Coincident sequence-specific RNA degradation of linked transgenes in the plant genome

The expression of transgenes in plant genomes can be inhibited by either transcriptional gene silencing or posttranscriptional gene silencing (PTGS). Overexpression of the chalcone synthase-A (CHS-A) transgene triggers PTGS of CHS-A and thus results in loss of flower pigmentation in petunia. We previously demonstrated that epigenetic inactivation of CHS-A transgene transcription leads to a reversion of the PTGS phenotype. Although neomycin phosphotransferase II (nptII), a marker gene co-introduced into the genome with the CHS-A transgene, is not normally silenced in petunia, even when CHS-A is silenced, here we found that nptII was silenced in a petunia line in which CHS-A PTGS was induced, but not in the revertant plants that had no PTGS of CHS-A. Transcriptional activity, accumulation of short interfering RNAs, and restoration of mRNA level after infection with viruses that had suppressor proteins of gene silencing indicated that the mechanism for nptII silencing was posttranscriptional. Read-through transcripts of the CHS-A gene toward the nptII gene were detected. Deep-sequencing analysis revealed a striking difference between the predominant size class of small RNAs produced from the read-through transcripts (22 nt) and that from the CHS-A RNAs (21 nt). These results implicate the involvement of read-through transcription and distinct phases of RNA degradation in the coincident PTGS of linked transgenes and provide new insights into the destabilization of transgene expression.

Public transport travel time variability definitions and monitoring

Public Transport Travel Time Variability (PTTV) is essential for understanding the deteriorations in the reliability of travel time, optimizing transit schedules and route choices. This paper establishes the key definitions of PTTV in which firstly include all buses, and secondly include only a single service from a bus route. The paper then analyzes the day-to-day distribution of public transport travel time by using Transit Signal Priority data. A comprehensive approach, using both parametric bootstrapping Kolmogorov-Smirnov test and Bayesian Information Creation technique is developed, recommends Lognormal distribution as the best descriptor of bus travel time on urban corridors. The probability density function of Lognormal distribution is finally used for calculating probability indicators of PTTV. The findings of this study are useful for both traffic managers and statisticians for planning and analyzing the transit systems.

Combined analysis of categorical and numerical descriptors of Australian groundnut accessions using nonlinear principal component analysis

For users of germplasm collections, the purpose of measuring characterization and evaluation descriptors, and subsequently using statistical methodology to summarize the data, is not only to interpret the relationships between the descriptors, but also to characterize the differences and similarities between accessions in relation to their phenotypic variability for each of the measured descriptors. The set of descriptors for the accessions of most germplasm collections consists of both numerical and categorical descriptors. This poses problems for a combined analysis of all descriptors because few statistical techniques deal with mixtures of measurement types. In this article, nonlinear principal component analysis was used to analyze the descriptors of the accessions in the Australian groundnut collection. It was demonstrated that the nonlinear variant of ordinary principal component analysis is an appropriate analytical tool because subspecies and botanical varieties could be identified on the basis of the analysis and characterized in terms of all descriptors. Moreover, outlying accessions could be easily spotted and their characteristics established. The statistical results and their interpretations provide users with a more efficient way to identify accessions of potential relevance for their plant improvement programs and encourage and improve the usefulness and utilization of germplasm collections.

