Functional investigation of five R2R3-MYB transcription factors associated with wood development in Eucalyptus using DAP-seq-ML

A multi-tiered transcriptional network regulates xylem differentiation and secondary cell wall (SCW) formation in plants, with evidence of both conserved and lineage-specific SCW network architecture. We aimed to elucidate the roles of selected R2R3-MYB transcription factors (TFs) linked to Eucalyptus wood formation by identifying genome-wide TF binding sites and direct target genes through an improved DAP-seq protocol combined with machine learning for target gene assignment (DAP-seq-ML). We applied this to five TFs including a well-studied SCW master regulator (EgrMYB2; homolog of AtMYB83), a repressor of lignification (EgrMYB1; homolog of AtMYB4), a TF affecting SCW thickness and vessel density (EgrMYB137; homolog of PtrMYB074) and two TFs with unclear roles in SCW regulation (EgrMYB135 and EgrMYB122). Each DAP-seq TF peak set (average 12,613 peaks) was enriched for canonical R2R3-MYB binding motifs. To improve the reliability of target gene assignment to peaks, a random forest classifier was developed from Arabidopsis DAP-seq, RNA-seq, chromatin, and conserved noncoding sequence data which demonstrated significantly higher precision and recall to the baseline method of assigning genes to proximal peaks. EgrMYB1, EgrMYB2 and EgrMYB137 predicted targets showed clear enrichment for SCW-related biological processes. As validation, EgrMYB137 overexpression in transgenic Eucalyptus hairy roots increased xylem lignification, while its dominant repression in transgenic Arabidopsis and Populus reduced xylem lignification, stunted growth, and caused downregulation of SCW genes. EgrMYB137 targets overlapped significantly with those of EgrMYB2, suggesting partial functional redundancy. Our results show that DAP-seq-ML identified biologically relevant R2R3-MYB targets supported by the finding that EgrMYB137 promotes SCW lignification in planta.

Haplotype mining panel for genetic dissection and breeding in Eucalyptus

To improve our understanding of genetic mechanisms underlying complex traits in plants, a comprehensive analysis of gene variants is required. Eucalyptus is an important forest plantation genus that is highly outbred. Trait dissection and molecular breeding in eucalypts currently relies on biallelic single-nucleotide polymorphism (SNP) markers. These markers fail to capture the large amount of haplotype diversity in these species, and thus multi-allelic markers are required. We aimed to develop a gene-based haplotype mining panel for Eucalyptus species. We generated 17 999 oligonucleotide probe sets for targeted sequencing of selected regions of 6293 genes implicated in growth and wood properties, pest and disease resistance, and abiotic stress responses. We identified and phased 195 834 SNPs using a read-based phasing approach to reveal SNP-based haplotypes. A total of 8915 target regions (at 4637 gene loci) passed tests for Mendelian inheritance. We evaluated the haplotype panel in four Eucalyptus species (E. grandis, E. urophylla, E. dunnii and E. nitens) to determine its ability to capture diversity across eucalypt species. This revealed an average of 3.13-4.52 haplotypes per target region in each species, and 33.36% of the identified haplotypes were shared by at least two species. This haplotype mining panel will enable the analysis of haplotype diversity within and between species, and provide multi-allelic markers that can be used for genome-wide association studies and gene-based breeding approaches.

qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)

BACKGROUND

Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of intuitive tools to browse and analyze the resulting large-scale genetic and genomic datasets remain a significant challenge. Furthermore, these integrative genomics approaches require innovative methods to dissect the flow and interconnectedness of biological information underlying complex trait variation. The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus. Since the Eucalyptus Genome Integrative Explorer (EucGenIE) is integrated within PlantGenIE, it shares genome and expression analysis tools previously implemented within the various subdomains (ConGenIE, PopGenIE and AtGenIE). Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking.

RESULTS

We have developed qtlXplorer ( https://eucgenie.org/QTLXplorer ) for visualizing and exploring systems genetics data from genome-wide association studies including quantitative trait loci (QTLs) and expression-based QTL (eQTL) associations. This module allows users to, for example, find co-located QTLs and eQTLs using an interactive version of Circos, or explore underlying genes using JBrowse. It provides users with a means to build systems genetics models and generate hypotheses from large-scale population genomics data. We also substantially upgraded the EucGenIE resource and show how it enables users to combine genomics and systems genetics approaches to discover candidate genes involved in biotic stress responses and wood formation by focusing on two multigene families, laccases and peroxidases.

CONCLUSIONS

qtlXplorer adds a new dimension, population genomics, to the EucGenIE and PlantGenIE environment. The resource will be of interest to researchers and molecular breeders working in Eucalyptus and other woody plant species. It provides an example of how systems genetics data can be integrated with functional genetics data to provide biological insight and formulate hypotheses. Importantly, integration within PlantGenIE enables novel comparative genomics analyses to be performed from population-scale data.

