Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution

Background Maize streak virus -strain A (MSV-A; Genus Mastrevirus, Family Geminiviridae), the maize-adapted strain of MSV that causes maize streak disease throughout sub-Saharan Africa, probably arose between 100 and 200 years ago via homologous recombination between two MSV strains adapted to wild grasses. MSV recombination experiments and analyses of natural MSV recombination patterns have revealed that this recombination event entailed the exchange of the movement protein - coat protein gene cassette, bounded by the two genomic regions most prone to recombination in mastrevirus genomes; the first surrounding the virion-strand origin of replication, and the second around the interface between the coat protein gene and the short intergenic region. Therefore, aside from the likely adaptive advantages presented by a modular exchange of this cassette, these specific breakpoints may have been largely predetermined by the underlying mechanisms of mastrevirus recombination. To investigate this hypothesis, we constructed artificial, low-fitness, reciprocal chimaeric MSV genomes using alternating genomic segments from two MSV strains; a grass-adapted MSV-B, and a maize-adapted MSV-A. Between them, each pair of reciprocal chimaeric genomes represented all of the genetic material required to reconstruct - via recombination - the highly maize-adapted MSV-A genotype, MSV-MatA. We then co-infected a selection of differentially MSV-resistant maize genotypes with pairs of reciprocal chimaeras to determine the efficiency with which recombination would give rise to high-fitness progeny genomes resembling MSV-MatA. Results Recombinants resembling MSV-MatA invariably arose in all of our experiments. However, the accuracy and efficiency with which the MSV-MatA genotype was recovered across all replicates of each experiment depended on the MSV susceptibility of the maize genotypes used and the precise positions - in relation to known recombination hotspots - of the breakpoints required to re-create MSV-MatA. Although the MSV-sensitive maize genotype gave rise to the greatest variety of recombinants, the measured fitness of each of these recombinants correlated with their similarity to MSV-MatA. Conclusions The mechanistic predispositions of different MSV genomic regions to recombination can strongly influence the accessibility of high-fitness MSV recombinants. The frequency with which the fittest recombinant MSV genomes arise also correlates directly with the escalating selection pressures imposed by increasingly MSV-resistant maize hosts.

New strategy toward dioxin risk reduction for local residents surrounding severe dioxin hotspots in Vietnam

Background A public health intervention program with active involvement of local related stakeholders was piloted in the Bien Hoa dioxin hot spot (2007-2009), and then expanded to the Da Nang dioxin hot spot in Vietnam (2009-2011). It aimed to reduce the risk of dioxin exposure through foods for local residents. This article presents the results of the intervention in Da Nang. Methodology To assess the results of this intervention program, pre-intervention and post-intervention knowledge-attitude-practice (KAP) surveys were implemented in 400 households, randomly selected from four wards surrounding Da Nang Airbase in 2009 and 2011, respectively. Results After the intervention, the knowledge on the existence of dioxin in food, dioxin exposure pathways, potential high risk foods and preventive measures significantly increased (p < 0.05). 98% were willing to follow advice on preventing dioxin exposure. Practices to reduce the risk of dioxin exposure also statistical significantly improved (p<0.05). After intervention, 60.4% of households undertook exposure preventive measures, significantly higher than that of the pre-intervention survey (39.6%; χ2 =40.15 , P<0.001). High risk foods had quite low rates of daily consumption (from 0% to 2.5%) and were significantly reduced (p<0.05). Conclusions This is seen as an effective intervention strategy toward reducing the risk of human exposure to dioxin at dioxin hot spots. While greater efforts are needed for remediating dioxin polluted areas inside airbases, there is also evidence to suggest that, during the past four decades, pollution has been expanding to the surrounding areas. For this reason, this model should be quickly expanded to the remaining dioxin hot spots in Vietnam to further reduce the exposure risk in these areas.

