A study of selected factors affecting efficacy of compost tea against several fungal pathogens of potato.

AIM: To investigate selected factors of two nonaerated compost teas (NCT) and mechanisms that influence the restriction of several fungal potato pathogens. METHODS AND RESULTS: Two NCTs, made from either commercial compost, (CCT) or vineyard compost (VCT), were tested for their ability to suppress potato pathogens. The VCT was more suppressive than CCT to mycelial growth of Alternaria solani and Rhizoctonia solani isolate 299, but not for R. solani isolate 422. Metagenomic studies of microbial diversity revealed that the CCT had higher fungal and bacterial diversity and richness than the VCT. Use of CCT significantly reduced lesion area of Alternaria alternata on detached leaves, however, a gum adjuvant did not lead to significantly greater control. Scanning microscopy showed that the spatial distribution of microbes from the CCT was altered with gum addition, to resemble what may have been a microbial biofilm. CONCLUSION: We confirmed that each NCT could suppress the mycelial growth of selected potato pathogens in culture, and CCT reduced A. alternata lesions on detached leaves. Factors including concentration, microbial communities and physio-chemical properties could not be consistently linked to NCT efficacy. SIGNIFICANCE AND IMPACT OF THE STUDY: This study particularly highlights the application of scanning microscopy to study the interaction between pathogens and putative NCT microbes on foliar surfaces. This adds insight to mechanisms of NCT efficacy, along with physico-chemical and microbial characterization of the teas. This study shows the potential for the use of NCTs as a crop protection tool of low-cost which could be of particular benefit in smallholder agriculture.

Diverse microbial communities in non-aerated compost teas suppress bacterial wilt.

Non-aerated compost teas (NCTs) are water extracts of composted organic materials and are used to suppress soil borne and foliar disease in many pathosystems. Greenhouse trials were used to test the effectiveness of NCTs to suppress potato bacterial wilt caused by Ralstonia solanacearum on plants grown in soils inoculated with a virulent isolate of the pathogen (biovar II). NCTs prepared from matured compost sources: agricultural waste (AWCT), vermicompost (VCT) and solid municipal waste (SMWCT) were evaluated at three initial application times (7 days before inoculation, at time of inoculation and 7 days after inoculation) prior to weekly applications, in a randomized complete-block design. AWCT applied initially at the time of inoculation resulted in the greatest disease suppression, with the disease severity index 2.5-fold less than the non-treated plants and the "area under the disease progress curve" (AUDPC) 3.2-fold less. VCT and SMWCT were less suppressive than AWCT regardless of initial application time. Next generation sequencing of the v4 region of 16S rRNA gene and the internal transcribed spacer region (ITS1) revealed that diversity and composition of the bacterial and fungal communities across the NCTs varied significantly. Dominant bacterial phyla such as Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, Verrucomicrobia, Chloroflexi, Planctomycetes, Acidobacteria, and a fungal phylum Ascomycota were detected in all NCTs. AWCT had optimum physico-chemical measurements with higher bacterial Shannon diversity indices (H) and fungal richness (S) than the other treatments. We conclude that bacterial wilt of potatoes grown in controlled conditions can be suppressed by a non-aerated compost tea with a high microbial diversity when applied at planting and weekly thereafter.

Evaluation of a permeable reactive barrier to capture and degrade hydrocarbon contaminants.

A permeable reactive barrier (PRB) was installed during 2005/2006 to intercept, capture and degrade a fuel spill at the Main Power House, Casey Station, Antarctica. Here, evaluation of the performance of the PRB is conducted via interpretation of total petroleum hydrocarbon (TPH) concentrations, degradation indices and most probable number (MPN) counts of total heterotroph and fuel degrading microbial populations. Results indicate that locations which contained the lowest TPH concentrations also exhibited the highest levels of degradation and numbers of fuel degrading microbes, based on the degradation indices and MPN methods selected. This provides insights to the most appropriate reactive materials for use in PRB's in cold and nutrient-limited environments.

Predictive model for the growth of spoilage bacteria on modified atmosphere packaged Atlantic salmon produced in Australia.

