An even pattern of xylan substitution is critical for interaction with cellulose in plant cell walls

Xylan and cellulose are abundant polysaccharides in vascular plants and essential for secondary cell wall strength. Acetate or glucuronic acid decorations are exclusively found on even-numbered residues in most of the glucuronoxylan polymer. It has been proposed that this even-specific positioning of the decorations might permit docking of xylan onto the hydrophilic face of a cellulose microfibril. Consequently, xylan adopts a flattened ribbon-like twofold helical screw conformation when bound to cellulose in the cell wall. Here we show that ESKIMO1/XOAT1/TBL29, a xylan-specific O-acetyltransferase, is necessary for generation of the even pattern of acetyl esters on xylan in Arabidopsis. The reduced acetylation in the esk1 mutant deregulates the position-specific activity of the xylan glucuronosyltransferase GUX1, and so the even pattern of glucuronic acid on the xylan is lost. Solid-state NMR of intact cell walls shows that, without the even-patterned xylan decorations, xylan does not interact normally with cellulose fibrils. We conclude that the even pattern of xylan substitutions seen across vascular plants therefore enables the interaction of xylan with hydrophilic faces of cellulose fibrils, and is essential for development of normal plant secondary cell walls.This work was part supported by the Leverhulme Trust grant for the Centre for Natural Material Innovation. J.W.-R., J.J.L. and O.M.T. are supported by studentships from Conicyt Chile and the Cambridge Trusts, the BBSRC Doctoral Training Partnership BB/J014540/1, and a BBSRC Novozymes iCASE award (BB/M015432/1) respectively. We thank K. B. Krogh for co-supervision of O.M.T. The UK 850 MHz solid-state NMR Facility used in this research was funded by EPSRC and BBSRC (Contract reference PR140003), as well as the University of Warwick including via part funding through Birmingham Science City Advanced Materials Projects 1 and 2 supported by Advantage West Midlands (AWM) and the European Regional Development Fund (ERDF)

Patterns and determinants of breastfeeding and complementary feeding practices in urban informal settlements, Nairobi Kenya

BackgroundThe World Health Organisation (WHO) recommends exclusive breastfeeding during the first six months of life for optimal growth, development and health. Breastfeeding should continue up to two years or more and nutritionally adequate, safe, and appropriately-fed complementary foods should be introduced at the age of six months to meet the evolving needs of the growing infant. Little evidence exists on breastfeeding and infant feeding practices in urban slums in sub-Saharan Africa. Our aim was to assess breastfeeding and infant feeding practices in Nairobi slums with reference to WHO recommendations. MethodsData from a longitudinal study conducted in two Nairobi slums are used. The study used information on the first year of life of 4299 children born between September 2006 and January 2010. All women who gave birth during this period were interviewed on breastfeeding and complementary feeding practices at recruitment and this information was updated twice, at four-monthly intervals. Cox proportional hazard analysis was used to determine factors associated with cessation of breastfeeding in infancy and early introduction of complementary foods. ResultsThere was universal breastfeeding with almost all children (99%) having ever been breastfed. However, more than a third (37%) were not breastfed in the first hour following delivery, and 40% were given something to drink other than the mothers' breast milk within 3 days after delivery. About 85% of infants were still breastfeeding by the end of the 11th month. Exclusive breastfeeding for the first six months was rare as only about 2% of infants were exclusively breastfed for six months. Factors associated with sub-optimal infant breastfeeding and feeding practices in these settings include child's sex; perceived size at birth; mother's marital status, ethnicity; education level; family planning (pregnancy desirability); health seeking behaviour (place of delivery) and; neighbourhood (slum of residence). ConclusionsThe study indicates poor adherence to WHO recommendations for breastfeeding and infant feeding practices. Interventions and further research should pay attention to factors such as cultural practices, access to and utilization of health care facilities, child feeding education, and family planning. <br/

Compositional analysis of bacterial communities in seawater, sediment, and sponges in the Misool coral reef system, Indonesia