A genome-wide SNP genotyping resource for tropical pine tree species

We performed gene and genome targeted SNP discovery towards the development of a genome-wide, multi-species genotyping array for tropical pines. Pooled RNA-seq data from shoots of seedlings from five tropical pine species was used to identify transcript-based SNPs resulting in 1.3 million candidate Affymetrix SNP probe sets. In addition, we used a custom 40K probe set to perform capture-seq in pooled DNA from 81 provenances representing the natural ranges of six tropical pine species in Mexico and Central America resulting in 563K candidate SNP probe sets. Altogether, 300K RNA-seq (72%) and 120K capture-seq (28%) derived SNP probe sets were tiled on a 420K screening array that was used to genotype 576 trees representing the 81 provenances and commercial breeding material. Based on the screening array results, 50K SNPs were selected for commercial SNP array production (Axiom 384 format, Thermo Fisher Scientific) including 20K polymorphic SNPs for P. patula, P. tecunumanii, P. oocarpa and P. caribaea, 15K for P. greggii and P. maximinoi, 13K for P. elliottii and 8K for P. pseudostrobus. We included 9.7K ancestry informative SNPs that will be valuable for species and hybrid discrimination. Of the 50K SNP markers, 25% are polymorphic in only one species, while 75% are shared by two or more species. The Pitro50K SNP chip will be useful for population genomics and molecular breeding in this group of pine species that, together with their hybrids, represent the majority of fast-growing tropical and subtropical pine plantations globally.

Benefits of maize resistance breeding and chemical control against northern leaf blight in smallholder farms in South Africa

Maize underpins food security in South Africa. An annual production of more than 10 million tons is a combination of the output of large-scale commercial farms plus an estimated 250 000 ha cultivated by smallholder farmers. Maize leaves are a rich source of nutrients for fungal pathogens. Farmers must limit leaf blighting by fungi to prevent sugars captured by photosynthesis being ‘stolen’ instead of filling the grain. This study aimed to fill the knowledge gap on the prevalence and impact of fungal foliar diseases in local smallholder maize fields. A survey with 1124 plant observations from diverse maize hybrids was conducted over three seasons from 2015 to 2017 in five farming communities in KwaZulu-Natal Province (Hlanganani, Ntabamhlophe, KwaNxamalala) and Eastern Cape Province (Bizana, Tabankulu). Northern leaf blight (NLB), common rust, Phaeosphaeria leaf spot, and grey leaf spot had overall disease incidences of 75%, 77%, 68% and 56%, respectively, indicating high disease pressure in smallholder farming environments. NLB had the highest disease severity (LSD test, p<0.05). A yield trial focused on NLB in KwaZulu-Natal showed that this disease reduced yields in the three most susceptible maize hybrids by 36%, 71% and 72%, respectively. Eighteen other hybrids in this trial did not show significant yield reductions due to NLB, which illustrates the progress made by local maize breeders in disease resistance breeding. This work highlights the risk to smallholder farmers of planting disease-susceptible varieties, and makes recommendations on how to exploit the advances of hybrid maize disease resistance breeding to develop farmer-preferred varieties for smallholder production.

What can trauma patients' experiences and perspectives tell us about the perceived quality of trauma care? a qualitative study set within the UK National Health Service

The global drive for improvements in the efficiency and quality of healthcare has led to the development of frameworks to assist in defining and measuring 'good quality care'. However, such frameworks lack a systematic or meaningful definition of what 'good quality care' means from the patients' perspective. The present research provides an in-depth analysis of patients' experiences in a hospital setting from a quality of care perspective. Forty-five adults (aged 16-70) hospitalised in one of four UK NHS trusts following an unintentional injury were interviewed about their experiences of care. The findings show variability in perceived quality of care within the same hospital episode which cannot be meaningfully captured by existing frameworks. The context of trauma care (e.g. distressing nature of injury, patient vulnerability, expectations of hospitalisation and participants' interaction with different service providers) defined the care experience and the value of being 'cared for'. Participants identified some aspects of good and care which related to holistic, person-centred and personalised care beyond the medical needs. Participants discussed the value of being understood, staff thinking of their needs beyond hospitalisation, staff trying 'their best' despite constrains of current care, having their emotional needs recognised and addressed and staff competence. Patients reported also poor quality of care and 'not being cared for' by specific staff groups which they expected to fulfil this role, rushed and unsympathetic care, lack of recognition for emotional impact of injury mapped onto existing quality frameworks e.g. safety, equity, accessibility and patient-centeredness as well as quality of interaction with providers, empathetic care which extended beyond medical needs, coordination of care, and the positivity of care delivery as important dimensions of quality care with implications for their recovery. The findings have implications for quality frameworks and theoretical definitions of quality of care; they demonstrate the importance of patient experience in addition to clinical effectiveness and safety as an essential dimension of quality care. In terms of practice, the findings support the need to incorporate knowledge and training of injured adults' psychological needs, and the value of interaction with professionals as a patient defined dimension of the quality of care.

eCALIBRATOR: A Comparative Tool to Identify Key Genes and Pathways for Eucalyptus Defense Against Biotic Stressors

