Stepwise kinetic equilibrium models of quantitative polymerase chain reaction.

BACKGROUND: Numerous models for use in interpreting quantitative PCR (qPCR) data are present in recent literature. The most commonly used models assume the amplification in qPCR is exponential and fit an exponential model with a constant rate of increase to a select part of the curve. Kinetic theory may be used to model the annealing phase and does not assume constant efficiency of amplification. Mechanistic models describing the annealing phase with kinetic theory offer the most potential for accurate interpretation of qPCR data. Even so, they have not been thoroughly investigated and are rarely used for interpretation of qPCR data. New results for kinetic modeling of qPCR are presented. RESULTS: Two models are presented in which the efficiency of amplification is based on equilibrium solutions for the annealing phase of the qPCR process. Model 1 assumes annealing of complementary targets strands and annealing of target and primers are both reversible reactions and reach a dynamic equilibrium. Model 2 assumes all annealing reactions are nonreversible and equilibrium is static. Both models include the effect of primer concentration during the annealing phase. Analytic formulae are given for the equilibrium values of all single and double stranded molecules at the end of the annealing step. The equilibrium values are then used in a stepwise method to describe the whole qPCR process. Rate constants of kinetic models are the same for solutions that are identical except for possibly having different initial target concentrations. Analysis of qPCR curves from such solutions are thus analyzed by simultaneous non-linear curve fitting with the same rate constant values applying to all curves and each curve having a unique value for initial target concentration. The models were fit to two data sets for which the true initial target concentrations are known. Both models give better fit to observed qPCR data than other kinetic models present in the literature. They also give better estimates of initial target concentration. Model 1 was found to be slightly more robust than model 2 giving better estimates of initial target concentration when estimation of parameters was done for qPCR curves with very different initial target concentration. Both models may be used to estimate the initial absolute concentration of target sequence when a standard curve is not available. CONCLUSIONS: It is argued that the kinetic approach to modeling and interpreting quantitative PCR data has the potential to give more precise estimates of the true initial target concentrations than other methods currently used for analysis of qPCR data. The two models presented here give a unified model of the qPCR process in that they explain the shape of the qPCR curve for a wide variety of initial target concentrations.

Widespread oxyregulation in tropical corals under hypoxia.

Hypoxia (low oxygen stress) is increasingly reported on coral reefs, caused by ocean deoxygenation linked to coastal nutrient pollution and ocean warming. While the ability to regulate respiration is a key driver of hypoxia tolerance in many other aquatic taxa, corals' oxyregulatory capabilities remain virtually unexplored. Here, we examine O2-consumption patterns across 17 coral species under declining O2 partial pressure (pO2). All corals showed ability to oxyregulate, but total positive regulation (Tpos) varied between species, ranging from 0.41 (Pocillopora damicornis) to 2.42 (P. acuta). On average, corals performed maximum regulation effort (Pcmax) at low pO2 (30% air saturation, corresponding to lower O2 levels measured on natural reef systems), and exhibited detectable regulation down to as low as <10% air saturation. Our study shows that corals are not oxyconformers as previously thought, suggesting oxyregulation is likely important for survival in dynamic O2 environments of shallow coral reefs subjected to hypoxic events.

An alternative cyclin-D1 splice site is not linked to inflammatory bowel disease-associated neoplasia.

BACKGROUND: Inflammatory bowel diseases (IBD) encompass inflammatory disorders affecting the gastrointestinal tract, primarily ulcerative colitis (UC) and Crohn's disease (CD). The risk of developing colorectal cancer (CRC) is increased in patients with IBD. The CCND1 protein is the regulatory subunit of an enzyme that inactivates the retinoblastoma protein, a tumor suppressor protein, and promotes progression through the G1-S phase of the cell cycle. The CCND1 870G-A gene polymorphism influences susceptibility to colorectal cancer. The mutant allele of CCND1 in IBD-associated neoplasia leads to a greater frequency of alternate splicing during transcription, resulting in a more stable CCND1 protein. This creates a higher concentration of CCND1, facilitating easier passage through the G1/S checkpoint, abnormal cell cycle progression, and possibly carcinogenesis. METHODS: We conducted a case-control study involving 396 individuals with IBD. IBD subgroups included CD, UC, and indeterminate colitis (IC). We studied patients with sporadic colorectal cancer (n=75) and patients without gastrointestinal disease as a control group (n=93). We extracted DNA from blood and performed polymerase chain reaction followed by high-performance liquid chromatography to screen for mutations. We confirmed the polymorphism at nucleotide A870G in exon 4. For statistical analysis, we used exact analyses of two-way contingency tables. Power calculations were done and correction for multiple testing was performed by computing the false discovery rate (FDR). RESULTS AND DISCUSSION: Our study had a power of 75% at a 0.05 significance level. A870G SNP allele frequency in the IBD group was 44.8%, compared to 51.6% in the control population. Only the IC group showed a significant association with CCND1 splice site after correction for multiple testing (FDR=0.042). There were no differences between the other IBD groups and controls. CONCLUSION: We found an association between CCND1 A870G SNP and IC group only (p=0.014, FDR=0.042). However, our data do not show an association between CCND1 A870G SNP and CD-associated or UC-associated neoplasia.

