Accelerating antibiotic discovery through artificial intelligence

By targeting invasive organisms, antibiotics insert themselves into the ancient struggle of the host-pathogen evolutionary arms race. As pathogens evolve tactics for evading antibiotics, therapies decline in efficacy and must be replaced, distinguishing antibiotics from most other forms of drug development. Together with a slow and expensive antibiotic development pipeline, the proliferation of drug-resistant pathogens drives urgent interest in computational methods that promise to expedite candidate discovery. Strides in artificial intelligence (AI) have encouraged its application to multiple dimensions of computer-aided drug design, with increasing application to antibiotic discovery. This review describes AI-facilitated advances in the discovery of both small molecule antibiotics and antimicrobial peptides. Beyond the essential prediction of antimicrobial activity, emphasis is also given to antimicrobial compound representation, determination of drug-likeness traits, antimicrobial resistance, and de novo molecular design. Given the urgency of the antimicrobial resistance crisis, we analyze uptake of open science best practices in AI-driven antibiotic discovery and argue for openness and reproducibility as a means of accelerating preclinical research. Finally, trends in the literature and areas for future inquiry are discussed, as artificially intelligent enhancements to drug discovery at large offer many opportunities for future applications in antibiotic development.

Pre-invasion assessment of exotic bark beetle-vectored fungi to detect tree-killing pathogens

Exotic diseases and pests of trees have caused continental-scale disturbances in forest ecosystems and industries, and their invasions are considered largely unpredictable. We tested the concept of pre-invasion assessment of not-yet invasive organisms, which enables empirical risk assessment of potential invasion and impact. Our example assesses fungi associated with Old World bark and ambrosia beetles and their potential to impact North American trees. We selected 55 Asian and European scolytine beetle species using host-use, economic, and regulatory criteria. We isolated 111 of their most consistent fungal associates and tested their effect on four important Southeastern American pine and oak species. Our test dataset found no highly virulent pathogens that should be classified as an imminent threat. Twenty-two fungal species were minor pathogens, which may require context-dependent response for their vectors at North American borders, while most of the tested fungi displayed no significant impact. Our results are significant in three ways: they ease the concerns over multiple overseas pests suspected of heightened potential risk; they provide basis for focus on the prevention of introduction and establishment of species that may be of consequence; and they demonstrate that pre-invasion assessment, if scaled up, can support practical risk assessment of exotic pathogens.

Promoting Effective Biosecurity Governance: Using Tripwires to Anticipate and Ameliorate Potentially Harmful Development Trends

Synthetic biology is a new, rapidly growing interdisciplinary field which seeks to use engineering techniques to alter and construct new biological components, devices, and systems. The rate of synthetic biology development and research has increased over the past two decades in both industry and academia (Ahteensuu 2017). Applications include medicine (new vaccines, delivery of therapeutics, and treatments), energy (biofuels), environmental remediation, food production, and general industry (detergents, adhesives, perfumes) (Evans and Selgelid 2015; Gronvall 2015). While synthetic biology heralds advances in these fields, its techniques could also be adapted for malicious purposes and used by terrorist organizations, rogue actors, or hostile nations to create dangerous pathogens, invasive organisms, or other disruptive biological agents (Yeh et al. 2012). Such potential makes synthetic biology a dual-use research area of concern (DURC) as the same techniques can be used to benefit or harm people, animals, environments, technology, or nations (Getz and Dellaire 2018). To cope with threats arising from synthetic biology’s dual-use nature, biosecurity is needed to prevent, detect, and attribute biological attacks.

Honey as a Source of Environmental DNA for the Detection and Monitoring of Honey Bee Pathogens and Parasites

Environmental DNA (eDNA) has been proposed as a powerful tool to detect and monitor cryptic, elusive, or invasive organisms. We recently demonstrated that honey constitutes an easily accessible source of eDNA. In this study, we extracted DNA from 102 honey samples (74 from Italy and 28 from 17 other countries of all continents) and tested the presence of DNA of nine honey bee pathogens and parasites (Paenibacillus larvae, Melissococcus plutonius, Nosema apis, Nosema ceranae, Ascosphaera apis,Lotmaria passim, Acarapis woodi, Varroa destructor, and Tropilaelaps spp.) using qualitative PCR assays. All honey samples contained DNA from V. destructor, confirming the widespread diffusion of this mite. None of the samples gave positive amplifications for N. apis, A. woodi, and Tropilaelaps spp. M. plutonius was detected in 87% of the samples, whereas the other pathogens were detected in 43% to 57% of all samples. The frequency of Italian samples positive for P. larvae was significantly lower (49%) than in all other countries (79%). The co-occurrence of positive samples for L. passim and A. apis with N. ceranae was significant. This study demonstrated that honey eDNA can be useful to establish monitoring tools to evaluate the sanitary status of honey bee populations.

