Analysis of early host responses for asymptomatic disease detection and management of specialty crops

The rapid and unabated spread of vector-borne diseases within US specialty crops threatens our agriculture, our economy, and the livelihood of growers and farm workers. Early detection of vector-borne pathogens is an essential step for the accurate surveillance and management of vector-borne diseases of specialty crops. Currently, we lack the tools that would detect the infectious agent at early (primary) stages of infection with a high degree of sensitivity and specificity. In this paper, we outline a strategy for developing an integrated suite of platform technologies to enable rapid, early disease detection and diagnosis of huanglongbing (HLB), the most destructive citrus disease. The research has two anticipated outcomes: i) identification of very early, disease-specific biomarkers using a knowledge base of translational genomic information on host and pathogen responses associated with early (asymptomatic) disease development; and ii) development and deployment of novel sensors that capture these and other related biomarkers and aid in presymptomatic disease detection. By combining these two distinct approaches, it should be possible to identify and defend the crop by interdicting pathogen spread prior to the rapid expansion phase of the disease. We believe that similar strategies can also be developed for the surveillance and management of diseases affecting other economically important specialty crops.

Computational annotation of genes differentially expressed along olive fruit development

BACKGROUND

Olea europaea L. is a traditional tree crop of the Mediterranean basin with a worldwide economical high impact. Differently from other fruit tree species, little is known about the physiological and molecular basis of the olive fruit development and a few sequences of genes and gene products are available for olive in public databases. This study deals with the identification of large sets of differentially expressed genes in developing olive fruits and the subsequent computational annotation by means of different software.

RESULTS

mRNA from fruits of the cv. Leccino sampled at three different stages [i.e., initial fruit set (stage 1), completed pit hardening (stage 2) and veraison (stage 3)] was used for the identification of differentially expressed genes putatively involved in main processes along fruit development. Four subtractive hybridization libraries were constructed: forward and reverse between stage 1 and 2 (libraries A and B), and 2 and 3 (libraries C and D). All sequenced clones (1,132 in total) were analyzed through BlastX against non-redundant NCBI databases and about 60% of them showed similarity to known proteins. A total of 89 out of 642 differentially expressed unique sequences was further investigated by Real-Time PCR, showing a validation of the SSH results as high as 69%. Library-specific cDNA repertories were annotated according to the three main vocabularies of the gene ontology (GO): cellular component, biological process and molecular function. BlastX analysis, GO terms mapping and annotation analysis were performed using the Blast2GO software, a research tool designed with the main purpose of enabling GO based data mining on sequence sets for which no GO annotation is yet available. Bioinformatic analysis pointed out a significantly different distribution of the annotated sequences for each GO category, when comparing the three fruit developmental stages. The olive fruit-specific transcriptome dataset was used to query all known KEGG (Kyoto Encyclopaedia of Genes and Genomes) metabolic pathways for characterizing and positioning retrieved EST records. The integration of the olive sequence datasets within the MapMan platform for microarray analysis allowed the identification of specific biosynthetic pathways useful for the definition of key functional categories in time course analyses for gene groups.

CONCLUSION

The bioinformatic annotation of all gene sequences was useful to shed light on metabolic pathways and transcriptional aspects related to carbohydrates, fatty acids, secondary metabolites, transcription factors and hormones as well as response to biotic and abiotic stresses throughout olive drupe development. These results represent a first step toward both functional genomics and systems biology research for understanding the gene functions and regulatory networks in olive fruit growth and ripening.

[Renal involvement in Fabry's disease: diagnosis, follow-up and enzyme replacement therapy]

Renal involvement in Fabry's disease in males starts at an early age with microalbuminuria and proteinuria and progresses rapidly towards end-stage renal disease requiring dialysis or renal transplantation. Renal involvement, together with cardiac and cerebral damage, is responsible for the severe morbidity and mortality in patients with Fabry's disease. In heterozygous female patients renal involvement has also been documented, but the onset of renal damage occurs later and the progression to end-stage renal disease is slower. Considering the relevance of renal damage in the prognosis of Fabry's disease, it is mandatory to point out the diagnostic criteria of Fabry's nephropathy and the modalities of follow-up of patients with renal involvement. The aim of this study is also to provide recommendations regarding the diagnosis, follow-up and indication for enzyme replacement therapy in patients with Fabry's disease.

