Phosphomannomutase 2 (PMM2) variants leading to hyperinsulinism-polycystic kidney disease are associated with early-onset inflammatory bowel disease and gastric antral foveolar hyperplasia

Phosphomannomutase 2 (PMM2) deficiency causes Congenital Disorder of Glycosylation (PMM2-CDG), but does not have a recognised association with Inflammatory Bowel Disease (IBD). A distinct clinical syndrome of hyperinsulinism and autosomal recessive polycystic kidney disease (HIPKD) arises in the context of a specific variant in the PMM2 promotor, either in homozygosity, or compound heterozygous with a deleterious PMM2 variant. Here, we describe the development of IBD in three patients with PMM2-HIPKD, with onset of IBD at 0, 6, and 10 years of age. In each case, intestinal inflammation coincided with the unusual finding of gastric antral foveolar hyperplasia. IBD disease was of variable severity at onset but well controlled with conventional and first-line biologic treatment approaches. The organ-level pattern of disease manifestations in PMM2-HIPKD-IBD may reflect a loss of cis-acting regulatory control by hepatocyte nuclear factor 4 alpha (HNF4A). Analysis of published transcriptomic data suggests that IBD most likely arises due to an impact on epithelial cellular function. We identify a specific pattern of variation in PMM2 as a novel association of early-onset IBD with distinctive gastric pathology

nQuack: An R package for predicting ploidal level from sequence data using site-based heterozygosity

Premise: Traditional methods of ploidal-level estimation are tedious; using DNA sequence data for cytotype estimation is an ideal alternative. Multiple statistical approaches to leverage sequence data for ploidy inference based on site-based heterozygosity have been developed. However, these approaches may require high-coverage sequence data, use inappropriate probability distributions, or have additional statistical shortcomings that limit inference abilities. We introduce nQuack, an open-source R package that addresses the main shortcomings of current methods. Methods and Results: nQuack performs model selection for improved ploidy predictions. Here, we implement expectation maximization algorithms with normal, beta, and beta-binomial distributions. Using extensive computer simulations that account for variability in sequencing depth, as well as real data sets, we demonstrate the utility and limitations of nQuack. Conclusions: Inferring ploidy based on site-based heterozygosity alone is difficult. Even though nQuack is more accurate than similar methods, we suggest caution when relying on any site-based heterozygosity method to infer ploidy.</p

MicroRNA Expression Profiling in Mild Asthmatic Human Airways and Effect of Corticosteroid Therapy

BACKGROUND: Asthma is a common disease characterised by reversible airflow obstruction, bronchial hyperresponsiveness and chronic inflammation, which is commonly treated using corticosteroids such as budesonide. MicroRNAs (miRNAs) are a recently identified family of non-protein encoding genes that regulate protein translation by a mechanism entitled RNA interference. Previous studies have shown lung-specific miRNA expression profiles, although their importance in regulating gene expression is unresolved. We determined whether miRNA expression was differentially expressed in mild asthma and the effect of corticosteroid treatment. METHODOLOGY/PRINCIPAL FINDINGS: We have examined changes in miRNA using a highly sensitive RT-PCR based approach to measure the expression of 227 miRNAs in airway biopsies obtained from normal and mild asthmatic patients. We have also determined whether the anti-inflammatory action of corticosteroids are mediated through miRNAs by determining the profile of miRNA expression in mild asthmatics, before and following 1 month twice daily treatment with inhaled budesonide. Furthermore, we have analysed the expression of miRNAs from individual cell populations from the airway and lung. We found no significant difference in the expression of 227 miRNAs in the airway biopsies obtained from normal and mild asthmatic patients. In addition, despite improved lung function, we found no significant difference in the miRNA expression following one month treatment with the corticosteroid, budesonide. However, analysis of bronchial and alveolar epithelial cells, airway smooth muscle cells, alveolar macrophages and lung fibroblasts demonstrate a miRNA expression profile that is specific to individual cell types and demonstrates the complex cellular heterogeneity within whole tissue samples. CONCLUSIONS: Changes in miRNA expression do not appear to be involved in the development of a mild asthmatic phenotype or in the anti-inflammatory action of the corticosteroid budesonid

Deepening democracy within Ireland's social partnership

Ireland's social partnership process, now under attack from a number of quarters, has repeatedly been charged with being 'undemocratic' in that it undermines the sovereign position of elected political representatives, with key policy formulation and decision-making taking place in fora outside the institutions of representative democracy. These critiques echo those against new forms of networked governance more globally. A key question therefore is how (and if) democracy may be deepened within social partnership or its potential successor(s). This article addresses this question by employing a post-liberal democratic framework to examine social partnership in practice, and by drawing lessons from another partnership process, Malawi's PRSP. Drawing from Malawi's experience, it is argued that democracy can be deepened within social partnership when governance deliberations and negotiations are conducted under conditions of vibrant public debate and genuine perspective-based representation, and when the communicative and discursive norms are widened to allow for such representation

A contemporary comparison of the effect of shunt type in hypoplastic left heart syndrome on the hemodynamics and outcome at stage 2 reconstruction