Ecological and social characterization of key resource areas in Kenyan rangelands

Key resource areas (KRAs), defined as dry season foraging zones for herbivores, were studied relative to the more extensive outlying rangeland areas (non-KRAs) in Kenya. Field surveys with pastoralists, ranchers, scientists and government officials delineated KRAs on the ground. Identified KRAs were mapped based on global positioning and local experts' information on KRAs accessibility and ecological attributes. Using the map of known KRAs and non-KRAs, we examined characteristics of soils, climate, topography, land use/cover attributes at KRAs relative to non-KRAs. How and why do some areas (KRAs) support herbivores during droughts when forage is scarce in other areas of the landscape? We hypothesized that KRAs have fundamental ecological and socially determined attributes that enable them to provide forage during critical times and we sought to characterize some of those attributes in this study. At the landscape level, KRAs took different forms based on forage availability during the dry season but generally occurred in locations of the landscape with aseasonal water availability and/or difficult to access areas during wet season forage abundance. Greenness trends for KRAs versus non-KRAs were evaluated with a 22-year dataset of Normalized Difference Vegetation Index (NDVI). Field surveys of KRAs provided qualitative information on KRAs as dry season foraging zones. At the scale of the study, soil attributes did not significantly differ for KRAs compared to non-KRAs. Slopes of KRA were generally steeper compared to non-KRAs and elevation was higher at KRAs. Field survey respondents indicated that animals and humans generally avoid difficult to access hilly areas using them only when all other easily accessible rangeland is depleted of forage during droughts. Understanding the nature of KRAs will support identification, protection and restoration of critical forage hotspots for herbivores by strengthening rangeland inventory, monitoring, policy formulation, and conservation efforts to improve habitats and human welfare. (c) 2007 Elsevier Ltd. All rights reserved.

Experimental evaluation of hotspot identification methods

Identifying crash “hotspots”, “blackspots”, “sites with promise”, or “high risk” locations is standard practice in departments of transportation throughout the US. The literature is replete with the development and discussion of statistical methods for hotspot identification (HSID). Theoretical derivations and empirical studies have been used to weigh the benefits of various HSID methods; however, a small number of studies have used controlled experiments to systematically assess various methods. Using experimentally derived simulated data—which are argued to be superior to empirical data, three hot spot identification methods observed in practice are evaluated: simple ranking, confidence interval, and Empirical Bayes. Using simulated data, sites with promise are known a priori, in contrast to empirical data where high risk sites are not known for certain. To conduct the evaluation, properties of observed crash data are used to generate simulated crash frequency distributions at hypothetical sites. A variety of factors is manipulated to simulate a host of ‘real world’ conditions. Various levels of confidence are explored, and false positives (identifying a safe site as high risk) and false negatives (identifying a high risk site as safe) are compared across methods. Finally, the effects of crash history duration in the three HSID approaches are assessed. The results illustrate that the Empirical Bayes technique significantly outperforms ranking and confidence interval techniques (with certain caveats). As found by others, false positives and negatives are inversely related. Three years of crash history appears, in general, to provide an appropriate crash history duration.

The influence of underreported crashes on hotspot identification

Hot spot identification (HSID) plays a significant role in improving the safety of transportation networks. Numerous HSID methods have been proposed, developed, and evaluated in the literature. The vast majority of HSID methods reported and evaluated in the literature assume that crash data are complete, reliable, and accurate. Crash under-reporting, however, has long been recognized as a threat to the accuracy and completeness of historical traffic crash records. As a natural continuation of prior studies, the paper evaluates the influence that under-reported crashes exert on HSID methods. To conduct the evaluation, five groups of data gathered from Arizona Department of Transportation (ADOT) over the course of three years are adjusted to account for fifteen different assumed levels of under-reporting. Three identification methods are evaluated: simple ranking (SR), empirical Bayes (EB) and full Bayes (FB). Various threshold levels for establishing hotspots are explored. Finally, two evaluation criteria are compared across HSID methods. The results illustrate that the identification bias—the ability to correctly identify at risk sites--under-reporting is influenced by the degree of under-reporting. Comparatively speaking, crash under-reporting has the largest influence on the FB method and the least influence on the SR method. Additionally, the impact is positively related to the percentage of the under-reported PDO crashes and inversely related to the percentage of the under-reported injury crashes. This finding is significant because it reveals that despite PDO crashes being least severe and costly, they have the most significant influence on the accuracy of HSID.