Sponge species have been deemed high microbial abundance (HMA) or low microbial abundance (LMA) based on the composition and abundance of their microbial symbionts. In the present study, we evaluated the richness and composition of bacterial communities associated with one HMA sponge (Xestospongia testudinaria; Demospongiae: Haplosclerida: Petrosiidae), one LMA sponge (Stylissa carteri; Demospongiae: Scopalinida - Scopalinidae), and one sponge with a hitherto unknown microbial community (Aaptos suberitoides; Demospongiae: Suberitida: Suberitidae) inhabiting the Misool coral reef system in the West Papua province of Indonesia. The bacterial communities of these sponge species were also compared with seawater and sediment bacterial communities from the same coastal coral reef habitat. Using a 16S rRNA gene barcoded pyrosequencing approach, we showed that the most abundant phylum overall was Proteobacteria. The biotope (sponge species, sediment or seawater) explained almost 84% of the variation in bacterial composition with highly significant differences in composition among biotopes and a clear separation between bacterial communities from seawater and S. carteri; X. testudinaria and A. suberitoides and sediment. The Chloroflexi classes SAR202 and Anaerolineae were most abundant in A. suberitoides and X. testudinaria and both of these species shared several OTUs that were largely absent in the remaining biotopes. This suggests that A. suberitoides is a HMA sponge. Although similar, the bacterial communities of S. carteri and seawater were compositionally distinct. These results confirm compositional differences between sponge and non-sponge biotopes and between HMA and LMA sponges.publishe

The Use of Orthologous Sequences to Predict the Impact of Amino Acid Substitutions on Protein Function

Computational predictions of the functional impact of genetic variation play a critical role in human genetics research. For nonsynonymous coding variants, most prediction algorithms make use of patterns of amino acid substitutions observed among homologous proteins at a given site. In particular, substitutions observed in orthologous proteins from other species are often assumed to be tolerated in the human protein as well. We examined this assumption by evaluating a panel of nonsynonymous mutants of a prototypical human enzyme, methylenetetrahydrofolate reductase (MTHFR), in a yeast cell-based functional assay. As expected, substitutions in human MTHFR at sites that are well-conserved across distant orthologs result in an impaired enzyme, while substitutions present in recently diverged sequences (including a 9-site mutant that “resurrects” the human-macaque ancestor) result in a functional enzyme. We also interrogated 30 sites with varying degrees of conservation by creating substitutions in the human enzyme that are accepted in at least one ortholog of MTHFR. Quite surprisingly, most of these substitutions were deleterious to the human enzyme. The results suggest that selective constraints vary between phylogenetic lineages such that inclusion of distant orthologs to infer selective pressures on the human enzyme may be misleading. We propose that homologous proteins are best used to reconstruct ancestral sequences and infer amino acid conservation among only direct lineal ancestors of a particular protein. We show that such an “ancestral site preservation” measure outperforms other prediction methods, not only in our selected set for MTHFR, but also in an exhaustive set of E. coli LacI mutants

Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences

BACKGROUND: Several lines of evidence suggest that codon usage in the Drosophila saltans and D. willistoni lineages has shifted towards a less frequent use of GC-ending codons. Introns in these lineages show a parallel shift toward a lower GC content. These patterns have been alternatively ascribed to either a shift in mutational patterns or changes in the definition of preferred and unpreferred codons in these lineages. RESULTS AND DISCUSSION: To gain additional insight into this question, we quantified background substitutional patterns in the saltans/willistoni group using inactive copies of a novel, Q-like retrotransposable element. We demonstrate that the pattern of background substitutions in the saltans/willistoni lineage has shifted to a significant degree, primarily due to changes in mutational biases. These differences predict a lower equilibrium GC content in the genomes of the saltans/willistoni species compared with that in the D. melanogaster species group. The magnitude of the difference can readily account for changes in intronic GC content, but it appears insufficient to explain changes in codon usage within the saltans/willistoni lineage. CONCLUSION: We suggest that the observed changes in codon usage in the saltans/willistoni clade reflects either lineage-specific changes in the definitions of preferred and unpreferred codons, or a weaker selective pressure on codon bias in this lineage

Malaria and Helminth Co-infections in School and Preschool Children: A Cross-sectional Study in Magu district, north-Western Tanzania.

