Trait databases: misuses and precautions

Trait‐based ecology has enjoyed increasing success, aided by the development of trait databases. However their reliability has hardly been tested. Sandel et al., in this issue, identified uncertainties in trait databases linked to missing species and variable sampling effort among species. This highlights the danger of using trait databases in a blind manner and the need for their thorough evaluation.     

Identification of citrullinated α-enolase as a candidate autoantigen in rheumatoid arthritis

Antibodies against citrullinated proteins are highly specific for rheumatoid arthritis (RA), but little is understood about their citrullinated target antigens. We have detected a candidate citrullinated protein by immunoblotting lysates of monocytic and granulocytic HL-60 cells treated with peptidylarginine deiminase. In an initial screen of serum samples from four patients with RA and one control, a protein of molecular mass 47 kDa from monocytic HL-60s reacted with sera from the patients, but not with the serum from the control. Only the citrullinated form of the protein was recognised. The antigen was identified by tandem mass spectrometry as α-enolase, and the positions of nine citrulline residues in the sequence were determined. Serum samples from 52 patients with RA and 40 healthy controls were tested for presence of antibodies against citrullinated and non-citrullinated α-enolase by immunoblotting of the purified antigens. Twenty-four sera from patients with RA (46%) reacted with citrullinated α-enolase, of which seven (13%) also recognised the non-citrullinated protein. Six samples from the controls (15%) reacted with both forms. α-Enolase was detected in the RA joint, where it co-localised with citrullinated proteins. The presence of antibody together with expression of antigen within the joint implicates citrullinated α-enolase as a candidate autoantigen that could drive the chronic inflammatory response in RA.     

The role of biomass allocation strategy in diversity loss due to fertilization

Proposed mechanisms for explaining biodiversity loss due to fertilization include interspecific competition and assemblage-level thinning. The interspecific competition hypothesis (ICH) assumes a link between population changes and species competitive ability, which is related to functional traits such as biomass allocation patterns. Based on a 2-year fertilization experiment in an alpine meadow on the Tibetan Plateau, we attempted to explore the relationships between individual and population responses. Individual response was measured by changes in plant biomass and biomass allocation, and population response was estimated by changes in species abundance. The results suggested that following fertilization (1) changes in individual biomass differ among species and functional groups, (2) reproductive allocation tends to decrease for all species whereas leaf allocation generally increases for grasses but decreases for forbs, (3) a strong positive correlation exists between species relative abundance change and individual biomass response, and (4) species relative abundance change has a positive correlation with leaf allocation response, a negative correlation with stem allocation response, and no significant correlation with reproductive allocation response. We conclude that the individual biomass responses and biomass allocation strategy can partly explain diversity loss due to fertilization, a result consistent with the ICH.     

Differential regulation of human eosinophil IL-3, IL-5, and GM-CSF receptor alpha-chain expression by cytokines: IL-3, IL-5, and GM-CSF down-regulate IL-5 receptor alpha expression with loss of IL-5 responsiveness,but up-regulate IL-3 receptor alpha expression

Our recent data suggested that tissue eosinophils may be relatively insensitive to anti-IL-5 treatment. We examined cross-regulation and functional consequences of modulation of eosinophil cytokine receptor expression by IL-3, IL-5 GM-CSF, and eotaxin. Incubation of eosinophils with IL-3, IL-5, or GM-CSF led to reduced expression of IL-5R alpha, which was sustained for up to 5 days. Eosinophils incubated with IL-5 or IL-3 showed diminished respiratory burst and mitogen-activated protein kinase kinase phosphorylation in response to further IL-5 stimulation. In contrast to these findings, eosinophil expression of IL-3R alpha was increased by IL-3, IL-5, and GM-CSF, whereas GM-CSF receptor alpha was down-regulated by GM-CSF, but was not affected by IL-3 or IL-5. CCR3 expression was down-regulated by IL-3 and was transiently reduced by IL-5 and GM-CSF, but rapidly returned toward baseline. Eotaxin had no effect on receptor expression for IL-3, IL-5, or GM-CSF. Up-regulation of IL-3R alpha by cytokines was prevented by a phosphoinositol 3-kinase inhibitor, whereas this and other signaling inhibitors had no effect on IL-5R alpha down-regulation. These data suggest dynamic and differential regulation of eosinophil receptors for IL-3, IL-5, and GM-CSF by the cytokine ligands. Since these cytokines are thought to be involved in eosinophil development and mobilization from the bone marrow and are present at sites of allergic inflammation, tissue eosinophils may have reduced IL-5R expression and responsiveness, and this may explain the disappointing effect of anti-IL-5 therapy in reducing airway eosinophilia in asthma.     

Cadherin-mediated differential cell adhesion controls slow muscle cell migration in the developing zebrafish myotome

Slow-twitch muscle fibers of the zebrafish myotome undergo a unique set of morphogenetic cell movements. During embryogenesis, slow-twitch muscle derives from the adaxial cells, a layer of paraxial mesoderm that differentiates medially within the myotome, immediately adjacent to the notochord. Subsequently, slow-twitch muscle cells migrate through the entire myotome, coming to lie at its most lateral surface. Here we examine the cellular and molecular basis for slow-twitch muscle cell migration. We show that slow-twitch muscle cell morphogenesis is marked by behaviors typical of cells influenced by differential cell adhesion. Dynamic and reciprocal waves of N-cadherin and M-cadherin expression within the myotome, which correlate precisely with cell migration, generate differential adhesive environments that drive slow-twitch muscle cell migration through the myotome. Removing or altering the expression of either protein within the myotome perturbs migration. These results provide a definitive example of homophilic cell adhesion shaping cellular behavior during vertebrate development.     

