Celiac disease microbiota and its applications

Intestinal microbiota plays an important role in maintaining the overall health of an individual. It can be affected by diet but also inflammation of the intestine due to various causes. In the last decade, particular attention has been paid to the study of the interaction between mucosal cells and intestinal microbiota, and to the host immune response to change in community structure. Here, we review the most significant studies on human microbiota in patients with celiac disease, and also the potential biotechnological use of microorganisms for the production of gluten-free products.     

Prioritizing causal disease genes using unbiased genomic features

Background

Cardiovascular disease (CVD) is the leading cause of death in the developed world. Human genetic studies, including genome-wide sequencing and SNP-array approaches, promise to reveal disease genes and mechanisms representing new therapeutic targets. In practice, however, identification of the actual genes contributing to disease pathogenesis has lagged behind identification of associated loci, thus limiting the clinical benefits.

Results

To aid in localizing causal genes, we develop a machine learning approach, Objective Prioritization for Enhanced Novelty (OPEN), which quantitatively prioritizes gene-disease associations based on a diverse group of genomic features. This approach uses only unbiased predictive features and thus is not hampered by a preference towards previously well-characterized genes. We demonstrate success in identifying genetic determinants for CVD-related traits, including cholesterol levels, blood pressure, and conduction system and cardiomyopathy phenotypes. Using OPEN, we prioritize genes, including FLNC, for association with increased left ventricular diameter, which is a defining feature of a prevalent cardiovascular disorder, dilated cardiomyopathy or DCM. Using a zebrafish model, we experimentally validate FLNC and identify a novel FLNC splice-site mutation in a patient with severe DCM.

Conclusion

Our approach stands to assist interpretation of large-scale genetic studies without compromising their fundamentally unbiased nature.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0534-8) contains supplementary material, which is available to authorized users.     

Productivity, 15N dynamics and water use efficiency in low‐ and high‐input switchgrass systems

Sustainable and environmentally benign switchgrass production systems need to be developed for switchgrass to become a large‐scale dedicated energy crop. An experiment was conducted in California from 2009 to 2011 to determine the sustainability of low‐ and high‐input irrigated switchgrass systems as a function of yield, irrigation requirement, crop N removal, N translocation from aboveground (AG) to belowground (BG) biomass during senescence, and fertilizer ¹⁵N recovery (FNR) in the AG and BG biomass (0–300 cm), and soil (0–300 cm). The low‐input system consisted of a single‐harvest (mid‐fall) irrigated until flowering (early summer), while the high‐input system consisted of a two‐harvest system (early summer and mid‐fall) irrigated throughout the growing season. Three N fertilization rates (0, 100, and 200 kg N ha^?1 yr^?1) were applied as subtreatments in a single application in the spring of each year. A single pulse of ¹⁵N enriched fertilizer was applied in the first year of the study to micro‐plots within the 100 kg N ha^?1 subplots. Average yields across years under optimal N rates (100 and 200 kg ha^?1 yr^?1 for low‐ and high‐input systems, respectively) were 20.7 and 24.8 Mg ha^?1. However, the low input (372 ha mm) required 47% less irrigation than the high‐input system (705 ha mm) and achieved higher irrigation use efficiency. In addition, the low‐input system had 46% lower crop N removal, 53% higher N stored in BG biomass, and a positive N balance, presumably due to 49% of ¹⁵N translocation from AG to BG biomass during senescence. Furthermore, at the end of 3 years, the low‐input system had lower fertilizer ¹⁵N removed by harvest (26%) and higher FNR remaining in the system in BG biomass plus soil (31%) than the high‐input system (45% and 21%, respectively). Based on these findings, low‐input systems are more sustainable than high‐input systems in irrigated Mediterranean climates.     

Backbone resonance assignment of Alt a 1, a unique β-barrel protein and the major allergen of Alternaria alternata

Alt a 1 is the major allergen of the fungus Alternaria alternata and can be found in the cell wall of its spores. It is a cysteine linked homodimeric protein with a unique β-barrel fold as recently revealed by X-ray crystallography. Despite the elucidation of its structure, its biological function remains unknown. For Alternaria-sensitized patients, contact leads to respiratory allergy and in severe cases to asthma-related death. Here we report the sequence-specific Alt a 1 backbone ¹H, ¹⁵N and ¹³C chemical shift assignment.     

Increased Inflammatory Response in Cytomegalovirus Seropositive Patients with Alzheimer’s Disease

Alzheimer’s disease (AD) has been associated with increased local inflammation in the affected brain regions, and in some studies also with elevated levels of proinflammatory cytokines in peripheral blood. Cytomegalovirus (CMV) is known to promote a more effector-oriented phenotype in the T-cell compartment, increasing with age. The aim of this study was to investigate the inflammatory response of peripheral blood mononuclear cells (PBMCs) from AD patients and non-demented (ND) controls. Using a multiplex Luminex xMAP assay targeting GM-CSF, IFN-γ, IL-1β, IL-2, IL-4, IL-5, IL-6, IL-8, IP-10 and TNF-α, cytokine profiles from PBMCs were analysed after stimulation with anti-CD3/CD28 beads, CMV pp65 peptide mix or amyloid β (Aβ) protofibrils, respectively. CMV seropositive AD subjects presented with higher IFN-γ levels after anti-CD3/CD28 and CMV pp65 but not after Aβ stimulation, compared to CMV seropositive ND controls. When analysing IFN-γ response to anti-CD3/CD28 stimulation on a subgroup level, CMV seropositive AD subjects presented with higher levels compared to both CMV seronegative AD and CMV seropositive ND subjects. Taken together, our data from patients with clinically manifest AD suggest a possible role of CMV as an inflammatory promoter in AD immunology. Further studies of AD patients at earlier stages of disease, could provide better insight into the pathophysiology.     