How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research

Over the past decade the mitochondrial (mt) genome has become the most widely used genomic resource available for systematic entomology. While the availability of other types of ‘–omics’ data – in particular transcriptomes – is increasing rapidly, mt genomes are still vastly cheaper to sequence and are far less demanding of high quality templates. Furthermore, almost all other ‘–omics’ approaches also sequence the mt genome, and so it can form a bridge between legacy and contemporary datasets. Mitochondrial genomes have now been sequenced for all insect orders, and in many instances representatives of each major lineage within orders (suborders, series or superfamilies depending on the group). They have also been applied to systematic questions at all taxonomic scales from resolving interordinal relationships (e.g. Cameron et al., 2009; Wan et al., 2012; Wang et al., 2012), through many intraordinal (e.g. Dowton et al., 2009; Timmermans et al., 2010; Zhao et al. 2013a) and family-level studies (e.g. Nelson et al., 2012; Zhao et al., 2013b) to population/biogeographic studies (e.g. Ma et al., 2012). Methodological issues around the use of mt genomes in insect phylogenetic analyses and the empirical results found to date have recently been reviewed by Cameron (2014), yet the technical aspects of sequencing and annotating mt genomes were not covered. Most papers which generate new mt genome report their methods in a simplified form which can be difficult to replicate without specific knowledge of the field. Published studies utilize a sufficiently wide range of approaches, usually without justification for the one chosen, that confusion about commonly used jargon such as ‘long PCR’ and ‘primer walking’ could be a serious barrier to entry. Furthermore, sequenced mt genomes have been annotated (gene locations defined) to wildly varying standards and improving data quality through consistent annotation procedures will benefit all downstream users of these datasets. The aims of this review are therefore to: 1. Describe in detail the various sequencing methods used on insect mt genomes; 2. Explore the strengths/weakness of different approaches; 3. Outline the procedures and software used for insect mt genome annotation, and; 4. Highlight quality control steps used for new annotations, and to improve the re-annotation of previously sequenced mt genomes used in systematic or comparative research.

Temperature variability and childhood pneumonia : an ecological study

Background Few data on the relationship between temperature variability and childhood pneumonia are available. This study attempted to fill this knowledge gap. Methods A quasi-Poisson generalized linear regression model combined with a distributed lag nonlinear model was used to quantify the impacts of diurnal temperature range (DTR) and temperature change between two neighbouring days (TCN) on emergency department visits (EDVs) for childhood pneumonia in Brisbane, from 2001 to 2010, after controlling for possible confounders. Results An adverse impact of TCN on EDVs for childhood pneumonia was observed, and the magnitude of this impact increased from the first five years (2001–2005) to the second five years (2006–2010). Children aged 5–14 years, female children and Indigenous children were particularly vulnerable to TCN impact. However, there was no significant association between DTR and EDVs for childhood pneumonia. Conclusions As climate change progresses, the days with unstable weather pattern are likely to increase. Parents and caregivers of children should be aware of the high risk of pneumonia posed by big TCN and take precautionary measures to protect children, especially those with a history of respiratory diseases, from climate impacts.

The complete mitochondrial genome of the yellow coaster, Acraea issoria (Lepidoptera: Nymphalidae: Heliconiinae: Acraeini): sequence, gene organization and a unique tRNA translocation event

In this paper, the complete mitochondrial genome of Acraea issoria (Lepidoptera: Nymphalidae: Heliconiinae: Acraeini) is reported; a circular molecule of 15,245 bp in size. For A. issoria, genes are arranged in the same order and orientation as the complete sequenced mitochondrial genomes of the other lepidopteran species, except for the presence of an extra copy of tRNAIle(AUR)b in the control region. All protein-coding genes of A. issoria mitogenome start with a typical ATN codon and terminate in the common stop codon TAA, except that COI gene uses TTG as its initial codon and terminates in a single T residue. All tRNA genes possess the typical clover leaf secondary structure except for tRNASer(AGN), which has a simple loop with the absence of the DHU stem. The sequence, organization and other features including nucleotide composition and codon usage of this mitochondrial genome were also reported and compared with those of other sequenced lepidopterans mitochondrial genomes. There are some short microsatellite-like repeat regions (e.g., (TA)9, polyA and polyT) scattered in the control region, however, the conspicuous macro-repeats units commonly found in other insect species are absent.