Most existing models for the spoilage of modified atmosphere packed Atlantic salmon are based on the growth of the spoilage organism Photobacterium phosphoreum. However, there is evidence that this organism is not the specific spoilage organism on salmon produced and packaged in Australia. We developed a predictive model for the growth of bacteria in Australian-produced Atlantic salmon stored under modified atmosphere conditions (30-98% carbon dioxide in nitrogen) at refrigeration temperatures (0-10 °C). As expected, both higher levels of carbon dioxide and lower temperatures decreased the observed growth rates of the total population. A Belehrádek-type model for growth rate fitted the data best with an acceptably low root mean square error. At low temperatures (∼0 °C) the growth rates in this study were similar to those predicted by other models but at higher temperatures (∼10 °C) the growth rates were significantly lower in the current study.

Dynamics of seawater bacterial communities in a shellfish hatchery.

Bacterial disease is a significant issue for larviculture of several species of shellfish, including oysters. One source of bacteria is the seawater used throughout the hatchery. In this study carried out at a commercial oyster hatchery in Tasmania, Australia, the diversity of the bacterial community and its relationship with larval production outcomes were studied over a 2-year period using terminal restriction fragment length polymorphism and tag-encoded pyrosequencing. The bacterial communities were very diverse, dominated by the Alphaproteobacteria, Gammaproteobacteria, Flavobacteria and Cyanobacteria. The communities were highly variable on scales of days, weeks and seasons. The difference between the intake seawater and treated clean seawater used in the hatchery was smaller than the observed temporal differences in the seawater throughout the year. No clear correlation was observed between production outcomes and the overall bacterial community structure. However, one group of Cyanobacterial sequences was more abundant when mass mortality events occurred than when healthy spat were produced although they were always present.

Use of near infrared spectroscopy to predict microbial numbers on Atlantic salmon.

The potential of a near infrared spectroscopy (NIR) method to detect as well as predict microbial spoilage on Atlantic salmon (Salmo salar) was investigated. Principal component analysis (PCA) of the NIR spectra showed clear separation between the fresh salmon fillets and those stored for nine days at 4°C indicating that NIR could detect spoilage. A partial least squares regression (PLS) prediction model for total aerobic plate counts after nine days was established using the NIR spectra collected when the fish was fresh to predict the number of bacteria that would be present nine days later. The calibration equation was good (R(2) = 0.95 and RMSE = 0.12 log cfu/g) although the error of the validation curve was larger (R(2) = 0.64 and RMSE = 0.32 log cfu/g). These results indicate that with further model development, it may be possible to use NIR to predict bacterial numbers, and hence shelf-life, in Atlantic salmon and other seafood.

Microbial communities on Australian modified atmosphere packaged Atlantic salmon.

The role of specific spoilage organisms (SSO) in products such as Atlantic salmon has been well documented. However, little is known about what other micro-organisms are present and these organisms may indirectly influence spoilage by their interactions with the SS0. We used a combination of culture-based and DNA-based methods to explore the microbial communities found on Atlantic salmon fillets packed in a modified atmosphere of carbon dioxide and nitrogen. After 15 days the communities were dominated by Shewanella spp. or Carnobacterium spp. and a variety of other genera were present in smaller numbers. Variability in the microbial community composition in packages processed on the same day was also observed. This was mostly due to differences in the presence of minor members of the community including species from genera such as Iodobacter, Serratia, Morganella and Yersinia. The combination of culture-based and culture-independent methods provided greater insight into the development of microbial communities on Atlantic salmon than would have been possible using only one method. This work highlights the potential importance of lactic acid bacteria (LAB) in fresh Atlantic salmon stored under modified atmosphere conditions.

The rate of removal and the compositional changes of diesel in Antarctic marine sediment.

