Suchergebnisse

[Background] The phylogenetic distribution of large-scale genome structure (i.e. mosaic compositional patchiness) has been explored mainly by analytical ultracentrifugation of bulk DNA. However, with the availability of large, good-quality chromosome sequences, and the recently developed computational methods to directly analyze patchiness on the genome sequence, an evolutionary comparative analysis can be carried out at the sequence level. [Results] The local variations in the scaling exponent of the Detrended Fluctuation Analysis are used here to analyze large-scale genome structure and directly uncover the characteristic scales present in genome sequences. Furthermore, through shuffling experiments of selected genome regions, computationally-identified, isochore-like regions were identified as the biological source for the uncovered large-scale genome structure. The phylogenetic distribution of short- and large-scale patchiness was determined in the best-sequenced genome assemblies from eleven eukaryotic genomes: mammals (Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus, and Canis familiaris), birds (Gallus gallus), fishes (Danio rerio), invertebrates (Drosophila melanogaster and Caenorhabditis elegans), plants (Arabidopsis thaliana) and yeasts (Saccharomyces cerevisiae). We found large-scale patchiness of genome structure, associated with in silico determined, isochore-like regions, throughout this wide phylogenetic range. [Conclusion] Large-scale genome structure is detected by directly analyzing DNA sequences in a wide range of eukaryotic chromosome sequences, from human to yeast. In all these genomes, large-scale patchiness can be associated with the isochore-like regions, as directly detected in silico at the sequence level. ; This work was supported by the Spanish Government (BIO2005-09116-C03-01) and Plan Andaluz de Investigación (CVI-162, P06-FQM-01858, P07-FQM-03163 and TIC-640).

The prevalence of poisoning events due to harmful algal blooms (HABs) has declined during the last two decades through monitoring programs and legislation, implemented mainly for bivalves. However, new toxin vectors and emergent toxins pose a challenge to public health. Several locations on the Portuguese coast were surveyed between 2009 and 2010 for three distinct biotoxin groups [saxitoxin (PST), spirolide (SPX) and okadaic acid (OA)], in 14 benthic species of mollusks and echinoderms. Our main goals were to detect new vectors and unravel the seasonal and geographical patterns of these toxins. PSTs were analyzed by the Lawrence method, SPXs by LC-MS/MS, and OA by LC-MS/MS and UPLC-MS/MS. We report 16 new vectors for these toxins in the North Atlantic. There were differences in toxin contents among species, but no significant geographical or seasonal patterns were found. Our results suggest that legislation should be adjusted to extend the monitoring of marine toxins to a wider range of species besides edible bivalves. ; info:eu-repo/semantics/publishedVersion

The potential hazard of 1080 baiting for predators to 14 species of non-target mammals in the pastoral
areas of Western Australia and a further six from Western Australia's Fitzgerald River National Park,
was assessed by comparing projected doses of 1080 (based on consumption of non-toxic bait by captive
animals in the absence of alternative food) with the approximate lethal dose of 1080 for each species.
These figures suggested that individuals from 12 species were potentially at risk from crackle baits, while
only individuals from Dasyurus hallucatus, Ningaui spp., Sminthopsis crassicaudata, Planigale maculata,
one population of Leggadina forresti and one population of Sminthopsis ooldea were potentially
endangered by meat baits.
Tests using the native mammals Zyzomys argurus and Pseudomys hermannsbergensis and laboratory
mice (Mus musculus) and laboratory rats (Rattus norvegicus) showed that individuals of all species
reduced their consumption of toxic bait relative to non-toxic bait, although this did not prevent three
of five rats and one of three P. hermannsbergensis from being killed.

Although attacks on humans by Australian magpies (Gymnorhina tibicen) are a source of significant wildlife–human conflict in urban areas of Australia, little is known about the patterns of attack by these birds. Such information is essential for the development of sound management plans for this species. We examined the attack behaviour of 48 aggressive magpies from Brisbane during September–October 1999, paying particular attention to the types of intruders targeted. All attacking birds were male. A clear majority (71%) of birds attacked only one intruder type, with about half attacking pedestrians only; similar proportions targeted cyclists (8%) only and mail deliverers (10%) only. While all intruding cyclists and mail deliverers were attacked, magpies did not attack all pedestrian intruders, suggesting possible discrimination within this category. Management implications for these intruder types are discussed.

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. ; Most animals, including sponges (Porifera), have species-specific microbiomes. Which genetic or environmental factors play major roles structuring the microbial community at the intraspecific level in sponges is, however, largely unknown. In this study, we tested whether geographic location or genetic structure of conspecific sponges influences their microbial assembly. For that, we used three sponge species with different rates of gene flow, and collected samples along their entire distribution range (two from the Mediterranean and one from the Southern Ocean) yielding a total of 393 samples. These three sponge species have been previously analysed by microsatellites or single nucleotide polymorphisms, and here we investigate their microbiomes by amplicon sequencing of the microbial 16S rRNA gene. The sponge Petrosia ficiformis, with highly isolated populations (low gene flow), showed a stronger influence of the host genetic distance on the microbial composition than the spatial distance. Host-specificity was therefore detected at the genotypic level, with individuals belonging to the same host genetic cluster harbouring more similar microbiomes than distant ones. On the contrary, the microbiome of Ircinia fasciculata and Dendrilla antarctica - both with weak population structure (high gene flow) - seemed influenced by location rather than by host genetic distance. Our results suggest that in sponge species with high population structure, the host genetic cluster influence the microbial community more than the geographic location. ; European Union's Horizon 2020 Research and Innovation Actions, Grant/Award Number: 679849; Marie Skłodowska-Curie Individual Fellowships, Grant/Award Number: 796011