Modelling snow cover duration improves predictions of functional and taxonomic diversity for alpine plant communities

Background and Aims Quantifying relationships between snow cover duration and plant community properties remains an important challenge in alpine ecology. This study develops a method to estimate spatial variation in energy availability in the context of a topographically complex, high-elevation watershed, which was used to test the explanatory power of environmental gradients both with and without snow cover in relation to taxonomic and functional plant diversity.Methods Snow cover in the French Alps was mapped at 15-m resolution using Landsat imagery for five recent years, and a generalized additive model (GAM) was fitted for each year linking snow to time and topography. Predicted snow cover maps were combined with air temperature and solar radiation data at daily resolution, summed for each year and averaged across years. Equivalent growing season energy gradients were also estimated without accounting for snow cover duration. Relationships were tested between environmental gradients and diversity metrics measured for 100 plots, including species richness, community-weighted mean traits, functional diversity and hyperspectral estimates of canopy chlorophyll content.Key Results Accounting for snow cover in environmental variables consistently led to improved predictive power as well as more ecologically meaningful characterizations of plant diversity. Model parameters differed significantly when fitted with and without snow cover. Filtering solar radiation with snow as compared without led to an average gain in R² of 0·26 and reversed slope direction to more intuitive relationships for several diversity metrics.Conclusions The results show that in alpine environments high-resolution data on snow cover duration are pivotal for capturing the spatial heterogeneity of both taxonomic and functional diversity. The use of climate variables without consideration of snow cover can lead to erroneous predictions of plant diversity. The results further indicate that studies seeking to predict the response of alpine plant communities to climate change need to consider shifts in both temperature and nival regimes.     

HIV-1 Genetic Diversity and Its Impact on Baseline CD4+T Cells and Viral Loads among Recently Infected Men Who Have Sex with Men in Shanghai,China

The HIV-1 epidemic among men who have sex with men (MSM) has been spreading throughout China. Shanghai, a central gathering place for MSM, is facing a continuously increasing incidence of HIV-1 infection. In order to better understand the dynamics of HIV-1 diversity and its influence on patient’s immune status at baseline on diagnosis, 1265 newly HIV-1-infected MSM collected from January 2009 to December 2013 in Shanghai were retrospectively analyzed for genetic subtyping, CD4+T cell counts, and viral loads. HIV-1 phylogenetic analysis revealed a broad viral diversity including CRF01_AE (62.13%), CRF07_BC (24.51%), subtype B (8.06%), CRF55_01B (3.24%), CER67_01B (0.95%), CRF68_01B (0.4%), CRF08_BC (0.08%) and CRF59_01B (0.08%). Twenty-four unique recombination forms (URFs) (1.98%) were identified as well. Bayesian inference analysis indicated that the introduction of CRF01_AE strain (1997) was earlier than CRF07_BC strain (2001) into MSM population in Shanghai based on the time of the most recent common ancestor (tMRCA). Three epidemic clusters and five sub-clusters were found in CRF01_AE. Significantly lower CD4+T cell count was found in individuals infected with CRF01_AE than in those infected with CRF07_BC infection (P<0.01), whereas viral load was significantly higher those infected with CRF01_AE than with CRF07_BC (P<0.01). In addition, the patients with >45 years of age were found to have lower CD4+T cell counts and higher viral loads than the patients with <25 years of age (P<0.05). This study reveals the presence of HIV-1 subtype diversity in Shanghai and its remarkable influence on clinical outcome. A real-time surveillance of HIV-1 viral diversity and phylodynamics of epidemic cluster, patient’s baseline CD4+T cell count and viral load would be of great value to monitoring of disease progression, intervention for transmission, improvement of antiretroviral therapy strategy and design of vaccines.     

Inflammation Anergy in Human Intestinal Macrophages Is Due to Smad-induced I��B�� Expression and NF-��B Inactivation

Human intestinal macrophages contribute to tissue homeostasis in noninflamed mucosa through profound down-regulation of pro-inflammatory cytokine release. Here, we show that this down-regulation extends to Toll-like receptor (TLR)-induced cytokine release, as intestinal macrophages expressed TLR3–TLR9 but did not release cytokines in response to TLR-specific ligands. Likely contributing to this unique functional profile, intestinal macrophages expressed markedly down-regulated adapter proteins MyD88 and Toll interleukin receptor 1 domain-containing adapter-inducing interferon β, which together mediate all TLR MyD88-dependent and -independent NF-κB signaling, did not phosphorylate NF-κB p65 or Smad-induced IκBα, and did not translocate NF-κB into the nucleus. Importantly, transforming growth factor-β released from intestinal extracellular matrix (stroma) induced identical down-regulation in the NF-κB signaling and function of blood monocytes, the exclusive source of intestinal macrophages. Our findings implicate stromal transforming growth factor-β-induced dysregulation of NF-κB proteins and Smad signaling in the differentiation of pro-inflammatory blood monocytes into noninflammatory intestinal macrophages.