Bird evolution: testing the Metaves clade with six new mitochondrial genomes

Background Evolutionary biologists are often misled by convergence of morphology and this has been common in the study of bird evolution. However, the use of molecular data sets have their own problems and phylogenies based on short DNA sequences have the potential to mislead us too. The relationships among clades and timing of the evolution of modern birds (Neoaves) has not yet been well resolved. Evidence of convergence of morphology remain controversial. With six new bird mitochondrial genomes (hummingbird, swift, kagu, rail, flamingo and grebe) we test the proposed Metaves/Coronaves division within Neoaves and the parallel radiations in this primary avian clade. Results Our mitochondrial trees did not return the Metaves clade that had been proposed based on one nuclear intron sequence. We suggest that the high number of indels within the seventh intron of the β-fibrinogen gene at this phylogenetic level, which left a dataset with not a single site across the alignment shared by all taxa, resulted in artifacts during analysis. With respect to the overall avian tree, we find the flamingo and grebe are sister taxa and basal to the shorebirds (Charadriiformes). Using a novel site-stripping technique for noise-reduction we found this relationship to be stable. The hummingbird/swift clade is outside the large and very diverse group of raptors, shore and sea birds. Unexpectedly the kagu is not closely related to the rail in our analysis, but because neither the kagu nor the rail have close affinity to any taxa within this dataset of 41 birds, their placement is not yet resolved. Conclusion Our phylogenetic hypothesis based on 41 avian mitochondrial genomes (13,229 bp) rejects monophyly of seven Metaves species and we therefore conclude that the members of Metaves do not share a common evolutionary history within the Neoaves.

Isolation and characterisation of novel microsatellite and mitochondrial DNA markers for the Eastern Water Dragon (Physignathus lesueurii)

Habitat fragmentation as a result of urbanisation is a growing problem for native lizard species. The Eastern Water Dragon (Physignathus lesueurii) is a social arboreal agamid lizard, native to Australia. This species represents an ideal model species to investigate the effect of urbanisation because of their prominent abundance in the urban landscape. Here we describe the isolation and characterisation of a novel set of 74 di-, tri-, and tetramicrosatellites from which 18 were selected and optimised into two multiplexes. The 18 microsatellites generated a total 148 alleles across the two populations. The number of alleles per locus varied from 2 to 18 alleles and measures of Ho and He varied from 0.395 to 0.877 and from 0.441 to 0.880, respectively. We also present primers for four novel mitochondrial DNA (mtDNA) markers. The combined length of the four mtDNA marker pairs was 2,528 bp which included 15 nucleotides changes. In comparison to threatened species, which are generally characterised by small population sizes, the Eastern Water Dragon represents an ideal model species to investigate the effect of urbanisation on their behavioural ecology and connectivity patterns among populations.

Risk of metabolic syndrome among children living in metropolitan Kuala Lumpur: A case control study

Background With the increasing prevalence of childhood obesity, the metabolic syndrome has been studied among children in many countries but not in Malaysia. Hence, this study aimed to compare metabolic risk factors between overweight/obese and normal weight children and to determine the influence of gender and ethnicity on the metabolic syndrome among school children aged 9-12 years in Kuala Lumpur and its metropolitan suburbs. Methods A case control study was conducted among 402 children, comprising 193 normal-weight and 209 overweight/obese. Weight, height, waist circumference (WC) and body composition were measured, and WHO (2007) growth reference was used to categorise children into the two weight groups. Blood pressure (BP) was taken, and blood was drawn after an overnight fast to determine fasting blood glucose (FBG) and full lipid profile, including triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C) and total cholesterol (TC). International Diabetes Federation (2007) criteria for children were used to identify metabolic syndrome. Results Participants comprised 60.9% (n = 245) Malay, 30.9% (n = 124) Chinese and 8.2% (n = 33) Indian. Overweight/obese children showed significantly poorer biochemical profile, higher body fat percentage and anthropometric characteristics compared to the normal-weight group. Among the metabolic risk factors, WC ≥90th percentile was found to have the highest odds (OR = 189.0; 95%CI 70.8, 504.8), followed by HDL-C≤1.03 mmol/L (OR = 5.0; 95%CI 2.4, 11.1) and high BP (OR = 4.2; 95%CI 1.3, 18.7). Metabolic syndrome was found in 5.3% of the overweight/obese children but none of the normal-weight children (p < 0.01). Overweight/obese children had higher odds (OR = 16.3; 95%CI 2.2, 461.1) of developing the metabolic syndrome compared to normal-weight children. Binary logistic regression showed no significant association between age, gender and family history of communicable diseases with the metabolic syndrome. However, for ethnicity, Indians were found to have higher odds (OR = 5.5; 95%CI 1.5, 20.5) compared to Malays, with Chinese children (OR = 0.3; 95%CI 0.0, 2.7) having the lowest odds. Conclusions We conclude that being overweight or obese poses a greater risk of developing the metabolic syndrome among children. Indian ethnicity is at higher risk compared to their counterparts of the same age. Hence, primary intervention strategies are required to prevent this problem from escalating.