Total nitrate uptake by an invasive benthic foraminifer in marine sediments

Oxygen availability impacts the marine nitrogen cycle at a range of spatial and temporal scales. Invasive organisms have shown to sustainably affect sediment geochemistry and benthic ecology. Nonionella sp. T1 was recently described as an invasive benthic foraminifer in the North Sea region. Here, we demonstrate the impact of this denitrifying species on the foraminifera fauna and the nitrogen cycle of the Gullmar Fjord (Sweden). The foraminifera contribution to benthic denitrification was estimated by coupling living foraminifera micro-distribution, denitrification rate measurement and sedimentary nitrate 2D distribution. Nonionella sp. T1 dominated the foraminifera fauna and could denitrify up to 50–100 % of nitrate porewater in oxygenated bottom waters of the fjord. Contrastingly, at the deepest hypoxic low-nitrate station, denitrifying foraminifera species were scarce and did not contribute to nitrogen removal (~ 5 %). Our study showed that benthic foraminifera can be a major contributor of nitrogen mitigation in oxic coastal ecosystems and should be included in ecological and diagenetic models aiming at understanding biogeochemical cycles coupled to nitrogen.

Introduction

This chapter introduces San Cristóbal Island, and specifically the village of El Progreso, which occupies a Zone of Special Use inside the Galápagos National Park. It outlines various problems faced by the park, especially those associated with invasive organisms and the growth of tourism. It juxtaposes the image of a people-free nature park with the growth of novel or emerging ecosystems, and discusses current disagreements in biological conservation. It presents the study of historic human landscape transformation within the framework of Historical Ecology by combining history, ecology, and archaeology. A chapter by chapter framework of the book is presented.

Research on Spartina alterniflora using molecular biological techniques: an overview

Biological invasion is a global issue. Since the double helix structure of DNA molecule was discovered in 1953, more scientific studies have focused on the structure and function of biological macromolecules in invasive organisms using molecular biology techniques, which has contributed to our understanding of their competitive advantages and invasion mechanisms. As a coastal invasive species, there has been considerable interest in Spartina alterniflora. Here we summarise previous studies investigating S. alterniflora using molecular biological techniques from the individual, population and application perspectives. We hope this article will be helpful in future studies on and in the management and utilisation of S. alterniflora in wetlands.

Spotlight on the monitoring of the invasion of a carabid beetle on an oceanic islandover a 100 year period

The flightless beetle Merizodus soledadinus, originating from the Falkland Islands, was introduced to the sub-Antarctic Kerguelen Islands. We compiled the existing information on ship visits and landings on these islands to confirm the introduction date of M. soledadinus. Using data available in the literature, in addition to collecting more than 2000 presence/absence records of M. soledadinus over the 1991-2018 period, we tracked changes of its abundance and geographical distribution. The range expansion of this nonflying insect was initially slow, but has accelerated over the past two decades in parallel to local increased abundances of the insect’s populations. Human activities may have facilitated colonization of some localities by M. soledadinus which is now widely present in the eastern part of the Kerguelen archipelago. This predatory insect represents a major threat for the native invertebrate fauna; in particular, the wingless flies Anatalanta aptera and Calycopteryx moseleyi which are locally displaced and/or eliminated by the beetle. If no control measures, let alone eradication, are practicable, it is essential to limit the transport of this invasive insect along with human activities. Since 2006, the Kerguelen Islands have had the status of a nature reserve, making these results of significant interests for the management of this archipelago, and more generally, emphasizing the importance of long-term biomonitoring programmes for assessing and predicting changes in the distribution of invasive organisms. Strict biosecurity measures have now been established at the Kerguelen Islands, with even greater attention paid to visits to remote sites not yet colonized by M. soledadinus.

Prevention of invasive species in the context of lower secondary education

Biological invasions are recognised as a potentially major threat to biodiversity and may have considerable economic and social effects. Public, including pupils, attitudes may have large implications for invasive species management in terms of prevention, early warning and eradication success, but significant is the relations between the lay public’s visions of nature, their knowledge about non-native species and their perceptions of invasive species management. The more direct experience people have with the impact of invasive species, the more likely they will be able to understand the potential benefits of management programmes. The aim of our work was to prepare educational materials about invasive organisms for elementary schools. Some of them were subsequently applied directly in practice as part of an excursion in a schoolyard in west Slovakia, where up to six species of invasive plants were identified in the close proximity to the school. Keywords: Biological invasions, prevention, education, excursion.