The predictive accuracy of survival between patient-reported versus clinician-reported pain in a cohort of 1,214 patients with metastatic cancer

9607

Background: Accurate assessment of pain involves cooperation between clinician and patient. However, in patients with metastatic disease agreement between clinician and patient ratings is known to be poor. The objectives of this meta-analysis are to investigate the degree of agreement between clinician- versus patient- reported cancer pain at entry in a cohort of patients with metastatic cancer and whether their ratings were associated with a difference in survival. Methods: Eight European Organisation for Research and Treatment of Cancer (EORTC) Randomized Controlled Trials (RCT), across different cancer sites, were eligible for this study. Pain was scored at baseline by the clinician [Common Toxicity Criteria (CTC)] and the patient (EORTC QLQ-C30). The Wilcoxon rank sign test was applied to investigate scoring differences between patient- versus clinician- reported pain and logistic regression to model whether clinical parameters, i.e., performance status, gender, age or cancer site, affected scoring differences. The model accuracy of both scorings was investigated with the Harrell's discrimination c-index (c) after correction for the clinical parameters. Results: 1214 patients provided valid patient- and clinician- reported pain data at entry. Cancer pain was specified as bone metastasis by 643 (53%) patients and not specified otherwise. The overall mean pain as scored by the clinician was 2.25 (standard deviation (SD) 1.1) and by the patient was 2.28 (SD=0.95) on a 1 to 4 scale. Scoring differences were found to be statistically significant for colorectal (p<.01), lung (p<.01), prostate (p<.01), and breast (p=0.03, but not for pancreatic cancer (p=0.49). Clinical parameters did not significantly affect the scoring differences. Pain as reported by patients (vs clinicians) showed similar predictive accuracy (c =0.62 vs 0.61, p=0.59). Conclusions: Our results provide further evidence that significant differences exist in pain reporting between clinicians and patients. Such results provide a rationale to include patient self reported pain assessment in future cancer RCTs to better assess disease status and survival prognosis.

No significant financial relationships to disclose.

Health-related quality of life indicators and overall quality of life: Results from a cluster analysis on baseline EORTC QLQ-C30 data from 6,739 cancer patients

e20576

Background: Increasingly randomized controlled trials in cancer research include Health-related Quality of Life (HRQoL) alongside traditional biomedical outcome measures. The majority of these trials focus on a general cancer HRQoL measure. The objective of this meta-analysis was to identify which HRQoL indicators influence a patient's overall quality of life, in order to better understand the changes in such a generic scale. Methods: Retrospective pooling of 29 European Organisation for Research and Treatment of Cancer (EORTC) clinical trials, among 10 cancer sites, yielded baseline EORTC QLQ-C30 data for a total of 6,739 patients. A cluster analysis, using Ward's method, was performed to determine how the 15 HRQoL indicators, and the Global Health scale (GH) in particular, cluster overall and by cancer characteristics. Cronbach's alpha coefficient (α) was used to measure internal consistency. Dendrograms of the HRQoL indicators were plotted for each cancer type. Results: Three main clusters emerged: a physical function related cluster (physical functioning, role functioning, fatigue and pain, α = 0.83), a psychological function related cluster (emotional functioning, cognitive functioning and insomnia, α = 0.64) and a gastrointestinal cluster (nausea and vomiting and appetite loss, α = 0.68). The GH scale was found to be part of the physical function cluster in the overall dataset (α = 0.85). This result was reproduced for both metastatic and non-metastatic patients. When looking across the 10 different cancer sites, the GH scale was mainly linked with a physical component in brain, head and neck, lung, melanoma, ovarian, pancreatic and prostate cancer. However, in breast and testicular cancer, GH was more strongly associated with the emotional scales. Conclusions: This study shows that the GH scale of the EORTC QLQ-C30 is most strongly linked with a patient's physical status. This result is consistent across stage of disease and most cancer sites. The different results seen in patients with breast and testicular cancer deserve additional investigation.

No significant financial relationships to disclose.