Preliminary validation of a novel high-resolution melt-based typing method based on the multilocus sequence typing scheme of Streptococcus pyogenes

The major limitation of current typing methods for Streptococcus pyogenes, such as emm sequence typing and T typing, is that these are based on regions subject to considerable selective pressure. Multilocus sequence typing (MLST) is a better indicator of the genetic backbone of a strain but is not widely used due to high costs. The objective of this study was to develop a robust and cost-effective alternative to S. pyogenes MLST. A 10-member single nucleotide polymorphism (SNP) set that provides a Simpson’s Index of Diversity (D) of 0.99 with respect to the S. pyogenes MLST database was derived. A typing format involving high-resolution melting (HRM) analysis of small fragments nucleated by each of the resolution-optimized SNPs was developed. The fragments were 59–119 bp in size and, based on differences in G+C content, were predicted to generate three to six resolvable HRM curves. The combination of curves across each of the 10 fragments can be used to generate a melt type (MelT) for each sequence type (ST). The 525 STs currently in the S. pyogenes MLST database are predicted to resolve into 298 distinct MelTs and the method is calculated to provide a D of 0.996 against the MLST database. The MelTs are concordant with the S. pyogenes population structure. To validate the method we examined clinical isolates of S. pyogenes of 70 STs. Curves were generated as predicted by G+C content discriminating the 70 STs into 65 distinct MelTs.

The effect of implementing a modified early warning scoring (MEWS) system on the adequacy of vital sign documentation

Introduction and objectives Early recognition of deteriorating patients results in better patient outcomes. Modified early warning scores (MEWS) attempt to identify deteriorating patients early so timely interventions can occur thus reducing serious adverse events. We compared frequencies of vital sign recording 24 h post-ICU discharge and 24 h preceding unplanned ICU admission before and after a new observation chart using MEWS and an associated educational programme was implemented into an Australian Tertiary referral hospital in Brisbane. Design Prospective before-and-after intervention study, using a convenience sample of ICU patients who have been discharged to the hospital wards, and in patients with an unplanned ICU admission, during November 2009 (before implementation; n = 69) and February 2010 (after implementation; n = 70). Main outcome measures Any change in a full set or individual vital sign frequency before-and-after the new MEWS observation chart and associated education programme was implemented. A full set of vital signs included Blood pressure (BP), heart rate (HR), temperature (T°), oxygen saturation (SaO2) respiratory rate (RR) and urine output (UO). Results After the MEWS observation chart implementation, we identified a statistically significant increase (210%) in overall frequency of full vital sign set documentation during the first 24 h post-ICU discharge (95% CI 148, 288%, p value <0.001). Frequency of all individual vital sign recordings increased after the MEWS observation chart was implemented. In particular, T° recordings increased by 26% (95% CI 8, 46%, p value = 0.003). An increased frequency of full vital sign set recordings for unplanned ICU admissions were found (44%, 95% CI 2, 102%, p value = 0.035). The only statistically significant improvement in individual vital sign recordings was urine output, demonstrating a 27% increase (95% CI 3, 57%, p value = 0.029). Conclusions The implementation of a new MEWS observation chart plus a supporting educational programme was associated with statistically significant increases in frequency of combined and individual vital sign set recordings during the first 24 h post-ICU discharge. There were no significant changes to frequency of individual vital sign recordings in unplanned admissions to ICU after the MEWS observation chart was implemented, except for urine output. Overall increases in the frequency of full vital sign sets were seen.

