Construction and elementary mode analysis of a metabolic model for Shewanella oneidensis MR-1.

A stoichiometric model describing the central metabolism of Shewanella oneidensis MR-1 wild-type and derivative strains was developed and used in elementary mode analysis (EMA). Shewanella oneidensis MR-1 can anaerobically respire a diverse pool of electron acceptors, and may be applied in several biotechnology settings, including bioremediation of toxic metals, electricity generation in microbial fuel cells, and whole-cell biocatalysis. The metabolic model presented here was adapted and verified by comparing the growth phenotypes of 13 single- and 1 double-knockout strains, while considering respiration via aerobic, anaerobic fumarate, and anaerobic metal reduction (Mtr) pathways, and utilizing acetate, n-acetylglucosamine (NAG), or lactate as carbon sources. The gene ppc, which encodes phosphoenolpyruvate carboxylase (Ppc), was determined to be necessary for aerobic growth on NAG and lactate, while not essential for growth on acetate. This suggests that Ppc is the only active anaplerotic enzyme when cultivated on lactate and NAG. The application of regulatory and substrate limitations to EMA has enabled creation of metabolic models that better reflect biological conditions, and significantly reduce the solution space for each condition, facilitating rapid strain optimization. This wild-type model can be easily adapted to include utilization of different carbon sources or secretion of different metabolic products, and allows the prediction of single- and multiple-knockout strains that are expected to operate under defined conditions with increased efficiency when compared to wild type cells.

Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.

OBJECTIVE: Our previous coeliac disease genome-wide association study (GWAS) implicated risk variants in the human leucocyte antigen (HLA) region and eight novel risk regions. To identify more coeliac disease loci, we selected 458 single nucleotide polymorphisms (SNPs) that showed more modest association in the GWAS for genotyping and analysis in four independent cohorts. DESIGN: 458 SNPs were assayed in 1682 cases and 3258 controls from three populations (UK, Irish and Dutch). We combined the results with the original GWAS cohort (767 UK cases and 1422 controls); six SNPs showed association with p<1 x 10(-04) and were then genotyped in an independent Italian coeliac cohort (538 cases and 593 controls). RESULTS: We identified two novel coeliac disease risk regions: 6q23.3 (OLIG3-TNFAIP3) and 2p16.1 (REL), both of which reached genome-wide significance in the combined analysis of all 2987 cases and 5273 controls (rs2327832 p = 1.3 x 10(-08), and rs842647 p = 5.2 x 10(-07)). We investigated the expression of these genes in the RNA isolated from biopsies and from whole blood RNA. We did not observe any changes in gene expression, nor in the correlation of genotype with gene expression. CONCLUSIONS: Both TNFAIP3 (A20, at the protein level) and REL are key mediators in the nuclear factor kappa B (NF-kappaB) inflammatory signalling pathway. For the first time, a role for primary heritable variation in this important biological pathway predisposing to coeliac disease has been identified. Currently, the HLA risk factors and the 10 established non-HLA risk factors explain approximately 40% of the heritability of coeliac disease.

Lack of association of MYO9B genetic variants with coeliac disease in a British cohort.

BACKGROUND AND AIMS: Development of coeliac disease involves an interaction between environmental factors (especially dietary wheat, rye, and barley antigens) and genetic factors (there is strong inherited disease susceptibility). The known human leucocyte antigen (HLA)-DQ2 and -DQ8 association explains only a minority of disease heritability. A recent study in the Dutch population suggested that genetic variation in the 3' region of myosin IXB (MYO9B) predisposes to coeliac disease. MYO9B is a Rho family GTPase activating protein involved in epithelial cell cytoskeletal organisation. MYO9B is hypothesised to influence intestinal permeability and hence intestinal antigen presentation. METHODS: Four single nucleotide polymorphisms were chosen to tag all common haplotypes of the MYO9B 3' haplotype block (exons 15-27). We genotyped 375 coeliac disease cases and 1366 controls (371 healthy and 995 population based). All individuals were of White UK Caucasian ethnicity. RESULTS: UK healthy control and population control allele frequencies were similar for all MYO9B variants. Case control analysis showed no significant association of any variant or haplotype with coeliac disease. CONCLUSIONS: Genetic variation in MYO9B does not have a major effect on coeliac disease susceptibility in the UK population. Differences between populations, a weaker effect size than originally described, or possibly a type I error in the Dutch study might explain these findings.

Synergy between TLR9 and NOD2 innate immune responses is lost in genetic Crohn's disease.