Many pests and pathogens threaten Eucalyptus plantations. The study of defense responses in this economically important wood and fiber crop enables the discovery of novel pathways and genes, which may be adopted to improve resistance. Various functional genomics experiments have been conducted in Eucalyptus-biotic stress interactions following the availability of the Eucalyptus grandis genome, however, comparisons between these studies were limited largely due to a lack of comparative tools. To this end, we developed eCALIBRATOR http://ecalibrator.bi.up.ac.za, a tool for the comparison of Eucalyptus biotic stress interaction. The tool, which is not limited to Eucalyptus, allows the comparison of various datasets, provides a visual output in the form of Venn diagrams and clustering and extraction of lists for gene ontology enrichment analyses. We also demonstrate the usefulness of the tool in revealing pathways and key gene targets to further functionally characterize. We identified 708 differentially expressed E. grandis genes in common among responses to the insect pest Leptocybe invasa, oomycete pathogen Phytophthora cinnamomi and fungus Chrysoporthe austroafricana. Within this set of genes, one of the Gene Ontology terms enriched was "response to organonitrogen compound," with NITRATE TRANSPORTER 2.5 (NRT2.5) being a key gene, up-regulated under susceptible interactions and down-regulated under resistant interactions. Although previous functional genetics studies in Arabidopsis thaliana support a role in nitrate acquisition and remobilization under long-term nitrate starvation, the importance of NRT2.5 in plant defense is unclear. The T-DNA mutants of AtNRT2.5 were more resistant to Pseudomonas syringae pv. tomato pv tomato DC3000 inoculation than the wild-type counterpart, supporting a direct role for NRT2.5 in plant defense. Future studies will focus on characterizing the Eucalyptus ortholog of NRT2.5.

A systems genetics analysis in Eucalyptus reveals coordination of metabolic pathways associated with xylan modification in wood-forming tissues

Acetyl- and methylglucuronic acid decorations of xylan, the dominant hemicellulose in secondary cell walls (SCWs) of woody dicots, affect its interaction with cellulose and lignin to determine SCW structure and extractability. Genes and pathways involved in these modifications may be targets for genetic engineering; however, little is known about the regulation of xylan modifications in woody plants. To address this, we assessed genetic and gene expression variation associated with xylan modification in developing xylem of Eucalyptus grandis × Eucalyptus urophylla interspecific hybrids. Expression quantitative trait locus (eQTL) mapping identified potential regulatory polymorphisms affecting gene expression modules associated with xylan modification. We identified 14 putative xylan modification genes that are members of five expression modules sharing seven trans-eQTL hotspots. The xylan modification genes are prevalent in two expression modules. The first comprises nucleotide sugar interconversion pathways supplying the essential precursors for cellulose and xylan biosynthesis. The second contains genes responsible for phenylalanine biosynthesis and S-adenosylmethionine biosynthesis required for glucuronic acid and monolignol methylation. Co-expression and co-regulation analyses also identified four metabolic sources of acetyl coenxyme A that appear to be transcriptionally coordinated with xylan modification. Our systems genetics analysis may provide new avenues for metabolic engineering to alter wood SCW biology for enhanced biomass processability.

Early risk factors for depression, anxiety and post-traumatic distress after hospital admission for unintentional injury: Multicentre cohort study

OBJECTIVE

To quantify psychological morbidity and identify baseline factors associated with depression, anxiety and post-traumatic distress symptoms up to 12 months post-injury.

METHODS

Multicentre cohort study of 668 adults, aged 16 to 70, admitted to 4 UK NHS hospital trusts. Data on injury, socio-demographic characteristics and health status was collected at recruitment. Depression, anxiety and post-traumatic distress were measured at 1, 2, 4 and 12 months post-injury. Multilevel linear regression assessed associations between patient and injury characteristics and psychological outcomes over 12 months follow-up.

RESULTS

Depression, anxiety and post-traumatic distress scores were highest 1 month post-injury, and remained above baseline at 2, 4 and 12 months post-injury. Moderate or severe injuries, previous psychiatric diagnoses, higher pre-injury depression and anxiety scores, middle age (45-64 years), greater deprivation and lower pre-injury quality of life (QoL) were associated with higher depression scores post-injury. Previous psychiatric diagnoses, higher pre-injury depression and anxiety scores, middle age, greater deprivation and lower pre-injury QoL were associated with higher anxiety scores post-injury. Traffic injuries or injuries from being struck by objects, multiple injures (≥3), being female, previous psychiatric diagnoses, higher pre-injury anxiety scores and greater deprivation were associated with higher post-traumatic distress scores post-injury.

CONCLUSION

A range of risk factors, identifiable shortly after injury, are associated with psychological morbidity occurring up to 12 months post-injury in a general trauma population. Further research is required to explore the utility of these, and other risk factors in predicting psychological morbidity on an individual patient basis.

Terpenes associated with resistance against the gall wasp, Leptocybe invasa, in Eucalyptus grandis

Leptocybe invasa is an insect pest causing gall formation on oviposited shoot tips and leaves of Eucalyptus trees leading to leaf deformation, stunting, and death in severe cases. We previously observed different constitutive and induced terpenes, plant specialized metabolites that may act as attractants or repellents to insects, in a resistant and susceptible clone of Eucalyptus challenged with L. invasa. We tested the hypothesis that specific terpenes are associated with pest resistance in a Eucalyptus grandis half-sib population. Insect damage was scored over 2 infestation cycles, and leaves were harvested for near-infrared reflectance (NIR) and terpene measurements. We used Bayesian model averaging for terpene selection and obtained partial least squares NIR models to predict terpene content and L. invasa infestation damage. In our optimal model, 29% of the phenotypic variation could be explained by 7 terpenes, and the monoterpene combination, limonene, α-terpineol, and 1,8-cineole, could be predicted with an NIR prediction ability of  .67. Bayesian model averaging supported α-pinene, γ-terpinene, and iso-pinocarveol as important for predicting L. invasa infestation. Susceptibility was associated with increased γ-terpinene and α-pinene, which may act as a pest attractant, whereas reduced susceptibility was associated with iso-pinocarveol, which may act to recruit parasitoids or have direct toxic effects.

