Phagocytic and serum killing of capsulate and non-capsulate Bacteroides fragilis

The relative susceptibilities of capsulate and non- capsulate variants of Bacteroides fragilis to serum and phagocytic killing were investigated. The capsule of B. fragilis did not confer resistance to serum killing. Phagocytic killing of non- capsulate B. fragilis occurred at bacterial concentrations of 1 X 10(6) and 1 X 10(7) cfu/ml. Capsulate B. fragilis organisms were also phagocytosed and killed at a concentration of 1 X 10(6) cfu/ml, but phagocytosis and killing were impaired at a concentration of 1 X 10(7) cfu/ml.

Immunochemical characterization of a polysaccharide antigen of Bacteroides fragilis with an IgM monoclonal antibody

An IgM mouse monoclonal antibody (McAb) Bf4 was produced to a surface polysaccharide of Bacteroides fragilis NCTC 9343. Immunoblotting showed that McAb Bf4 reacted strongly with a high molecular mass structure which was sensitive to oxidation with periodate but resisted protease treatment. An inhibition enzyme-linked immunosorbent assay (ELISA) indicated that McAb Bf4 did not cross react with the sixteen Bacteroides species and strains tested. Cells of B. fragilis NCTC 9343 recovered from the various interfaces of a Percoll discontinuous density gradient were tested in the inhibition ELISA. Bacteria from the 0-20%, 20-40% and 40-60% interfaces inhibited the ELISA; however, cells from the 60-80% interface did not. Electron microscopy with immunogold labelling showed that McAb Bf4 did not react with the extracellular fibrous network on bacteria recovered from the 0-20% interface, or the extracellular electron dense layer on cells from the 60-80% interface; however, it was associated with a surface structure on cells from the 20-40% interface. Growth in vivo did not enrich for bacteria with this structure.

Foraging trip time-activity budgets and reproductive success in the black-legged kittiwake

Seabirds are central place foragers during the breeding season and, as marine food resources are often patchily distributed, flexibility in foraging behaviour may be important in maintaining prey delivery rates to chicks. We developed a methodological approach using a combination of GPS data loggers and temperature-depth recorders that allowed us to describe the behaviour of surface-feeding seabirds. Specifically, we tested whether differences in foraging behaviour of black-legged kittiwakes Rissa tridactyla could be linked with reproductive success by comparing 2 consecutive years at 2 sites. At Rathlin Island (Northern Ireland) during 2010, foraging differed markedly from that during 2009 and from that at Lambay Island (Republic of Ireland) during both years. Birds exhibited foraging trips of greater duration, travelled a greater total distance, spent more time in transit and spent longer recuperating on the surface of the water. This notable shift was associated with a decline in breeding success, with greater loss of eggs to predation and lower prey delivery rates, resulting in the starvation of 15 % of chicks. We suggest that food resources were reduced or geographically less accessible during 2010, with suitable foraging areas located further from the colony. Birds did not invest greater amounts of time attempting to catch prey. Thus, our results indicate that kittiwakes at Rathlin modulated their foraging behaviour not by increasing foraging effort through feeding more intensively within prey patches but by extending their range to increase the probability of encountering more profitable prey patches. © Inter-Research 2012.

Non-adherence to therapy in children with cystic fibrosis

Hawthorne N., Hawwa A.F., Shields M.D., Reid A.J., McElnay J.C. (2011) Non-adherence to therapy in children with cystic fibrosis. Pediatric Pulmonology, 46: 408.

Non-adherence in children with cystic fibrosis

Hawthorne N., Hawwa A., McElnay J., Shields M., Reid A. (2011) Non-adherence in children with cystic fibrosis. Journal of Pharmacy and Pharmaceutical Sciences, 14: 209s

Collectives of diagnostic biomarkers identify high-risk subpopulations of hematuria patients: exploiting heterogeneity in large-scale biomarker data

Background: Ineffective risk stratification can delay diagnosis of serious disease in patients with hematuria. We applied a systems biology approach to analyze clinical, demographic and biomarker measurements (n = 29) collected from 157 hematuric patients: 80 urothelial cancer (UC) and 77 controls with confounding pathologies.

Methods: On the basis of biomarkers, we conducted agglomerative hierarchical clustering to identify patient and biomarker clusters. We then explored the relationship between the patient clusters and clinical characteristics using Chi-square analyses. We determined classification errors and areas under the receiver operating curve of Random Forest Classifiers (RFC) for patient subpopulations using the biomarker clusters to reduce the dimensionality of the data.

Results: Agglomerative clustering identified five patient clusters and seven biomarker clusters. Final diagnoses categories were non-randomly distributed across the five patient clusters. In addition, two of the patient clusters were enriched with patients with ‘low cancer-risk’ characteristics. The biomarkers which contributed to the diagnostic classifiers for these two patient clusters were similar. In contrast, three of the patient clusters were significantly enriched with patients harboring ‘high cancer-risk” characteristics including proteinuria, aggressive pathological stage and grade, and malignant cytology. Patients in these three clusters included controls, that is, patients with other serious disease and patients with cancers other than UC. Biomarkers which contributed to the diagnostic classifiers for the largest ‘high cancer- risk’ cluster were different than those contributing to the classifiers for the ‘low cancer-risk’ clusters. Biomarkers which contributed to subpopulations that were split according to smoking status, gender and medication were different.