Diesels and lubricants used at research stations can persist in terrestrial and marine sediments for decades, but knowledge of their effects on the surrounding environments is limited. In a 5 year in situ investigation, marine sediment spiked with Special Antarctic Blend (SAB) diesel was placed on the seabed of O'Brien Bay near Casey Station, Antarctica and sampled after 5, 56, 65, 104 and 260 weeks. The rates and possible mechanisms of removal of the diesel from the marine sediments are presented here. The hydrocarbons within the spiked sediment were removed at an overall rate of 4.7mg total petroleum hydrocarbons kg(-1) sediment week(-1), or 245mgkg(-1)year(-1), although seasonal variation was evident. The concentration of total petroleum hydrocarbons fell markedly from 2020±340mgkg(-1) to 800±190mgkg(-1), but after 5 years the spiked sediment was still contaminated relative to natural organic matter (160±170mgkg(-1)). Specific compounds in SAB diesel preferentially decreased in concentration, but not as would be expected if biodegradation was the sole mechanism responsible. Naphthalene was removed more readily than n-alkanes, suggesting that aqueous dissolution played a major role in the reduction of SAB diesel. 1,3,5,7-Teramethyladamantane and 1,3-dimethyladamantane were the most recalcitrant isomers in the spiked marine sediment. Dissolution of aromatic compounds from marine sediment increases the availability of more soluble, aromatic compounds in the water column. This could increase the area of contamination and potentially broaden the region impacted by ecotoxicological effects from shallow sediment dwelling fauna, as noted during biodegradation, to shallow (<19m) water dwelling fauna.

Quality of life of children with sleep-disordered breathing treated with adenotonsillectomy.

OBJECTIVE: To assess the quality of life of UK children with sleep-disordered breathing undergoing adenotonsillectomy, by using the Obstructive Sleep Apnoea 18 questionnaire and determining score changes and effect sizes. DESIGN: Prospective, longitudinal study. SETTING: The otolaryngology department of a university teaching hospital in Northern England. PARTICIPANTS: Twenty-eight children for whom adenotonsillectomy was planned as treatment for sleep-disordered breathing, and who had either a clinical history consistent with obstructive sleep apnoea or a polysomnographic diagnosis. MAIN OUTCOME MEASURE: The Obstructive Sleep Apnoea 18 questionnaire, a previously validated, disease-specific quality of life assessment tool; changes in questionnaire scores and effect sizes were assessed. METHODS: The Obstructive Sleep Apnoea 18 questionnaire was administered to each child's parent pre-operatively, then again at the follow-up appointment. Questionnaire scores ranged from 1 to 7. Score changes were analysed using the paired t-test; effect sizes were calculated using 95 per cent confidence intervals. RESULTS: Complete data were obtained for 22 children (mean age, 61 months). Ten had undergone pre-operative polysomnography. Twenty-one children underwent adenotonsillectomy (one underwent tonsillectomy). Median follow up was eight weeks (interquartile range, six to 11 weeks). Following surgery, the overall mean score improvement was 2.6 (p < 0.0001) and the mean effect size 2.4 (95 per cent confidence interval 1.9 to 2.8). There were significant improvements in each of the individual questionnaire domains, i.e. sleep disturbance (mean score change 3.9, p < 0.0001), physical suffering (2.2, p < 0.0001), emotional distress (2.0, p = 0.0001), daytime problems (1.8, p = 0.0001) and caregiver concerns (2.6, p < 0.0001). CONCLUSION: In these children with sleep-disordered breathing treated by adenotonsillectomy, Obstructive Sleep Apnoea 18 questionnaire results indicated significantly improved mean score changes and effect sizes across all questionnaire domains, comparing pre- and post-operative data.

Impact of primary tumour stage on survival in dogs with solitary lung tumours.