Malaria vectors in the Democratic Republic of the Congo: the mechanisms that confer insecticide resistance in Anopheles gambiae and Anopheles funestus

Background

The Democratic Republic of the Congo (DRC) is characterized as a holoendemic malaria area with the main vectors being Anopheles funestus and members of the Anopheles gambiae complex. Due to political instability and socio-economic challenges in the region, knowledge of insecticide resistance status and resistance mechanisms in these vectors is limited. Mosquitoes were collected from a mining site in the north-eastern part of the country and, following identification, were subjected to extensive testing for the target-site and biochemical basis of resistance. Quantitative real-time PCR was used to assess a suite of 10 genes frequently involved in pyrethroid and dichlorodiphenyltrichloroethane (DDT) resistance in An. gambiae females and males. In An. funestus, gene expression microarray analysis was carried out on female mosquitoes.

Results

In both species, deltamethrin resistance was recorded along with high resistance and suspected resistance to DDT in An. gambiae and An. funestus, respectively. A total of 85% of An. gambiae carried the kdr mutations as either homozygous resistant (RR) (L1014S, L1014F or both) or heterozygous (RS), however only 3% carried the rdl mutant allele (RS) and no ace-1 mutations were recorded. Synergist assays indicated a strong role for P450s in deltamethrin resistance in both species. In An. gambiae, analysis of transcription levels showed that the glutathione-S-transferase, GSTS1-2, produced the highest fold change in expression (7.6-fold in females and 31-fold in males) followed by GSTE2, thioredoxin peroxidase (TPX2), and cytochrome oxidases (CYP6M2 and CYP6P1). All other genes tested produced fold change values below 2. Microarray analysis revealed significant over-transcription of cuticular proteins as well as CYP6M7, CYP6P9a and CYP6P9b in insecticide resistant An. funestus.

Conclusions

These data show that high levels of deltamethrin resistance in the main malaria vector species, conferred by enzymatic detoxification, are present in the DRC.

Electronic supplementary material

The online version of this article (10.1186/s12936-017-2099-y) contains supplementary material, which is available to authorized users.

Identification of the Eucalyptus grandis chitinase gene family and expression characterization under different biotic stress challenges

Eucalyptus grandis (W. Hill ex Maiden) is an Australian Myrtaceae tree grown for timber in many parts of the world and for which the annotated genome sequence is available. Known to be susceptible to a number of pests and diseases, E. grandis is a useful study organism for investigating defense responses in woody plants. Chitinases are widespread in plants and cleave glycosidic bonds of chitin, the major structural component of fungal cell walls and arthropod exoskeletons. They are encoded by an important class of genes known to be up-regulated in plants in response to pathogens. The current study identified 67 chitinase gene models from two families known as glycosyl hydrolase 18 and 19 (36 GH18 and 31 GH19) within the E. grandis genome assembly (v1.1), indicating a recent gene expansion. Sequences were aligned and analyzed as conforming to currently recognized plant chitinase classes (I-V). Unlike other woody species investigated to date, E. grandis has a single gene encoding a putative vacuolar targeted Class I chitinase. In response to Leptocybe invasa (Fisher & La Salle) (the eucalypt gall wasp) and Chrysoporthe austroafricana (Gryzenhout & M.J. Wingf. 2004) (causal agent of fungal stem canker), this Class IA chitinase is strongly up-regulated in both resistant and susceptible plants. Resistant plants, however, indicate greater constitutive expression and increased up-regulation than susceptible plants following fungal challenge. Up-regulation within fungal resistant clones was further confirmed with protein data. Clusters of putative chitinase genes, particularly on chromosomes 3 and 8, are significantly up-regulated in response to fungal challenge, while a cluster on chromosome 1 is significantly down-regulated in response to gall wasp. The results of this study show that the E. grandis genome has an expanded group of chitinase genes, compared with other plants. Despite this expansion, only a single Class I chitinase is present and this gene is highly up-regulated within diverse biotic stress conditions. Our research provides insight into a major class of defense genes within E. grandis and indicates the importance of the Class I chitinase.

Psychological morbidity and health-related quality of life after injury: multicentre cohort study

PURPOSE

To demonstrate the impact of psychological morbidity 1 month post-injury on subsequent post-injury quality of life (HRQoL) in a general injury population in the UK to inform development of trauma care and rehabilitation services.