Global sequence variation in the histidine-rich proteins 2 and 3 of Plasmodium falciparum: implications for the performance of malaria rapid diagnostic tests

Background Accurate diagnosis is essential for prompt and appropriate treatment of malaria. While rapid diagnostic tests (RDTs) offer great potential to improve malaria diagnosis, the sensitivity of RDTs has been reported to be highly variable. One possible factor contributing to variable test performance is the diversity of parasite antigens. This is of particular concern for Plasmodium falciparum histidine-rich protein 2 (PfHRP2)-detecting RDTs since PfHRP2 has been reported to be highly variable in isolates of the Asia-Pacific region. Methods The pfhrp2 exon 2 fragment from 458 isolates of P. falciparum collected from 38 countries was amplified and sequenced. For a subset of 80 isolates, the exon 2 fragment of histidine-rich protein 3 (pfhrp3) was also amplified and sequenced. DNA sequence and statistical analysis of the variation observed in these genes was conducted. The potential impact of the pfhrp2 variation on RDT detection rates was examined by analysing the relationship between sequence characteristics of this gene and the results of the WHO product testing of malaria RDTs: Round 1 (2008), for 34 PfHRP2-detecting RDTs. Results Sequence analysis revealed extensive variations in the number and arrangement of various repeats encoded by the genes in parasite populations world-wide. However, no statistically robust correlation between gene structure and RDT detection rate for P. falciparum parasites at 200 parasites per microlitre was identified. Conclusions The results suggest that despite extreme sequence variation, diversity of PfHRP2 does not appear to be a major cause of RDT sensitivity variation.

Climate variability, climate change and land degradation

Effective response by government and individuals to the risk of land degradation requires an understanding of regional climate variations and the impacts of climate and management on condition and productivity of land and vegetation resources. Analysis of past land degradation and climate variability provides some understanding of vulnerability to current and future climate changes and the information needs for more sustainable management. We describe experience in providing climate risk assessment information for managing for the risk of land degradation in north-eastern Australian arid and semi-arid regions used for extensive grazing. However, we note that information based on historical climate variability, which has been relied on in the past, will now also have to factor in the influence of human-induced climate change. Examples illustrate trends in climate for Australia over the past decade and the impacts on indicators of resource condition. The analysis highlights the benefits of insights into past trends and variability in rainfall and other climate variables based on extended historic databases. This understanding in turn supports more reliable regional climate projections and decision support information for governments and land managers to better manage the risk of land degradation now and in the future.

Pasture Degradation and Recovery in Australia's Rangelands : Learning from History

"The extended drought periods in each degradation episode have provided a test of the capacity of grazing systems (i.e. land, plants, animals, humans and social structure) to handle stress. Evidence that degradation was already occurring was identified prior to the extended drought sequences. The sequence of dry years, ranging from two to eight years, exposed and/or amplified the degradation processes. The unequivocal evidence was provided by: (a) the physical 'horror' of bare landscapes, erosion scalds and gullies and dust storms; (b) the biological devastation of woody weeds and animal suffering/deaths or forced sales, and; (c) the financial and emotional plight of graziers and their families due to reduced production in some cases leading to abandonment of properties or, sadly, deaths (e.g. McDonald 1991, Ker Conway 1989)."--Publisher website

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.

Autotransporters of Escherichia coli : a sequence-based characterization

Autotransporter (AT) proteins are found in all Escherichia coli pathotypes and are often associated with virulence. In this study we took advantage of the large number of available E. coli genome sequences to perform an in-depth bioinformatic analysis of AT-encoding genes. Twenty-eight E. coli genome sequences were probed using an iterative approach, which revealed a total of 215 AT-encoding sequences that represented three major groups of distinct domain architecture: (i) serine protease AT proteins, (ii) trimeric AT adhesins and (iii) AIDA-I-type AT proteins. A number of subgroups were identified within each broad category, and most subgroups contained at least one characterized AT protein; however, seven subgroups contained no previously described proteins. The AIDA-I-type AT proteins represented the largest and most diverse group, with up to 16 subgroups identified from sequence-based comparisons. Nine of the AIDA-I-type AT protein subgroups contained at least one protein that possessed functional properties associated with aggregation and/or biofilm formation, suggesting a high degree of redundancy for this phenotype. The Ag43, YfaL/EhaC, EhaB/UpaC and UpaG subgroups were found in nearly all E. coli strains. Among the remaining subgroups, there was a tendency for AT proteins to be associated with individual E. coli pathotypes, suggesting that they contribute to tissue tropism or symptoms specific to different disease outcomes.