Analysis of the cleavage site specificity of the endopeptidase involved in the maturation of the large subunit of hydrogenase 3 from Escherichia coli

The maturation of [NiFe]-hydrogenases is a catalysed process in which the activities of at least seven proteins are involved. The last step consists of the endoproteolytic cleavage of the precursor of the large subunit after the [NiFe]-metal centre has been assembled. The amino acid sequence requirements for the endopeptidase HycI involved in the C-terminal processing of HycE, the large subunit of the hydrogenase 3 from Escherichia coli, were investigated. Mutational alteration of the amino acid residues neighbouring the cleavage site showed that proteolysis still occurred when chemically similar amino acids were exchanged. Processing was blocked, however, in a variant in which the methionine at the C-terminal side was replaced by a glutamate residue. Truncation of the precursor from the C-terminal end rendered variants amenable to maturation even when two-thirds of the extension were removed but abolished proteolysis upon further deletion of a cluster of six basic amino acids. A construct in which the C-terminal extension from the large subunit of the hydrogenase 2 was fused to the mature part of the large subunit of hydrogenase 3 was neither processed by HycI nor by HybD, the endopeptidase specific for the large subunit of hydrogenase 2. The maturation endopeptidase, therefore, exhibits a relaxed sequence constraint in recognition of its cleavage site and does not require the entire C-terminal extension. The results point to an interaction of the C-terminus with some domain of the large subunit, rendering a conformation amenable to recognition by the endopeptidase.     

Multiple common susceptibility variants near BMP pathway loci GREM1, BMP4, and BMP2 explain part of the missing heritability of colorectal cancer

Genome-wide association studies (GWAS) have identified 14 tagging single nucleotide polymorphisms (tagSNPs) that are associated with the risk of colorectal cancer (CRC), and several of these tagSNPs are near bone morphogenetic protein (BMP) pathway loci. The penalty of multiple testing implicit in GWAS increases the attraction of complementary approaches for disease gene discovery, including candidate gene- or pathway-based analyses. The strongest candidate loci for additional predisposition SNPs are arguably those already known both to have functional relevance and to be involved in disease risk. To investigate this proposition, we searched for novel CRC susceptibility variants close to the BMP pathway genes GREM1 (15q13.3), BMP4 (14q22.2), and BMP2 (20p12.3) using sample sets totalling 24,910 CRC cases and 26,275 controls. We identified new, independent CRC predisposition SNPs close to BMP4 (rs1957636, P = 3.93×10(-10)) and BMP2 (rs4813802, P = 4.65×10(-11)). Near GREM1, we found using fine-mapping that the previously-identified association between tagSNP rs4779584 and CRC actually resulted from two independent signals represented by rs16969681 (P = 5.33×10(-8)) and rs11632715 (P = 2.30×10(-10)). As low-penetrance predisposition variants become harder to identify-owing to small effect sizes and/or low risk allele frequencies-approaches based on informed candidate gene selection may become increasingly attractive. Our data emphasise that genetic fine-mapping studies can deconvolute associations that have arisen owing to independent correlation of a tagSNP with more than one functional SNP, thus explaining some of the apparently missing heritability of common diseases.     

Prolonged activation of tumor necrosis factor (TNF)-alpha and its soluble receptors in chronic heart failure patients both in the compensated and decompensated state. Interplay between their levels and metalloproteinase-3