METHODS

Multicentre cohort study of 16-70-year-olds admitted to 4 UK hospitals following injury. Psychological morbidity and HRQoL (EQ-5D-3L) were measured at recruitment and 1, 2, 4 and 12 months post-injury. A reduction in EQ-5D compared to retrospectively assessed pre-injury levels of at least 0.074 was taken as the minimal important difference (MID). Multilevel logistic regression explored relationships between psychological morbidity 1 month post-injury and MID in HRQoL over the 12 months after injury.

RESULTS

A total of 668 adults participated. Follow-up rates were 77% (1 month) and 63% (12 months). Substantial reductions in HRQoL were seen; 93% reported a MID at 1 month and 58% at 12 months. Problems with pain, mobility and usual activities were commonly reported at each time point. Depression and anxiety scores 1 month post-injury were independently associated with subsequent MID in HRQoL. The relationship between depression and HRQoL was partly explained by anxiety and to a lesser extent by pain and social functioning. The relationship between anxiety and HRQoL was not explained by factors measured in our study.

CONCLUSIONS

Hospitalised injuries result in substantial reductions in HRQoL up to 12 months later. Depression and anxiety early in the recovery period are independently associated with lower HRQoL. Identifying and managing these problems, ensuring adequate pain control and facilitating social functioning are key elements in improving HRQoL post-injury.

Systems genetics reveals a transcriptional network associated with susceptibility in the maize-grey leaf spot pathosystem

We used a systems genetics approach to elucidate the molecular mechanisms of the responses of maize to grey leaf spot (GLS) disease caused by Cercospora zeina, a threat to maize production globally. Expression analysis of earleaf samples in a subtropical maize recombinant inbred line population (CML444 × SC Malawi) subjected in the field to C. zeina infection allowed detection of 20 206 expression quantitative trait loci (eQTLs). Four trans-eQTL hotspots coincided with GLS disease QTLs mapped in the same field experiment. Co-expression network analysis identified three expression modules correlated with GLS disease scores. The module (GY-s) most highly correlated with susceptibility (r = 0.71; 179 genes) was enriched for the glyoxylate pathway, lipid metabolism, diterpenoid biosynthesis and responses to pathogen molecules such as chitin. The GY-s module was enriched for genes with trans-eQTLs in hotspots on chromosomes 9 and 10, which also coincided with phenotypic QTLs for susceptibility to GLS. This transcriptional network has significant overlap with the GLS susceptibility response of maize line B73, and may reflect pathogen manipulation for nutrient acquisition and/or unsuccessful defence responses, such as kauralexin production by the diterpenoid biosynthesis pathway. The co-expression module that correlated best with resistance (TQ-r; 1498 genes) was enriched for genes with trans-eQTLs in hotspots coinciding with GLS resistance QTLs on chromosome 9. Jasmonate responses were implicated in resistance to GLS through co-expression of COI1 and enrichment of genes with the Gene Ontology term 'cullin-RING ubiquitin ligase complex' in the TQ-r module. Consistent with this, JAZ repressor expression was highly correlated with the severity of GLS disease in the GY-s susceptibility network.

The Eucalyptus grandis NBS-LRR Gene Family: Physical Clustering and Expression Hotspots

Eucalyptus grandis is a commercially important hardwood species and is known to be susceptible to a number of pests and pathogens. Determining mechanisms of defense is therefore a research priority. The published genome for E. grandis has aided the identification of one important class of resistance (R) genes that incorporate nucleotide binding sites and leucine-rich repeat domains (NBS-LRR). Using an iterative search process we identified NBS-LRR gene models within the E. grandis genome. We characterized the gene models and identified their genomic arrangement. The gene expression patterns were examined in E. grandis clones, challenged with a fungal pathogen (Chrysoporthe austroafricana) and insect pest (Leptocybe invasa). One thousand two hundred and fifteen putative NBS-LRR coding sequences were located which aligned into two large classes, Toll or interleukin-1 receptor (TIR) and coiled-coil (CC) based on NB-ARC domains. NBS-LRR gene-rich regions were identified with 76% organized in clusters of three or more genes. A further 272 putative incomplete resistance genes were also identified. We determined that E. grandis has a higher ratio of TIR to CC classed genes compared to other woody plant species as well as a smaller percentage of single NBS-LRR genes. Transcriptome profiles indicated expression hotspots, within physical clusters, including expression of many incomplete genes. The clustering of putative NBS-LRR genes correlates with differential expression responses in resistant and susceptible plants indicating functional relevance for the physical arrangement of this gene family. This analysis of the repertoire and expression of E. grandis putative NBS-LRR genes provides an important resource for the identification of novel and functional R-genes; a key objective for strategies to enhance resilience.

Stereotactic radiosurgery for lung cancer

Lung cancer is the most common cause of cancer death in both men and women in the United States. Anatomic lobectomy is the standard treatment and offers the best results for curative treatment of early stage non-small cell lung cancer (NSCLC). With an aging population, a significant proportion of patients are not surgical candidates at the time of diagnosis. In medically inoperable patients, standard external beam radiation has been offered as treatment, with suboptimal results. Stereotactic radiosurgery (SRS), a term coined by Leksell describes an approach using multiple convergent beams, precise localization with a stereotactic coordinate system, and rigid immobilization. It provides precise delivery of beams from multiple collimated paths which maximizes radiation delivery to the tumor, and minimizes the exposure of normal tissue. Early results with SRS are very encouraging, and prospective trials are underway in our institution and others to evaluate its role in early stage NSCLC. In article we review the role of stereotactic radiosurgery for the treatment of lung cancer.