Relationships among health-related quality of life indicators in cancer patients: A pooled study of baseline EORTC QLQ-C30 data from 6,739 patients

9612

Background: Cancer patients frequently experience multiple and co-occuring problems due to their illness and therapies. Clusters are defined as groups of two or more Health-Related Quality of Life (HRQoL) indicators that occur concurrently and may or may not have a common related cause. The objective of this meta-analysis was to identify how HRQoL indicators cluster among cancer patients. Methods: Retrospective pooling of 29 European Organisation for Research and Treatment of Cancer (EORTC) randomized clinical trials, among 10 cancer sites, yielded baseline EORTC QLQ-C30 HRQoL data for a total of 6739 patients. A cluster analysis was performed to identify clusters among the 15 HRQoL scales, via Ward's method. Cronbach's alpha coefficient (α) was used to measure internal consistency. Dendrograms of the HRQoL indicators were plotted for the overall data and for each cancer site. Results: Three main clusters emerged from the pooled dataset: a physical function-related cluster, consisting of physical and role functioning, fatigue and pain (α = 0.83); a psychological function-related cluster, consisting of emotional and cognitive functioning and insomnia (α = 0.64); and a gastrointestinal cluster, consisting of nausea and vomiting and appetite loss (α = 0.68). The same clusters were found in patients with metastatic and non-metastatic disease. The gastrointestinal cluster was reproduced in all 10 cancer sites. We found that pain was not correlated with the other variables of the physical function cluster for patients with brain, colorectal or pancreatic cancer. For the psychological component cluster, cognitive functioning was not correlated with the other variables of the cluster for breast or pancreatic cancer patients, while insomnia was found not to be correlated with the other variables of the cluster for prostate cancer patients. Conclusions: This study shows that relationships among HRQoL indicators exist and that three major constructs can be found: a physical, a psychological and a gastrointestinal component. Understanding these relationships may aid diagnostic criteria, and assessment, management, and prioritization of symptom care.

No significant financial relationships to disclose.

Computer-assisted diagnosis (CAD) in mammography: comparison of diagnostic accuracy of a new algorithm (Cyclopus, Medicad) with two commercial systems

PURPOSE

The study compares the diagnostic accuracy (correct identification of cancer) of a new computer-assisted diagnosis (CAD) system (Cyclopus) with two other commercial systems (R2 and CADx).

MATERIALS AND METHODS

Cyclopus was tested on a set of 120 mammograms on which the two compared commercial systems had been previously tested. The set consisted of mammograms reported as negative, preceding 31 interval cancers reviewed as screening error or minimal sign, and of 89 verified negative controls randomly selected from the same screening database.

RESULTS

Cyclopus sensitivity was 74.1% (R2=54.8%; CADx=41.9%) and was higher for interval cancers reviewed as screening error (90.9%; R2=54.5%; CADx=81.8%) compared with those reviewed as minimal sign (65.0%; R2=55.0%; CADx=20.0%). Specificity was 15.7% (R2=29.2%; CADx=17.9%). Overall accuracy was 30.8% (R2=35.8%; CADx=24.1%). The positive predictive value of a case with CAD marks [regions of interest (ROI)] was 23.4% (23/98; R2=16.0%; CADx=15.1%). Average ROI number per view among negative controls was 1.13 (R2=0.93; CADx=0.99). Cyclopus was more sensitive for masses compared with isolated microcalcifications (208 vs 62 ROI; R2=90 vs 213; CADx=192 vs 130).

CONCLUSIONS

Compared with two other commercial systems, Cyclopus was more sensitive (R2 p=0.14; CADx p=0.02) and less specific (R2 p=0.02; CADx p=0.64).

