Socio‐economic impact classification of alien taxa (SEICAT)

1 Many alien taxa are known to cause socio‐economic impacts by affecting the different constituents of human well‐being (security; material and non‐material assets; health; social, spiritual and cultural relations; freedom of choice and action). Attempts to quantify socio‐economic impacts in monetary terms are unlikely to provide a useful basis for evaluating and comparing impacts of alien taxa because they are notoriously difficult to measure and important aspects of human well‐being are ignored. 2 Here, we propose a novel standardised method for classifying alien taxa in terms of the magnitude of their impacts on human well‐being, based on the capability approach from welfare economics. The core characteristic of this approach is that it uses changes in peoples' activities as a common metric for evaluating impacts on well‐being. 2 Impacts are assigned to one of five levels, from Minimal Concern to Massive, according to semi‐quantitative scenarios that describe the severity of the impacts. Taxa are then classified according to the highest level of deleterious impact that they have been recorded to cause on any constituent of human well‐being. The scheme also includes categories for taxa that are not evaluated, have no alien population, or are data deficient, and a method for assigning uncertainty to all the classifications. To demonstrate the utility of the system, we classified impacts of amphibians globally. These showed a variety of impacts on human well‐being, with the cane toad (Rhinella marina) scoring Major impacts. For most species, however, no studies reporting impacts on human well‐being were found, i.e. these species were data deficient. 2 The classification provides a consistent procedure for translating the broad range of measures and types of impact into ranked levels of socio‐economic impact, assigns alien taxa on the basis of the best available evidence of their documented deleterious impacts, and is applicable across taxa and at a range of spatial scales. The system was designed to align closely with the Environmental Impact Classification for Alien Taxa (EICAT) and the Red List, both of which have been adopted by the International Union of Nature Conservation (IUCN), and could therefore be readily integrated into international practices and policies

A vision for global monitoring of biological invasions

Managing biological invasions relies on good global coverage of species distributions. Accurate information on alien species distributions, obtained from international policy and cross-border co-operation, is required to evaluate trans-boundary and trading partnership risks. However, a standardized approach for systematically monitoring alien species and tracking biological invasions is still lacking. This Perspective presents a vision for global observation and monitoring of biological invasions. We show how the architecture for tracking biological invasions is provided by a minimum information set of Essential Variables, global collaboration on data sharing and infrastructure, and strategic contributions by countries. We show how this novel, synthetic approach to an observation system for alien species provides a tangible and attainable solution to delivering the information needed to slow the rate of new incursions and reduce the impacts of invaders. We identify three Essential Variables for Invasion Monitoring; alien species occurrence, species alien status and alien species impact. We outline how delivery of this minimum information set by joint, complementary contributions from countries and global community initiatives is possible. Country contributions are made feasible using a modular approach where all countries are able to participate and strategically build their contributions to a global information set over time. The vision we outline will deliver wide-ranging benefits to countries and international efforts to slow the rate of biological invasions and minimize their environmental impacts. These benefits will accrue over time as global coverage and information on alien species increases

No saturation in the accumulation of alien species worldwide

Although research on human-mediated exchanges of species has substantially intensified during the last centuries, we know surprisingly little about temporal dynamics of alien species accumulations across regions and taxa. Using a novel database of 45,813 first records of 16,926 established alien species, we show that the annual rate of first records worldwide has increased during the last 200 years, with 37% of all first records reported most recently (1970–2014). Inter-continental and inter-taxonomic variation can be largely attributed to the diaspora of European settlers in the nineteenth century and to the acceleration in trade in the twentieth century. For all taxonomic groups, the increase in numbers of alien species does not show any sign of saturation and most taxa even show increases in the rate of first records over time. This highlights that past efforts to mitigate invasions have not been effective enough to keep up with increasing globalization

Identification of Novel Native Autoantigens in Rheumatoid Arthritis

The majority of patients diagnosed with rheumatoid arthritis (RA) have developed autoantibodies against neoepitopes in proteins that have undergone post-translational modification, e.g., citrullination or carbamylation. There is growing evidence of their molecular relevance and their potential utility to improve diagnosis, patient stratification, and prognosis for precision medicine. Autoantibodies reacting to native proteins may also have a role in RA pathogenesis, however, their reactivity patterns remain much less studied. We hypothesized that a high-density protein array technology could shed light onto the normal and disease-related autoantibodies produced in healthy and RA patient subgroups. In an exploratory study, we investigated the global reactivity of autoantibodies in plasma pools from 15 anti-cyclic citrullinated peptide (CCP)-positive and 10 anti-CCP-negative RA patients and 10 healthy donors against more than 1600 native and unmodified human proteins using a high-density protein array. A total of 102 proteins recognized by IgG autoantibodies were identified, hereof 86 were recognized by antibodies from CCP-positive RA patients and 76 from anti-CCP-negative RA patients, but not by antibodies from healthy donors. Twenty-four of the identified autoantigens have previously been identified in synovial fluid. Multiple human proteins in their native conformation are recognized by autoantibodies from anti-CCP-positive as well as anti-CCP-negative RA patients

