Iron deficiency interrupts energy transfer from a disconnected part of the antenna to the rest of Photosystem II

Iron deficiency changed markedly the shape of the leaf chlorophyll fluorescence induction kinetics during a dark-light transition, the so-called Kautsky effect. Changes in chlorophyll fluorescence lifetime and yield were observed, increasing largely the minimal and the intermediate chlorophyll fluorescence levels, with a marked dip between the intermediate and the maximum levels and loss of the secondary peak after the maximum. During the slow changes, the lifetime-yield relationship was found to be linear and curvilinear (towards positive lifetime values) in control and Fe-deficient leaves, respectively. These results suggested that part of the Photosystem II antenna in Fe-deficient leaves emits fluorescence with a long lifetime. In dark-adapted Fe-deficient leaves, measurements in the picosecond-nanosecond time domain confirmed the presence of a 3.3-ns component, contributing to 15% of the total fluorescence. Computer simulations revealed that upon illumination such contribution is also present and remains constant, indicating that energy transfer is partially interrupted in Fe-deficient leaves. Photosystem II-enriched membrane fractions containing different pigment-protein complexes were isolated from control and Fe-deficient leaves and characterized spectrophotometrically. The photosynthetic pigment composition of the fractions was also determined. Data revealed the presence of a novel pigment-protein complex induced by Fe deficiency and an enrichment of internal relative to peripheral antenna complexes. The data suggest a partial disconnection between internal Photosystem II antenna complexes and the reaction center, which could lead to an underestimation of the Photosystem II efficiency in dark-adapted, low chlorophyll Fe-deficient leaves, using chlorophyll fluorescence. This revised version was published online in August 2006 with corrections to the Cover Date.     

Growth of cranial synchondroses and sutures requires polycystin-1

In vertebrates, coordinated embryonic and postnatal growth of the craniofacial bones and the skull base is essential during the expansion of the rostrum and the brain. Identification of molecules that regulate skull growth is important for understanding the nature of craniofacial defects and for development of non-invasive biologically based diagnostics and therapies.Here we report on spatially restricted growth defects at the skull base and in craniofacial sutures of mice deficient for polycystin-1 (Pkd1). Mutant animals reveal a premature closure of both presphenoid and sphenooccipital synchondroses at the cranial base. Furthermore, knockout mice lacking Pkd1 in neural crest cells are characterized by impaired postnatal growth at the osteogenic fronts in craniofacial sutures that are subjected to tensile forces. Our data suggest that polycystin-1 is required for proliferation of subpopulations of cranial osteochondroprogenitor cells of both mesodermal and neural crest origin during skull growth. However, the Erk1/2 signalling pathway is up-regulated in the Pkd1-deficient skeletal tissue, similarly to that previously reported for polycystic kidney.     

Controversies in the laboratory diagnosis of celiac disease in children; new haplotypes discovered

The latest consensus on celiac disease in 2008, under the auspices of the International Societies of Pediatric Gastroenterology, Hepatology and Nutrition, shows that HLA DQ2/DQ8 typing indicates the highest negative predictive value for celiac disease, which would exclude the diagnosis of celiac disease. In Romania, there are no studies on the implication of HLA-DQ2/DQ8 in celiac disease in children. The aim of our study was to analyze the significance of genetic tests, with a focus on negative HLA-DQ2/DQ8 cases, as well as to determine the main haplotypes involved in celiac disease in children. We tested in 37 children with old celiac disease, confirmed based on the presence of intestinal villi changes on duodenal biopsy, the IgA anti-tissue transglutaminase antibodies (TgA-IgA) by ELISA and the IgA anti-endomysium antibodies (EmA-IgA) by indirect immunofluorescence, compared to HLA-DQ2/DQ8 typing by polymerase chain reaction (PCR). In 25 children, the determined HLA haplotypes predominantly belonged to DQ2, and in 3 children we report the presence of a new haplotype, DR3-DQ2/DR4-DQ8, formed by pattern 1, DR3-DQ2-the DQA1*0501 and DQB1*0201 alleles, and pattern 5, DR4-DQ8-the DQA1*0301 and DQB1*0302 alleles. In 9 children, genetic tests were negative for celiac disease. The identification of HLA-DQ2/DQ8 provides additional data in the diagnosis of celiac disease, but a rigid algorithm in the diagnosis of celiac disease has no practical applicability.     

