Breaking free from thermodynamic constraints: thermal acclimation and metabolic compensation in a freshwater zooplankton species.

Respiration rates of ectothermic organisms are affected by environmental temperatures, and sustainable metabolism at high temperatures sometimes limits heat tolerance. Organisms are hypothesized to exhibit acclimatory metabolic compensation effects, decelerating their metabolic processes below Arrhenius expectations based on temperature alone. We tested the hypothesis that either heritable or plastic heat tolerance differences can be explained by metabolic compensation in the eurythermal freshwater zooplankton crustacean Daphnia magna We measured respiration rates in a ramp-up experiment over a range of assay temperatures (5-37°C) in eight genotypes of D. magna representing a range of previously reported acute heat tolerances and, at a narrower range of temperatures (10-35°C), in D. magna with different acclimation history (either 10 or 25°C). We discovered no difference in temperature-specific respiration rates between heat-tolerant and heat-sensitive genotypes. In contrast, we observed acclimation-specific compensatory differences in respiration rates at both extremes of the temperature range studied. Notably, there was a deceleration of oxygen consumption at higher temperature in 25°C-acclimated D. magna relative to their 10°C-acclimated counterparts, observed in active animals, a pattern corroborated by similar changes in filtering rate and, partly, by changes in mitochondrial membrane potential. A recovery experiment indicated that the reduction of respiration was not caused by irreversible damage during exposure to a sublethal temperature. Response time necessary to acquire the respiratory adjustment to high temperature was lower than for low temperature, indicating that metabolic compensation at lower temperatures requires slower, possibly structural changes.

Haplotype analysis on chromosome 6p of tumor necrosis factor alpha, vascular endothelial growth factor A, and interleukin-17F alleles associated with corneal transplant rejection.

OBJECTIVE: The aim of this work was to investigate single-nucleotide polymorphisms (SNPs) in multiple genes on chromosome 6p in corneal transplant recipients known to be at increased risk of failure through immunologic rejection (ie, "high-risk" corneal transplants). Tumor necrosis factor alpha (TNF-α) is a key immunoregulatory cytokine in the ocular environment, interacting with a variety of factors in a synergistic way and playing a crucial role in many stages of the inflammatory response. Vascular endothelial growth factor (VEGF) is one of the most important angiogenic factors, supporting both hemangiogenesis and lymphangiogenesis, both key in transplant tolerance and rejection. Interleukin-17 (IL-17) is a multifunctional cytokine produced by T-helper 17 cells, exerting specific effector functions during an immune response. Association of SNPs in all 3 genes with corneal transplant outcome was therefore investigated. METHODS: Three hundred five corneal transplant recipients were followed for 3 years, and episodes of allograft rejection were recorded. With the use of patient DNA, 6 SNPs of 3 different genes on chromosome 6p were investigated. The TNF-α promoter SNP -308 G/A (rs1800629) was analyzed with the use of induced heteroduplex generation; 2 VEGF-A functional variants were analyzed, -2578 (rs699947) C/A and -1154 (rs1570360) G/A, with the use of Taqman genotyping assays; and 3 nonsynonymous IL-17F SNPs in exon 3 (negative strand), (rs2397084) A/G, (rs11465553) G/A, and (rs763780) A/G, were investigated with the use of direct sequencing. Haplotypes were inferred with the use of PHASE using positive strand alleles, and exact measures of association were determined with the use of Mid-P exact chi-square. RESULTS: Six common haplotypes were inferred, with the haplotype TNF-α (rs1800629), VEGF-A (rs699947), (rs1570360), IL-17F (rs763780), (rs11465553), and (rs2397084) ACGTCT having a significant association with corneal transplant rejection (odds ratio, 1.78; 95% confidence interval, 1.01-3.11; P = .04). CONCLUSIONS: The results suggest that patients carrying a combination of SNPs for TNF-α, VEGF-A, and IL-17F of ACGTCT haplotype may have an increased risk of corneal allograft rejection compared with patients carrying other haplotypes.

