SIGNing a symbiotic treaty with gut microbiota

Beneficial microbes hold great promise for the treatment of a wide range of immune and inflammatory disorders. In this issue of The EMBO Journal, Lightfoot and colleagues report how the food‐grade bacterium Lactobacillus acidophilus helps the immune system to limit experimental colitis in mice through interaction between SIGNR3 and surface layer protein A (SlpA) in L. acidophilus. These results pave the way for future development of novel therapies for inflammatory diseases, including inflammatory bowel disease.     

Negative refraction angular characterization in one-dimensional photonic crystals

Background

Photonic crystals are artificial structures that have periodic dielectric components with different refractive indices. Under certain conditions, they abnormally refract the light, a phenomenon called negative refraction. Here we experimentally characterize negative refraction in a one dimensional photonic crystal structure; near the low frequency edge of the fourth photonic bandgap. We compare the experimental results with current theory and a theory based on the group velocity developed here. We also analytically derived the negative refraction correctness condition that gives the angular region where negative refraction occurs.

Methodology/Principal Findings

By using standard photonic techniques we experimentally determined the relationship between incidence and negative refraction angles and found the negative refraction range by applying the correctness condition. In order to compare both theories with experimental results an output refraction correction was utilized. The correction uses Snell''s law and an effective refractive index based on two effective dielectric constants. We found good agreement between experiment and both theories in the negative refraction zone.

Conclusions/Significance

Since both theories and the experimental observations agreed well in the negative refraction region, we can use both negative refraction theories plus the output correction to predict negative refraction angles. This can be very useful from a practical point of view for space filtering applications such as a photonic demultiplexer or for sensing applications.     

Harmonic Analysis of the Fluorescence Response of Bimane Adducts of Colicin E1 at Helices 6, 7, and 10

The pre-channel state of helices 6, 7, and 10 (Val⁴⁴⁷–Gly⁴⁷⁵ and Ile⁵⁰⁸–Ile⁵²²) of colicin E1 was investigated by a site-directed fluorescence labeling technique. A total of 44 cysteine variants were purified and covalently labeled with monobromobimane fluorescent probe. A variety of fluorescence properties of the bimane fluorophore were measured for both the soluble and membrane-bound states of the channel peptide, including the fluorescence emission maximum, fluorescence anisotropy, and membrane bilayer penetration depth. Using site-directed fluorescence labeling combined with our novel helical periodicity analysis method, the data revealed that helices 6, 7, and 10 are separate amphipathic α-helices with a calculated periodicity of T = 3.34 ± 0.08 for helix 6, T = 3.56 ± 0.03 for helix 7, and T = 2.99 ± 0.12 for helix 10 in the soluble state. In the membrane-bound state, the helical periodicity was determined to be T = 3.00 ± 0.15 for helix 6, T = 3.68 ± 0.03 for helix 7, and T = 3.47 ± 0.04 for helix 10. Dual fluorescence quencher analysis showed that both helices 6 and 7 adopt a tilted topology that correlates well with the analysis based on the fluorescence anisotropy profile. These data provide further support for the umbrella model of the colicin E1 channel domain.     

Gender differences in ancestral contribution and admixture in Venezuelan populations

The origin of the contribution of uniparental heritage were analyzed in 615 samples of individuals proceeding from 13 towns classified according to historic differences in their emergence and development as African-derived, European-derived, and admixed/urban. Mitochondrial and Y-chromosome haplogroups were identified by PCR-restriction fragment length polymorphism. The results were compared with previous estimates of admixture made with autosomal markers and with historic aspects. The results show a predominantly indigenous genetic contribution through the female, being more prevalent in urban populations; the African contribution, although dispersed, presents a larger concentration in the African-derived towns, whereas the European contribution is limited to populations with this origin, reflecting isolation and the conservation of the distribution pattern of genes of the Colonial era. With regard to admixture through males, it is almost exclusively of European origin, whereas the African contribution is basically concentrated in the African-derived towns, and the Amerindian lineages are almost nonexistent. The genome of paternal heredity, as opposed to the autosomal and the mitochondrial, shows a homogeneous pattern of admixture that is independent of the origin of the population studied, suggesting that European genes have been introduced into the Venezuelan population through male immigrations, whereas the indigenous contribution has been preserved in the Venezuelan genetic pool through the women. These results provide evidence of the heterogeneity in the genetic origin of the Venezuelan population, which should be taken into account in forensic and epidemiologic genetic studies.     

Structural response of Caribbean dry forests to hurricane winds: a case study from Guánica Forest, Puerto Rico