Covalent modifications of antitetanus F(ab')2 fragments with natural and synthetic polyamines and their effects on the antibody endocytosis in cultured HL60 cells

For antibody therapeutics to succeed when intracellular target molecules are involved, a strategy must be applied to increase the delivery of antibodies into cells to reach their targets. Antibody cationization by chemical conjugation of a polyamine could be one such strategy. Both natural polyamines with increasing net charge valencies (putrescine, PUT; spermidine, SPD; and spermine, SPM) and a synthetic polyamine (hexamethylenediamine, HMD) can be used to cationize antibodies, but no comparison of the respective effects of these polyamines on intracellular delivery of antibodies has been performed yet. This study describes the covalent modification of antitetanus F(ab') 2 with these four polyamines using different reaction conditions, and compares the effects of these modifications on antibody interaction with cultured HL60 cells. The cationized antibodies retained > or =80% of the binding activity of the unmodified F(ab') 2 with regard to tetanus toxin, as measured by an antigen-binding capture enzyme immunoassay. This same method was used to quantify the amount of cell-associated F(ab') 2 following incubation with HL60 cells. Cationization was shown to enhance cell interaction of the F(ab') 2 : the higher the number of coupled polyamine molecules, the greater the amount of antibody associated with the cells. Moreover, coupling the F(ab') 2 to the SPD and SPM polyamines had greater effect on cell interaction than coupling the F(ab') 2 to the PUT and HMD diamines. Internalization of the cationized antibodies by the HL60 cells was demonstrated by confocal microscopy. This technique also showed that SPD and SPM were more effective than PUT and HMD in terms of intracellular delivery of the F(ab') 2 . It follows from all these results that electrostatic interaction involving charge density plays a predominant role in the endocytic transport mechanism of the F(ab') 2 modified with these polyamines. However, coupling the F(ab') 2 to SPM and SPD yielded the same maximum effects in terms of cell interaction, although coupling SPM was expected to increase the antibody net charge valency more than coupling SPD. This finding suggests that the effective global charge for the cell interaction and uptake of polyamine-modified antibodies does not simply correspond to the addition of the ionizable amine functions on the coupled polyamines, and that other factors may come into play.     

An Exponential Combination Procedure for Set-Based Association Tests in Sequencing Studies

State-of-the-art next-generation-sequencing technologies can facilitate in-depth explorations of the human genome by investigating both common and rare variants. For the identification of genetic factors that are associated with disease risk or other complex phenotypes, methods have been proposed for jointly analyzing variants in a set (e.g., all coding SNPs in a gene). Variants in a properly defined set could be associated with risk or phenotype in a concerted fashion, and by accumulating information from them, one can improve power to detect genetic risk factors. Many set-based methods in the literature are based on statistics that can be written as the summation of variant statistics. Here, we propose taking the summation of the exponential of variant statistics as the set summary for association testing. From both Bayesian and frequentist perspectives, we provide theoretical justification for taking the sum of the exponential of variant statistics because it is particularly powerful for sparse alternatives—that is, compared with the large number of variants being tested in a set, only relatively few variants are associated with disease risk—a distinctive feature of genetic data. We applied the exponential combination gene-based test to a sequencing study in anticancer pharmacogenomics and uncovered mechanistic insights into genes and pathways related to chemotherapeutic susceptibility for an important class of oncologic drugs.     

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

Although genome-wide association studies (GWAS) of complex traits have yielded more reproducible associations than had been discovered using any other approach, the loci characterized to date do not account for much of the heritability to such traits and, in general, have not led to improved understanding of the biology underlying complex phenotypes. Using a web site we developed to serve results of expression quantitative trait locus (eQTL) studies in lymphoblastoid cell lines from HapMap samples (http://www.scandb.org), we show that single nucleotide polymorphisms (SNPs) associated with complex traits (from http://www.genome.gov/gwastudies/) are significantly more likely to be eQTLs than minor-allele-frequency–matched SNPs chosen from high-throughput GWAS platforms. These findings are robust across a range of thresholds for establishing eQTLs (p-values from 10⁻⁴–10⁻⁸), and a broad spectrum of human complex traits. Analyses of GWAS data from the Wellcome Trust studies confirm that annotating SNPs with a score reflecting the strength of the evidence that the SNP is an eQTL can improve the ability to discover true associations and clarify the nature of the mechanism driving the associations. Our results showing that trait-associated SNPs are more likely to be eQTLs and that application of this information can enhance discovery of trait-associated SNPs for complex phenotypes raise the possibility that we can utilize this information both to increase the heritability explained by identifiable genetic factors and to gain a better understanding of the biology underlying complex traits.     