Malaria, schistosomiasis and soil transmitted helminth infections (STH) are important parasitic infections in Sub-Saharan Africa where a significant proportion of people are exposed to co-infections of more than one parasite. In Tanzania, these infections are a major public health problem particularly in school and pre-school children. The current study investigated malaria and helminth co-infections and anaemia in school and pre-school children in Magu district, Tanzania. School and pre-school children were enrolled in a cross-sectional study. Stool samples were examined for Schistosoma mansoni and STH infections using Kato Katz technique. Urine samples were examined for Schistosoma haematobium using the urine filtration method. Blood samples were examined for malaria parasites and haemoglobin concentrations using the Giemsa stain and Haemoque methods, respectively. Out of 1,546 children examined, 1,079 (69.8%) were infected with one or more parasites. Malaria-helminth co-infections were observed in 276 children (60% of all children with P. falciparum infection). Malaria parasites were significantly more prevalent in hookworm infected children than in hookworm free children (p = 0.046). However, this association was non-significant on multivariate logistic regression analysis (OR = 1.320, p = 0.064). Malaria parasite density decreased with increasing infection intensity of S. mansoni and with increasing number of co-infecting helminth species. Anaemia prevalence was 34.4% and was significantly associated with malaria infection, S. haematobium infection and with multiple parasite infections. Whereas S. mansoni infection was a significant predictor of malaria parasite density, P. falciparum and S. haematobium infections were significant predictors of anaemia. These findings suggest that multiple parasite infections are common in school and pre-school children in Magu district. Concurrent P. falciparum, S. mansoni and S. haematobium infections increase the risk of lower Hb levels and anaemia, which in turn calls for integrated disease control interventions. The associations between malaria and helminth infections detected in this study need further investigation

Relative Impacts of Adult Movement, Larval Dispersal and Harvester Movement on the Effectiveness of Reserve Networks

Movement of individuals is a critical factor determining the effectiveness of reserve networks. Marine reserves have historically been used for the management of species that are sedentary as adults, and, therefore, larval dispersal has been a major focus of marine-reserve research. The push to use marine reserves for managing pelagic and demersal species poses significant questions regarding their utility for highly-mobile species. Here, a simple conceptual metapopulation model is developed to provide a rigorous comparison of the functioning of reserve networks for populations with different admixtures of larval dispersal and adult movement in a home range. We find that adult movement produces significantly lower persistence than larval dispersal, all other factors being equal. Furthermore, redistribution of harvest effort previously in reserves to remaining fished areas (‘fishery squeeze’) and fishing along reserve borders (‘fishing-the-line’) considerably reduce persistence and harvests for populations mobile as adults, while they only marginally changes results for populations with dispersing larvae. Our results also indicate that adult home-range movement and larval dispersal are not simply additive processes, but rather that populations possessing both modes of movement have lower persistence than equivalent populations having the same amount of ‘total movement’ (sum of larval and adult movement spatial scales) in either larval dispersal or adult movement alone

River Restoration in Spain: Theoretical and Practical Approach in the Context of the European Water Framework Directive.

River restoration is becoming a priority in many countries because of increasing the awareness of environmental degradation. In Europe, the EU Water Framework Directive (WFD) has significantly reinforced river restoration, encouraging the improvement of ecological status for water bodies. To fulfill the WFD requirements, the Spanish Ministry of the Environment developed in 2006 a National Strategy for River Restoration whose design and implementation are described in this paper. At the same time many restoration projects have been conducted, and sixty of them have been evaluated in terms of stated objectives and pressures and implemented restoration measures. Riparian vegetation enhancement, weir removal and fish passes were the most frequently implemented restoration measures, although the greatest pressures came from hydrologic alteration caused by flow regulation for irrigation purposes. Water deficits in quantity and quality associated with uncontrolled water demands seriously affect Mediterranean rivers and represent the main constraint to achieving good ecological status of Spanish rivers, most of them intensively regulated. Proper environmental allocation of in-stream flows would need deep restrictions in agricultural water use which seem to be of very difficult social acceptance. This situation highlights the need to integrate land-use and rural development policies with water resources and river management, and identifies additional difficulties in achieving the WFD objectives and good ecological status of rivers in Mediterranean countries