Assessment of oxygen consumption in response to progressive hypoxia.

A new method is presented for describing the rate of oxygen consumption in response to progressive hypoxia. The method consists of screening candidate functions describing the relationship between Vo2 (oxygen consumption rate) and Po2 (ambient oxygen concentration) by testing each for fit to observed data for a single curve and the function that best fits is chosen using lowest AICc value as the criterion. Descriptive statistics are then extracted from the selected function that best describes the pattern present in the curve. Several new descriptive statistics for the pattern of response are proposed which are based on the null model of simple diffusion and no regulation. The method quantifies deviation from the null model at each point on the curve and measures both positive and negative deviation which occur when the curve changes more slowly or more rapidly than the null model predicts, respectively. The new descriptive statistics generalize the traditional one used in the past, the critical oxygen tension (Pc), and allow interpretation of a variety of shapes of curves which cannot be analyzed with conventional methods. Because the method is descriptive, it does not implicate any specific mechanisms in generating the response. The method is applied to data from 68 animals in 14 different species groups reported in the literature. The overall results suggest the existence of substantial diversity in response types among animals, which requires a more complex description than has traditionally been used.

Characterization of N-acetyltransferase 1 and 2 polymorphisms and haplotype analysis for inflammatory bowel disease and sporadic colorectal carcinoma.

BACKGROUND: N-acetyltransferase 1 (NAT1) and 2 (NAT2) are polymorphic isoenzymes responsible for the metabolism of numerous drugs and carcinogens. Acetylation catalyzed by NAT1 and NAT2 are important in metabolic activation of arylamines to electrophilic intermediates that initiate carcinogenesis. Inflammatory bowel diseases (IBD) consist of Crohn's disease (CD) and ulcerative colitis (UC), both are associated with increased colorectal cancer (CRC) risk. We hypothesized that NAT1 and/or NAT2 polymorphisms contribute to the increased cancer evident in IBD. METHODS: A case control study was performed with 729 Caucasian participants, 123 CRC, 201 CD, 167 UC, 15 IBD dysplasia/cancer and 223 controls. NAT1 and NAT2 genotyping were performed using Taqman based techniques. Eight single nucleotide polymorphisms (SNPs) were characterized for NAT1 and 7 SNPs for NAT2. Haplotype frequencies were estimated using an Expectation-Maximization (EM) method. Disease groups were compared to a control group for the frequencies at each individual SNP separately. The same groups were compared for the frequencies of NAT1 and NAT2 haplotypes and deduced NAT2 phenotypes. RESULTS: No statistically significant differences were found for any comparison. Strong linkage disequilibrium was present among both the NAT1 SNPs and the NAT2 SNPs. CONCLUSION: This study did not demonstrate an association between NAT1 and NAT2 polymorphisms and IBD or sporadic CRC, although power calculations indicate this study had sufficient sample size to detect differences in frequency as small as 0.05 to 0.15 depending on SNP or haplotype.

Bioactivity of anacardic acid against colorado potato beetle (Leptinotarsa decemlineata) larvae.

Anacardic acid (2-hydroxy-6-alkylbenzoic acid) produced and secreted from glandular trichomes of zonal geranium (Pelargonium x hortorum; Geraniaceae family) provides resistance to small pests (aphids and spider mites). To assess the potential bioactivity of anacardic acid against larger insect pests and to determine if an alternate mode of application (ingestion rather than the topical application) could impart resistance to pests, the effects of anacardic acid consumption on the development of Colorado potato beetle larvae were tested. Analysis of dose-response curves indicated a significant effect on weight gain and mortality. Assessment of food preference (treated versus untreated) indicated larvae avoid food containing anacardic acid and have a lower feeding rate on food containing anacardic acid. On the basis of these results, it is suggested that anacardic acid, applied as a chemical spray or through bioengineering production in crop plants, may provide a new tool in the arsenal to minimize damage to plants caused by pests.