INTRODUCTION: Recent clinical and experimental studies indicate that upregulation of the TNF system can contribute to the progression of cardiac remodeling and heart failure decompensation, by promoting alterations in cardiomyocyte biology and extracellular matrix metabolism. Extracellular matrix turnover is regulated by the matrix metalloproteinases (MMPs), which are endogenous enzymes responsible for extracellular collagen degradation. The present study investigates the fluctuation of serum levels of TNF-alpha, soluble TNF receptor-1 (sTNFR1) and -2 (sTNFR2), in patients with chronic heart failure both during acute decompensation and the stable state of the syndrome. The second goal of this study was to determine if a relationship exists between serum MMPs profiles (MMP-1, MMP-2, MMP-3) and circulating TNF-alpha or its soluble receptors. METHODS: Our patient group consisted of 52 patients with chronic heart failure (NYHA III-IV; mean age: 65 +/- 4 years; hypertensive cardiomyopathy: 20, ischemic cardiomyopathy: 17, dilated cardiomyopathy: 10, valvular disease: 5), who were hospitalized for acute decompensation of the syndrome. Our control group consisted of 30 healthy subjects (mean age: 57 +/- 6 years). Serum levels of TNF-alpha, sTNFR1, sTNFR2 and MMP-1,-2,-3 were measured in heart failure patients by ELISA at admission and after one month as follow-up. Values are expressed as medians and interquartile ranges. RESULTS: In our patient group, we observed a statistically significant increase in the levels of sTNFR1 and sTNFR2 at admission (sTNFR1: 5.15 ng\mL, 4.49-8.90 ng\mL, P < 0.001, sTNFR2: 13.40 ng\mL, 6.10-21.50 ng\mL, P < 0.001), and at one-month follow-up (sTNFR1: 5.30 ng\mL, 4.61-6.90 ng\mL, P < 0.001, sTNFR2: 21.80 ng\mL, 11.50-25.20 ng\mL, P < 0.001), compared to the control group (sTNFR1: 3.83 ng\mL, 3.70-3.95 ng\mL, sTNFR2: 4.00 ng\mL, 3.40-5.40 ng\mL). There was a statistically significant difference in the levels of sTNFR2 between admission and follow-up (P < 0.05). Significant correlations between serum MMP-3 and sTNFR2 levels both at admission and follow up (r -/+ 0.460, P -/+ 0.005 and r -/+ 0.338, P -/+ 0.044, respectively) were also found. CONCLUSIONS: Soluble TNF receptors are elevated in heart failure patients both in acute decompensation and stable phase. We have detected higher levels of soluble TNFR2 during the compensated phase of heart failure, suggesting that TNFR2 receptors appear to stabilize the cytokine and thereby prolong its half-life and biological functions. Finally, TNF system-mediated cardiac remodeling may exist through the activation of MMP-3 signaling pathways.     

Estimating pneumonia deaths of post-neonatal children in countries of low or no death certification in 2008

Background

Pneumonia is the leading cause of child deaths globally. The aims of this study were to: a) estimate the number and global distribution of pneumonia deaths for children 1–59 months for 2008 for countries with low (<85%) or no coverage of death certification using single-cause regression models and b) compare these country estimates with recently published ones based on multi-cause regression models.

Methods and Findings

For 35 low child-mortality countries with <85% coverage of death certification, a regression model based on vital registration data of low child-mortality and >85% coverage of death certification countries was used. For 87 high child-mortality countries pneumonia death estimates were obtained by applying a regression model developed from published and unpublished verbal autopsy data from high child-mortality settings. The total number of 1–59 months pneumonia deaths for the year 2008 for these 122 countries was estimated to be 1.18 M (95% CI 0.77 M–1.80 M), which represented 23.27% (95% CI 17.15%–32.75%) of all 1–59 month child deaths. The country level estimation correlation coefficient between these two methods was 0.40.

Interpretation

Although the overall number of post-neonatal pneumonia deaths was similar irrespective to the method of estimation used, the country estimate correlation coefficient was low, and therefore country-specific estimates should be interpreted with caution. Pneumonia remains the leading cause of child deaths and is greatest in regions of poverty and high child-mortality. Despite the concerns about gender inequity linked with childhood mortality we could not estimate sex-specific pneumonia mortality rates due to the inadequate data. Life-saving interventions effective in preventing and treating pneumonia mortality exist but few children in high pneumonia disease burden regions are able to access them. To achieve the United Nations Millennium Development Goal 4 target to reduce child deaths by two-thirds in year 2015 will require the scale-up of access to these effective pneumonia interventions.     

Long term sequelae from childhood pneumonia; systematic review and meta-analysis

Background

The risks of long term sequelae from childhood pneumonia have not been systematically assessed. The aims of this study were to: (i) estimate the risks of respiratory sequelae after pneumonia in children under five years; (ii) estimate the distribution of the different types of respiratory sequelae; and (iii) compare sequelae risk by hospitalisation status and pathogen.

Methods

We systematically reviewed published papers from 1970 to 2011. Standard global burden of disease categories (restrictive lung disease, obstructive lung disease, bronchiectasis) were labelled as major sequelae. ‘Minor’ sequelae (chronic bronchitis, asthma, other abnormal pulmonary function, other respiratory disease), and multiple impairments were also included. Thirteen papers were selected for inclusion. Synthesis was by random effects meta-analysis and meta-regression.

Results

Risk of at least one major sequelae was 5.5% (95% confidence interval [95% CI] 2.8–8.3%) in non hospitalised children and 13.6% [6.2–21.1%]) in hospitalised children. Adenovirus pneumonia was associated with the highest sequelae risk (54.8% [39.2–70.5%]) but children hospitalised with no pathogen isolated also had high risk (17.6% [10.9–24.3%]). The most common type of major sequela was restrictive lung disease (5.4% [2.5–10.2%]) . Potential confounders such as loss to follow up and median age at infection were not associated with sequelae risk in the final models.

