Lipopolysaccharide from Gut-Associated Lymphoid-Tissue-Resident Alcaligenes faecalis: Complete Structure Determination and Chemical Synthesis of Its Lipid A

Alcaligenes faecalis is the predominant Gram-negative bacterium inhabiting gut-associated lymphoid tissues, Peyer's patches. We previously reported that an A. faecalis lipopolysaccharide (LPS) acted as a weak agonist for Toll-like receptor 4 (TLR4)/myeloid differentiation factor-2 (MD-2) receptor as well as a potent inducer of IgA without excessive inflammation, thus suggesting that A. faecalis LPS might be used as a safe adjuvant. In this study, we characterized the structure of both the lipooligosaccharide (LOS) and LPS from A. faecalis. We synthesized three lipid A molecules with different degrees of acylation by an efficient route involving the simultaneous introduction of 1- and 4′-phosphates. Hexaacylated A. faecalis lipid A showed moderate agonistic activity towards TLR4-mediated signaling and the ability to elicit a discrete interleukin-6 release in human cell lines and mice. It was thus found to be the active principle of the LOS/LPS and a promising vaccine adjuvant candidate

A global perspective on marine photosynthetic picoeukaryote community structure

A central goal in ecology is to understand the factors affecting the temporal dynamics and spatial distribution of microorganisms and the underlying processes causing differences in community structure and composition. However, little is known in this respect for photosynthetic picoeukaryotes (PPEs), algae that are now recognised as major players in marine CO2 fixation. Here, we analysed dot blot hybridisation and cloning–sequencing data, using the plastid-encoded 16S rRNA gene, from seven research cruises that encompassed all four ocean biomes. We provide insights into global abundance, α- and β-diversity distribution and the environmental factors shaping PPE community structure and composition. At the class level, the most commonly encountered PPEs were Prymnesiophyceae and Chrysophyceae. These taxa displayed complementary distribution patterns, with peak abundances of Prymnesiophyceae and Chrysophyceae in waters of high (25:1) or low (12:1) nitrogen:phosphorus (N:P) ratio, respectively. Significant differences in phylogenetic composition of PPEs were demonstrated for higher taxonomic levels between ocean basins, using Unifrac analyses of clone library sequence data. Differences in composition were generally greater between basins (interbasins) than within a basin (intrabasin). These differences were primarily linked to taxonomic variation in the composition of Prymnesiophyceae and Prasinophyceae whereas Chrysophyceae were phylogenetically similar in all libraries. These data provide better knowledge of PPE community structure across the world ocean and are crucial in assessing their evolution and contribution to CO2 fixation, especially in the context of global climate change

Legacy of Amazonian Dark Earth soils on forest structure and species composition

This is the final version. Available from the publisher via the DOI in this record.Aim: Amazonian forests predominantly grow on highly weathered and nutrient poor soils. Anthropogenically enriched Amazonian Dark Earths (ADE), traditionally known as Terra Preta de Índio, were formed by pre-Columbian populations. ADE soils are characterized by increased fertility and have continued to be exploited following European colonization. Here, we evaluated the legacy of land-use and soil enrichment on the composition and structure in ADE and non-ADE (NDE) forests. Location: Eastern and southern Amazonia. Time period: Pre-Columbia – 2014. Methods: We sampled nine pairs of ADE and adjacent NDE forest plots in eastern and southern Amazonia. In each plot, we collected soil samples at 0–10 and 10–20 cm depth and measured stem diameter, height, and identified all individual woody plants (palms, trees and lianas) with diameter ≥ 10 cm. We compared soil physicochemical properties, vegetation diversity, floristic composition, aboveground biomass, and percentage of useful species. Results: In the nine paired plots, soil fertility was significantly higher in ADE soil. We sampled 4,191 individual woody plants representing 404 species and 65 families. The floristic composition of ADE and NDE forests differed significantly at both local and regional levels. In southern Amazonia, ADE forests had, on average, higher aboveground biomass than other forests of the region, while in eastern Amazonia, biomass was similar to that of NDE forests. Species richness of both forest types did not differ and was within the range of existing regional studies. The differences in composition between large and small diameter tree recruits may indicate long-term recovery and residual effects from historical land-use. Additionally, the proportion of edible species tended to be higher in the ADE forests of eastern and southern Amazonia. Main conclusions: The marked differences in soil fertility, floristic composition and aboveground biomass between ADE and NDE forests are consistent with a small-scale long-term land-use legacy and a regional increase in tree diversity

Padrão geográfico de diversidade genética em populações naturais de Pau-rosa (Aniba rosaeodora), na Amazônia Central

