Single-nucleotide polymorphisms in the IL2RA gene are associated with age at diagnosis in late-onset Finnish type 1 diabetes subjects

The onset of type 1 diabetes can occur at any age, with as many as half of all cases diagnosed after age 15. Despite this wide distribution in age at diagnosis, most genetic studies focus on cases diagnosed in childhood or during early adulthood. To better understand the genetics of late-onset type 1 diabetes, we collected a Finnish case/control cohort with all cases diagnosed between ages 15 and 40. We genotyped 591 probands and 1,538 control subjects at regions well established as susceptibility loci in early onset type 1 diabetes. These loci were then tested for disease association and age-at-diagnosis effects. Using logistic regression, we found that single-nucleotide polymorphisms (SNPs) at the INS, PTPN22, and IFIH1 loci were associated with late-onset disease (OR (95%CI)?=?0.57(0.47–0.69), p?=?2.77?×?10^?9; OR (95%CI)?=?1.50 (1.27–1.78), p?=?3.98?×?10^?6; and OR (95%CI)?=?0.81(0.71–0.93), p?=?0.0028, respectively). In contrast, a disease association was not detected for two SNPs at the IL2RA locus (rs11594656 and rs41295061). Despite this, we did find an independent age-at-diagnosis effect for each IL2RA SNP using a multivariate Cox proportional hazards model (p?=?0.003, 0.002, respectively). Taken together, polymorphisms at the IL2RA locus were a major determinant of age at diagnosis in our cohort with an effect at par with the HLA-DQ2/DQ8 genotype as measured by hazard ratios. These findings suggest that the IL2RA locus controls both the susceptibility to disease and its time of occurrence. Thus, we believe the IL2/IL2R axis represents a potential therapeutic target for delaying the onset of disease.     

A phylogenetic circumscription of Polytrichastrum (Polytrichaceae): Reassessment of sporophyte morphology supports molecular phylogeny

Mosses arguably possess the most structurally complex sporangia of any extant land plants, a consequence of being the monosporangiophyte lineage most strongly adapted to terrestrial environments. Morphological and functional variation in the mechanisms that regulate spore release in one of the major classes of mosses, the Polytrichopsida, is largely unexplored, while recent research indicates that the most distinctive structure, the peristome, has evolved independently in the Polytrichopsida and in other mosses. The genus Polytrichastrum was separated from Polytrichum on the basis of such sporangial characters, although the critical features had until recently only been examined using light microscopy, and strong evidence from molecular data indicated that Polytrichastrum as currently circumscribed is polyphyletic. Here we use Bayesian ancestral character state reconstruction in conjunction with extensive scanning electron micrographic studies to elucidate probable morphology at ancestral nodes and define natural taxa. As well as clarifying the structure, evolution, and aspects of development of the peristome-epiphragm complex in this highly prominent group of mosses, the results provide a basis for a revised phylogenetic taxonomy in which the species of Polytrichastrum sect. Aporotheca are recognized once more within Polytrichum.     

Effects of acquired obesity on endothelial function in monozygotic twins

Objective: To determine whether acquired obesity or accompanying metabolic changes such as adiponectin deficiency, insulin resistance, dyslipidemia, or visceral fat are associated, independent of genetic influences, with endothelial dysfunction by studying young adult monozygotic (MZ) twin pairs discordant for obesity. Research Methods and Procedures: Nine obesity‐discordant (intra‐pair difference in BMI, 3.8 to 10.1 kg/m²) and nine concordant (0 to 2.3 kg/m²) 24‐ to 27‐year‐old MZ twin pairs were identified from a population‐based FinnTwin16‐sample. Endothelial function was measured by blood flow responses to intrabrachial infusions of an endothelium‐dependent (acetylcholine) and an endothelium‐independent (sodium nitroprusside) vasodilator. Whole body insulin sensitivity was measured using the euglycemic insulin clamp technique, and forearm and body composition were measured with magnetic resonance imaging and DXA. In addition, serum levels of adiponectin, high‐sensitivity C‐reactive protein, and lipids were determined. Results: The heavier co‐twins of the discordant pairs had significantly lower whole body insulin sensitivity than the leaner co‐twins. Blood flows/muscle volume during infusions of acetylcholine and sodium nitroprusside were not altered by obesity. However, intra‐pair differences in serum adiponectin, intra‐abdominal fat, and C‐reactive protein were significantly correlated with those in endothelial function. Only the relationship between intra‐pair differences in adiponectin and endothelial function persisted in multiple linear regression analysis. Obesity‐concordant co‐twins had comparable insulin sensitivity and endothelial function. Discussion: In young adult MZ twins discordant for obesity, acquired adiponectin deficiency rather than obesity per se is an independent correlate of endothelial dysfunction.     