Understanding high traffic injury risks for children in low socioeconomic areas: a qualitative study of parents' views

OBJECTIVE

To gain an in-depth qualitative understanding of parents' views about their children's exposure to road traffic injury risk in low socioeconomic areas.

DESIGN

Focus groups facilitated by a moderator with content analysis of data.

SETTING

Focus groups were conducted in 10 low socioeconomic English districts that also have high rates of child pedestrian injury. Research was conducted in community venues within each area.

SUBJECTS

Parents of children aged 9-14 years living in low socioeconomic areas.

RESULTS

Parents believe that children play in their local streets for the following reasons: they like playing out with friends near home; there are few safe, secure, and well-maintained public spaces for children; children are excluded from affordable leisure venues because of their costs; insufficient parental responsibility. For children that play in the street, the key sources of risk identified by parents were: illegal riding and driving around estates and on the pavements; the speed and volume of traffic; illegal parking; drivers being poorly informed about where children play; children's risk-taking behavior.

CONCLUSIONS

Intervention programs need to take into account multiple reasons why children in low socioeconomic areas become exposed to hazardous environments thereby increasing their risk of injury. Multi-agency partnerships involving the community are increasingly needed to implement traditional road safety approaches, such as education, engineering, and enforcement, and provide safe and accessible public space, affordable activities for children, and greater support for parents.

Intimate partner sexual abuse among women on methadone

This article reports findings on the prevalence and correlates of intimate partner sexual abuse (using the Revised Conflict Tactics Scale) among a sample of women in methadone treatment in New York City. Results indicate that, during the course of the intimate relationship, approximately 15% of women had experienced intimate partner sexual assault and 47% were sexually assaulted and/or coerced. Nine percent had experienced intimate partner sexual assault and 38% intimate partner sexual coercion in the past year of the relationship. Bivariate analyses revealed that women who were sexually abused in the 12 months prior to the interview tended also to be physically abused by intimate partners. Women who were unemployed, poor, crack-cocaine or injecting-drug users, and were physically and/or sexually abused as children, were at increased risk of experiencing intimate partner sexual abuse in adulthood. In multivariate models, only extreme poverty and sexual abuse in childhood emerged as risk factors for intimate partner sexual abuse in adulthood.

Minimally invasive surgical staging for esophageal cancer

BACKGROUND

The incidence of esophageal adenocarcinoma is increasing in the United States, and the 5-year survival rate is dismal. Preliminary data suggest that conventional imaging is inaccurate in staging esophageal cancer and could limit accurate assessment of new treatments. The objective of this study was to compare minimally invasive surgical staging (MIS) with conventional imaging for staging esophageal cancer.

METHODS

Patients with potentially resectable esophageal cancer were eligible. Staging by conventional methods used computed tomography (CT) scan of the chest and abdomen, and endoscopic ultrasound (EUS), whereas MIS used laparoscopy and videothoracoscopy. Conventional staging results were compared to those from MIS.

RESULTS

In 53 patients, the following stages were assigned by CT scan and EUS: carcinoma in situ (CIS; n = 1), I (n = 1), II (n = 23), III (n = 20), IV (n = 8). In 17 patients (32.1%), MIS demonstrated inaccuracies in the conventional imaging, reassigning a lower stage in 10 patients and a more advanced stage in 7 patients.

CONCLUSIONS

In 32.1% of patients with esophageal cancer, MIS changed the stage originally assigned by CT scan and EUS. Therefore, MIS should be applied to evaluate the accuracy of new noninvasive imaging methods and to assess new therapies for esophageal cancer.

Primary structure of the sialodacryoadenitis virus genome: sequence of the structural-protein region and its application for differential diagnosis

Sialodacryoadenitis virus (SDAV) is a coronavirus that is commonly found in laboratory rats and that causes sialodacryoadenitis and respiratory illness. We cloned and sequenced the 3' terminal 9.8 kb of the genomic RNA and analyzed the structure of the viral genome. As with mouse hepatitis coronaviruses (MHVs), the SDAV genome was able to code for a spike protein, a small membrane protein, a membrane-associated protein, and a nucleocapsid protein. In addition, the hemagglutinin-esterase gene capable of encoding a protein of 439 amino acids (aa) was identified. The putative functional site for acetylesterase activity was present in the HE protein as Phe-Gly-Asp-Ser (FGDS), suggesting that the SDAV HE protein might have retained the esterase activity. Immediately upstream of the HE gene and downstream of the polymerase 1b gene, the NS2 nonstructural-protein gene was identified with a coding capacity of 274 aa. A motif of UCUAAAC was identified as a potential transcription signal for subgenomic mRNA synthesis. Large insertions of 172, 127, and 44 aa were detected in the N-terminal half of the predicted S protein of SDAV when its sequence was compared to the sequences of MHV 2, MHV JHM, and MHV A59, respectively. The sequence information on the SDAV S-protein gene was applied to a differential diagnostic PCR to detect and distinguish the rat coronavirus from mouse coronaviruses. This is the first report on the comprehensive genetic information of any rat coronavirus.

