Summary
Understanding how invasions by exotic plant species occur has been and still is a fundamental goal in the field of invasion ecology. Recently, research focus has shifted to below‐ground ...mechanisms of invasion, which has provided valuable insights into the role of soil microbes in the invasion process.
Research on how soil microbes drive plant invasions has produced a multitude of potential mechanisms and hypotheses, and we have taken this timely opportunity to organize these hypotheses, explore interrelations among them and with other drivers of invasion and identify areas requiring more in‐depth study.
Synthesis. This special feature brings together current research on soil microbes as drivers and responders of invasion, highlighting the methods that can be used to advance our understanding of how, when and which soil microbes play a role in the invasion process. Further advances in the field can be made by increasing realism in experiments, making wider use of molecular methods and culturing of microbial isolates and considering the importance of microbes relative to other invasion drivers.
This special feature brings together current research on soil microbes as drivers and responders of invasion, highlighting the methods that can be used to advance our understanding of how, when and which soil microbes play a role in the invasion process. Further advances in the field can be made by increasing realism in experiments, making wider use of molecular methods and culturing of microbial isolates and considering the importance of microbes relative to other invasion drivers.
The Ecology and Evolution of Alien Plants van Kleunen, Mark; Bossdorf, Oliver; Dawson, Wayne
Annual review of ecology, evolution, and systematics,
11/2018, Volume:
49, Issue:
1
Journal Article
Peer reviewed
Open access
We review the state of the art of alien plant research with emphasis on conceptual advances and knowledge gains on general patterns and drivers, biotic interactions, and evolution. Major advances ...include the identification of different invasion stages and invasiveness dimensions (geographic range, habitat specificity, local abundance) and the identification of appropriate comparators while accounting for propagule pressure and year of introduction. Developments in phylogenetic and functional trait research bear great promise for better understanding of the underlying mechanisms. Global patterns are emerging with propagule pressure, disturbance, increased resource availability, and climate matching as major invasion drivers, but species characteristics also play a role. Biotic interactions with resident communities shape invasion outcomes, with major roles for species diversity, enemies, novel weapons, and mutualists. Mounting evidence has been found for rapid evolution of invasive aliens and evolutionary responses of natives, but a mechanistic understanding requires tighter integration of molecular and phenotypic approaches. We hope the open questions identified in this review will stimulate further research on the ecology and evolution of alien plants.
•We studied the molecular interactions of various molecules (approved drugs, in vivo tested compounds) as potential blocking agents against the SARS-CoV-2 spike protein.•Five SARS-CoV-2 lineages were ...investigated (alpha, beta, gamma, delta, and C.36).•Our research incorporated various computational methods including molecular docking, ADME predictions, and molecular dynamics simulations coupled with MM/PBSA calculations.•The results of the MD simulations and MM/PBSA calculations indicated that the most favorable inhibitors were zafirlukast, pranlukast, canderastan cilexetil, saquanivir and simeprevir. Zafirlukast and simeprevir showed the most promising binding profile with an average binding energy of around –22 kcal/mol. Most of these drugs were previously considered as inhibitors of other SARS-CoV-2 proteins indicating a possible dual action on the virus.
For the last two years, the COVID-19 pandemic has continued to bring consternation on most of the world. According to recent WHO estimates, there have been more than 5.6 million deaths worldwide. The virus continues to evolve all over the world, thus requiring both vigilance and the necessity to find and develop a variety of therapeutic treatments, including the identification of specific antiviral drugs. Multiple studies have confirmed that SARS‐CoV‐2 utilizes its membrane-bound spike protein to recognize human angiotensin-converting enzyme 2 (ACE2). Thus, preventing spike-ACE2 interactions is a potentially viable strategy for COVID-19 treatment as it would block the virus from binding and entering into a host cell. This work aims to identify potential drugs using an in silico approach. Molecular docking was carried out on both approved drugs and substances previously tested in vivo. This step was followed by a more detailed analysis of selected ligands by molecular dynamics simulations to identify the best molecules that thwart the ability of the virus to interact with the ACE2 receptor. Because the SARS-CoV-2 virus evolves rapidly due to a plethora of immunocompromised hosts, the compounds were tested against five different known lineages. As a result, we could identify substances that work well on individual lineages and those showing broader efficacy. The most promising candidates among the currently used drugs were zafirlukast and simeprevir with an average binding affinity of –22 kcal/mol for spike proteins originating from various lineages. The first compound is a leukotriene receptor antagonist that is used to treat asthma, while the latter is a protease inhibitor used for hepatitis C treatment. From among the in vivo tested substances that concurrently exhibit promising free energy of binding and ADME parameters (indicating a possible oral administration) we selected the compound BDBM50136234. In conclusion, these molecules are worth exploring further by in vitro and in vivo studies against SARS-CoV-2.
RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. ...However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures.
Scientists' warning on invasive alien species Pyšek, Petr; Hulme, Philip E.; Simberloff, Dan ...
Biological reviews of the Cambridge Philosophical Society,
December 2020, Volume:
95, Issue:
6
Journal Article
Peer reviewed
Open access
ABSTRACT
Biological invasions are a global consequence of an increasingly connected world and the rise in human population size. The numbers of invasive alien species – the subset of alien species ...that spread widely in areas where they are not native, affecting the environment or human livelihoods – are increasing. Synergies with other global changes are exacerbating current invasions and facilitating new ones, thereby escalating the extent and impacts of invaders. Invasions have complex and often immense long‐term direct and indirect impacts. In many cases, such impacts become apparent or problematic only when invaders are well established and have large ranges. Invasive alien species break down biogeographic realms, affect native species richness and abundance, increase the risk of native species extinction, affect the genetic composition of native populations, change native animal behaviour, alter phylogenetic diversity across communities, and modify trophic networks. Many invasive alien species also change ecosystem functioning and the delivery of ecosystem services by altering nutrient and contaminant cycling, hydrology, habitat structure, and disturbance regimes. These biodiversity and ecosystem impacts are accelerating and will increase further in the future. Scientific evidence has identified policy strategies to reduce future invasions, but these strategies are often insufficiently implemented. For some nations, notably Australia and New Zealand, biosecurity has become a national priority. There have been long‐term successes, such as eradication of rats and cats on increasingly large islands and biological control of weeds across continental areas. However, in many countries, invasions receive little attention. Improved international cooperation is crucial to reduce the impacts of invasive alien species on biodiversity, ecosystem services, and human livelihoods. Countries can strengthen their biosecurity regulations to implement and enforce more effective management strategies that should also address other global changes that interact with invasions.
•We discuss the two main schools of thought in RNA 3D modeling: fundamental principles (‘Greek science’) versus knowledge-based (‘Babylonian science’).•We discuss the RNA Puzzles experiment for ...evaluation of RNA 3D structure prediction methods.•We discuss methods for modeling RNA–metal ion interactions.•We discuss methods for modeling RNA interactions with proteins and small molecule ligands.
RNA molecules have key functions in cellular processes beyond being carriers of protein-coding information. These functions are often dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is difficult, which has prompted the development of computational methods for structure prediction from sequence. Recent progress in 3D structure modeling of RNA and emerging approaches for predicting RNA interactions with ions, ligands and proteins have been stimulated by successes in protein 3D structure modeling.
One of the best-known general patterns in island biogeography is the species–isolation relationship (SIR), a decrease in the number of native species with increasing island isolation that is linked ...to lower rates of natural dispersal and colonization on remote oceanic islands. However, during recent centuries, the anthropogenic introduction of alien species has increasingly gained importance and altered the composition and richness of island species pools. We analyzed a large dataset for alien and native plants, ants, reptiles, mammals, and birds on 257 (sub) tropical islands, and showed that, except for birds, the number of naturalized alien species increases with isolation for all taxa, a pattern that is opposite to the negative SIR of native species. We argue that the reversal of the SIR for alien species is driven by an increase in island invasibility due to reduced diversity and increased ecological naiveté of native biota on the more remote islands.
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