Functional tumor necrosis factor alpha polymorphisms and haplotype analysis in high-risk corneal transplantation.

BACKGROUND: Tumor necrosis factor alpha (TNF-α) plays a critical role in diverse cellular processes including ocular immune tolerance, inflammation, and allograft rejection. The ubiquitous transcription factor nuclear factor kappa B (NF-κB) regulates expression of numerous genes. Induction of the TNF-α pathway is involved in the inflammatory response and loss of transplant tolerance. OBJECTIVES: We investigated functional single nucleotide polymorphisms (SNPs) in the promoter region of TNF-α and an insertion/deletion (indel) polymorphism of NF-κB1 in corneal transplant recipients considered to be at increased risk of immunological rejection (ie, high-risk corneal transplantations) and looked for any associations with corneal transplantation outcome. PATIENTS AND METHODS: Three hundred eighty-four full thickness corneal transplant recipients were followed for 3 years and episodes of reversible and irreversible allograft rejection were recorded. Using DNA obtained from these patients, 5 SNPs located in the promoter region -1031 T/C rs1799964, -863 C/A (rs1800630), -857 C/T (rs1799724), -308 G/A (rs1800629), and -238 G/A (rs361525), and one SNP upstream from the transcription start site (+489) rs1800610 of TNF-α were analyzed using induced heteroduplex generation. A functional NF-κB1 indel (-94) was also investigated. Haplotypes were inferred by PHASE and associations with rejection were determined by chi-square analysis. RESULTS: The TNF-α haplotype TCTGGA was significantly associated with reduced risk of corneal graft rejection (Pc < .005) and TCTAGA was associated with increased risk of rejection (Pc < .005) in high-risk corneal transplants. There was no association with the NF-κB1 indel (Pc > .05). CONCLUSION: According to haplotype frequencies, our results suggest that the TCTGGA haplotype may confer additional protection against risk of immunological rejection whereas TCTAGA may increase risk of corneal allograft rejection in the high-risk setting. However, both haplotypes were relatively rare and thus would not warrant genotyping for individual patient selection for anti-TNF therapy.

Evaluation of NFKB1A variants in patients with knee osteoarthritis.

A key feature of osteoarthritis (OA) is articular cartilage loss mediated by numerous catabolic factors including pro-inflammatory cytokines. Cytokine expression is modulated by the nuclear factor κB (NF-κB) family of transcription factors that are in turn, regulated by the inhibitor of NF-κB IκBα encoded by NFKB1A. We examined eight, previously reported common germline polymorphisms to determine whether NFKB1A variants are associated with knee OA. Eight common single-nucleotide polymorphisms (SNPs) across the NFKB1A gene were genotyped in 189 cases with knee OA and 197 healthy controls. Allele, genotype and haplotype frequencies were compared between case and control groups and stratified according to gender due to the increased prevalence of female OA. Serum concentrations of four biochemical markers elevated in OA were compared with genotype for each knee OA case. None of the SNPs showed an association with knee OA; however, stratification of the data for gender showed an increased frequency of the rs8904 variant allele in the female knee OA case group (P = 0.02). Six common haplotypes were identified (H1-H6). H6 was marginally more prevalent in the knee OA group (P = 0.05). The rs8904 variant was associated with increased levels of hyaluronan (HA), a marker of synovial inflammation at 12 and 24 months compared to baseline levels. The nearby rs696 variant demonstrated increased levels of C-reactive protein (CRP) at 12 months and HA at 12 and 24 months. A reduction in CRP levels at 12 months was observed for the rs2233419 variant. These findings provide evidence for the association of NFKB1A variants and knee OA.

Association between CCL2 haplotypes and knee osteoarthritis.

We examined five single nucleotide polymorphisms (SNPs) and reconstructed 5-locus haplotypes of the CCL2 gene, in knee osteoarthritis (OA) cases and in controls. The CCL2 rs2857657 variant (G) allele was observed more frequently in female knee OA cases than in controls. One haplotype (H5) was observed exclusively in the control group (f = 2.3%). Genetic variation in the CCL2 gene may be associated with knee OA.