Short answer versus multiple choice examination questions for first year chemistry

Multiple choice (MC) examinations are frequently used for the summative assessment of large classes because of their ease of marking and their perceived objectivity. However, traditional MC formats usually lead to a surface approach to learning, and do not allow students to demonstrate the depth of their knowledge or understanding. For these reasons, we have trialled the incorporation of short answer (SA) questions into the final examination of two first year chemistry units, alongside MC questions. Students’ overall marks were expected to improve, because they were able to obtain partial marks for the SA questions. Although large differences in some individual students’ performance in the two sections of their examinations were observed, most students received a similar percentage mark for their MC as for their SA sections and the overall mean scores were unchanged. In-depth analysis of all responses to a specific question, which was used previously as a MC question and in a subsequent semester in SA format, indicates that the SA format can have weaknesses due to marking inconsistencies that are absent for MC questions. However, inclusion of SA questions improved student scores on the MC section in one examination, indicating that their inclusion may lead to different study habits and deeper learning. We conclude that questions asked in SA format must be carefully chosen in order to optimise the use of marking resources, both financial and human, and questions asked in MC format should be very carefully checked by people trained in writing MC questions. These results, in conjunction with an analysis of the different examination formats used in first year chemistry units, have shaped a recommendation on how to reliably and cost-effectively assess first year chemistry, while encouraging higher order learning outcomes.

Experiences with implementing common mathematical operations using field programmable gate arrays

Many computationally intensive scientific applications involve repetitive floating point operations other than addition and multiplication which may present a significant performance bottleneck due to the relatively large latency or low throughput involved in executing such arithmetic primitives on commod- ity processors. A promising alternative is to execute such primitives on Field Programmable Gate Array (FPGA) hardware acting as an application-specific custom co-processor in a high performance reconfig- urable computing platform. The use of FPGAs can provide advantages such as fine-grain parallelism but issues relating to code development in a hardware description language and efficient data transfer to and from the FPGA chip can present significant application development challenges. In this paper, we discuss our practical experiences in developing a selection of floating point hardware designs to be implemented using FPGAs. Our designs include some basic mathemati cal library functions which can be implemented for user defined precisions suitable for novel applications requiring non-standard floating point represen- tation. We discuss the details of our designs along with results from performance and accuracy analysis tests.

A rep-based hairpin inhibits replication of diverse maize streak virus isolates in a transient assay

Centre for High-Performance Computing, Rosebank, Cape Town, South Africa Maize streak disease, caused by the A strain of the African endemic geminivirus, maize streak mastrevirus (MSV-A), threatens the food security and livelihoods of subsistence farmers throughout sub-Saharan Africa. Using a well-established transient expression assay, this study investigated the potential of a spliceable-intron hairpin RNA (hpRNA) approach to interfere with MSV replication. Two strategies were explored: (i) an inverted repeat of a 662 bp region of the MSV replication-associated protein gene (rep), which is essential for virus replication and is therefore a good target for post-transcriptional gene silencing; and (ii) an inverted repeat of the viral long intergenic region (LIR), considered for its potential to trigger transcriptional silencing of the viral promoter region. After co-bombardment of cultured maize cells with each construct and an infectious partial dimer of the cognate virus genome (MSV-Kom), followed by viral replicativeform-specific PCR, it was clear that, whilst the hairpin rep construct (pHPrepDI662) completely inhibited MSV replication, the LIR hairpin construct was ineffective in this regard. In addition, pHPrepDI662 inhibited or reduced replication of six MSV-A genotypes representing the entire breadth of known MSV-A diversity. Further investigation by real-time PCR revealed that the pHPrepDI662 inverted repeat was 22-fold more effective at reducing virus replication than a construct containing the sense copy, whilst the antisense copy had no effect on replication when compared with the wild type. This is the first indication that an hpRNA strategy targeting MSV rep has the potential to protect transgenic. © 2011 SGM.