Angiotensin receptor antagonists and ACE inhibitors

BACKGROUND

ACE inhibitors are valuable and effective drugs in the treatment of hypertension, heart failure, myocardial infarction and nephropathy. Angiotensin receptor antagonists, which have recently been introduced into clinical practice, have the potential to replace ACE inhibitor therapy in many patients.

OBJECTIVE

To review the mechanisms of action, indications and side effects of ACE inhibitors and angiotensin receptor antagonists and to highlight similarities and differences between the two drug classes.

DISCUSSION

Angiotensin receptor antagonists have the theoretical advantage of being more effective in blocking the effects of angiotensin II at angiotensin type I receptors. The potential disadvantage of not potentiating bradykinin may be compensated by the unopposed action of angiotensin II on vascular angiotensin type II receptors, which appear to mediate similar beneficial cardiovascular effects to bradykinin. Angiotensin II receptor antagonists have a lower incidence of adverse effects than ACE inhibitors as they do not produce cough and appear much less likely to produce angioedema. Although ACE inhibitors are the most commonly prescribed antihypertensive drug class in Australia, they are underused for the treatment of heart failure and left ventricular dysfunction following myocardial infarction. Angiotensin receptor antagonists may become alternative therapies to ACE inhibitors in these disorders. However, at present they are only indicated for the treatment of hypertension.

Postoperative portable chest radiographs: optimum use in thoracic surgery

PURPOSE

Daily portable chest radiographs are routinely ordered in many institutions after thoracic surgery. Our purpose was to assess the efficacy and cost of this practice and to determine the optimum use of postoperative x-ray studies.

METHODS

A prospective review of all portable chest x-ray films after 100 consecutive elective thoracotomies (DRG 75) was conducted. Each x-ray study initiated a three-part survey. First, the surgeon listed whether the x-ray study was routine and the anticipated management had it not been available. The radiologist then interpreted and scored the x-ray study as follows: negative, expected findings; A, minor findings necessitating no intervention; B, minor findings necessitating intervention; or C, major findings necessitating intervention. Finally, the x-ray film and the interpretation were returned to the surgeon. Any interventions necessitated by the x-ray study were recorded.

RESULTS

In 6 months, 99 patients underwent 82 pulmonary resections and 18 other major procedures. In the postoperative period, 769 portable chest x-ray studies were ordered, median five per patient (range 2 to 49). Of these, 731 (95%) were routine and 38 (5%), nonroutine. Severity scores were as follows: negative in 106 (13.8%), A in 558 (72.5%), B in 59 (7.7%), and C in 46 (6.0%). X-ray findings altered management in 43 of 769 studies (5.6%): in 33 routine (4.5%), in 10 nonroutine (26.3%), in 13 A (2.3%), in 22 B (37.3%), and in 8 C (17.4%).

CONCLUSIONS

These results demonstrate that routine daily portable chest x-ray studies have a minimal impact on management. It is, in fact, nonroutine x-ray studies that more often alter management. Had routine portable chest x-ray studies, which cost $114 each in our institution, been limited to one immediately after the operation, only 133 such studies (100 routine and 33 nonroutine) would have been needed in the care of these patients. Elimination of 636 (82.7%) x-ray studies reduces the cost of care by $725 per patient ($286,000 annually). For major thoracic procedures, it is safe, efficacious, and cost effective to eliminate routine postoperative portable chest x-ray studies and order nonroutine portable studies only when clinically indicated.

Posttranscriptional regulation of macrophage tissue factor expression by antioxidants

Tissue factor (TF) expression by cells of monocyte/macrophage lineage represents an important mechanism underlying the initiation of fibrin deposition at sites of extravascular inflammation. Recent evidence suggests a role for oxidant stress in the signalling pathway of various cell types by virtue of its ability to induce DNA binding of various transcription factors, including nuclear factor kappa B and AP-1. The effect of antioxidant treatment on lipopolysaccharide (LPS)-induced TF expression was examined in murine peritoneal macrophages and human monocytes. Both pyrrolidine dithiocarbamate, an oxidant scavenger, and N-acetyl-cysteine, a precursor of the endogenous antioxidant glutathione, inhibited stimulation of macrophage procoagulant activity by LPS. Northern blot analysis showed that neither of these agents reduced LPS-stimulated TF mRNA accumulation, thereby suggesting a posttranscriptional mechanism for the effect. Immunofluorescence studies of human monocytes using polyclonal anti-TF antibody showed that N-acetyl-cysteine treatment prevented the characteristic plasmalemmal localization of TF antigen that occurs in response to LPS. Western blot analysis showed that N-acetyl-cysteine reduced the accumulation of the 47-kD mature glycoprotein in LPS-treated cells, a finding consistent with the results of the immunofluorescence studies. Furthermore, these conditions did not result in an accumulation of the less mature forms of TF. When considered together, these data suggest that antioxidants exert their effects by impairing translation and/or by causing degradation of newly translated protein. The effect of antioxidants on tumor necrosis factor appeared to be species specific, with no effect on LPS-induced tumor necrosis factor in murine cells, but with inhibition in human monocytes. The posttranscriptional effect of antioxidants on TF expression data suggests a novel mechanism whereby these agents might modulate monocyte/macrophage activation.