OBJECTIVES: The objective of this study was to determine simple prognostic criteria for differentiation of canine solitary lung tumour cases into those that will and will not benefit from thoracic surgery. METHODS: This was a retrospective study using the records of cases presented to Davies Veterinary Specialists, Hitchin, UK, from December 1998 to December 2005. Survival analyses were performed using the Kaplan-Meier and logrank methods. Potentially significant variables were evaluated by multivariate Cox analysis. RESULTS: Forty-two patients met the inclusion criteria. Primary tumour stage T1, absence of neoplastic lymph nodes and metastases, and papillary tumour type were statistically significant favourable prognostic indicators on univariate analysis. Multivariate analysis attributed significance to primary tumour stage T1 and papillary type only. Median survival times were 555 days for T1N0M0 tumours of papillary type and 72 days for the remainder. CLINICAL SIGNIFICANCE: Survival time following surgery in dogs with primary lung tumours was poor except in clinical stage T1N0M0 cases. These data support use of clinical techniques to dichotomise cases as T1N0M0 or other, improving decision making in thoracic surgery. These data validate initiation of prospective studies examining the role of chemotherapy in the management of advanced cases.

Prohibitin, a protein downregulated by androgens, represses androgen receptor activity.

Prohibitin (PHB) is a cell cycle regulatory protein, known to repress E2F1-mediated gene activation via recruitment of transcriptional regulatory factors such as retinoblastoma and histone deacetylase 1 (HDAC1). We previously identified PHB as a target protein of androgen signaling in prostate cancer cells and showed that downregulation of PHB is required for androgen-induced cell cycle entry in these cells. We now present evidence that PHB, which has 54% homology at the protein level to the oestrogen receptor corepressor REA (repressor of oestrogen receptor activity), can repress androgen receptor (AR)-mediated transcription and androgen-dependent cell growth. Depletion of endogenous PHB resulted in an increase in expression of the androgen-regulated prostate-specific antigen gene. The repression appears to be specific to androgen and closely related receptors, as it is also evident for the glucocorticoid and progesterone, but not oestrogen, receptors. In spite of interaction of PHB with HDAC1, HDAC activity is not required for this repression. Although AR and PHB could be co-immunoprecipitated, no direct interaction was detectable, suggesting that PHB forms part of a repressive complex with the AR. Competition with the co-activator SRC1 further suggests that formation of a complex with AR, PHB and other cofactors is the mechanism by which repression is achieved. It appears then that repression of AR activity is one mechanism by which PHB inhibits androgen-dependent growth of prostate cells. Further, this study implies that the AR itself could, by mediating downregulation of a corepressor, be involved in the progression of prostate tumours to the hormone refractory stage.

Prevalence of Campylobacter species, Helicobacter pylori and Arcobacter species in stool samples from the Venda region, Limpopo, South Africa: studies using molecular diagnostic methods.

OBJECTIVES: This study determined the prevalence of Campylobacter spp., Helicobacter pylori and Arcobacter spp. in stool samples from Venda in relation to diarrhea, intestinal inflammation and HIV status using specific molecular methods. METHODS: Stool samples were collected from hospital patients (255) and primary school children (67). Genomic DNA was extracted from the stools and molecular methods including PCR, PCR followed by restriction analysis and multiplex PCR were used to test for the different organisms. The lactoferrin content of the stools was determined using commercial kits from TechLab (Blacksburg, VA, USA). RESULTS: The prevalence of the different organisms was 50.6% for H. pylori, 10.2% for C. jejuni, 6.2% for A. butzleri, 6.5% for C. coli, 3.1% for C. concisus, 2.8% for A. cryaerophilus and 1.9% for A. skirrowii. Of all the organisms, only C. jejuni was significantly associated with diarrhea (84.8%) (chi2=21.025, P<0.001) and elevated levels of lactoferrin (78.8%) (chi2=16.919, P<0.005) and was an important pathogen associated with diarrhea among HIV positive individuals (22.8%). CONCLUSIONS: Campylobacter infections are common causes of gastroenteritis in Venda. Non-C. jejuni/coli Campylobacters such as C. concisus as well as A. butzleri and H. pylori may be involved in gastrointestinal diseases in the region but further studies are needed to confirm this hypothesis.

Mechanisms of androgen receptor repression in prostate cancer.