Aim Tropical dry forests in the Caribbean have an uniquely short, shrubby structure with a high proportion of multiple‐stemmed trees compared to dry forests elsewhere in the Neotropics. Previous studies have shown that this structure can arise without the loss of main stems from cutting, grazing, or other human intervention. The Caribbean has a high frequency of hurricanes, so wind may also influence forest stature. Furthermore, these forests also tend to grow on soils with low amounts of available phosphorus, which may also influence structure. The objective of this study was to assess the role of high winds in structuring dry forest, and to determine whether soil nutrient pools influence forest response following hurricane disturbance. Location Guánica Forest, Puerto Rico. Methods Over 2000 stems in five plots were sampled for hurricane effects within 1 week after Hurricane Georges impacted field sites in 1998. Sprout initiation, growth, and mortality were analysed for 1407 stems for 2 years after the hurricane. Soil nutrient pools were measured at the base of 456 stems to assess association between nutrients and sprout dynamics. Results Direct effects of the hurricane were minimal, with stem mortality at < 2% and structural damage to stems at 13%, although damage was biased toward stems of larger diameter. Sprouting response was high – over 10 times as many trees had sprouts after the hurricane as before. The number of sprouts on a stem also increased significantly. Sprouting was common on stems that only suffered defoliation or had no visible effects from the hurricane. Sprout survival after 2 years was also high (> 86%). Soil nutrient pools had little effect on forest response as a whole, but phosphorus supply did influence sprout dynamics on four of the more common tree species. Main conclusions Hurricanes are able to influence Caribbean tropical dry forest structure by reducing average stem diameter and basal area and generating significant sprouting responses. New sprouts, with ongoing survival, will maintain the high frequency of multi‐stemmed trees found in this region. Sprouting is not limited to damaged stems, indicating that trees are responding to other aspects of high winds, such as short‐term gravitational displacement or sway. Soil nutrients play a secondary role in sprouting dynamics of a subset of species. The short, shrubby forest structure common to the Caribbean can arise naturally as a response to hurricane winds.     

Bryophyte Species Diversity in Secondary Forests Dominated by the Introduced Species Spathodea campanulata Beauv. in Puerto Rico

The introduced tree species Spathodea campanulata (Bignoniaceae) forms novel forests in Puerto Rico, these having emerged after the abandonment of fields in the mid‐20th century and resulting in forests with a new species composition. We assessed bryophyte species richness in these novel forests and sought correlations with geological substrate, past land use, forest edge and patch area, forest structure, elevation, microhabitat diversity, tree species richness, and microclimatic conditions. Transects were established (edge and forest interior) in nine moist forest patches dominated by Spathodea in north‐central Puerto Rico. These Spathodea forest patches ranged from 0.6 to 9 ha. ANOVA, Chi‐square, correlation, and cluster analyses were used in data analyses. We found 57 bryophyte species. There was a significant difference in bryophyte richness among patches. Those on karst exhibited highest bryophyte richness due to microhabitat diversity, past land use, and shorter hydroperiods. Alluvial sites scored lowest in bryophyte species richness, and forest structure was important for bryophyte communities on these sites. Significant differences in temperature, relative humidity, and light intensity were observed between edge and forest interior. These appeared important for establishing bryophyte species cover but not richness and composition. Microhabitat diversity, patch area, and forest age were more related to bryophyte species richness than elevation, exposed edge, and tree species richness, regardless of geologic substrate. Collectively, Spathodea patches were similar to mature forests on the Island with respect to bryophyte species richness and composition. Novel Spathodea forests have conservation value due to their habitat suitability for bryophyte communities.     

Altered phosphorylation and localization of the A-type channel, Kv4.2 in status epilepticus

Extracelluar signal-regulated kinase (ERK) pathway activation has been demonstrated following convulsant stimulation; however, little is known about the molecular targets of ERK in seizure models. Recently, it has been shown that ERK phosphorylates Kv4.2 channels leading to down-regulation of channel function, and substantially alters dendritic excitability. In the kainate model of status epilepticus (SE), we investigated whether ERK phosphorylates Kv4.2 and whether the changes in Kv4.2 were evident at a synaptosomal level during SE. Western blotting was performed on rat hippocampal whole cell, membrane, synaptosomal, and surface biotinylated extracts following systemic kainate using an antibody generated against the Kv4.2 ERK sites and for Kv4.2, ERK, and phospho-ERK. ERK activation was associated with an increase in Kv4.2 phosphorylation during behavioral SE. During SE, ERK activation and Kv4.2 phosphorylation were evident at the whole cell and synaptosomal levels. In addition, while whole-cell preparations revealed no alterations in total Kv4.2 levels, a decrease in synaptosomal and surface expression of Kv4.2 was evident after prolonged SE. These results demonstrate ERK pathway coupling to Kv4.2 phosphorylation. The finding of decreased Kv4.2 levels in hippocampal synaptosomes and surface membranes suggest additional mechanisms for decreasing the dendritic A-current, which could lead to altered intrinsic membrane excitability during SE.     

Identification of GntR as regulator of the glucose metabolism in Pseudomonas aeruginosa

In contrast to Escherichia coli, glucose metabolism in pseudomonads occurs exclusively through the Entner‐Doudoroff (ED) pathway. This pathway, as well as the three routes to generate the initial ED pathway substrate, 6‐phosphogluconate, is regulated by the PtxS, HexR and GtrS/GltR systems. With GntR (PA2320) we report here the identification of an additional regulator in Pseudomonas aeruginosa PAO1. GntR repressed its own expression as well as that of the GntP gluconate permease. In contrast to PtxS and GtrS/GltR, GntR did not modulate expression of the toxA gene encoding the exotoxin A virulence factor. GntR was found to bind to promoters P_gntR and P_gntP and the consensus sequence of its operator was defined as 5′‐AC‐N‐AAG‐N‐TAGCGCT‐3′. Both operator sites overlapped with the RNA polymerase binding site and we show that GntR employs an effector mediated de‐repression mechanism. The release of promoter bound GntR is induced by gluconate and 6‐phosphogluconate that bind with similar apparent affinities to the GntR/DNA complex. GntR and PtxS are paralogous and may have evolved from a common ancestor. The concerted action of four regulatory systems in the regulation of glucose metabolism in Pseudomonas can be considered as a model to understand complex regulatory circuits in bacteria.