Large-Scale Wind Disturbances Promote Tree Diversity in a Central Amazon Forest

Canopy gaps created by wind-throw events, or blowdowns, create a complex mosaic of forest patches varying in disturbance intensity and recovery in the Central Amazon. Using field and remote sensing data, we investigated the short-term (four-year) effects of large (>2000 m²) blowdown gaps created during a single storm event in January 2005 near Manaus, Brazil, to study (i) how forest structure and composition vary with disturbance gradients and (ii) whether tree diversity is promoted by niche differentiation related to wind-throw events at the landscape scale. In the forest area affected by the blowdown, tree mortality ranged from 0 to 70%, and was highest on plateaus and slopes. Less impacted areas in the region affected by the blowdown had overlapping characteristics with a nearby unaffected forest in tree density (583±46 trees ha⁻¹) (mean±99% Confidence Interval) and basal area (26.7±2.4 m² ha⁻¹). Highly impacted areas had tree density and basal area as low as 120 trees ha⁻¹ and 14.9 m² ha⁻¹, respectively. In general, these structural measures correlated negatively with an index of tree mortality intensity derived from satellite imagery. Four years after the blowdown event, differences in size-distribution, fraction of resprouters, floristic composition and species diversity still correlated with disturbance measures such as tree mortality and gap size. Our results suggest that the gradients of wind disturbance intensity encompassed in large blowdown gaps (>2000 m²) promote tree diversity. Specialists for particular disturbance intensities existed along the entire gradient. The existence of species or genera taking an intermediate position between undisturbed and gap specialists led to a peak of rarefied richness and diversity at intermediate disturbance levels. A diverse set of species differing widely in requirements and recruitment strategies forms the initial post-disturbance cohort, thus lending a high resilience towards wind disturbances at the community level.     

Interspecific Small Molecule Interactions between Clinical Isolates of Pseudomonas aeruginosa and Staphylococcus aureus from Adult Cystic Fibrosis Patients

Pseudomonas aeruginosa and Staphylococcus aureus are the most prevalent pathogens in airway infections of cystic fibrosis (CF) patients. We studied how these pathogens coexist and interact with each other. Clinical isolates of both species were retrieved from adult CF patients. Culture supernatants from 63 P. aeruginosa isolates triggered a wide range of biofilm-stimulatory activities when added to the culture of a control S. aureus strain. The extent of biofilm formation by S. aureus was positively correlated to the levels of the 2-alkyl-4-(1H)-quinolones (AQs) Pseudomonas Quinolone Signal (PQS) and 2-heptyl-4-hydroxy quinoline N-oxide (HQNO) produced by the P. aeruginosa isolates. Supernatants from P. aeruginosa isogenic mutants deficient in PQS and HQNO production stimulated significantly less biofilm formation by S. aureus than that seen with the parental strain PA14. When studying co-isolated pairs of P. aeruginosa and S. aureus retrieved from patients showing both pathogens, P. aeruginosa supernatants stimulated less biofilm production by the S. aureus counterparts compared to that observed using the control S. aureus strain. Accordingly, some P. aeruginosa isolates produced low levels of exoproducts and also some of the clinical S. aureus isolates were not stimulated by their co-isolates or by PA14 despite adequate production of HQNO. This suggests that colonization of the CF lungs promotes some type of strain selection, or that co-existence requires specific adaptations by either or both pathogens. Results provide insights on bacterial interactions in CF.     

Land Use and Land Cover Change Dynamics across the Brazilian Amazon: Insights from Extensive Time-Series Analysis of Remote Sensing Data

Throughout the Amazon region, the age of forests regenerating on previously deforested land is determined, in part, by the periods of active land use prior to abandonment and the frequency of reclearance of regrowth, both of which can be quantified by comparing time-series of Landsat sensor data. Using these time-series of near annual data from 1973–2011 for an area north of Manaus (in Amazonas state), from 1984–2010 for south of Santarém (Pará state) and 1984–2011 near Machadinho d’Oeste (Rondônia state), the changes in the area of primary forest, non-forest and secondary forest were documented from which the age of regenerating forests, periods of active land use and the frequency of forest reclearance were derived. At Manaus, and at the end of the time-series, over 50% of regenerating forests were older than 16 years, whilst at Santarém and Machadinho d’Oeste, 57% and 41% of forests respectively were aged 6–15 years, with the remainder being mostly younger forests. These differences were attributed to the time since deforestation commenced but also the greater frequencies of reclearance of forests at the latter two sites with short periods of use in the intervening periods. The majority of clearance for agriculture was also found outside of protected areas. The study suggested that a) the history of clearance and land use should be taken into account when protecting deforested land for the purpose of restoring both tree species diversity and biomass through natural regeneration and b) a greater proportion of the forested landscape should be placed under protection, including areas of regrowth.