Characterization of genotype-phenotype relationships and stratification by the CARD15 variant genotype for inflammatory bowel disease susceptibility loci using multiple short tandem repeat genetic markers.

The classification of ulcerative colitis (UC), Crohn disease (CD), and indeterminate colitis (IC) as forms of inflammatory bowel disease (IBD) is based on clinical, radiological, and histological criteria. The genetic basis of IBD is well founded, and susceptibility loci have been identified on several different chromosomes. We aimed to define genotype-phenotype relationships and interactions with the IBD susceptibility gene CARD15for various IBD susceptibility loci (IBD1, IBD2, IBD5, IBD6, IBD7, and chromosome 4) by characterizing previously described peak LOD score short tandem repeat (STR) markers. The study population consisted of 484 severely affected Caucasian patients with IBD, 144 healthy controls, and 348 nonaffected first-degree relatives of IBD patients. Associations were defined with the use of population- and family-based methodology. Correction for multiple testing was performed with a method based on an experimental false discovery rate. We provide novel evidence to show that IBD2 is involved in susceptibility to IC and terminal ileal CD in this population, with overrepresentation of IBD2 STR D12S83 (GenBank Z16592.1) allele 7 (g.49_60del[CA](6)) in IC (q = 0.038, P = 0.014) and underrepresentation of allele 8 (g.51_60del[CA](5)) in terminal ileal CD (q = 0.038, P = 0.016). The association of IBD2 with IC was confirmed by family-based testing. We also provide novel evidence to show that IBD5 is involved in susceptibility to IC and colonic/ileocolonic CD in this population, with overrepresentation of IBD5 STR D5S1984 (GenBank Z52623.1) allele 5 (g.183_186del[CA](2)) in both IC (q = 0.040, P = 0.005) and colonic/ileocolonic CD (q = 0.040, P = 0.004). Evidence is also given for potential interactions between CARD15and IBD2/IBD5. Other findings include an association of IBD2 with UC, and an association of IBD1 with terminal ileal and colonic/ileocolonic CD.

Evaluation of SLC11A1 as an inflammatory bowel disease candidate gene.

BACKGROUND: Significant evidence suggests that a promoter polymorphism within the gene SLC11A1 is involved in susceptibility to both autoimmune and infectious disorders. The aim of this study was to evaluate whether SLC11A1 has a role in the susceptibility to inflammatory bowel disease (IBD) by characterizing a promoter polymorphism within the gene and two short tandem repeat (STR) markers in genetic proximity to SLC11A1. METHODS: The studied population consisted of 484 Caucasians with IBD, 144 population controls, and 348 non-IBD-affected first-degree relatives of IBD patients. IBD subjects were re-categorized at the sub-disease phenotypic level to characterize possible SLC11A1 genotype-phenotype correlations. Polymorphic markers were amplified from germline DNA and typed using gel electrophoresis. Genotype-phenotype correlations were defined using case-control, haplotype, and family-based association studies. RESULTS: This study did not provide compelling evidence for SLC11A1 disease association; most significantly, there was no apparent evidence of SLC11A1 promoter allele association in the studied Crohn's disease population. CONCLUSION: Our results therefore refute previous studies that have shown SLC11A1 promoter polymorphisms are involved in susceptibility to this form of IBD.

Dietary phytoestrogens and photoperiodic response in a male songbird, the Dark-eyed Junco (Junco hyemalis).

Many commercial bird diets are made with soy products that contain phytoestrogens (i.e., plant compounds that have weak agonist activity at estrogen receptors), but the effects of these compounds on bird physiology and behavior are largely unknown. The primary phytoestrogens present in soy are the isoflavones genistin and diadzin, which have been shown to affect reproductive measures in many taxa. Two groups of wild-caught male Dark-eyed Juncos (Junco hyemalis) were fed a diet either made with water-washed soy protein (soy(+)) or made with soy protein that had been alcohol-washed to extract isoflavones (soy(-)). Both groups exhibited a photoperiodic response to long days. Plasma luteinizing hormone (LH) concentrations increased within the first week of long day (LD) exposure for both groups, and over the course of the experiment LH was higher in the soy(+) group, although concentrations for both groups were lower than have been reported in free-living juncos. The rate of cloacal protuberance (CP) growth was significantly affected by diet, with the soy(-) birds beginning to increase their CPs about a week faster than soy(+) birds after exposure to LD. There was no group difference in food intake, fat score, body mass, or behavioral measures during the study or in testis weight at the end of the study. Although effects of dietary phytoestrogens detected were subtle (i.e., rate of CP growth), those investigating subtle effects of hormonally active substances (e.g., endocrine disruptors) or environmental cues affecting the reproductive axis in songbirds may want to consider eliminating phytoestrogens from their experimental diets.

