An annotated checklist of the orchids of Nepal

An annotated checklist comprised of 458 taxa of orchids known from Nepal is provided, including 104 genera, 437 species, 16 varieties, 3 subspecies and 2 forma and 18 endemic species. In Nepal, orchid species are distributed from 60–5200 m a.s.l. In the checklist, notes on altitudinal ranges, habit, habitat, global distribution, phenology, etc. are presented.     

Impact of Parthenium hysterophorus L. invasion on plant species composition and soil properties of grassland communities in Nepal

Parthenium hysterophorus (Asteraceae) is a noxious plant that is considered one of the most invasive species in the world. We studied changes in the composition of plant species and soil properties related to the invasion of P. hysterophorus in three grassland communities of central Nepal. We collected vegetation and soil data along transects that were established in densely invaded to non-invaded areas within homogenous grassland stands. We found significant differences between invaded, transitional and non-invaded plots in species composition and soil properties. There were fewer species in non-invaded than transitional and invaded plots. By P. hysterophorus invasion both native and non-native species were supported or replaced, respectively. The concentrations of soil nitrogen and organic matter were significantly higher in transitional and invaded plots than in non-invaded plots. Soil pH, phosphorus and potassium were highest in the invaded plots, lowest in the non-invaded and intermediate in the transitional plots. Due to changes in above-ground vegetation and below-ground soil nutrient contents, P. hysterophorus invasion is likely to have an overall negative effect on the functioning of the entire ecosystem. Therefore, management of noxious P. hysterophorus is necessary to prevent future problems.     

Mobilizing metaphors: the popular use of keystone,flagship and umbrella species concepts

Misrepresentation of terminology is a major impediment for attempts at enhancing public conservation literacy. Despite being critically important for improving conservation practice, there have been few systematic analyses of the popular use of conservation terminology. This paper draws from science communication studies and metaphor analysis, to examine how keystone, flagship and umbrella species concepts are used and represented in non-academic contexts. 557 news articles containing these terms were systematically analyzed. Mammals featured in 60% of articles on keystones, 55% on flagships and 63% on umbrella species. Number of articles explaining the terms keystone (35%) and flagship (31%) was low, and keystones were the most misrepresented term. Keystones were metaphorically linked with balance, flagships with representation and umbrella species with protection. These metaphors influenced public interpretation of scientific terminology, oriented actions towards select species, and led to a valuation of such actions. Together, the findings highlight three important aspects of popular use of conservation terminology: (1) communication is largely biased towards mammals, (2) everyday language plays a vital role in the interpretation of concepts, and (3) metaphors influence peoples’ actions and understanding. Conservation biologists need to engage with issues of language if public conservation literacy is to be improved. Further evaluations of concepts with high public and policy relevance, systematic identification of communication shortfalls, and linguistic assessments prior to promoting new terms are potential ways of achieving this.     

The interferon type I signature towards prediction of non-response to rituximab in rheumatoid arthritis patients

Introduction

B cell depletion therapy is efficacious in rheumatoid arthritis (RA) patients failing on tumor necrosis factor (TNF) blocking agents. However, approximately 40% to 50% of rituximab (RTX) treated RA patients have a poor response. We investigated whether baseline gene expression levels can discriminate between clinical non-responders and responders to RTX.

Methods

In 14 consecutive RA patients starting on RTX (test cohort), gene expression profiling on whole peripheral blood RNA was performed by Illumina^® HumanHT beadchip microarrays. Supervised cluster analysis was used to identify genes expressed differentially at baseline between responders and non-responders based on both a difference in 28 joints disease activity score (ΔDAS28 < 1.2) and European League against Rheumatism (EULAR) response criteria after six months RTX. Genes of interest were measured by quantitative real-time PCR and tested for their predictive value using receiver operating characteristics (ROC) curves in an independent validation cohort (n = 26).

Results

Genome-wide microarray analysis revealed a marked variation in the peripheral blood cells between RA patients before the start of RTX treatment. Here, we demonstrated that only a cluster consisting of interferon (IFN) type I network genes, represented by a set of IFN type I response genes (IRGs), that is, LY6E, HERC5, IFI44L, ISG15, MxA, MxB, EPSTI1 and RSAD2, was associated with ΔDAS28 and EULAR response outcome (P = 0.0074 and P = 0.0599, respectively). Based on the eight IRGs an IFN-score was calculated that reached an area under the curve (AUC) of 0.82 to separate non-responders from responders in an independent validation cohort of 26 patients using Receiver Operator Characteristics (ROC) curves analysis according to ΔDAS28 < 1.2 criteria. Advanced classifier analysis yielded a three IRG-set that reached an AUC of 87%. Comparable findings applied to EULAR non-response criteria.

Conclusions

This study demonstrates clinical utility for the use of baseline IRG expression levels as a predictive biomarker for non-response to RTX in RA.     

Inhibiting citrullination in rheumatoid arthritis: taking fuel from the fire

Citrullination is a post-translational modification catalysed by peptidylarginine deiminase and is a common feature of inflammation. The presence of anti-citrullinated protein/peptide antibodies (ACPA), however, is unique to rheumatoid arthritis. Several lines of evidence suggest that ACPA are important in the pathogenesis of rheumatoid arthritis. A popular hypothesis for this pathogenesis is a two-hit model. The first hit gives rise to ACPA, and the second hit, an unrelated episode of synovial inflammation accompanied by citrullination, is perpetuated by the pre-existing antibodies. This model suggests that reducing citrullination might ameliorate disease. Recent findings indicate that citrullination closely correlates with inflammation, and that glucocorticoids decrease peptidylarginine deiminase expression independent of their other anti-inflammatory effects.     

Community assembly in Lake Tanganyika cichlid fish: quantifying the contributions of both niche‐based and neutral processes

The cichlid family features some of the most spectacular examples of adaptive radiation. Evolutionary studies have highlighted the importance of both trophic adaptation and sexual selection in cichlid speciation. However, it is poorly understood what processes drive the composition and diversity of local cichlid species assemblages on relatively short, ecological timescales. Here, we investigate the relative importance of niche‐based and neutral processes in determining the composition and diversity of cichlid communities inhabiting various environmental conditions in the littoral zone of Lake Tanganyika, Zambia. We collected data on cichlid abundance, morphometrics, and local environments. We analyzed relationships between mean trait values, community composition, and environmental variation, and used a recently developed modeling technique (STEPCAM) to estimate the contributions of niche‐based and neutral processes to community assembly. Contrary to our expectations, our results show that stochastic processes, and not niche‐based processes, were responsible for the majority of cichlid community assembly. We also found that the relative importance of niche‐based and neutral processes was constant across environments. However, we found significant relationships between environmental variation, community trait means, and community composition. These relationships were caused by niche‐based processes, as they disappeared in simulated, purely neutrally assembled communities. Importantly, these results can potentially reconcile seemingly contrasting findings in the literature about the importance of either niche‐based or neutral‐based processes in community assembly, as we show that significant trait relationships can already be found in nearly (but not completely) neutrally assembled communities; that is, even a small deviation from neutrality can have major effects on community patterns.