Compilation of somatic mutations of the CDKN2 gene in human cancers : non-random distribution of base substitutions

The CDKN2 gene, encoding the cyclin-dependent kinase inhibitor p16, is a tumour suppressor gene that maps to chromosome band 9p21-p22. The most common mechanism of inactivation of this gene in human cancers is through homozygous deletion; however, in a smaller proportion of tumours and tumour cell lines intragenic mutations occur. In this study we have compiled a database of over 120 published point mutations in the CDKN2 gene from a wide variety of tumour types. A further 50 deletions, insertions, and splice mutations in CDKN2 have also been compiled. Furthermore, we have standardised the numbering of all mutations according to the full-length 156 amino acid form of p16. From this study we are able to define several hot spots, some of which occur at conserved residues within the ankyrin domains of p16. While many of the hotspots are shared by a number of cancers, the relative importance of each position varies, possibly reflecting the role of different carcinogens in the development of certain tumours. As reported previously, the mutational spectrum of CDKN2 in melanomas differs from that of internal malignancies and supports the involvement of UV in melanoma tumorigenesis. Notably, 52% of all substitutions in melanoma-derived samples occurred at just six nucleotide positions. Nonsense mutations comprise a comparatively high proportion of mutations present in the CDKN2 gene, and possible explanations for this are discussed.

Haplotype analysis of two recurrent CDKN2A mutations in 10 melanoma families : evidence for common founders and independent mutations

Germ-line mutations in CDKN2A have been shown to predispose to cutaneous malignant melanoma. We have identified 2 new melanoma kindreds which carry a duplication of a 24bp repeat present in the 5' region of CDKN2A previously identified in melanoma families from Australia and the United States. This mutation has now been reported in 5 melanoma families from 3 continents: Europe, North America, and Australasia. The M53I mutation in exon 2 of CDKN2A has also been documented in 5 melanoma families from Australia and North America. The aim of this study was to determine whether the occurrence of the mutations in these families from geographically diverse populations represented mutation hotspots within CDKN2A or were due to common ancestors. Haplotypes of 11 microsatellite markers flanking CDKN2A were constructed in 5 families carrying the M53I mutation and 5 families carrying the 24bp duplication. There were some differences in the segregating haplotypes due primarily to recombinations and mutations within the short tandem-repeat markers; however, the data provide evidence to indicate that there were at least 3 independent 24bp duplication events and possibly only 1 original M53I mutation. This is the first study to date which indicates common founders in melanoma families from different continents.

Street-level drug law enforcement : a meta-analytical review

Our paper presents the results of a meta-analytical review of street level drug law enforcement. We conducted a series of meta-analyses to compare and contrast the effectiveness of four types of drug law enforcement approaches, including community-wide policing, problem-oriented/ partnership approaches that were geographically focused, hotspots policing and standard, unfocused law enforcement efforts. We examined the relative impact of these different crime control tactics on streetlevel drug problems as well as associated problems such as property crime, disorder and violent crime. The results of the meta-analyses, together with examination of forest plots, reveal that problem-oriented policing and geographically-focused interventions involving cooperative partnerships between police and third parties tend to be more effective at controlling drug problems than community-wide policing efforts that are unfocused and spread out across a community. But geographically focused and community-wide drug law enforcement interventions that leverage partnerships are more effective at dealing with drug problems than traditional, law enforcement-only interventions. Our results suggest that the key to successful drug law enforcement lies in the capacity of the police to forge productive partnerships with third parties rather than simply increasing police presence or intervention (e.g., arrests) at drug hotspots.

CARDIAC-ARIA: Measuring the Accessibility to Cardiovascular Services in Rural and Remote Australia Via Applied Geographical Spatial Technology (GIS)

Background/aims: Cardiovascular disease (CVD) continues to impose a heavy burden in terms of cost, disability and death in Australia. Recent evidence suggests that increasing remoteness, where cardiac services are scarce, is linked to an increased risk of dying from CVD. Fatal CVD events are reported to be between 20% and 50% higher in rural areas compared to major cities. Method: This project, with its extensive use of Geographic Information Systems (GIS) technology, will rank 11,338 rural and remote population centres to identify geographical ‘hotspots’ where there is likely to be a mismatch between the demand for and actual provision of cardiovascular services. It will, therefore, guide more equitable provision of services to rural and remote communities. Outcomes: The CARDIAC-ARIA project is designed to; map the type and location of cardiovascular services currently available in Australia, relative to the distribution of individuals who currently have symptomatic CVD; determine, by expert panel, what are the minimal requirements for comprehensive cardiovascular health support in metropolitan and rural communities and derive a rating classification based on the Accessibility and Remoteness Index of Australia (ARIA) for each of Australia's 11,338 rural and remote population centres. Conclusion: This unique, innovative and highly collaborative project has the potential to deliver a powerful tool to highlight and combat the burden imposed by cardiovascular disease (CVD) in Australia.