Identification of quantitative proteomic differences between Mycobacterium tuberculosis lineages with altered virulence

Evidence currently suggests that as a species Mycobacterium tuberculosis exhibits very little genomic sequence diversity. Despite limited genetic variability, members of the M. tuberculosis complex (MTBC) have been shown to exhibit vast discrepancies in phenotypic presentation in terms of virulence, elicited immune response and transmissibility. Here, we used qualitative and quantitative mass spectrometry tools to investigate the proteomes of seven clinically-relevant mycobacterial strains four M. tuberculosis strains, M. bovis, M. bovis BCG, and M. avium that show varying degrees of pathogenicity and virulence, in an effort to rationalize the observed phenotypic differences. Following protein preparation, liquid chromatography mass spectrometry (LC MS/MS) and data capture were carried out using an LTQ Orbitrap Velos. Data analysis was carried out using a novel bioinformatics strategy, which yielded high protein coverage and was based on high confidence peptides. Through this approach, we directly identified a total of 3788 unique M. tuberculosis proteins out of a theoretical proteome of 4023 proteins and identified an average of 3290 unique proteins for each of the MTBC organisms (representing 82% of the theoretical proteomes), as well as 4250 unique M. avium proteins (80% of the theoretical proteome). Data analysis showed that all major classes of proteins are represented in every strain, but that there are significant quantitative differences between strains. Targeted selected reaction monitoring (SRM) assays were used to quantify the observed differential expression of a subset of 23 proteins identified by comparison to gene expression data as being of particular relevance to virulence. This analysis revealed differences in relative protein abundance between strains for proteins which may promote bacterial fitness in the more virulent W. Beijing strain. These differences may contribute to this strain's capacity for surviving within the host and resisting treatment, which has contributed to its rapid spread. Through this approach, we have begun to describe the proteomic portrait of a successful mycobacterial pathogen. Data are available via ProteomeXchange with identifier PXDO04165

Classifying LISA gravitational wave burst signals using Bayesian evidence

We consider the problem of characterisation of burst sources detected with the Laser Interferometer Space Antenna (LISA) using the multi-modal nested sampling algorithm, MultiNest. We use MultiNest as a tool to search for modelled bursts from cosmic string cusps, and compute the Bayesian evidence associated with the cosmic string model. As an alternative burst model, we consider sine-Gaussian burst signals, and show how the evidence ratio can be used to choose between these two alternatives. We present results from an application of MultiNest to the last round of the Mock LISA Data Challenge, in which we were able to successfully detect and characterise all three of the cosmic string burst sources present in the release data set. We also present results of independent trials and show that MultiNest can detect cosmic string signals with signal-to-noise ratio (SNR) as low as ~7 and sine-Gaussian signals with SNR as low as ~8. In both cases, we show that the threshold at which the sources become detectable coincides with the SNR at which the evidence ratio begins to favour the correct model over the alternative.Comment: 21 pages, 11 figures, accepted by CQG; v2 has minor changes for consistency with accepted versio

Rare, Potentially Pathogenic Variants in ZNF469 Are Not Enriched in Keratoconus in a Large Australian Cohort of European Descent

Purpose: The Zinc Finger Protein 469 (ZNF469) gene has been proposed as a candidate gene for keratoconus due to the association of an upstream polymorphism (rs9938149) with the disease in two independent studies, and the role of the gene in the autosomal recessive disease Brittle Cornea Syndrome. Coding variants in ZNF469 have been assessed for association with keratoconus in several small studies, with conflicting results. We assessed rare, potentially pathogenic variants in ZNF469 for enrichment in keratoconus patients in a cohort larger than all previous studies combined. Methods: ZNF469 was sequenced in 385 Australian keratoconus patients of European descent, 346 population controls, and 230 ethnically matched screened controls by either whole exome sequencing or targeted gene sequencing. The frequency of rare and very rare potentially pathogenic variants was compared between cases and controls using χ2 or Fisher\u27s exact tests and further explored using a gene based test (Sequence Kernel Association Test [SKAT]), weighting on the rarity of variants. Results: A total of 49 rare, including 33 very rare, potentially pathogenic variants were identified across all groups. No enrichment of rare or very rare potentially pathogenic variants in ZNF469 was observed in our cases compared to the control groups following analysis using χ2 or Fisher\u27s exact tests. This finding was further supported by the SKAT results, which found no significant difference in the frequency of variants predicted to be damaging between cases and either control group (P = 0.06). Conclusions: Rare variants in ZNF469 do not contribute to keratoconus susceptibility and do not account for the association at rs9938149