Tumour necrosis factor receptor superfamily member 11B polymorphisms and association with knee osteoarthritis in women.

We examined single-nucleotide polymorphisms (SNPs) across the tumour necrosis factor receptor superfamily member 11B (TNFRSF11B) gene and knee OA. We identified alleles in a VNTR region in intron 3 that was observed exclusively in women OA cases (P = 0.007, Pc = 0.042). Our results reveal that a previously unreported association between a VNTR genotype in TNFRSF11B and knee OA in women.

Evaluation of IL18 and IL18R1 polymorphisms: genetic susceptibility to knee osteoarthritis.

We examined single-nucleotide polymorphisms (SNPs) in IL18 and IL18/R1 genes and knee OA. IL18 rs1946518 wild-type allele was more frequently observed in cases (P = 0.04). Haplotype 1 was more frequently observed in cases (P = 0.04). Genetic variation in the promoter region of IL18, but not IL18R1, may be associated with OA.

Local inflammatory markers and systemic endotoxin in aggressive periodontitis.

While much research has focused on local and systemic factors contributing to periodontal disease, little is known regarding mechanisms linking these factors. We have previously reported a systemic hyper-inflammatory response to bacterial endotoxin in localized aggressive periodontitis (LAP). The objectives of this study were to delineate cyto/chemokines in gingival crevicular fluid (GCF) and evaluate systemic levels of endotoxin associated with LAP. Clinical parameters, GCF, and peripheral blood were collected from: 34 LAP, 10 healthy siblings, and nine healthy unrelated control individuals. Cyto/chemokines were quantified in GCF, systemic endotoxin levels were quantified in plasma, and correlation analysis was performed among all parameters. Nine mediators were elevated in LAP diseased sites as compared with healthy sites (TNFα, INFγ, IL1ß, IL2, IL6, IL10, Il12p40, GMCSF, and MIP1α, p < 0.001), while MCP1, IL4, and IL8 were elevated in healthy sites (p < 0.01). Four- to five-fold-higher endotoxin levels were detected in LAP plasma compared with that from healthy participants (p < 0.0001), which correlated with all clinical parameters and most cyto/chemokines analyzed. In conclusion, higher systemic levels of endotoxin were found in LAP, which correlates with an exacerbated local inflammatory response and clinical signs of disease. (Clinicaltrials.gov number, NCT01330719).

Association between a common IL10 distal promoter haplotype and IgE production in individuals with atopic dermatitis.

Atopic dermatitis (AD) is a genetically determined inflammatory skin disease characterized by abnormal cytokine production, including increased production of interleukin 10 (IL10). Single nucleotide polymorphisms (SNP) and haplotypes in the IL10 gene promoter region on chromosome 1q31-32 have been implicated in several inflammatory diseases, but generally, only SNPs proximal to the transcription start site (TSS) have been investigated. The aim of this study was to identify proximal, distal and combined haplotype sets in the IL10 promoter region and to study their association with clinical phenotypes in atopic dermatitis. SNPs at positions -3575, -2849, -2779, -2763, -1082, -851, -819 and -592 in the IL10 promoter region were genotyped in individuals with atopic dermatitis (n= 47) and nonatopic control subjects (n= 40) using polymerase chain reaction-based techniques and induced heteroduplex generator (IHG) analysis. Pan-promoter, TSS-proximal and TSS-distal haplotypes were reconstructed using phase analysis. Fifteen haplotypes representing all eight SNPs were identified. Subgrouping identified four 4-locus and three 3-locus TSS-proximal haplotypes; and nine 4-locus TSS-distal haplotypes. No difference was found in haplotype or SNP frequencies between the AD and control groups, or between patients with mild or severe disease. However, a common 4-locus TSS-distal haplotype (TGAC) was significantly increased in patients with IgE levels over 1000 kIU L(-1). This study is the first to analyse the association between haplotype groups in the IL10 promoter region and clinical phenotypes in AD. We have demonstrated a significant association between the TSS-distal haplotype TGAC, and IgE levels in AD patients. It remains to be shown if there is an association between the TGAC haplotype and IL10 production, which might account for the stimulation of IgE production.