Class I and II HLA genes are associated with susceptibility and age at onset in Finnish families with type 1 diabetes

OBJECTIVES: We explored the properties of the long-term survivor model (LTS) in the genetic association studies and studied allelic and haplotypic associations between the age at onset and partially latent susceptibility of type 1 diabetes (T1DM) and Human Leucocyte Antigen (HLA) A, B and DR loci. METHODS: The authors applied the long-term survivor model (LTS) for sibships collected in a population-based registry during a calendar time period. The method uses sibs that could not become probands and includes the proband's age at onset during the recruitment period. Association between the candidate gene and the partially latent susceptibility is modeled with logistic regression and the age at onset with a two-parameter gamma distribution, where a scale parameter depends on the candidate genotypes. We also performed a simulation study of nuclear families to compare the power of the likelihood ratio tests of the genetic association based on the LTS model with those obtained using family-based association method (FBAT) and bias of the case-pseudo control design. In addition, we analysed allele and haplotype associations between HLA A, B and DR loci (IDDM1) with T1DM, using population-based ascertainment of 705 sibships with complete HLA information. RESULTS: A simulation study showed that the estimates of the genetic association using an ascertainment-corrected LTS model are virtually unbiased and that the relative risk estimates obtained from case-pseudo control design (TDT) are negatively biased. In the analysis of the Finnish T1DM families we found that only B62 (p < 0.05) is positively significantly associated with susceptibility after adjusting for the haplotype effects. Five alleles were significantly associated with age at onset (B8 and DR3, p < 0.01; A2, B60 and DR6, p < 0.05). No significant three-locus haplotype associations with the susceptibility were found, but A3B18DR4 (p < 0.001) haplotype was associated with older age at onset than average. CONCLUSIONS: Estimates of genetic relative risk obtained from the case-pseudo control design are negatively biased and the prospective LTS model is an appropriate choice, when there are non-susceptible subjects in the population with variable age at onset. Based on the analysis of T1DM, we conclude that there are gene(s) in the HLA region that are associated with susceptibility and/or age at onset of T1DM, and this should be taken into account in future studies.     

Ethylene insensitivity modulates ozone-induced cell death in birch

We have used genotypic variation in birch (Betula pendula Roth) to investigate the roles of ozone (O(3))-induced ethylene (ET), jasmonic acid, and salicylic acid in the regulation of tissue tolerance to O(3). Of these hormones, ET evolution correlated best with O(3)-induced cell death. Disruption of ET perception by transformation of birch with the dominant negative mutant allele etr1-1 of the Arabidopsis ET receptor gene ETR1 or blocking of ET perception with 1-methylcyclopropene reduced but did not completely prevent the O(3)-induced cell death, when inhibition of ET biosynthesis with aminooxyacetic acid completely abolished O(3) lesion formation. This suggests the presence of an ET-signaling-independent but ET biosynthesis-dependent component in the ET-mediated stimulation of cell death in O(3)-exposed birch. Functional ET signaling was required for the O(3) induction of the gene encoding beta-cyanoalanine synthase, which catalyzes detoxification of the cyanide formed during ET biosynthesis. The results suggest that functional ET signaling is required to protect birch from the O(3)-induced cell death and that a decrease in ET sensitivity together with a simultaneous, high ET biosynthesis can potentially cause cell death through a deficient detoxification of cyanide.     

Coronary artery diameter can be assessed reliably with transthoracic echocardiography

We studied whether diameters of coronary arteries can be measured accurately with the use of transthoracic echocardiography (TTE). By knowing the anatomic diameter of the coronary artery together with coronary flow velocity it is possible to measure coronary flow volume more precisely by TTE. However, the suitability of TTE for measurement of diameters of all main epicardial coronary arteries has not been systematically validated. We measured the diameters of the left main (LM), left anterior descending (LAD), left circumflex (LCX), and right coronary arteries (RCA) with the use of TTE [manual two-dimensional (2D), color-Doppler, and automated 2D analysis] in 30 patients who had normal coronary anatomy. We compared these diameters to those measured with quantitative coronary angiography (QCA). We could measure diameters of LM, LAD, LCX, and RCA by TTE in up to 37%, 63%, 7%, and 60% of patients, respectively. The overall correlation coefficients between TTE and QCA measurements were 0.83 (P < 0.01) with manual 2D analysis, 0.82 (P < 0.01) with automated 2D analysis, and 0.94 (P < 0.01) with a color-Doppler-based analysis. Interobserver variability of TTE measurements was low (coefficient of variation 5.4 +/- 4.6-7.5 +/- 8.8%). TTE is an accurate method to evaluate coronary artery diameter in patients with healthy coronary arteries.     