Hotspot Identification: A Full Bayesian Hierarchical Modeling Approach

This study proposes a full Bayes (FB) hierarchical modeling approach in traffic crash hotspot identification. The FB approach is able to account for all uncertainties associated with crash risk and various risk factors by estimating a posterior distribution of the site safety on which various ranking criteria could be based. Moreover, by use of hierarchical model specification, FB approach is able to flexibly take into account various heterogeneities of crash occurrence due to spatiotemporal effects on traffic safety. Using Singapore intersection crash data(1997-2006), an empirical evaluate was conducted to compare the proposed FB approach to the state-of-the-art approaches. Results show that the Bayesian hierarchical models with accommodation for site specific effect and serial correlation have better goodness-of-fit than non hierarchical models. Furthermore, all model-based approaches perform significantly better in safety ranking than the naive approach using raw crash count. The FB hierarchical models were found to significantly outperform the standard EB approach in correctly identifying hotspots.

Impacts of invasive plants on Australian rangelands

In Australia, the spread and dominance of non-native plant species has been identified as a serious threat to rangeland biodiversity and ecosystem functioning. Rangelands extend over 70% of Australia’s land mass or more than 6 million km2. These rangelands consist of a diverse set of ecosystems including grasslands, shrub-lands, and woodlands spanning numerous climatic zones, ranging from arid to mesic. Because of the high economic, social, and environmental values, sustainable management of these vast landscapes is critical for Australia’s future. More than 2 million people live in these areas and major industries are ranching, mining, and tourism. In terms of biodiversity values, 53 of 85 of Australia’s biogeographical regions and 5 of 15 identified biodiversity hotspots are found in rangelands.

Global genetic diversity and geographical and host-species distribution of beak and feather disease virus isolates

Psittacine beak and feather disease (PBFD) has a broad host range and is widespread in wild and captive psittacine populations in Asia, Africa, the Americas, Europe and Australasia. Beak and feather disease circovirus (BFDV) is the causative agent. BFDV has an ~2 kb single stranded circular DNA genome encoding just two proteins (Rep and CP). In this study we provide support for demarcation of BFDV strains by phylogenetic analysis of 65 complete genomes from databases and 22 new BFDV sequences isolated from infected psittacines in South Africa. We propose 94% genome-wide sequence identity as a strain demarcation threshold, with isolates sharing > 94% identity belonging to the same strain, and strain subtypes sharing> 98% identity. Currently, BFDV diversity falls within 14 strains, with five highly divergent isolates from budgerigars probably representing a new species of circovirus with three strains (budgerigar circovirus; BCV-A, -B and -C). The geographical distribution of BFDV and BCV strains is strongly linked to the international trade in exotic birds; strains with more than one host are generally located in the same geographical area. Lastly, we examined BFDV and BCV sequences for evidence of recombination, and determined that recombination had occurred in most BFDV and BCV strains. We established that there were two globally significant recombination hotspots in the viral genome: the first is along the entire intergenic region and the second is in the C-terminal portion of the CP ORF. The implications of our results for the taxonomy and classification of circoviruses are discussed. © 2011 SGM.

Spatial mapping of city-wide PBDE levels using an exponential decay model

Passive air samplers (PAS) consisting of polyurethane foam (PUF) disks were deployed at 6 outdoor air monitoring stations in different land use categories (commercial, industrial, residential and semi-rural) to assess the spatial distribution of polybrominated diphenyl ethers (PBDEs) in the Brisbane airshed. Air monitoring sites covered an area of 1143 km2 and PAS were allowed to accumulate PBDEs in the city's airshed over three consecutive seasons commencing in the winter of 2008. The average sum of five (∑5) PBDEs (BDEs 28, 47, 99, 100 and 209) levels were highest at the commercial and industrial sites (12.7 ± 5.2 ng PUF−1), which were relatively close to the city center and were a factor of 8 times higher than residential and semi-rural sites located in outer Brisbane. To estimate the magnitude of the urban ‘plume’ an empirical exponential decay model was used to fit PAS data vs. distance from the CBD, with the best correlation observed when the particulate bound BDE-209 was not included (∑5-209) (r2 = 0.99), rather than ∑5 (r2 = 0.84). At 95% confidence intervals the model predicts that regardless of site characterization, ∑5-209 concentrations in a PAS sample taken between 4–10 km from the city centre would be half that from a sample taken from the city centre and reach a baseline or plateau (0.6 to 1.3 ng PUF−1), approximately 30 km from the CBD. The observed exponential decay in ∑5-209 levels over distance corresponded with Brisbane's decreasing population density (persons/km2) from the city center. The residual error associated with the model increased significantly when including BDE-209 levels, primarily due to the highest level (11.4 ± 1.8 ng PUF−1) being consistently detected at the industrial site, indicating a potential primary source at this site. Active air samples collected alongside the PAS at the industrial air monitoring site (B) indicated BDE-209 dominated congener composition and was entirely associated with the particulate phase. This study demonstrates that PAS are effective tools for monitoring citywide regional differences however, interpretation of spatial trends for POPs which are predominantly associated with the particulate phase such as BDE-209, may be restricted to identifying ‘hotspots’ rather than broad spatial trends.