Characterization of sky-region morphological-temporal airborne collision detection

Automated airborne collision-detection systems are a key enabling technology for facilitat- ing the integration of unmanned aerial vehicles (UAVs) into the national airspace. These safety-critical systems must be sensitive enough to provide timely warnings of genuine air- borne collision threats, but not so sensitive as to cause excessive false-alarms. Hence, an accurate characterisation of detection and false alarm sensitivity is essential for understand- ing performance trade-offs, and system designers can exploit this characterisation to help achieve a desired balance in system performance. In this paper we experimentally evaluate a sky-region, image based, aircraft collision detection system that is based on morphologi- cal and temporal processing techniques. (Note that the examined detection approaches are not suitable for the detection of potential collision threats against a ground clutter back- ground). A novel collection methodology for collecting realistic airborne collision-course target footage in both head-on and tail-chase engagement geometries is described. Under (hazy) blue sky conditions, our proposed system achieved detection ranges greater than 1540m in 3 flight test cases with no false alarm events in 14.14 hours of non-target data (under cloudy conditions, the system achieved detection ranges greater than 1170m in 4 flight test cases with no false alarm events in 6.63 hours of non-target data). Importantly, this paper is the first documented presentation of detection range versus false alarm curves generated from airborne target and non-target image data.

Comparison of PCR, nested PCR, and random amplified polymorphic DNA PCR for detection and typing of Ureaplasma urealyticum in specimens from pregnant women

A PCR assay, using three primer pairs, was developed for the detection of Ureaplasma urealyticum, parvo biovar, mba types 1, 3, and 6, in cultured clinical specimens. The primer pairs were designed by using the polymorphic base positions within a 310- to 311-bp fragment of the 5* end and upstream control region of the mba gene. The specificity of the assay was confirmed with reference serovars 1, 3, 6, and 14 and by the amplified-fragment sizes (81 bp for mba 1, 262 bp for mba 3, and 193 bp for mba 6). A more sensitive nested PCR was also developed. This involved a first-step PCR, using the primers UMS-125 and UMA226, followed by the nested mba-type PCR described above. This nested PCR enabled the detection and typing of small numbers of U. urealyticum cells, including mixtures, directly in original clinical specimens. By using random amplified polymorphic DNA (RAPD) PCR with seven arbitrary primers, we were also able to differentiate the two biovars of U. urealyticum and to identify 13 RAPD-PCR subtypes. By applying these subtyping techniques to clinical samples collected from pregnant women, we established that (i) U. urealyticum is often a persistent colonizer of the lower genital tract from early midtrimester until the third trimester of pregnancy, (ii) mba type 6 was isolated significantly more often (P 5 0.048) from women who delivered preterm than from women who delivered at term, (iii) no particular ureaplasma subtype(s) was associated with placental infections and/or adverse pregnancy outcomes, and (iv) the ureaplasma subtypes most frequently isolated from women were the same subtypes most often isolated from infected placentas.

Re-imagining utopias: The bat/human project

The making of the modern world has long been fuelled by utopian images that are blind to ecologi- cal reality. Botanical gardens are but one example – who typically portray themselves as miniature, isolated 'edens on earth', whereas they are now in many cases self-evidently also the vital ‘lungs’ of crowded cities, as well as critical habitats for threat- ened biodiversity. In 2010 the 'Remnant Emergency Art lab' set out to question utopian thinking through a creative provocation called the 'Botanical Gardens ‘X-Tension’ - an imagined city-wide, distributed, network of 'ecological gardens' suited to both bat and human needs, in order to ask, what now needs to be better understood, connected and therefore ultimately conserved.

Comprehensive evaluation of DNA barcoding for the molecular species identification of forensically important Australian Sarcophagidae (Diptera)

Carrion-breeding Sarcophagidae (Diptera) can be used to estimate the post-mortem interval (PMI) in forensic cases. Difficulties with accurate morphological identifications at any life stage and a lack of documented thermobiological profiles have limited their current usefulness of these flies. The molecular-based approach of DNA barcoding, which utilises a 648-bp fragment of the mitochondrial cytochrome oxidase subunit I gene, was previously evaluated in a pilot study for the discrimination between 16 Australian sarcophagids. The current study comprehensively evaluated DNA barcoding on a larger taxon set of 588 adult Australian sarcophagids. A total of 39 of the 84 known Australian species were represented by 580 specimens, which includes 92% of potentially forensically important species. A further eight specimens could not be reliably identified, but included as six unidentifable taxa. A neighbour-joining phylogenetic tree was generated and nucleotide sequence divergences were calculated using the Kimura-two-parameter distance model. All species except Sarcophaga (Fergusonimyia) bancroftorum, known for high morphological variability, were resolved as reciprocally monophyletic (99.2% of cases), with most having bootstrap support of 100. Excluding S. bancroftorum, the mean intraspecific and interspecific variation ranged from 0.00-1.12% and 2.81-11.23%, respectively, allowing for species discrimination. DNA barcoding was therefore validated as a suitable method for the molecular identification of the Australian Sarcophagidae, which will aid in the implementation of this fauna in forensic entomology.