Anti-androgens used in prostate cancer therapy inhibit AR (androgen receptor) activity via largely unknown mechanisms. Although initially successful in most cases, they eventually fail and the disease progresses. We need to elucidate how anti-androgens work to understand why they fail, and prolong their effects or design further therapies. Using a cellular model, we found different anti-androgens have diverse effects on subcellular localization of AR, revealing that they work via different mechanisms and suggesting that an informed sequential treatment regime may benefit patients. In the presence of the anti-androgens bicalutamide and hydroxyflutamide, a significant proportion of the AR is translocated to the nucleus but remains inactive. Receptor inhibition under these conditions is likely to involve recruitment of co-repressor proteins, which interact with antagonist-occupied receptor but inhibit receptor-dependent transcription. Which co-repressors are required in vivo for AR repression by anti-androgens is not clear, but one candidate is the Notch effector Hey1. This inhibits ligand-dependent activity of the AR but not other steroid receptors. Further, it is excluded from the nucleus in most human prostate cancers, suggesting that abnormal subcellular distribution of co-repressors may contribute to the aberrant hormonal responses observed in prostate cancer. A decrease in co-repressor function is one possible explanation for the development of anti-androgen-resistant prostate cancer, and this suggests that it may not occur at the gross level of protein expression.

Use of the internet by colorectal cancer patients.

OBJECTIVE: To identify the frequency of Internet use by colorectal cancer patients. MATERIALS AND METHODS: Fifty patients interviews. RESULTS: Only four patients (8%) had used the internet to access information about colorectal cancer though 36% would have used it if a site had been recommended. CONCLUSION: The Internet is a resource rarely used by patients but there is potential for its use as an adjunct to written and verbal information.

Overexpression of CEBPbeta correlates with decreased TFF1 in gastric cancer.

CCAAT element binding protein beta (C/EBPbeta) is an important regulator of cell growth, differentiation and in promoting tumor invasiveness. C/EBPbeta is located on chromosome 20q, which is amplified in many solid tumors including gastric cancers (GC). We sought to characterize the status of C/EBPbeta expression in GCs, which was recently found to repres TFF1 gene. Microarray analysis revealed overexpression of C/EBPbeta in 25 of 27 (93%) GC when compared to 12 normal gastric tissue samples. RT-PCR analysis confirmed the overexpression of C/EBPbeta transcripts in 54 of 59 (91%) GC. In total, 15 of 18 gastric tumors exhibited at least fivefold higher C/EBPbeta transcript levels compared to their corresponding adjacent normal gastric tissue samples. Moreover, immunohistochemistry analysis demonstrated increased nuclear staining of C/EBPbeta in 10 of 13 GC and at least fourfold overexpression of C/EBPbeta in three primary GC compared to adjacent normal gastric tissue. Furthermore, a striking correlation of decreased TFF1 expression with increased C/EBPbeta was observed in the gastric tumors studied. Microarray analysis demonstrated a loss of TFF1 expression in all 27 GC cases examined, of which 25 exhibited high C/EBPbeta expression compared to normal gastric tissue. RT-PCR analysis revealed loss of TFF1 expression in 56 of 59 gastric tumors in which 54 of these tumors exhibited overexpression of C/EBPbeta. Immunohistochemical analysis revealed overexpression of C/EBPbeta in 10 of 13 gastric tumors that exhibited low expression of TFF1 at the protein level. Thus, overexpression of the transcription factor C/EBPbeta in the majority of GCs is a novel finding.

Mechanisms of androgen receptor signalling via steroid receptor coactivator-1 in prostate.