BACKGROUND: Nucleotide binding oligomerisation domain 2 (NOD2; also known as CARD15) mutations are associated with Crohn's disease but how mutations cause disease is poorly understood. Innate immune responses are reportedly enhanced by combined NOD2 ligand (muramyl dipeptide, MDP) and Toll-like receptor 4 ligand (TLR4, lipopolysaccharide) stimulation. Intestinal TLR signalling has a dual role-maintaining intestinal homeostasis and protection from injury as well as initiating inflammatory responses. TLR9 is functional in the intestinal epithelium where it is most strongly expressed in Paneth cells. AIMS: To study possible interactions between CpG DNA (TLR9 ligand) and MDP using primary human cells of differing NOD2 genotypes. SUBJECTS: NOD2 wild-type healthy controls (n = 7) and NOD2 homozygous Crohn's disease patients (n = 19), age and sex matched. METHODS: Peripheral blood mononuclear cells were stimulated with CpG DNA and MDP. Cytokines were measured by enzyme linked immunosorbent assay. RESULTS: Tumour necrosis factor alpha (TNF-alpha) and interleukin 8 (IL-8) responses to CpG DNA were similar in NOD2 wild-type and homozygous mutant cells. Concomitant NOD2 stimulation had a marked synergistic effect on CpG DNA induced TNF-alpha responses at 10-100 ng/ml MDP. A mean 2.1-fold increase in CpG DNA induced TNF-alpha responses and a mean 3.7-fold increase in IL-8 responses were observed in NOD2 wild-type cells with 10 ng/ml MDP. This effect was abolished in NOD2 homozygous cells. CONCLUSIONS: NOD2 stimulation normally enhances innate immune responses to CpG DNA. This marked synergistic effect is lost in Crohn's disease patients homozygous for NOD2 mutations, with implications for TLR mediated intestinal homeostasis and inflammation.

Effect of obesity on screening mammography: outcomes analysis of 88,346 consecutive examinations.

OBJECTIVE: We determined differences in the rates of recall, biopsy, and cancer detection for screening mammography as a function of adiposity. MATERIALS AND METHODS: Eighty-eight thousand three hundred forty-six consecutive screening mammography examinations were performed from April 1985 to August 1997. Patient weights were normalized to ideal weight correcting for height and were subdivided into adiposity cohorts including underweight by greater than 10%; ideal weight +/- 10%; overweight by 11-24%; overweight by 25-39%; and overweight by greater than 40%. The rates of recall, biopsy, cancer detection, and cancer stage were calculated and were analyzed using the chi-square test for trend. Cancer size was analyzed using linear regression analysis. RESULTS: Reliable (p < 0.05) and meaningful differences were seen between cohorts of increasing adiposity for rates of recall, biopsy, and cancer detection. An increase in recall rate occurred with progressively increasing adiposity (3.88%, 4.89%, 5.11%, 5.47%, 5.55% [p < 0.0001]). The rate of biopsy also increased with increasing adiposity (0.98%, 1.31%, 1.35%, 1.59%, 1.65% [p < 0.0002]), as did the rate of screening-detected cancer (number of cases of cancer per 1000 women screened) (3.74, 4.29, 5.34, 4.70, 6.04 [p < 0.015]). Finally, increased adiposity also correlated with increased median cancer size (p < 0.02) and with more advanced stage at diagnosis (p = 0.046). CONCLUSION: Increasing adiposity correlates with progressive increases in the rates of recall, biopsy, and cancer detection for women undergoing screening mammography. Increasing adiposity also correlates with increased cancer size and stage, providing further support for obesity as a risk factor for breast cancer.

Outcome analysis for women undergoing annual versus biennial screening mammography: a review of 24,211 examinations.