IgG-F-actin antibodies in celiac disease and dermatitis herpetiformis

Anti-actin antibodies are found in 52-85% of patients with autoimmune hepatitis or chronic active hepatitis and in 22% of patients with primary biliary cirrhosis. In patients with celiac disease, anti-actin antibodies correlate with the degree of villous atrophy. Studies on their involvement in celiac disease and dermatitis herpetiformis in Romania have not been done. The purpose of this study was to evaluate of the quality of IgG anti-F-actin antibodies (IgG-AAA) tests compared with IgA tissue transglutaminase antibodies (IgA-TgA) having IgA endomysial antibody (IgA-EmA) as gold standard in celiac disease and dermatitis herpetiformis and to see if there is any relationship between them. The study included 70 pediatric patients with celiac disease under gluten-free diets and 10 adult patients with dermatitis herpetiformis, during 2010. The IgG-AAA antibodies levels were determined by ELISA. Assessing the qualities of IgG-AAA compared to IgA-TgA, we obtained the following values sensitivity (Se) 27.8%, specificity (Sp) 79.4%, respectively Se 88.9%, Sp 79.4% in celiac disease and Se 33.3%, Sp 100%, respectively Se 100%, Sp 100% in dermatitis herpetiformis. Also, there was a prevalence of 24.3% and 30% of IgG-AAA in the two groups of patients, but no statistically significant associations were found. Therefore, we concluded that IgG-AAA can not replace IgA-TgA in children patients with celiac disease under gluten-free diets and in adult patients with dermatitis herpetiformis. AAA-IgG serum activity in both diseases exist, but without a relationship of association with them.     

PRIMAL: Fast and Accurate Pedigree-based Imputation from Sequence Data in a Founder Population

Founder populations and large pedigrees offer many well-known advantages for genetic mapping studies, including cost-efficient study designs. Here, we describe PRIMAL (PedigRee IMputation ALgorithm), a fast and accurate pedigree-based phasing and imputation algorithm for founder populations. PRIMAL incorporates both existing and original ideas, such as a novel indexing strategy of Identity-By-Descent (IBD) segments based on clique graphs. We were able to impute the genomes of 1,317 South Dakota Hutterites, who had genome-wide genotypes for ~300,000 common single nucleotide variants (SNVs), from 98 whole genome sequences. Using a combination of pedigree-based and LD-based imputation, we were able to assign 87% of genotypes with >99% accuracy over the full range of allele frequencies. Using the IBD cliques we were also able to infer the parental origin of 83% of alleles, and genotypes of deceased recent ancestors for whom no genotype information was available. This imputed data set will enable us to better study the relative contribution of rare and common variants on human phenotypes, as well as parental origin effect of disease risk alleles in >1,000 individuals at minimal cost.     

Is interleukin-17 a proatherogenic biomarker?

The importance of chronic inflammation in atherogenesis and cytokine involvement in all stages of atherosclerotic plaque development is now obvious. Our approach of the significant cytokines involved in atherogenesis or cardiovascular diseases is based on a correlation between clinical research and experiments on animal models. The contribution of IL-17 in atherogenesis remains controversial. In this study we investigated the role of IL-17 in cardiovascular diseases and in atherosclerosis associated with pathological aging. We performed a case-control study, enrolling subjects aged over 65 years in both groups. We included 40 patients with cardiovascular disorders and 10 healthy volunteers. IL-17 levels were measured in the serum of patients and healthy controls, along with serum total cholesterol and triglycerides. Significantly higher levels of IL-17 were obtained in patients compared to healthy controls (p<0.001). The level of this biomarker correlated significantly with two biochemical parameters - serum total cholesterol and triglycerides (the Pearson coefficient showed statistical significance, p=0.033, respectively p=0.043). We did not find any correlation between IL-17 and these two parameters in the control group. Our study is useful in understanding the physiopathological implications of IL-17 in the atherogenesis process. This could represent a starting point for future studies, including research regarding the therapeutic potential of IL-17 in pathological aging.