Xylan decoration patterns and the plant secondary cell wall molecular architecture.

The molecular architecture of plant secondary cell walls is still not resolved. There are several proposed structures for cellulose fibrils, the main component of plant cell walls and the conformation of other molecules is even less well known. Glucuronic acid (GlcA) substitution of xylan (GUX) enzymes, in CAZy family glycosyl transferase (GT)8, decorate the xylan backbone with various specific patterns of GlcA. It was recently discovered that dicot xylan has a domain with the side chain decorations distributed on every second unit of the backbone (xylose). If the xylan backbone folds in a similar way to glucan chains in cellulose (2-fold helix), this kind of arrangement may allow the undecorated side of the xylan chain to hydrogen bond with the hydrophilic surface of cellulose microfibrils. MD simulations suggest that such interactions are energetically stable. We discuss the possible role of this xylan decoration pattern in building of the plant cell wall.We thank Nadine Anders for helpful comments on the manuscript. The work was supported by a Leverhulme Trust Programme Grant : The Centre for Natural Material Innovation and the Biotechnology and Biological Sciences Research Council grant numbers [BB/K005537/1] and [BB/G016240/1].This is the author accepted manuscript. The final version is available from Portland Press via http://dx.doi.org/10.1042/BST2015018

The injectable-only contraceptive medroxyprogesterone acetate, unlike norethisterone acetate and progesterone, regulates inflammatory genes in endocervical cells via the glucocorticoid receptor

Clinical studies suggest that the injectable contraceptive medroxyprogesterone acetate (MPA) increases susceptibility to infections such as HIV-1, unlike the injectable contraceptive norethisterone enanthate (NET-EN). We investigated the differential effects, molecular mechanism of action and steroid receptor involvement in gene expression by MPA as compared to NET and progesterone (P4) in the End1/E6E7 cell line model for the endocervical epithelium, a key point of entry for pathogens in the female genital mucosa. MPA, unlike NET-acetate (NET-A) and P4, increases mRNA expression of the anti-inflammatory GILZ and IκBα genes. Similarly, MPA unlike NET-A, decreases mRNA expression of the pro-inflammatory IL-6, IL-8 and RANTES genes, and IL-6 and IL-8 protein levels. The predominant steroid receptor expressed in the End1/E6E7 and primary endocervical epithelial cells is the glucocorticoid receptor (GR), and GR knockdown experiments show that the anti-inflammatory effects of MPA are mediated by the GR. Chromatin-immunoprecipitation results suggest that MPA, unlike NET-A and P4, represses pro-inflammatory cytokine gene expression in cervical epithelial cells via a mechanism involving recruitment of the GR to cytokine gene promoters, like the GR agonist dexamethasone. This is at least in part consistent with direct effects on transcription, without a requirement for new protein synthesis. Dose response analysis shows that MPA has a potency of ∼24 nM for transactivation of the anti-inflammatory GILZ gene and ∼4-20 nM for repression of the pro-inflammatory genes, suggesting that these effects are likely to be relevant at injectable contraceptive doses of MPA. These findings suggest that in the context of the genital mucosa, these GR-mediated glucocorticoid-like effects of MPA in cervical epithelial cells are likely to play a critical role in discriminating between the effects on inflammation caused by different progestins and P4 and hence susceptibility to genital infections, given the predominant expression of the GR in primary endocervical epithelial cells

Assessing the conservation status of mangroves in Rakhine, Myanmar

Ecosystem degradation is a key challenge that human society faces, as ecosystems provide services that are tied to human well-being. Particularly, mangrove ecosystems provide important services to communities but are suffering heavy degradation, loss and potential collapse due to anthropogenic activities. The IUCN Red List of Ecosystems is a transparent and consistent framework for assessing ecosystems' risk of collapse and is increasingly used to inform legislation and ecosystem management globally. Satellite data have become increasingly common in environmental monitoring due to their extensive spatial and temporal coverage. Here, recent advances in analyses using satellite-derived data were implemented to reassess the conservation status of the ‘Rakhine mangrove forest on mud’, an important intertidal ecosystem in Myanmar, extending a previous national Red List assessment that assessed the ecosystem as Critically Endangered. By incorporating additional data sources and analyses, the extended assessment produced more robust results and reduced the uncertainty in the previous assessment. Overall, the ecosystem was assessed as Critically Endangered (range: Vulnerable to Critically Endangered) as a result of historical mangrove extent loss. Recent losses and biotic disruptions were also observed, which would have led to the ecosystem being assessed as Vulnerable. While the final outcome of the Red List assessment remained at Critically Endangered due to the historical state of the mangroves pre-dating the temporal coverage from satellite data, the uncertainty of the ecosystem's status was reduced, and the reassessment highlighted the recent areal changes and mangrove degradation that has occurred. The importance of conducting reassessments when new data become available is discussed, and a template for future mangrove Red List assessments that use satellite data as their primary source of information to improve the robustness of their results is presented

The pattern of xylan acetylation suggests xylan may interact with cellulose microfibrils as a twofold helical screw in the secondary plant cell wall of Arabidopsis thaliana.