OBJECTIVE: Our goal was to determine differences in outcome measures between women undergoing annual versus biennial screening mammography. MATERIALS AND METHODS: A retrospective review of prospectively collected data on 24,211 consecutive screening mammography examinations was performed in women aged 40-79 years, all of whom had undergone previous normal screening mammography. Annual screening and biennial screening were defined as examinations performed 10-14 months and 22-26 months, respectively, after previous normal screening mammography. The rates of recall, biopsy, cancer detection, and interval cancer for annual and biennial screening cohorts were calculated, as were tumor size, lymph node status, and stage of invasive cancer. Interval cancer cases were identified by linkage with a regional tumor registry. RESULTS: Of the 4306 biennially screened women, 160 were recalled (3.7%), 45 were biopsied (1.0%), and cancer was detected in 19 (0.44%). Of the 19,905 annually screened women, 518 were recalled (2.6%), 150 were biopsied (0.75%), and cancer was detected in 71 (0.36%). Of the 3278 registry-linked biennially screened women, five had interval cancer (0.15%); of the 15,031 registry-linked annually screened women, 10 had interval cancer (0.07%). For biennial screening-detected cancer and interval invasive cancer combined, the median tumor size was 15 mm, 24% had lymph node metastasis, and 29% were stage 2 or higher. For annual screening-detected cancer, these measures were 11 mm, 14% positive nodes, and 17% stage 2+ cancer, respectively. CONCLUSION: Annual screening mammography results in lower recall rates than does biennial screening (p < .0001). Moreover, annual screening results in the detection of smaller tumors that have a more favorable prognosis (p = .04).

Health benefits for the terminally ill: reality and perception.

This paper examines the availability and scope of hospice benefits as well as employers' attitudes and knowledge about care for the terminally ill. Data are drawn from a national random sample of 1,502 employers with 200 or more workers and from focus groups with employee benefits managers and their insurance advisers, brokers, and consultants. Major findings are that 83 percent of employers offer explicit hospice benefits, with most other firms covering hospice through high-cost case management. Most employers support the concept of hospice care because they believe that it reduces medical expenses.

Carbofuran poisoning in herons: diagnosis using cholinesterase reactivation techniques.

Exposure to the carbamate insecticide carbofuran was detected using brain cholinesterase (ChE) reactivation techniques in heron carcasses collected from a potential pesticide exposure incident. Great egrets (Nycticorax nycticorax), great blue herons (Ardea herodias), and black-crowned night herons (Casmerodius albus) were exposed to carbofuran (2,3-dihydro-2,2-dimethyl-7-benzofuranyl methylcarbamate) either by dermal exposure while wading or through ingestion of contaminated food items. Carcasses may have been in the field up to 5 days prior to collection. Brain ChE, substantially inhibited in most samples, increased 7.9-208% in the reactivation assay after 4 to 96 hours at 37 C, providing evidence of exposure to a carbamate pesticide. Crayfish (Procambarus clarkii) identified in the crops of some herons contained carbofuran residues of up to 0.6 parts per million wet weight, providing additional evidence of exposure. Reactivated brain ChE in several samples approached the range of control values.

Development and optimization of reactivation techniques for carbamate-inhibited brain and plasma cholinesterases in birds and mammals.

Two biochemical assays were developed which promote and measure the induced reactivation of carbamate-inhibited cholinesterases in avian and mammalian brain and plasma samples. The effects of inhibitor concentration, temperature, and the extent of dilution on the achievement of a steady state equilibrium and the subsequent level and rate of recovery of brain cholinesterase activity were investigated. A similar procedure for reactivation of carbamate-inhibited plasma cholinesterase activity involved the removal of excess carbamate from a small sample volume (< 400 microliters). Both methods begin by measuring cholinesterase activity immediately following dilution and involve an incubation period during which conditions for spontaneous reactivation of the inhibited enzymes are maximized. Both assays are suitable for large-scale, rapid use and appear able to restore inhibited cholinesterase activity to levels closely approximating that of control values for each species tested. These methods will not only maximize the usefulness of cholinesterases in monitoring carbamate pesticide exposure but should prove to be extremely useful tools in the forensic assessment of carbamate exposure in human and wildlife pesticide incidents.

Secondary poisoning hazard of fenthion to American kestrels.

The possibility that fenthion, an organophosphorus pesticide, could represent a secondary poisoning hazard to birds of prey was tested, using American kestrels (Falco sparverius) and house sparrows (Passer domesticus) as representative models of a naturally occurring predator-prey interaction. Fourteen kestrels were presented with live sparrows exposed previously to perches containing Rid-A-Bird 1100 solution (11% fenthion active ingredient). Eleven kestrels died within twenty-four h after consuming one fenthion-exposed sparrow. Two kestrels died after consumption of a second fenthion-exposed sparrow on day 2, and a final kestrel died after partially consuming a third fenthion-exposed sparrow on day 3. Brain cholinesterase (ChE) activity in kestrels was depressed to levels diagnostic of poisoning by a ChE-inhibiting compound. The majority of fenthion contamination of sparrows was external, with the highest amounts measured on the feet. The detection of fenthion residues in kestrel gastro-intestinal tracts confirmed secondary fenthion poisoning.