Haplotype uncertainty in association studies.

Inferring haplotypes from genotype data is commonly undertaken in population genetic association studies. Within such studies the importance of accounting for uncertainty in the inference of haplotypes is well recognised. We investigate the effectiveness of correcting for uncertainty using simple methods based on the output provided by the PHASE haplotype inference methodology. In case-control analyses investigating non-Hodgkin lymphoma and haplotypes associated with immune regulation we find little effect of making adjustment for uncertainty in inferred haplotypes. Using simulation we introduce a higher degree of haplotype uncertainty than was present in our study data. The simulation represents two genetic loci, physically close on a chromosome, forming haplotypes. Considering a range of allele frequencies, degrees of linkage between the loci, and frequency of missing genotype data, we detail the characteristics of genetic regions which may be susceptible to the influence of haplotype uncertainty. Within our evaluation we find that bias is avoided by considering haplotype probabilities or using multiple imputation, provided that for each of these methods haplotypes are inferred separately for case and control populations; furthermore using multiple imputation provides the facility to incorporate haplotype uncertainty in the estimation of confidence intervals. We discuss the implications of our findings within the context of the complexity of haplotype inference for larger marker rich regions as would typically be encountered in genetic analyses.

Cytokine gene polymorphism in human disease: on-line databases, Supplement 3.

Within the past few years, the focus on cytokine single nucleotide polymorphism (SNP) function and association with human diseases has increased considerably. This third supplement to the Cytokine Gene Polymorphism in Human Disease: On-line database describes the positive associations of cytokine SNPs in human diseases described in articles published from 2002 up to 2005. A file containing a list of all SNPs investigated in this period of time and their association with human disease or expression pattern can be downloaded from the internet address http://www.nanea.dk/cytokinesnps/. The web pages also contain other features and downloads that could be useful when planning cytokine SNP association studies.

Haplotypes of the low-density lipoprotein receptor-related protein 5 (LRP5) gene: are they a risk factor in osteoarthritis?

OBJECTIVE: Several genome-wide scans have revealed an osteoarthritis (OA)-susceptibility locus on chromosome 11q in close proximity to the low-density lipoprotein receptor-related protein 5 (LRP5) gene. The regulation of bone mass is under the control of LRP5 and since increased bone mass is thought to play a role in the pathology of OA we examined LRP5 polymorphisms and haplotypes to determine if variants of this locus may predispose to OA. METHODS: A UK control population of 187 individuals was examined for five commonly occurring polymorphisms against a cohort of 158 DNAs from patients with knee OA. An additional UK cohort was also examined to confirm the findings of the first study; this second group consisted of 110 knee OA patients. Haplotype analysis was also performed on patient and control DNAs. RESULTS: A study of individual polymorphisms revealed no association with disease. However, haplotype analysis of the initial two populations revealed a common haplotype (C-G-C-C-A) that provided a 1.6-fold increased risk of OA (P(c)=0.021). The data obtained from the second cohort confirmed the initial findings, with a 1.6-fold increased risk observed within this cohort for the risk haplotype (P=0.012). CONCLUSIONS: A closer investigation of LRP5 and associated Wnt signalling molecules in OA will help determine disease aetiology and the development of novel treatment strategies that specifically target the bone compartment.

Vascular endothelial growth factor gene polymorphism and acute respiratory distress syndrome.