Conclusions: The systems biology approach applied in this study allowed the hematuric patients to cluster naturally on the basis of the heterogeneity within their biomarker data, into five distinct risk subpopulations. Our findings highlight an approach with the promise to unlock the potential of biomarkers. This will be especially valuable in the field of diagnostic bladder cancer where biomarkers are urgently required. Clinicians could interpret risk classification scores in the context of clinical parameters at the time of triage. This could reduce cystoscopies and enable priority diagnosis of aggressive diseases, leading to improved patient outcomes at reduced costs. © 2013 Emmert-Streib et al; licensee BioMed Central Ltd.

Standardization of diagnostic biomarker concentrations in urine; the hematuria caveat

Sensitive and specific urinary biomarkers can improve patient outcomes in many diseases through informing early diagnosis. Unfortunately, to date, the accuracy and translation of diagnostic urinary biomarkers into clinical practice has been disappointing. We believe this may be due to inappropriate standardization of diagnostic urinary biomarkers. Our objective was therefore to characterize the effects of standardizing urinary levels of IL-6, IL-8, and VEGF using the commonly applied standards namely urinary creatinine, osmolarity and protein. First, we report results based on the biomarker levels measured in 120 hematuric patients, 80 with pathologically confirmed bladder cancer, 27 with confounding pathologies and 13 in whom no underlying cause for their hematuria was identified, designated “no diagnosis”. Protein levels were related to final diagnostic categories (p = 0.022, ANOVA). Osmolarity (mean = 529 mOsm; median = 528 mOsm) was normally distributed, while creatinine (mean = 10163 µmol/l, median = 9350 µmol/l) and protein (0.3297, 0.1155 mg/ml) distributions were not. When we compared AUROCs for IL-6, IL-8 and VEGF levels, we found that protein standardized levels consistently resulted in the lowest AUROCs. The latter suggests that protein standardization attenuates the “true” differences in biomarker levels across controls and bladder cancer samples. Second, in 72 hematuric patients; 48 bladder cancer and 24 controls, in whom urine samples had been collected on recruitment and at follow-up (median = 11 (1 to 20 months)), we demonstrate that protein levels were approximately 24% lower at follow-up (Bland Altman plots). There was an association between differences in individual biomarkers and differences in protein levels over time, particularly in control patients.

Modelling recovery of Celtic Sea demersal fish community size-structure

The Large Fish Indicator (LFI) is a size-based indicator of fish community state. The indicator describes the proportion by biomass of a fish community represented by fish larger than some size threshold. From an observed peak value of 0.49 in 1990, the Celtic Sea LFI declined until about 2000 and then fluctuated around 0.10 throughout the 2000s. This decline in the LFI reflected a period of diminishing ‘large’ fish biomass, probably related to high levels of size selective fishing. During the study period, fishing mortality was maintained at consistently high values. Average biomass of ‘small’ fish fluctuated across the whole time series, showing a weak positive trend in recent years. Inter-annual variation in the LFI was increasingly driven by fluctuation in small fish biomass as large fish biomass declined. Simulations using a size-based ecosystem model suggested that recovery in Celtic Sea fish community size-structure (LFI) could demand at least 20% reductions in fishing pressure and occur on decadal timescales.

Balancing Inflammatory, Lipid, and Xenobiotic Signaling Pathways by VSL#3, a Biotherapeutic Agent, in the Treatment of Inflammatory Bowel Disease

Background: The interleukin 10 knockout mouse (IL10-KO) is a model of human inflammatory bowel disease (IBD) used to Study host microbial interactions and the action of potential therapeutics. Using Affymetrix data analysis, important signaling pathways and transcription factors relevant to gut inflammation and antiinflammatory probiotics were identified.

Methods: Affymetrix microarray analysis on both wildtype (WT) and IL10-KO mice orally administered with and without the probiotic VSL#3 was performed and the results validated by real-time polymerase chain reaction (PCR), immunocytochemistry, proteomics, and histopathology. Changes in metabolically active bacteria were assessed with denaturing gradient gel electrophoresis (DGGE).

Results: Inflammation in IL10-KO mice was characterized by differential regulation of inflammatory, nuclear receptor, lipid, and xenobiotic signaling pathways. Probiotic intervention resulted in downregulation of CXCL9 (fold change [FC] = -3.98, false discovery rate [FDR] = 0.019), CXCL10 (FC = -4.83, FDR = 0.0008), CCL5 (FC -3.47 FDR = 0.017), T-cell activation (Itgal [FC = -4.72, FDR = 0.00009], Itgae [FC = -2.54 FDR = 0.0044]) and the autophagy gene IRGM (FC = -1.94, FDR = 0.01), a recently identified susceptibility gene in human IBD. Consistent with a marked reduction in integrins, probiotic treatment decreased the number of CCL5+ CD3+ double-positive T Cells and upregulated galectin2, which triggers apoptosis of activated T cells. Importantly, genes associated with lipid and PPAR signaling (PPAR alpha [FC = 2.36, FDR = 0.043], PPARGC1 alpha [FC 2.58, FDR = 0.016], Nrld2 [FC = 3.11, FDR = 0.0067]) were also upregulated. Altered microbial diversity was noted in probiotic-treated mice.

Conclusions: Bioinformatics analysis revealed important immune response. phagocytic and inflammatory pathways dominated by elevation of T-helper cell 1 type (TH1) transcription factors in IL10-KO mice. Probiotic intervention resulted in a site-specific reduction of these pathways but importantly upregulated PPAR, xenobiotic, and lipid signaling genes. potential antagonists of NF-kappa B inflammatory pathways.