a teacher-researcher community, but cross-generational networks. Our aim was to build the capacities of both generations to address long-standing educational problems in new ways that drew overtly on their different and complementary resources.

Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant

Background Invasive species pose a significant threat to global economies, agriculture and biodiversity. Despite progress towards understanding the ecological factors associated with plant invasions, limited genomic resources have made it difficult to elucidate the evolutionary and genetic factors responsible for invasiveness. This study presents the first expressed sequence tag (EST) collection for Senecio madagascariensis, a globally invasive plant species. Methods We used pyrosequencing of one normalized and two subtractive libraries, derived from one native and one invasive population, to generate an EST collection. ESTs were assembled into contigs, annotated by BLAST comparison with the NCBI non-redundant protein database and assigned gene ontology (GO) terms from the Plant GO Slim ontologies. Key Results Assembly of the 221 746 sequence reads resulted in 12 442 contigs. Over 50 % (6183) of 12 442 contigs showed significant homology to proteins in the NCBI database, representing approx. 4800 independent transcripts. The molecular transducer GO term was significantly over-represented in the native (South African) subtractive library compared with the invasive (Australian) library. Based on NCBI BLAST hits and literature searches, 40 % of the molecular transducer genes identified in the South African subtractive library are likely to be involved in response to biotic stimuli, such as fungal, bacterial and viral pathogens. Conclusions This EST collection is the first representation of the S. madagascariensis transcriptome and provides an important resource for the discovery of candidate genes associated with plant invasiveness. The over-representation of molecular transducer genes associated with defence responses in the native subtractive library provides preliminary support for aspects of the enemy release and evolution of increased competitive ability hypotheses in this successful invasive. This study highlights the contribution of next-generation sequencing to better understanding the molecular mechanisms underlying ecological hypotheses that are important in successful plant invasions.