The androgen receptor (AR) is a member of the nuclear receptor superfamily. These ligand-activated transcription factors usually contain two activation functions, a ligand-independent activation function 1(AF1) in the divergent N-terminal domain and a ligand-dependent AF2 in the more conserved C-terminal ligand-binding domain. To promote transcription from target promoters, DNA-bound nuclear receptors recruit coactivator proteins that promote transcription by modifying histones within nucleosomes, resulting in altered topology of chromatin to allow access of the basal transcriptional machinery, or stabilising the pre-initiation complex. It is well known that most coactivators interact with AF2 of many nuclear receptors via conserved, helical LxxLL motifs (where L is leucine and x is any amino acid). The AF2 of the AR is very weak, but we were able to demonstrate that its intrinsic ligand-dependent activity is potentiated by steroid receptor coactivator-1 (SRC1) and that this region interacts with coactivators via LxxLL motifs. However, a mutant SRC1 coactivator with no functional LxxLL motifs was still able to potentiate AR activity. We found that SRC1 can also be recruited to (and increase activity of) AF1 of the AR via a conserved, glutamine-rich region. Point mutations within this region abolish SRC1 interaction with AF1 and also abolish or severely impair its ability to potentiate AR activity on all promoters tested. Thus the AR interacts with SRC1 via two different regions and the AF1 interaction is functionally the more important, although the contribution of the two interactions varies in a promoter-dependent fashion. SRC1 then potentiates receptor activity via recruitment of CBP/p300, a histone acetyltranferase. This is important in the context of prostate cancer as SRC1 and other coactivators including CBP are coexpressed with AR in the luminal epithelial cells of the prostate, where over 90% of prostate tumours arise. There is a need for effective second-line prostate cancer therapy aimed at blocking the AR pathway when anti-androgen therapy has failed. Since there is growing evidence that nuclear receptor cofactors may be implicated in the progression of hormone-dependent tumours to hormone-independent states, novel targets could include the interaction of AR with coactivator proteins. We suggest that the N-terminal interaction would be a more specific and effective target in the case of prostate cancer than the LxxLL/AF2 interaction.

Inactivation of the E-cadherin gene in sporadic diffuse-type gastric cancer.

Loss of the cell adhesion molecule E-cadherin has been observed in a variety of human carcinomas, and germline E-cadherin mutations have been found in several familial cases of diffuse gastric cancer. We sought to determine the prevalence and nature of E-cadherin alterations in "sporadic" gastric carcinomas. We performed comprehensive sequencing of the coding region, loss of heterozygosity (LOH) analysis, and immunohistochemical protein expression determination on 40 sporadic gastric adenocarcinomas. In total, 7 of 25 diffuse-type cancers harbored genetic alterations in the E-cadherin gene. Novel mutations predicted to significantly compromise protein function were found within 4 of these cancers, 2 of which harbored alterations resulting in biallelic inactivation of the gene product. Three diffuse cancers failed to amplify Exon 8 of E-cadherin, suggesting the presence of a homozygous abnormality. Notably, one germline E-cadherin mutation was also identified within these "sporadic" diffuse cancers. Significant gene mutations were not found in the 14 intestinal-type or histologically mixed cancer. Immunohistochemistry revealed aberrant or negative protein expression in seven diffuse-type tumors, four of which correlated with the genetic alterations. Both diffuse and intestinal-type tumors exhibited low rates of LOH, suggesting that allelic loss at the locus is not a common mechanism for E-cadherin inactivation during gastric tumorigenesis. Our observations suggest that inactivation of the E-cadherin gene occurs only in a subset of diffuse-type gastric cancers, as the majority of cases did not contain genetic alterations or identifiable protein abnormalities. Germline E-cadherin alterations, although rare, may underlie some diffuse gastric cancer cases that have important biologic and practical implications

Molecular classification of human carcinomas by use of gene expression signatures.

Classification of human tumors according to their primary anatomical site of origin is fundamental for the optimal treatment of patients with cancer. Here we describe the use of large-scale RNA profiling and supervised machine learning algorithms to construct a first-generation molecular classification scheme for carcinomas of the prostate, breast, lung, ovary, colorectum, kidney, liver, pancreas, bladder/ureter, and gastroesophagus, which collectively account for approximately 70% of all cancer-related deaths in the United States. The classification scheme was based on identifying gene subsets whose expression typifies each cancer class, and we quantified the extent to which these genes are characteristic of a specific tumor type by accurately and confidently predicting the anatomical site of tumor origin for 90% of 175 carcinomas, including 9 of 12 metastatic lesions. The predictor gene subsets include those whose expression is typical of specific types of normal epithelial differentiation, as well as other genes whose expression is elevated in cancer. This study demonstrates the feasibility of predicting the tissue origin of a carcinoma in the context of multiple cancer classes.