Rosewood (Aniba rosaeodora Ducke, Lauraceae) is an Amazonian evergreen tree and a source of the purest linalool, the main component of its essential oil, which is very valuable in the international perfumery market. After decades of over-exploitation it is currently considered as threatened. We evaluated the genetic diversity and its distribution in four populations in Central Amazonia. Thirty-five reliable RAPD markers were generated, of which 32 were polymorphic (91.4%). Variation was higher within the populations (76.5%; p < 0.0001) and geographic distribution contributed to population differentiation (23.4%; p < 0.0001). The Amazon River had a small influence on gene flow (3.3%; p < 0.0001), but we identified evidence of gene flow across the river. There were significant differences in marker frequencies (p < 0.05), in agreement with the low gene flow (Nm = 2.02). The correlation between genetic distance and gene flow was - 0.95 (p = 0.06) and between geographic distance and gene flow was -0.78 (p = 0.12). There was a geographic cline of variability across an East-West axis, influenced as well by the Amazon River, suggesting the river could be a barrier to gene flow. Although threatened, these Rosewood populations retain high diversity, with the highest levels in the Manaus population, which has been protected for over 42 years in a Reserve.O Pau-rosa (Aniba rosaeodora Ducke, Lauraceae) é uma árvore amazônica fonte do mais puro linalol, o qual é o principal componente do seu óleo essencial e muito valioso no mercado internacional de perfumaria. Após várias décadas de intensa exploração, a espécie foi levada à categoria de ameaçada de extinção. Quatro populações naturais distribuídas na bacia Amazônia Central foram avaliadas quanto ao nível e a distribuição da diversidade genética. Trinta e cinco marcadores RAPD reprodutíveis foram gerados, dos quais 32 foram polimórficos (91,4%). A diversidade foi maior dentro das populações (76,5%; p < 0,0001) e a distribuição geográfica contribuiu para a diferenciação entre as populações (23,4%; p < 0,0001). A AMOVA indicou que pode haver uma influência parcial do Rio Amazonas no fluxo gênico (3,3%; p < 0,0001), mas foram identificadas evidências de fluxo gênico atravessando o rio. Houve diferenças significativas nas freqüências dos marcadores (p < 0,05) e o fluxo gênico estimado foi relativamente baixo (Nm = 2,02). A correlação entre a distância genética e o fluxo gênico foi de - 0,95 (p = 0,06) e para a distância geográfica e o fluxo gênico foi de - 0,78 (p = 0,12). Houve um padrão geográfico de variabilidade ao longo do eixo Leste - Oeste, influenciado também pelo Rio Amazonas, o que sugere que o rio poderia funcionar como uma barreira para o fluxo gênico. Apesar de ameaçadas, estas populações de Pau-rosa possuem alta diversidade, com o maior valor na população de Manaus, que vem sendo protegida por 42 anos em uma reserva

An exploratory evaluation of the Ward and Hudson Offending Pathways model with sex offenders who have intellectual disability

Background It was predicted that offenders with intellectual disability ( ID) categorised according to Ward & Hudson's ( 1998b) self- regulation theory as having an Approach goal would have higher levels of distorted cognitions, less victim empathy, and a history of more prolific offending compared to those with an Avoidant goal. Offenders categorised as having a Passive strategy were hypothesised to have lower levels of general intellectual functioning, and more known offences and convictions compared to those with an Active strategy. Method Using a cross- sectional independent groups design, the offence pathways of 34 men with ID who were taking part in group cognitive behavioural therapy were rated by therapists. Participants assigned to each pathway were then compared using measures of sexual knowledge, distorted cognitions, and victim empathy. Cronbach's alpha for the measures was found to be acceptable. Results Offenders with an Approach goal were found to have higher levels of distorted cognitions and more denial about the negative impact of their offending upon their victims on one measure of distorted cognitions, while on another measure of distorted cognitions there were no differences. There were no differences between Approach and Avoidant offenders in terms of victim empathy, socio- sexual knowledge, severity of offending, and victim type. Offenders with a Passive strategy were found to have lower levels of general intellectual functioning than offenders with an Active strategy, but did not have more known offences and convictions. Conclusions The findings provide partial support for the usefulness of the Offending Pathways model in understanding the sexual offence processes of men with ID. The difficulties with this study are further discussed, together with the theoretical implication

A chronic strain of the cystic fibrosis pathogen Pandoraea pulmonicola expresses a heterogenous hypo-acylated lipid A

Pandoraea sp. is an emerging Gram-negative pathogen in cystic fibrosis causing severe and persistent inflammation and damage of the lungs. The molecular mechanisms underlying the high pathogenicity of Pandoraea species are still largely unknown. As Gram-negatives, Pandoraea sp. express lipopolysaccharides (LPS) whose recognition by the host immune system triggers an inflammatory response aimed at the bacterial eradication from the infected tissues. The degree of the inflammatory response strongly relies on the fine structure of the LPS and, in particular, of its glycolipid moiety, i.e. the lipid A. Here we report the structure of the lipid A isolated from the LPS of a chronic strain of P. pulmonicola (RL 8228), one of the most virulent identified so far among the Pandoraea species. Our data demonstrated that the examined chronic strain produces a smooth-type LPS with a complex mixture of hypoacylated lipid A species displaying, among other uncommon characteristics, the 2-hydroxylation of some of the acyl chains and the substitution by an additional glucosamine on one or both the phosphate groups

Genetic mapping of a major gene affecting onion bulb fructan content

The non-structural dry matter content of onion bulbs consists principally of fructose, glucose, sucrose and fructans. The objective of this study was to understand the genetic basis for the wide variation observed in the relative amounts of these carbohydrates. Bulb carbohydrate composition was evaluated in progeny from crosses between high dry matter storage onion varieties and sweet, low dry matter varieties. When samples were analysed on a dry weight basis, reducing sugar and fructan content exhibited high negative correlations and bimodal segregation suggestive of the action of a major gene. A polymorphic SSR marker, ACM235, was identified which exhibited strong disequilibrium with bulb fructan content in F2:3 families from the `W202A¿ × `Texas Grano 438¿ mapping population evaluated in two environments. This marker was mapped to chromosome 8 in the interspecific population `Allium cepa × A. roylei¿. Mapping in the `Colossal Grano PVP¿ × `Early Longkeeper P12¿ F2 population showed that a dominant major gene conditioning high-fructan content lay in the same genomic region. QTL analysis of total bulb fructan content in the intraspecific mapping population `BYG15-23¿ × `AC43¿ using a complete molecular marker map revealed only one significant QTL in the same chromosomal region. This locus, provisionally named Frc, may account for the major phenotypic differences in bulb carbohydrate content between storage and sweet onion varietie