Conclusions

All children with pneumonia diagnosed by a health professional should be considered at risk of long term sequelae. Evaluation of childhood pneumonia interventions should include potential impact on long term respiratory sequelae.     

Instrumental variable estimation of the causal effect of plasma 25-hydroxy-vitamin D on colorectal cancer risk: a mendelian randomization analysis

Vitamin D deficiency has been associated with several common diseases, including cancer and is being investigated as a possible risk factor for these conditions. We reported the striking prevalence of vitamin D deficiency in Scotland. Previous epidemiological studies have reported an association between low dietary vitamin D and colorectal cancer (CRC). Using a case-control study design, we tested the association between plasma 25-hydroxy-vitamin D (25-OHD) and CRC (2,001 cases, 2,237 controls). To determine whether plasma 25-OHD levels are causally linked to CRC risk, we applied the control function instrumental variable (IV) method of the mendelian randomization (MR) approach using four single nucleotide polymorphisms (rs2282679, rs12785878, rs10741657, rs6013897) previously shown to be associated with plasma 25-OHD. Low plasma 25-OHD levels were associated with CRC risk in the crude model (odds ratio (OR): 0.76, 95% Confidence Interval (CI): 0.71, 0.81, p: 1.4×10(-14)) and after adjusting for age, sex and other confounding factors. Using an allele score that combined all four SNPs as the IV, the estimated causal effect was OR 1.16 (95% CI 0.60, 2.23), whilst it was 0.94 (95% CI 0.46, 1.91) and 0.93 (0.53, 1.63) when using an upstream (rs12785878, rs10741657) and a downstream allele score (rs2282679, rs6013897), respectively. 25-OHD levels were inversely associated with CRC risk, in agreement with recent meta-analyses. The fact that this finding was not replicated when the MR approach was employed might be due to weak instruments, giving low power to demonstrate an effect (<0.35). The prevalence and degree of vitamin D deficiency amongst individuals living in northerly latitudes is of considerable importance because of its relationship to disease. To elucidate the effect of vitamin D on CRC cancer risk, additional large studies of vitamin D and CRC risk are required and/or the application of alternative methods that are less sensitive to weak instrument restrictions.     

Metal insertion into NiFe-hydrogenases

The synthesis and the insertion of the metallocentre of NiFe-hydrogenases is a complex process, in which seven maturation enzymes plus ATP, GTP and carbamoyl phosphate are involved. The review summarizes what is known about the properties and activities of these auxiliary proteins, and postulates a pathway along which maturation may take place.     

Attenuation of intestinal ischemia/reperfusion induced liver and lung injury by intraperitoneal administration of (-)-epigallocatechin-3-gallate

The aim of this study was to evaluate the effect of ( - )-epigallocatechin-3-gallate (EGCG), a natural antioxidant, on liver and lungs after warm intestinal ischemia/reperfusion (I/R). Thirty male Wistar rats were equally divided into a sham-operation group, an intestinal I/R group and an intestinal I/R group pretreated with EGCG intraperitoneally. Intestinal ischemia was induced by occlusion of the superior mesenteric artery for 60 min followed by reperfusion for 120 min. Immediately after reperfusion, liver, lung and blood samples were collected and analyzed. Results showed that intestinal I/R increased the levels of aspartate (AST) and alanine (ALT) transaminase in serum to 987 and 752 IU/l, respectively. Malondialdehyde (MDA) increased in liver to 1.524 nmol/g in the group subjected to intestinal I/R compared to 0.995 nmol/g in the sham operation group. MDA was also increased in lungs to 1.581 nmol/g compared to 0.896 nmol/g in the sham operation group. Myeloperoxidase (MPO) increased in liver, after intestinal I/R, to 5.16 U/g compared to 1.59 U/g in the sham operation group. MPO was also increased in lungs to 3.89 U/g compared to 1.65 U/g in the sham operation group. Pretreatment with EGCG decreased serum levels of AST and ALT to 236 and 178 IU/l, respectively. It also decreased mean MDA levels in liver and lungs to 1.061 and 1.008 nmol/g, respectively, and mean MPO levels in liver and lungs to 1.88 and 1.71 U/g, respectively. Light microscopy and transmission electron microscopy examinations showed significant alteration in liver and lungs and protection of liver and lung parenchyma in the animals treated with EGCG.     