CARD15 genotype-phenotype relationships in a small inflammatory bowel disease population with severe disease affection status.

Inflammatory bowel disease (IBD; MIM# 266600) is subdivided on the basis of clinical findings as either Crohn's disease (CD), ulcerative colitis (UC), or indeterminate colitis (IC). Three previously described mutations within the IBD susceptibility gene CARD15 (R702W, G908R, 1007fs) increase susceptibility to CD with a terminal ileal and/or ileocolonic location and fibrostenosing behavior. We undertook an association study using 477 unrelated IBD patients (248 CD, 172 UC, 57 IC) and 104 population controls to determine whether these previously described associations could be replicated in a small, accurately phenotyped cohort. Case-control and family-based approaches were employed to analyze CARD15 mutant allele and haplotype data. Analyses were initially performed in unstratified IBD cohorts. The R702W mutant allele was associated with CD on case-control analysis (q=0.036, P=.004), and 1007fs with CD on pedigree disequilibrium testing (P=.020). All 3 CARD15 mutations increased susceptibility to a variety of CD subphenotypic manifestations, including early-onset CD in individuals with a family history of IBD, and CD complicated by extraintestinal disease. We also present evidence to suggest that R702W may predispose to a more generalized form of CD. Additionally, we confirm that CARD15 mutations are associated with terminal ileal/ileocolonic, and to a lesser extent, fibrostenosing CD.

The acute and delayed effects of hydrostatic dilation on rat femoral arteries.

The technique of intraoperative vessel dilation is sometimes used to facilitate microvascular anastomosis and prevent vasospasm. Although this technique is not new, its application has not gained widespread acceptance mainly due to concerns raised about potential damage to the vessels acutely and during the postoperative period, leading to decreased vessel patency. The goal of this study was to determine the acute and delayed histologic effects of hydrostatic dilation on rat femoral arteries and to compare the response of dilated arteries to vasodilating and vasoconstricting agents. The femoral arteries in 22 rats were used in 2 experimental groups; 9 in the acute group and 13 in the delayed group. Six animals served as controls. After the vessels were exposed, a microcatheter was inserted into a segment of the vessel that had been isolated between 2 vessel clamps. Saline was infused into the artery until a pressure of 300 mm Hg was attained and then maintained for 60 seconds. In the acute group, the animals were euthanized at the end of the dilation, while in the delayed group the animals were euthanized 24 hours later. Hydrostatic dilation of rat femoral arteries was found to increased vessel diameter acutely, with subsequent relief and prevention of vasospasm during the ensuing 24 hours. Histologically, there was no increased damage of the vessel walls in the dilated vessels compared with control vessels. Based on the data reported in this study, hydrostatic dilation of rat microvessels appears to be safe and may be used to technically facilitate microanastomoses and decrease vasospasm.

T-cell receptor gamma: a microsatellite marker for colorectal cancer.

BACKGROUND: T-cell receptor gamma (TCR-gamma) is involved in maintaining host cell integrity and homeostasis of the human immune system. We hypothesize that polymorphism of the TCR-gamma complex may be involved in the pathogenesis of colorectal cancer. METHODS: The microsatellite markers D7S1818 and D7S2206 located within the TCR-gamma antigen locus on chromosome 7p were amplified by polymerase chain reaction, and genotypes were determined for 22 patients with early onset of colorectal cancer (<60 years old) and for 38 population-based control subjects. RESULTS: Genotype BC of D7S1818 (P = .049) and haplotype AC of D7S1818/D7S2206 (P < or = .003) were associated with colorectal cancer as compared with the control population (extended Fisher's exact test). CONCLUSIONS: This study identifies a novel genetic and clinical association between TCR-gamma and early-onset colorectal cancer. Many young patients do not fulfill the criteria for hereditary colorectal cancer syndromes and are therefore not identified by established screening programs. Markers such as D7S1818 and D7S2206 may become useful in the identification of patients at risk of developing colorectal cancer and permit earlier therapeutic intervention.