ObjectiveWe compare the hemodynamics and perioperative course of shunt type in hypoplastic left heart syndrome at the time of stage 2 reconstruction and longer-term survival.MethodsWe retrospectively reviewed the echocardiograms, catheterizations, and hospital records of all patients who had a stage 1 reconstruction between January 2002 and May 2005 and performed a cross-sectional analysis of hospital survivors.ResultsOne hundred seventy-six patients with hypoplastic left heart syndrome and variants underwent a stage 1 reconstruction with either a right ventricle–pulmonary artery conduit (n = 62) or a modified Blalock–Taussig shunt (n = 114). The median duration of follow-up is 29.1 months (range, 0-57 months). By means of Kaplan–Meier analysis, there is no difference in survival at 3 years (right ventricle–pulmonary artery conduit: 73% [95% confidence limit, 59%–83%] vs modified Blalock–Taussig shunt: 69% [95% confidence limit, 59%–77%]; P = .6). One hundred twenty-four patients have undergone stage 2 reconstruction (78 modified Blalock–Taussig shunts and 46 right ventricle–pulmonary artery conduits). At the time of the stage 2 reconstruction, patients with right ventricle–pulmonary artery conduits were younger (153 days [range, 108–340 days]; modified Blalock–Taussig shunt, 176 days [range, 80–318 days]; P = .03), had lower systemic oxygen saturation (73% [range, 58%–85%] vs 77% [range, 57%–89%], P < .01), and had higher preoperative hemoglobin levels (15.8 g/dL [range, 13–21 g/dL] vs 14.8 g/dL [range, 12–19 g/dL], P < .01) compared with those of the modified Blalock–Taussig shunt group. By means of echocardiographic evaluation, there was a higher incidence of qualitative ventricular dysfunction in patients with right ventricle–pulmonary artery conduits (14/46 [31%] vs 9/73 [12%], P = .02). However, no difference was observed in common atrial pressure or the arteriovenous oxygen difference.ConclusionInterim analyses suggest no advantage of one shunt type over another. This report raises concern of late ventricular dysfunction and outcome in patients with a right ventricle–pulmonary artery conduit

The global development project contested: the local politics of the PRSP process in Malawi

Development, in an age of globalizations, has indeed become a global project. However, this project remains contested and contestable. While much attention has been given to this contestation at a macro-policy level, the dynamics of such contestations on the ground remain less studied. Noting that development projects, policies and programs are themselves products of power relations and social struggles, this paper focuses on the dynamics of these relations and struggles in relation to the dissemination of the global development project in Malawi. Drawing from the experiences and fractious journey from 2000 to 2006 of the broad-based civil society network involved in Malawi’s ongoing PRSP process, the paper shows how local actors draw creatively on globalized discourses of participation and representation to contest and confound the objectives of the elites, thereby complicating the channels through which the global development project is promulgated

Utilizing "Omic" technologies to identify and prioritize novel sources of resistance to the oomycete pathogen <i>Phytophthora infestans</i> in potato germplasm collections

The biggest threat to potato production world-wide is late blight, caused by the oomycete pathogen Phytophthora infestans. A screen of 126 wild diploid Solanum accessions from the Commonwealth Potato Collection (CPC) with P. infestans isolates belonging to the genotype 13-A2 identified resistances in the species S. bulbocastanum, S. capsicibaccatum, S. microdontum, S. mochiquense, S. okadae, S. pinnatisectum, S. polyadenium, S. tarijense and S. verrucosum. Effector-omics, allele mining and diagnostic RenSeq (dRenSeq) were utilized to investigate the nature of resistances in S. okadae accessions. dRenSeq in resistant S. okadae accessions 7129, 7625, 3762 and a bulk of 20 resistant progeny confirmed the presence of full-length Rpi-vnt1.1 under stringent mapping conditions and corroborated allele mining results in the accessions 7129 and 7625 as well as Avr-vnt1 recognition in transient expression assays. In contrast, susceptible S. okadae accession 3761 and a bulk of 20 susceptible progeny lacked sequence homology in the 5’ end compared to the functional Rpi-vnt1.1 gene. Further evaluation of S. okadae accessions with late blight isolates that have a broad spectrum of virulence demonstrated that, although S. okadae accessions 7129, 7625 and 7629 contain functional Rpi-vnt1.1, they also carry a novel resistance gene. We provide evidence that existing germplasm collection are important sources of novel resistances and that ‘omic’ technologies such as dRenSeq-based genomics and effector-omics are efficacious tools to rapidly explore the diversity within these collections

Mass Azithromycin and Malaria Parasitemia in Niger: Results from a Community-Randomized Trial.

Studies designed to determine the effects of mass administration of azithromycin on trachoma have suggested that mass azithromycin distributions may also reduce the prevalence of malaria. These studies have typically examined the impact of a small number of treatments over short durations. In this prespecified substudy of a cluster-randomized trial for trachoma, we compared malaria parasitemia prevalence in 24 communities in Niger randomized to receive either annual or biannual mass azithromycin distributions over 3 years. The 12 communities randomized to annual azithromycin received three treatments during the high-transmission season, and the 12 communities randomized to biannual azithromycin received a total of six treatments: three during the high-transmission season and three during the low-transmission season. Blood samples were taken to assess malariometric indices among children in all study communities at a single time point during the high-transmission season after 3 years of the intervention. No significant differences were identified in malaria parasitemia, parasite density, or hemoglobin concentration between the annual and biannual treatment arms. When compared with annual mass azithromycin alone, additional mass azithromycin distributions given during the low-transmission season did not significantly reduce the subsequent prevalence of malaria parasitemia or parasite density after 3 years, as measured during the high-transmission season