Comparative Performance of Four Methods for High-throughput Glycosylation Analysis of Immunoglobulin G in Genetic and Epidemiological Research

The biological and clinical relevance of glycosylation is becoming increasingly recognized, leading to a growing interest in large-scale clinical and population-based studies. In the past few years, several methods for high-throughput analysis of glycans have been developed, but thorough validation and standardization of these methods is required before significant resources are invested in large-scale studies. In this study, we compared liquid chromatography, capillary gel electrophoresis, and two MS methods for quantitative profiling of N-glycosylation of IgG in the same data set of 1201 individuals. To evaluate the accuracy of the four methods we then performed analysis of association with genetic polymorphisms and age. Chromatographic methods with either fluorescent or MS-detection yielded slightly stronger associations than MS-only and multiplexed capillary gel electrophoresis, but at the expense of lower levels of throughput. Advantages and disadvantages of each method were identified, which should inform the selection of the most appropriate method in future studies.Glycans are important structural and functional components of the majority of proteins, but because of their structural complexity and the absence of a direct genetic template our current understanding of the role of glycans in biological processes lags significantly behind the knowledge about proteins or DNA (1, 2). However, a recent comprehensive report endorsed by the US National Academies concluded that “glycans are directly involved in the pathophysiology of every major disease and that additional knowledge from glycoscience will be needed to realize the goals of personalized medicine” (3).It is estimated that the glycome (defined as the complete set of all glycans) of a eukaryotic cell is composed of more than a million different glycosylated structures (1), which contain up to 10,000 structural glycan epitopes for interaction with antibodies, lectins, receptors, toxins, microbial adhesins, or enzymes (4). Our recent population-based studies indicated that the composition of the human plasma N-glycome varies significantly between individuals (5, 6). Because glycans have important structural and regulatory functions on numerous glycoproteins (7), the observed variability suggests that differences in glycosylation might contribute to a large part of the human phenotypic variability. Interestingly, when the N-glycome of isolated immunoglobulin G (IgG)¹ was analyzed, it was found to be even more variable than the total plasma N-glycome (8), indicating that the combined analysis of all plasma glycans released from many different glycoproteins blurs signals of protein-specific regulation of glycosylation.A number of studies have investigated the role of glycans in human disease, including autoimmune diseases and cancer (9, 10). However, most human glycan studies have been conducted with very small sample sizes. Given the complex causal pathways involved in pathophysiology of common complex disease, and thus the likely modest effect sizes associated with individual factors, the majority of these studies are very likely to be substantially underpowered. In the case of inflammatory bowel disease, only 20% of reported inflammatory bowel disease glycan associations were replicated in subsequent studies, suggesting that most are false positive findings and that there is publication bias favoring the publication of positive findings (11). This situation is similar to that which occurred in the field of genetic epidemiology in the past when many underpowered candidate gene studies were published and were later found to consist of mainly false positive findings (12, 13). It is essential, therefore, that robust and affordable methods for high-throughput analysis are developed so that adequately powered studies can be conducted and the publication of large numbers of small studies reporting false positive results (which could threaten the credibility of glycoscience) be avoided.Rapid advances of technologies for high-throughput genome analysis in the past decade enabled large-scale genome-wide association studies (GWAS). GWAS has become a reliable tool for identification of associations between genetic polymorphisms and various human diseases and traits (14). Thousands of GWAS have been conducted in recent years, but these have not included the study of glycan traits until recently. The main reason was the absence of reliable tools for high-throughput quantitative analysis of glycans that could match the measurements of genomic, biochemical, and other traits in their cost, precision, and reproducibility. However, several promising high-throughput technologies for analysis of N-glycans were developed (8, 15–20) recently. Successful implementation of high-throughput analytical techniques for glycan analysis resulted in publication of four initial GWAS of the human glycome (21–24).In this study, we compared ultra-performance liquid chromatography with fluorescence detection (UPLC-FLR), multiplex capillary gel electrophoresis with laser induced fluorescence detection (xCGE-LIF), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), and liquid chromatography electrospray mass spectrometry (LC-ESI-MS) as tools for mid-to-high-throughput glycomics and glycoproteomics. We have analyzed IgG N-glycans by all four methods in 1201 individuals from European populations. The analysis of associations between glycans and ∼300,000 single-nucleotide genetic polymorphisms was performed and correlation between glycans and age was studied in all four data sets to identify the analytical method that shows the strongest potential to uncover biological mechanisms underlying protein glycosylation.