A novel strategy for microarray quality control using Bayesian networks

MOTIVATION: High-throughput microarray technologies enable measurements of the expression levels of thousands of genes in parallel. However, microarray printing, hybridization and washing may create substantial variability in the quality of the data. As erroneous measurements may have a drastic impact on the results by disturbing the normalization schemes and by introducing expression patterns that lead to incorrect conclusions, it is crucial to discard low quality observations in the early phases of a microarray experiment. A typical microarray experiment consists of tens of thousands of spots on a microarray, making manual extraction of poor quality spots impossible. Thus, there is a need for a reliable and general microarray spot quality control strategy. RESULTS: We suggest a novel strategy for spot quality control by using Bayesian networks, which contain many appealing properties in the spot quality control context. We illustrate how a non-linear least squares based Gaussian fitting procedure can be used in order to extract features for a spot on a microarray. The features we used in this study are: spot intensity, size of the spot, roundness of the spot, alignment error, background intensity, background noise, and bleeding. We conclude that Bayesian networks are a reliable and useful model for microarray spot quality assessment. SUPPLEMENTARY INFORMATION: http://sigwww.cs.tut.fi/TICSP/SpotQuality/.     

Speciation by host switch and adaptive radiation in a fish parasite genus Gyrodactylus (Monogenea,Gyrodactylidae)

Four hundred Gyrodactylus species have been formally described, but the estimated number of species in this fish ectoparasite genus of Monogenean Platyhelminthes is more than 20,000. The unusually high species richness has lead to the hypotheses of speciation and adaptive radiation via host switching. These hypotheses were tested by reconstructing a molecular phylogeny for the subgenus G. (Limnonephrotus) which is a group of freshwater parasites, including five species infecting wild and farmed salmonids. The highly variable ITS1 and ITS2 segments and the conservative 5.8S ribosomal gene were sequenced in 22 species plus two species representing the subgenus G. (Paranephrotus) as an outgroup. The phylogeny was compared with host systematics: the species were collected from six fish families (Cyprinidae, Salmonidae, Percidae, Esocidae, Gasterosteidae, and Gobitidae). The phylogenetic analysis demonstrated that G. (Limnonephrotus) is a monophyletic group that was originally hosted by cyprinids. The speciation has occurred in two episodes, the older one manifested in genetic distances 25-33% (4-6 Myr BP). The latter speciation burst occurred in one clade only, perhaps one million years ago. This clade has been morphologically identified as a wageneri species group. It is a monophyletic group of 18 species [studied here] and contains all five salmonid parasites, but also parasites, on cyprinids, percids, esocids, and gasterosteids. In G. (Limnonephrotus), eight host switches crossing the host family barrier were observed, and at least three of them were followed by repetitive speciation. Seven host-switch events were statistically confirmed by bootstrapping. The suggested model of speciation by host switch was accepted, and interestingly the adaptive radiation seems to be a consequence of host switch to a new family (key innovation model). The molecular and ecological evolution rate of Gyrodactylus parasites is manyfold in comparison to host species, and the phylogenies are largely independent and disconnected.     

Monoclonal antibodies, immunofluorometric assay, and detection of human semenogelin in male reproductive tract: no association with in vitro fertilizing capacity of sperm

Semenogelin plays an important role in sperm clotting and is degraded into smaller fragments by prostate-specific antigen (PSA) during clot liquefaction. Semenogelin and its fragments inhibit sperm motility in vitro. We studied the expression of semenogelin I mRNA and its localization in various tissues of the male genital tract. We also studied semenogelin concentrations with respect to sperm parameters and the outcome of in vitro fertilization. Semenogelin protein was detected by immunohistochemical staining and semenogelin I mRNA was detected by Northern blot analysis in the seminal vesicles and ampullary part of the vas deferens, whereas specimens from the prostate, epididymis, testis, and the female genital tract were negative. Using monoclonal antibodies against semenogelin, an immunofluorometric assay was developed to measure semenogelin levels in seminal plasma and to evaluate possible correlations with sperm parameters and fertilization in vitro. No correlation was found between the semenogelin concentration and the volume of the ejaculate, sperm concentration, sperm motility, or in vitro fertilization rate. Semenogelin levels were positively correlated with the total protein concentration in seminal plasma, and there was an inverse correlation between the concentration of semenogelin and that of PSA. The levels of semenogelin appear to bear no relationship to the in vitro fertilization capacity of the spermatozoa.