Gene regulation in parthenocarpic tomato fruit

Parthenocarpy is potentially a desirable trait for many commercially grown fruits if undesirable changes to structure, flavour, or nutrition can be avoided. Parthenocarpic transgenic tomato plants (cv MicroTom) were obtained by the regulation of genes for auxin synthesis (iaaM) or responsiveness (rolB) driven by DefH9 or the INNER NO OUTER (INO) promoter from Arabidopsis thaliana. Fruits at a breaker stage were analysed at a transcriptomic and metabolomic level using microarrays, real-time reverse transcription-polymerase chain reaction (RT-PCR) and a Pegasus III TOF (time of flight) mass spectrometer. Although differences were observed in the shape of fully ripe fruits, no clear correlation could be made between the number of seeds, transgene, and fruit size. Expression of auxin synthesis or responsiveness genes by both of these promoters produced seedless parthenocarpic fruits. Eighty-three percent of the genes measured showed no significant differences in expression due to parthenocarpy. The remaining 17% with significant variation (P <0.05) (1748 genes) were studied by assigning a predicted function (when known) based on BLAST to the TAIR database. Among them several genes belong to cell wall, hormone metabolism and response (auxin in particular), and metabolism of sugars and lipids. Up-regulation of lipid transfer proteins and differential expression of several indole-3-acetic acid (IAA)- and ethylene-associated genes were observed in transgenic parthenocarpic fruits. Despite differences in several fatty acids, amino acids, and other metabolites, the fundamental metabolic profile remains unchanged. This work showed that parthenocarpy with ovule-specific alteration of auxin synthesis or response driven by the INO promoter could be effectively applied where such changes are commercially desirable.

Mammaglobin B expression in human endometrial cancer

Mammaglobin B (MGB-2) is an uteroglobin gene family member recently found highly differentially expressed in ovarian cancer by gene expression profiling. To evaluate its potential as a novel endometrial cancer biomarker, in this study we quantified and compared MGB-2 expression at messenger RNA and protein levels in endometrial tumors (endometrioid endometrial cancer [EEC]) with different grades of differentiation. MGB-2 expression was evaluated by real-time polymerase chain reaction (PCR) and immunohistochemistry (IHC) in fresh frozen biopsies and paraffin-embedded tissues derived from a total of 70 patients including 50 primary EEC and 20 normal endometria (NECs). High levels of MGB-2 gene expression were detected in 10 of 11 EEC G1 cases (91%), 16 of 17 EEC G2 cases (94%), and 6 of 22 EEC G3 cases (27%) by real-time PCR. In contrast, normal endometrial cells expressed low to negligible levels of MGB-2 by real-time PCR (P= 0.002 EEC vs NEC). Well- and moderately differentiated EECs overexpressed MGB-2 gene at significant higher levels when compared to NECs (P< 0.01). Pairwise differences between both G2 and G1 vs G3 cases for MGB-2 relative gene expression values were also statistically significant (G2 vs G3 P< 0.001, G1 vs G3 P= 0.016). MGB-2 protein expression was detected in 31 (86%) of 36 EEC and 0 of 5 atrophic NEC controls, while seven of eight (88%) of the proliferative/secretory/hyperplastic NECs focally expressed MGB-2 by IHC. MGB-2 is highly expressed in EEC, particularly in well- and moderately differentiated tumors, and may represent a novel molecular marker for EEC.

Light induces expression of a dehydrin-encoding gene during seedling de-etiolation in sunflower (Helianthus annuus L.)

The effects of light quality on the expression of a sunflower dehydrin-encoding gene, HaDhn1, were studied during seedling de-etiolation. Seeds were germinated in the dark and, after 5 days, seedlings were maintained well watered and de-etiolated under different lights for 3, 6, 12, and 24h. Exposure to white light stimulated HaDhn1 transcript accumulation in the cotyledons of these seedlings, contrary to seedlings grown in the dark. HaDhn1 transcripts increased also treating plantlets with monochromatic lights, especially red light. The increase of HaDhn1 transcripts is provoked by the formation of the active form of phytochrome. Further experiments, performed saturating active phytochrome by yellow light, in combination or not with blue light, showed that also cryptochrome can increase HaDhn1 transcripts accumulation after exposure to light. In situ analysis of HaDhn1 expression domains in cotyledons of light-treated seedlings showed a hybridisation signal spread in all mesophyll cells, especially in the basal portion and in the vascular tissue. In the distal portion of the cotyledons, less intense signal was observed. Western blot analysis indicated that HaDhn1 transcription is not followed by dehydrin-protein accumulation. The isolated putative promoter sequence of the HaDhn1 gene showed that different putative cis-elements recognisable by transcription factors occur in the isolated sequence, including a putative light-responsive G-box. On the whole, our results indicate that HaDhn1 gene expression is induced by light during de-etiolation, in absence of water stress.