The interaction between xylan and cellulose microfibrils is important for secondary cell wall properties in vascular plants; however, the molecular arrangement of xylan in the cell wall and the nature of the molecular bonding between the polysaccharides are unknown. In dicots, the xylan backbone of β-(1,4)-linked xylosyl residues is decorated by occasional glucuronic acid, and approximately one-half of the xylosyl residues are O-acetylated at C-2 or C-3. We recently proposed that the even, periodic spacing of GlcA residues in the major domain of dicot xylan might allow the xylan backbone to fold as a twofold helical screw to facilitate alignment along, and stable interaction with, cellulose fibrils; however, such an interaction might be adversely impacted by random acetylation of the xylan backbone. Here, we investigated the arrangement of acetyl residues in Arabidopsis xylan using mass spectrometry and NMR. Alternate xylosyl residues along the backbone are acetylated. Using molecular dynamics simulation, we found that a twofold helical screw conformation of xylan is stable in interactions with both hydrophilic and hydrophobic cellulose faces. Tight docking of xylan on the hydrophilic faces is feasible only for xylan decorated on alternate residues and folded as a twofold helical screw. The findings suggest an explanation for the importance of acetylation for xylan-cellulose interactions, and also have implications for our understanding of cell wall molecular architecture and properties, and biological degradation by pathogens and fungi. They will also impact strategies to improve lignocellulose processing for biorefining and bioenergy.The work conducted by TT and NN was supported by a grant from the BBSRC: BB/G016240/1 BBSRC Sustainable Energy Centre Cell Wall Sugars Programme (BSBEC) to PD and DNB. The work of PD was supported by the European Community’s Seventh Framework Programme SUNLIBB (FP7/2007-2013) under the grant agreement #251132. The NMR facility infrastructure was supported by the BBSRC and the Wellcome Trust. TCFG thanks CNPq (Brazil) for a graduate fellowship (grant # 140978/2009-7). MSS thanks CEPROBIO (grant # 490022/2009- 0) and FAPESP for funding (grant #2013/08293-7).This is the accepted version of the following article: "Busse-Wicher, M; Gomes, T.C.F; Tryfona, T; Nikolovski, N; Stott, K; Grantham, N.J; Bolam, D.N; Skaf, M.S; Dupree, P. (2014) "The pattern of xylan acetylation suggests xylan may interact with cellulose microfibrils as a two-fold helical screw in the secondary plant cell wall of Arabidopsis thaliana." The Plant Journal. Accepted article [electronic] 10.1111/tpj.12575", which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1111/tpj.12575/abstrac

Threatened ecosystems of Myanmar. An IUCN Red List of ecosystems assessment. Version 1.0.

[Excerpt:] Myanmar's Red List of Ecosystems is a tool to understand our threats and plan for conservation and sustainable management. Forests constitute the dominant ecosystems in Myanmar, and we are blessed with high forest cover (42.92%) and diversity, with 36 of our 64 ecosystems identified as forest and mangrove. These forests and biodiversity underpin a range of ecosystem services which are central to Myanmar’s sustainable development, supporting human and resource needs, and contributing to a more stable climate. The loss of forests and our biodiversity leads to degradation and deterioration of ecosystem services and threatens Myanmar’s irreplaceable ecological heritage. We often discuss ecosystem services but this study documents Myanmar’s terrestrial ecosystem typology and spatial distribution for the first time. This is one of the first ecosystem red lists developed within ASEAN and this will inform our implementation for decades to come to inform legislation, land-use planning, protected area expansion, monitoring and reporting, and ecosystem management. To sustain our forests and our biodiversity we need to sustainably manage all of these incredible ecosystems

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

Bordetella pertussis Infection Exacerbates Influenza Virus Infection through Pertussis Toxin-Mediated Suppression of Innate Immunity