BACKGROUND: Non-cardiogenic pulmonary oedema is a characteristic feature of the acute respiratory distress syndrome (ARDS). The properties of vascular endothelial growth factor (VEGF) as a potent vascular permogen and mitogen have led to investigation of its potential role in this condition. Lower VEGF plasma levels have been linked to the presence of the T allele in the +936 CT polymorphism. We hypothesised that the presence of the T allele would be associated with the development and severity of ARDS. METHODS: A cohort of 137 normal subjects, 117 ventilated patients with ARDS, and 103 "at risk" of ARDS were genotyped for the VEGF+936 CT polymorphism. The severity of physiological disturbance and mortality was determined in the ventilated cohorts. RESULTS: The CT and TT genotype frequencies were increased in ARDS patients compared with both normal subjects (OR 2.01, 95% CI 1.13 to 3.58, p = 0.02) and those "at risk" (OR 2.05, 95% CI 1.02 to 2.20, p = 0.03). In patients with ARDS but not those "at risk", CT and TT genotypes were associated with a higher mean APACHE III score (80.9 (4.3) v 69.3 (2.9), p<0.05). CONCLUSION: These data support a role for VEGF in the pathogenesis of ARDS and its associated physiological derangement.

Prevalence and treatment of carpal tunnel syndrome in renal haemodialysis.

The purpose of this study was to investigate the prevalence and aetiology of carpal tunnel syndrome (CTS) and the effect of open carpal tunnel decompression (CTD) in a group of patients on renal haemodialysis. In 91 patients attending a Renal Unit who were assessed only by clinical means, the prevalence of CTS was 7.1%. CTS development was not significantly correlated with known risk factors, in particular duration of dialysis and presence of an artero-venous fistula on the symptomatic limb. CTD led to a mean symptom-free period of 12 years. In summary, CTS is a frequent and serious disease affecting renal dialysis patients, but its aetiology remains uncertain. Nevertheless, CTD is an effective and lasting treatment for this condition.

Fluid shear stress induces beta-catenin signaling in osteoblasts.

beta-Catenin plays a dual role in cells: one at cell-cell junctions and one regulating gene transcription together with TCF (T-cell Factor) in the nucleus. Recently, a role for beta-catenin in osteoblast differentiation and gene expression has begun to be elucidated. Herein we investigated the effects of fluid shear stress (FSS) on beta-catenin signaling. FSS is a well-characterized anabolic stimulus for osteoblasts; however, the molecular mechanisms for the effects of this stimulation remain largely unknown. We found that 1 hour of laminar FSS (10 dynes/cm(2)) induced translocation of beta-catenin to the nucleus and activated a TCF-reporter gene. Analysis of upstream signals that may regulate beta-catenin signaling activity revealed two potential mechanisms for increased beta-catenin signaling. First, FSS induced a transient, but significant, increase in the phosphorylation of both glycogen synthase kinase 3beta (GSK-3beta) and Akt. Second, FSS reduced the levels of beta-catenin associated with N-cadherin, suggesting that less sequestration of beta-catenin by cadherins occurs in osteoblasts subjected to FSS. Functional analysts of potential genes regulated by beta-catenin signaling in osteoblasts revealed two novel observations. First, endogenous, nuclear beta-catenin purified from osteoblasts formed a complex with a TCF -binding element in the cyclooxygenase-2 promoter, and, second, overexpression of either a constitutively active beta-catenin molecule or inhibition of GSK-3beta activity increased basal cyclooxygenase-2 levels. Together, these data demonstrate for the first time that FSS modulates the activity of both GSK-3beta and beta-catenin and that these signaling molecules regulate cyclooxygenase-2 expression in osteoblasts.

Extended haplotypes and linkage disequilibrium in the IL1R1-IL1A-IL1B-IL1RN gene cluster: association with knee osteoarthritis.