Two novel mutations and a previously unreported intronic polymorphism in the NOTCH3 gene

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a hereditary disease of small vessel caused by mutations in the NOTCH3 gene (NCBI Gene ID: 4854) located on chromosome 19p13.1. NOTCH3 consists of 33 exons which encode a protein of 2321 amino acids. Exons 3 and 4 were found to be mutation hotspots, containing more than 65% of all CADASIL mutations. We performed direct sequencing on an ABI 3130 Genetic Analyser to screen for mutations and polymorphisms on 300 patients who were clinically suspected to have CADASIL. First, exons 3 and 4 were screened in NOTCH3 and if there were no variations found, then extended CADASIL testing (exons 2, 11, 18 and 19) was offered to patients. Here we report two novel non-synonymous mutations identified in the NOTCH3 gene. The first mutation, located in exon 4 was found in a 49-year-old female and causes an alanine to valine amino acid change at position 202 (605C > T). The second mutation, located in exon 11, was found in a 66-year-old female and causes a cysteine to arginine amino acid change at position 579 (1735T > C). We also report a 46-year-old male with a known polymorphism Thr101Thr (rs3815188) and an unreported polymorphism NM_000435.2:c.679+60G>A observed in intron 4 of the NOTCH3 gene. Although Ala202Ala (rs1043994) is a common polymorphism in the NOTCH3 gene, our reported novel mutation (Ala202Val) causes an amino acid change at the same locus. Our other reported mutation (Cys579Arg) correlates well with other known mutations in NOTCH3, as the majority of the CADASIL-associated mutations in NOTCH3 generally occur in the EGF-like (epidermal growth factor-like) repeat domain, causing a change in the number of cysteine residues. The intronic polymorphism NM_000435.2:c.679+60G>A lies close to the intron–exon boundary and may affect the splicing mechanism in the NOTCH3 gene.

Platelet-derived endothelial cell growth factor expression and angiogenesis in cervical intraepithelial neoplasia and squamous cell carcinoma of the cervix

Growth and metastatic spread of invasive carcinoma depends on angiogenesis, the formation of new blood vessels. Platelet-derived endothelial cell growth factor (PD-ECGF) is an angiogenic growth factor for a number of solid tumors, including lung, bladder, colorectal, and renal cell cancer. Cervical intraepithelial neoplasia (CIN) is the precursor to squamous cell cervical carcinoma (SCC). Mean vessel density (MVD) increases from normal cervical tissue, through low- and high-grade CIN to SCC. We evaluated PD-ECGF immunoreactivity and correlated its expression with MVD in normal, premalignant, and malignant cervical tissue. PD-ECGF expression was assessed visually within the epithelial tissues and scored on the extent and intensity of staining. MVD was calculated by counting the number of vessels positive for von Willebrand factor per unit area subtending normal or CIN epithelium or within tumor hotspots for SCC. Cytoplasmic and/or nuclear PD-ECGF immunoreactivity was seen in normal epithelium. PD-ECGF expression significantly increased with histologic grade from normal, through low- and high-grade CIN, to SCC (P < .02). A progressive significant increase in the microvessel density was also seen, ranging from a mean of 28 vessels for normal tissue to 57 for SCC (P < .0005). No correlation was found between PD-ECGF expression and MVD (P = .45). We conclude that PD-ECGF expression and MVD increase as the cervix transforms from a normal to a malignant phenotype. PD-ECGF is thymidine phosphorylase, a key enzyme in the activation of fluoropyrimidines, including 5-fluorouracil. Evaluation of PD-ECGF thymidine phosphorylase expression may be important in designing future chemotherapeutic trials in cervical cancer. Copyright (C) 2000 by W.B. Saunders Company.