Rust-Bio - a fast and safe bioinformatics library

We present Rust-Bio, the first general purpose bioinformatics library for the innovative Rust programming language. Rust-Bio leverages the unique combination of speed, memory safety and high-level syntax offered by Rust to provide a fast and safe set of bioinformatics algorithms and data structures with a focus on sequence analysis

The genome sequence and effector complement of the flax rust pathogen Melampsora lini

Rust fungi cause serious yield reductions on crops, including wheat, barley, soybean, coffee, and represent real threats to global food security. Of these fungi, the flax rust pathogen Melampsora lini has been developed most extensively over the past 80 years as a model to understand the molecular mechanisms that underpin pathogenesis. During infection, M. lini secretes virulence effectors to promote disease. The number of these effectors, their function and their degree of conservation across rust fungal species is unknown. To assess this, we sequenced and assembled de novo the genome of M. lini isolate CH5 into 21,130 scaffolds spanning 189 Mbp (scaffold N50 of 31 kbp). Global analysis of the DNA sequence revealed that repetitive elements, primarily retrotransposons, make up at least 45% of the genome. Using ab initio predictions, transcriptome data and homology searches, we identified 16,271 putative protein-coding genes. An analysis pipeline was then implemented to predict the effector complement of M. lini and compare it to that of the poplar rust, wheat stem rust and wheat stripe rust pathogens to identify conserved and species-specific effector candidates. Previous knowledge of four cloned M. lini avirulence effector proteins and two basidiomycete effectors was used to optimize parameters of the effector prediction pipeline. Markov clustering based on sequence similarity was performed to group effector candidates from all four rust pathogens. Clusters containing at least one member from M. lini were further analyzed and prioritized based on features including expression in isolated haustoria and infected leaf tissue and conservation across rust species. Herein, we describe 200 of 940 clusters that ranked highest on our priority list, representing 725 flax rust candidate effectors. Our findings on this important model rust species provide insight into how effectors of rust fungi are conserved across species and how they may act to promote infection on their hosts.This work was funded by a grant from the CSIRO Transformational Biology Capability Platform to Adnane Nemri. Claire Anderson was supported by an ARC Discovery Grant (DP120104044) awarded to David A. Jones and Peter N. Dodds

Combating stem and leaf rust of wheat: Historical perspective, impacts, and lessons learned

millions fed, food security, wheat rust, stem rust, leaf rust, Norman Borlaug,

Pre-terrestrial origin of rust in the Nakhla meteorite

The authors present quantative elemental compositions and summarize textural evidence for the pre-terrestrial origin of rust on the Nakhla meteorite. The material in question is called 'rust' because its phase composition remains unknown. Compelling evidence for the pre-terrestrial origin of the rust is found in rust veins truncated by fusion crust and preserved as faults in sutured igneous crystals. Rust veins that approach the meteorite's fusion crust become discontinuous and exhibit vugs that suggest partial decrepitation; no veins that penetrate the fusion crust have been found. Because the rust probably contains volatile compounds, it is reasonable to expect that heating near the ablation surface (formed during atmospheric entry to Earth) would encourage devolatilization of the rust. Hence, the absence of rust veins in fusion crust and vugs in rust veins near fusion crust clearly imply that the rust existed in the meteorite before atmospheric entry

Unstated contributions: how artistic inquiry can inform inter-disciplinary research

Since 1990, many creative disciplines, such as art, design and performance, have engaged increasingly with academic research. Accompanying this has been a good deal of interest in ways to employ their professional and creative practices as instruments of inquiry, just as previous disciplines have developed research methods that employ their specialist skills and knowledge. This raises questions about how research in the creative disciplines might contribute to knowledge and understanding. Research and practice in these fields may deal with matter that changes meaning with time or context, especially in art, where audiences may be expected to complete the meaning of creative works for themselves. This paper offers an oversight of these issues. It sets out some examples from the wider community that illustrate how incomplete or tacit contributions to inquiry can be a valuable and sometimes necessary part of the enterprise of creating knowledge, establishing a research model that is relevant in many areas, especially where disciplines collaborate. It goes on to set out tentative principles for such contributions.</p

Media Framing of Financial Mechanisms for Resolving Human–Predator Conflict in Namibia

The decline in carnivore populations is largely exacerbated by lethal methods used to reduce livestock depredation. Financial mechanisms are designed to limit lethal control by reducing the cost of depredation. The media can affect how the general public feel about issues like financial mechanisms but no study has been undertaken to understand the framing of this topic. This article filled this gap by using content analysis of newspapers to analyze economic incentives designed to mitigate human–carnivore conflict in Namibia. Forty-six percent of the articles were framed positively toward incentives, 24% ambivalently, 19% negatively, and 11% neutrally. Compensation was commonly framed positively whereas community-based conservation, trophy hunting, and tourism were framed ambivalently. Incentives were framed more negatively where perceived costs outweighed benefits. These results can help conservationists plan more effective communication interventions and anticipate issues that can affect the success of mitigation strategies