The interleukin-1 gene cluster is a key regulator in a number of chronic disease processes. We explored the linkage between nine polymorphic loci in the IL1R1 promoter, eight in the IL1A-IL1B-IL1RN gene complex, and their association with osteoarthritis (OA), a common complex disease associated with low-level inflammation. Using 195 healthy controls, we identified eight novel polymorphisms in the IL1R1 exon 1A region. We found limited LD between IL1R1 and the IL1A-IL1B-IL1RN cluster, although LD within these two individual groups was high. To test association with knee OA, we genotyped 141 patients from Bristol (UK) at the 17 loci. IL1R1 promoter haplotypes showed no association with disease. However, within the IL1A-IL1B-IL1RN complex, we identified a common haplotype conferring a four-fold risk of OA (P=0.00043; Pc=0.0043) and one IL1B-IL1RN haplotype conferring a four-fold reduced risk (P=0.0036; Pc=0.029). To replicate these associations, we subsequently examined 163 knee OA patients from London. Here, the effects of the haplotypes were confirmed: the risk IL1A-IL1B-IL1RN haplotype conferred a two-fold risk of OA (P=0.02), and the protective IL1B-IL1RN haplotype conferred a five-fold reduced risk of OA (P=0.0000008). These results may help to explain the genome-wide scan linkage data and functional observations concerning association between IL-1 and OA.

Identification of two novel single nucleotide polymorphisms in the promoter of the human interleukin-18 receptor alpha.

Single-strand conformational polymorphism (SSCP) was used to identify single nucleotide polymorphisms (SNPs) in the promoter region of the human interleukin-18 receptor alpha (IL-18Ralpha). Two SNPs were identified at positions -69 and -638 relative to the transcriptional start site. Two-way comparison of the two SNPs revealed strong linkage disequilibrium (chi2 = 63.45, P < 0.001). Three haplotypes were identified, namely C-69C-638, T-69C-638 and C-69T-638, with frequencies of 0.26, 0.39 and 0.35, respectively.

TNFalpha polymorphism frequencies in HPV-associated cervical dysplasia.

OBJECTIVES: Persistent high-risk HPV infection of the uterine cervix is associated with CIN and cervical carcinoma. Women with a reduced pro-inflammatory response to HPV are likely to be susceptible to viral persistence, and therefore, potentially more vulnerable to cervical neoplasia. In this study, we investigate whether nucleotide sequence polymorphisms in the TNFalpha (TNFSF2) gene (which can modify gene transcription up to 9-fold) might influence susceptibility to, or evolution of, CIN. METHODS: Induced heteroduplex analysis was used to identify polymorphisms at positions TNFalpha -308 and -238 in women with normal cervical cytology and with cervical disease. Patients with low-grade disease were HPV typed using general primer GP5+/6+ PCR/EIA and reverse line blotting, and were reassessed for disease status at 6 and 24 months. RESULTS: CIN patients as a group had a significantly higher frequency of TNFalpha -308 low-secretor genotypes (GG) compared to controls, and this effect was most pronounced in the CIN1 group (P = 0.01 and P = 0.004, respectively). TNFalpha polymorphism frequencies at position -238 were similar for patients and controls. Neither polymorphism was associated with the presence of HPV infection at recruitment or disease outcome at 6 or 24 months. CONCLUSIONS: These findings support the hypothesis that susceptibility to CIN is influenced by TNFalpha -308 polymorphism.

Discrimination of suballeles present at the TNFd microsatellite locus using induced heteroduplex analysis.

Polymorphism at the TNFd locus has been implicated in a number of disease association studies. The TNFd locus consists of three regions of (GA)(n) repeats separated by an imperfect repeat of two guanine bases. TNFd alleles are genotyped by the number of repeats in the first (GA)(n) repeat region, and until now the second repeat region had been thought to be nonpolymorphic. We report the existence of suballeles present within the TNFd microsatellite locus, detected using induced heteroduplex generator (IHG) technology. These alleles cannot be detected using conventional typing strategies as they represent altered distribution of the (GA)(n) repeats or sequence variation within the repeat. The suballeles affect the frequencies of the conventional d3 and d4 alleles leading to significantly altered allele frequencies. Some studies have associated the d3 and d4 alleles with disease outcome. We re-analysed one such study cohort using IHG technology and demonstrated a high proportion of incorrectly assigned TNFd3 alleles.