Association of FOBT-assessed faecal Hb content with colonic lesions detected in the Florence screening programme

We assessed the correlation between quantitative results of immunological faecal occult blood testing (I-FOBT) and colonic lesions (191 colorectal cancers, 890 adenomas) detected at colonoscopy in 2597 FOBT+ (cutoff 100 ng ml⁻¹ Hb) subjects. At univariate analysis, a higher average faecal Hb content was significantly associated with male gender (P=0.003), age (P=0.02), and colonoscopy findings (P=0.000). Among adenomas, higher faecal Hb content was significantly associated with size (P=0.0000), presence of severe dysplasia (P=0.0001), presence of villous component (P=0.0002), and location in the left colon (P=0.003). At multivariate analysis adjusting for potential confounders, age (P=0.03), size (P=0.0000), and location in the left colon (P=0.0005) were confirmed as having an independent association with higher faecal Hb content. Immunological FOBT is confirmed to be a specific screening test to detect cancer and adenoma, with a low positivity rate (3.7%) and a high positive predictive value (41.5%). Faecal Hb content is significantly higher for those lesions (cancer and high-risk adenomas) screening is aimed at detecting.

Dietary habits, lifestyle and cardiovascular risk factors in a clinically healthy Italian population: the 'Florence' diet is not Mediterranean

OBJECTIVE

To evaluate dietary habits and lifestyle of Italian subjects, to provide current data on adequacy of the nutritional guidelines and recommendations especially in relation to primary prevention of cardiovascular diseases and to assess the influence of dietary habits on lipid profile and homocysteine levels.

DESIGN

Cross-sectional.

SETTING

Population-based study.

SUBJECTS

A sample of 520 clinically healthy subjects (211 males, 309 females) with a mean age of 46 y, living in Florence area, Italy.

INTERVENTIONS

Dietary pattern was assessed by trained dietitians through a semiquantitative food questionnaire. Fasting blood samples were drawn for assessment of lipid profile, homocysteine and circulating vitamins.

RESULTS

Contribution from total fats was over 30% in about 70% of subjects and intake of saturated fatty acids (SFA) was above the recommended values in at least 40% of the study population. Furthermore, almost the whole (99.6%) population reported low intake of polyunsaturated fatty acids (PUFA). High levels of total cholesterol were present in over 40% of the study population, whereas abnormal values of LDL-cholesterol were observed in about 30%. High levels of homocysteine were found in 11.7% of the study population. An extremely high percentage of subjects reported low intake of vitamins, especially with regard to folic acid (89%), vitamin B(6) (70.1%) and vitamin E (99.6%). In a multiple linear regression model, circulating levels of vitamin B(12) and folic acid, and intake of alcohol and vitamin C resulted in being independently associated with homocysteine plasma levels.

CONCLUSIONS

In a typical Mediterranean country, general outlines of Mediterranean diet are not completely followed, especially concerning total fats, SFA, PUFA and vitamins' intake.

SPONSORSHIP

Ministero della Salute (Italy) - 'Progetto per la Salute e la Prevenzione di Malattia' 2001-2003.

Anderson-Fabry disease with cerebrovascular complications in two Italian families

We describe four patients with cerebrovascular complications from two unrelated Italian families with Anderson-Fabry disease. Clinical examination, neuroimaging (MRI), biochemical and genetic analyses were carried out in all the patients. Alpha-galactosidase A activity was detected by fluorimetric assay and genetic analysis was performed by DNA sequencing. Family 1. A male patient presented recurrent strokes when he was 34 years old, albuminuria and subsequently progressive renal failure to renal transplantation. Family 2. A male patient, aged 32 years, had diplopia for a few days and then recurrent strokes with left spastic hemiparesis and internuclear ophthalmoplegia. A female patient, aged 48 years, presented L-dopa-responsive parkinsonism, and her sister had stroke when she was 55 years old. MRI was abnormal in all the patients and showed lacunar infarctions in the periventricular white matter, basal ganglia and pons. Lesions were detected by MRI even before stroke in a female patients. In patients with Anderson-Fabry disease, stroke is a frequent complication, and may be the first threatening clinical manifestation. In young people with undefined stroke, even without signs of renal involvement, it is important to consider the diagnosis of Anderson-Fabry disease and so to perform clinical examination and biochemical analyses. The pre-clinical stage of cerebrovascular involvement may be evaluable by MRI.