Reliable thirty-hour lung preservation by donor lung hyperinflation

We examined the hypothesis that the degree of inflation of the lungs at the time of harvest may have an important role in postpreservation function. Lungs of donor dogs randomly assigned to groups 1 (n = 5) and 2 (n = 5) were ventilated with large tidal volumes (tidal volume, 25 ml/kg; positive end-expiratory pressure, 5 cm H2O; respiratory rate, 12 breaths/min, inspired oxygen fraction 1.0) and were inflated to 30 cm H2O for 15 seconds before pulmonary artery flush and again immediately before tracheal crossclamping. In group 3 (n = 5) donor lungs were normally ventilated (tidal volume, 12.5 ml/kg, positive end-expiratory pressure 0 cm H2O; respiratory rate 12 breaths/min, inspired oxygen fraction, 1.0) and were not hyperinflated before pulmonary artery flushing; the trachea was crossclamped at end-inspiration. In groups 1 and 3 a large bolus (25 micrograms/kg) of prostaglandin E1 was injected into the pulmonary artery before flushing and was also added to the pulmonary artery flush solution (500 micrograms/L). A rapid (approximately 50 seconds), high-volume mm Hg), hypothermic (4 degrees C) pulmonary artery flush was performed in all hypothermic (4 degrees C) pulmonary artery flush was performed in all groups with modified Euro-Collins solution. Heart-lung blocks were stored at 4 degrees C for approximately 29 hours before left single lung allografting. An inflatable cuff was placed around the recipient right pulmonary artery, allowing independent study of the transplanted lung. Hyperinflated lungs harvested with or without prostaglandin E1 provided equivalently excellent early posttransplant function (arterial oxygen tension [mean +/- standard deviation]: group 1; 503 +/- 45, vs group 2; 529 +/- 150 mm Hg; inspired oxygen fraction 1.0). Mean arterial oxygen tension was significantly lower in group 3 (116 +/- 78 mm Hg) than in either groups 1 or 2 (p < 0.0002 for either comparison). Copious reperfusion pulmonary edema was a constant feature in group 3 but was not seen in groups 1 and 2. All 10 recipients in groups 1 and 2 survived the 3-day assessment period without difficulty; two of the five recipients in group 3 died during initial unilateral perfusion of the transplanted lung. Donor hyperventilation and inflation to 30 cm H2O before hypothermic storage can help provide excellent posttransplantation lung function after 30-hour preservation, with or without prostaglandin E1 pretreatment. We speculate that this improvement may be due to effects of increased lung volume on pulmonary vascular tone and/or surfactant metabolism.

Variant Philadelphia translocations in chronic myeloid leukemia: correlation with cancer breakpoints, fragile sites and oncogenes

Four cases of variant Philadelphia (Ph1) translocations were found in 72 patients (5.5%) with Ph1-positive chronic myeloid leukemia (CML). One previously unreported case was a simple variant translocation, namely, 46,XY,t(11;17)(q13;p13),t(17;22)(q25;q22); 46,XY,t(1;21)(q32;q11),t(11;17)(q13;p13), t(17;22)(q25;q11). Complex variant translocations were observed in three cases, namely, 46,XY,t(5;9;22)(q31;q34;q11),46,XX,t(8;9;22) (q22;q34;q11) and 46,XX,t(9;15;22) (q34;q15;q11). The chromosomal breakpoints in the cases of variant Ph1 translocations were the following: 1q32, 5q31, 8q22, 11q13, 15q15, 17p13, 17q25 and 21q11. Eight of the eight (100%) breakpoints were located in Giemsa-negative bands. Furthermore, seven of the eight (87%) variant Ph1 breakpoints correspond to the breakpoints present in consistent cancer arrangements. Three of the eight (38%) correspond to fragile sites and four of the eight (50%) correspond to oncogenes.

Effect of a fibrin(ogen)-derived vasoactive peptide on polymorphonuclear leukocyte emigration

A vasoactive peptide known to increase vascular permeability and corresponding to residues 30-43 of the human fibrinogen B beta-chain induced polymorphonuclear leukocyte emigration in rabbit skin in vivo. The leukocyte emigration was much stronger after 2 h than after 0.5 h. Addition of prostaglandin E2 (PGE2) did not influence the chemotactic activity, which might possibly be explained by a known PGI2 releasing capacity of this peptide. PGE2 enhanced the leukocyte emigration due to leukotriene B4.

The effect of gamma irradiation of human cells and somatic cell hybridization on sister chromatid exchange frequencies in the hamster chromosomes of hamster-human hybrid lines

Sister chromatid exchange (SCE) frequency was studied in human/hamster hybrid lines in which the human cells had been exposed to gamma irradiation at doses of 0, 10, 20, and 40 grays. A higher SCE frequency was found in the hamster chromosomes in the hybrid lines than was found in the hamster parental cell line CHW1103. There was also a dose-dependent increase of SCE frequency in the unirradiated hamster chromosomes in the hybrid lines in which the human parental cells had been irradiated.