Pertussis (whooping cough) is frequently complicated by concomitant infections with respiratory viruses. Here we report the effect of Bordetella pertussis infection on subsequent influenza virus (PR8) infection in mouse models and the role of pertussis toxin (PT) in this effect. BALB/c mice infected with a wild-type strain of B. pertussis (WT) and subsequently (up to 14 days later) infected with PR8 had significantly increased pulmonary viral titers, lung pathology and mortality compared to mice similarly infected with a PT-deficient mutant strain (ΔPT) and PR8. Substitution of WT infection by intranasal treatment with purified active PT was sufficient to replicate the exacerbating effects on PR8 infection in BALB/c and C57/BL6 mice, but the effects of PT were lost when toxin was administered 24 h after virus inoculation. PT had no effect on virus titers in primary cultures of murine tracheal epithelial cells (mTECs) in vitro, suggesting the toxin targets an early immune response to increase viral titers in the mouse model. However, type I interferon responses were not affected by PT. Whole genome microarray analysis of gene expression in lung tissue from PT-treated and control PR8-infected mice at 12 and 36 h post-virus inoculation revealed that PT treatment suppressed numerous genes associated with communication between innate and adaptive immune responses. In mice depleted of alveolar macrophages, increase of pulmonary viral titers by PT treatment was lost. PT also suppressed levels of IL-1β, IL-12, IFN-γ, IL-6, KC, MCP-1 and TNF-α in the airways after PR8 infection. Furthermore PT treatment inhibited early recruitment of neutrophils and NK cells to the airways. Together these findings demonstrate that infection with B. pertussis through PT activity predisposes the host to exacerbated influenza infection by countering protective innate immune responses that control virus titers

Use of Intravascular Imaging During Chronic Total Occlusion Percutaneous Coronary Intervention: Insights From a Contemporary Multicenter Registry

Background: Intravascular imaging can facilitate chronic total occlusion (CTO) percutaneous coronary intervention. Methods and Results: We examined the frequency of use and outcomes of intravascular imaging among 619 CTO percutaneous coronary interventions performed between 2012 and 2015 at 7 US centers. Mean age was 65.4±10 years and 85% of the patients were men. Intravascular imaging was used in 38%: intravascular ultrasound in 36%, optical coherence tomography in 3%, and both in 1.45%. Intravascular imaging was used for stent sizing (26.3%), stent optimization (38.0%), and CTO crossing (35.7%, antegrade in 27.9%, and retrograde in 7.8%). Intravascular imaging to facilitate crossing was used more frequently in lesions with proximal cap ambiguity (49% versus 26%, P<0.0001) and with retrograde as compared with antegrade‐only cases (67% versus 31%, P<0.0001). Despite higher complexity (Japanese CTO score: 2.86±1.19 versus 2.43±1.19, P=0.001), cases in which imaging was used for crossing had similar technical and procedural success (92.8% versus 89.6%, P=0.302 and 90.1% versus 88.3%, P=0.588, respectively) and similar incidence of major cardiac adverse events (2.7% versus 3.2%, P=0.772). Use of intravascular imaging was associated with longer procedure (192 minutes [interquartile range 130, 255] versus 131 minutes [90, 192], P<0.0001) and fluoroscopy (71 minutes [44, 93] versus 39 minutes [25, 69], P<0.0001) time. Conclusions: Intravascular imaging is frequently performed during CTO percutaneous coronary intervention both for crossing and for stent selection/optimization. Despite its use in more complex lesion subsets, intravascular imaging was associated with similar rates of technical and procedural success for CTO percutaneous coronary intervention. Clinical Trial Registration URL: http://www.clinicaltrials.gov. Unique identifier: NCT02061436

Forest condition in the Congo Basin for the assessment of ecosystem conservation status

Quantifying ecological condition, notably the extent of forest degradation is important for understanding and designing measures to protect biodiversity and enhancing the capacity of forests to deliver ecosystem services. Conservation planning, particularly the prioritization of management interventions for forests, is often lacking spatial data on forest degradation, and it is often overlooked within decision-making processes. We develop a continuous metric termed Forest Condition (FC) which aims to measure the degree of forest degradation on a scale from 0 to 100, incorporating the temporal history of forest change over any spatial extent. We parameterize this metric based on estimated changes in above ground biomass in the context of forest fragmentation over time to estimate a continuous measure of forest degradation for Congo Basin countries. We estimate that just <70% of Congo Basin forests remain fully intact, a decrease from 78% in the year 2000. FC was validated by direct remote sensing measurements from Landsat imagery for DRC. Results showed that FC was significantly positively correlated with forest canopy cover, gap area per hectare, and magnitude of temporal change in Normalized Burn Ratio. We tested the ability of FC to distinguish primary and secondary degradation and deforestation and found significant differences in gap area and spectral anomalies to validate our theoretical model. We apply the IUCN Red List of Ecosystems criteria to demonstrate the integration of forest condition to assess the risk of ecosystem collapse. Based on this assessment, we found that without including FC in the assessment of biotic disruption, 12 ecosystems representing over 11% of forested area in 2015 would not have been assigned a threat status, and an additional 9 ecosystems would have a lower threat status. Our overall assessment of ecosystems found about half of all Congo Basin ecosystem types, accounting for 20% of all forest area are threatened to some degree, including 4 ecosystems (<1% of total area) which are critically engendered. FC is a transferrable and scalable assessment to support forest monitoring, planning, and management