The complete mitochondrial genome of the flesh fly, Sarcophaga impatiens Walker (Diptera: Sarcophagidae)

Approximately 2500 fly species comprise the Sarcophagidae family worldwide. The complete mitochondrial genome of the carrion-breeding, forensically important Sarcophaga impatiens Walker (Diptera: Sarcophagidae) from Australia was sequenced. The 15,169 bp circular genome contains the 37 genes found in a typical Metazoan genome: 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. It also contains one non-coding A+T-rich region. The arrangement of the genes was the same as that found in the ancestral insect. All the protein initiation codons are ATN, except for cox1 that begins with TCG (encoding S). The 22 tRNA anticodons of S. impatiens are consistent with those observed in Drosophila yakuba, and all form the typical cloverleaf structure, except for tRNA-Ser(AGN) that lacks the DHU arm. The mitochondrial genome of Sarcophaga presented will be valuable for resolving phylogenetic relationships within the family Sarcophagidae and the order Diptera, and could be used to identify favourable genetic markers for species identifications for forensic purposes.

The moderating effect of knowledge sharing on the relationship between manufacturing activities and business performance

This paper investigates the critical role of knowledge sharing (KS) in leveraging manufacturing activities, namely integrated supplier management (ISM) and new product development (NPD) to improve business performance (BP) within the context of Taiwanese electronic manufacturing companies. The research adopted a sequential mixed method research design, which provided both quantitative empirical evidence as well as qualitative insights, into the moderating effect of KS on the relationships between these two core manufacturing activities and BP. First, a questionnaire survey was administered, which resulted in a sample of 170 managerial and technical professionals providing their opinions on KS, NPD and ISM activities and the BP level within their respective companies. On the basis of the collected data, factor analysis was used to verify the measurement model, followed by correlation analysis to explore factor interrelationships, and finally moderated regression analyses to extract the moderating effects of KS on the relationships of NPD and ISM with BP. Following the quantitative study, six semi-structured interviews were conducted to provide qualitative in-depth insights into the value added from KS practices to the targeted manufacturing activities and the extent of its leveraging power. Results from quantitative statistical analysis indicated that KS, NPD and ISM all have a significant positive impact on BP. Specifically, IT infrastructure and open communication were identified as the two types of KS practices that could facilitate enriched supplier evaluation and selection, empower active employee involvement in the design process, and provide support for product simplification and the modular design process, thereby improving manufacturing performance and strengthening company competitiveness. The interviews authenticated many of the empirical findings, suggesting that in the contemporary manufacturing context KS has become an integral part of many ISM and NPD activities and when embedded properly can lead to an improvement in BP. The paper also highlights a number of useful implications for manufacturing companies seeking to leverage their BP through innovative and sustained KS practices.

The strategic importance of tacit knowledge management activities in construction

Purpose: Tacit knowledge is perceived as the most strategically important resource of the construction organisation, and the only renewable and sustainable base for its activities and competitiveness. Knowledge management (KM) activities that deal with tacit knowledge are essential in helping an organisation to achieve its long-term organisational objectives. The purpose of this paper is to provide empirical evidence for the stronger strategic role of tacit KM in comparison to explicit KM. Design/methodology/approach: A questionnaire survey was administered in 2005 to a sample of construction contractors operating in Hong Kong to elicit opinions on the internal business environment, intensity of KM activities as executed by targeted organisations, and contribution of these activities to business performance (BP). A total of 149 usable responses were received from 99 organisations representing about 38 per cent of the sampling frame. The statistical analyses helped to map the reported KM activities into two groups that, respectively, deal with tacit and explicit knowledge. The sensitivity to variations of organisational policies and strength of association with BP in relation to the two groups of KM activities were also compared empirically. A total of 15 interviews with the managerial and professional staff of leading contractors was undertaken to provide insightful narratives of KM implementations. Findings: The effective implementation of organisational policies, such as encouraging innovations and strengthening strategic guidance for KM, would facilitate human interactions of tacit KM. Higher intensity of activities in managing tacit knowledge would ultimately help the organisations to achieve economic gain in the long run. Originality/value: The stronger strategic role of tacit KM is empirically investigated and established within the context of construction organisations.