Context The mitigation of feral pig (Sus scrofa) impacts in north Queensland's World Heritage tropical rainforests is constrained by the lack of an effective and target-specific poison baiting method. Aims This study aimed to determine whether easily implemented bait presentation methods or seasonal variation in bait acceptability could be used to selectively reduce the consumption of feral pig baits by non-target species. Methods We exposed manufactured feral pig baits to pigs and non-target species in the field, and compared bait encounter, sampling and consumption rates for different functional groups of species among three different types of bait presentation and composition. We then exposed baits under different seasonal conditions and related bait encounter and consumption by different functional groups to seasonally variable phenomena. Key results Shallow burial greatly reduced bait consumption by most non-target species, but not dingoes (Canis lupus dingo). Nocturnal bait distribution and seasonal baiting were less useful. Pigs showed substantial seasonal variation in physiological condition, suggesting that pigs should be more susceptible to consuming novel foods, such as baits, after periods of low rainfall. However, few pigs consumed the manufactured baits used in this study. Conclusions Manufactured baits are not currently suitable for widespread use in the region. However, shallow burial should provide an effective method of reducing non-target bait-take if baits can be made more attractive and acceptable to pigs and less acceptable to dingoes. Implications Future efforts to enable effective feral pig control in the region should focus on developing baiting materials that are more attractive to pigs and unappealing to dingoes.

As the therapeutic use of sacred plants and fungi becomes increasingly accepted by Western medicine, a tug of war has been taking place between those who advocate the traditional consumption of whole organisms and those who defend exclusively the utilization of purified compounds. The attempt to reduce organisms to single active principles is challenged by the sheer complexity of traditional medicine. Ayahuasca, for example, is a concoction of at least two plant species containing multiple psychoactive substances with complex interactions. Similarly, cannabis contains dozens of psychoactive substances whose specific combinations in different strains correspond to different types of therapeutic and cognitive effects. The "entourage effect" refers to the synergistic effects of the multiple compounds present in whole organisms, which may potentiate clinical efficacy while attenuating side effects. In opposition to this view, mainstream pharmacology is adamant about the need to use purified substances, presumably more specific and safe. In this chapter, I will review the evidence on both sides to discuss the scientific, economic, and political implications of this controversy. The evidence indicates that it is time to embrace the therapeutic complexity of psychedelics. ; 2019-07-30

Meat-based baits are currently used for the control of the exotic red fox (Vulpes vulpes) in south-eastern Australia. Thirty-one quadrupedal endemic mammals are considered to be potentially bait consuming (PBC) and may be exposed to bait toxicants. Mechanical toxicant ejectors may be more selective if some PBC species cannot apply enough upward force to trigger them. A simple relationship between body mass and pulling force was sought to enable estimates of ejector specificity to be made. The pulling force applied to ejector baits was measured for the red fox and six endemic mammals. The relationship between body mass and pulling force was highly significant (P < 0.001) and the resulting regression equation was used to estimate the highest pulling forces for 31 quadrupedal mammals based upon the largest body mass recorded for each species. In a sample of 640 foxes, taken by a range of methods in south-eastern Australia, the lowest adult body mass detected from January to September was 3 kg and declined only when cubs were present in the population from October to December. An ejector trigger force of 26.46 N was estimated to allow foxes weighing >3 kg to trigger the device, while eliminating exposure of 26 of the 31 PBC mammals. Appropriate toxicant selection and dose rates may ensure that four out of five susceptible mammals are less likely to be affected by unwanted exposure.

ABSTRACT Most animals, including sponges (Porifera), have species‐specific microbiomes. Which genetic or environmental factors play major roles structuring the microbial community at the intraspecific level in sponges is, however, largely unknown. In this study, we tested whether geographic location or genetic structure of conspecific sponges influences their microbial assembly. For that, we used three sponge species with different rates of gene flow, and collected samples along their entire distribution range (two from the Mediterranean and one from the Southern Ocean) yielding a total of 393 samples. These three sponge species have been previously analysed by microsatellites or single nucleotide polymorphisms, and here we investigate their microbiomes by amplicon sequencing of the microbial 16S rRNA gene. The sponge Petrosia ficiformis, with highly isolated populations (low gene flow), showed a stronger influence of the host genetic distance on the microbial composition than the spatial distance. Host‐specificity was therefore detected at the genotypic level, with individuals belonging to the same host genetic cluster harbouring more similar microbiomes than distant ones. On the contrary, the microbiome of Ircinia fasciculata and Dendrilla antarctica ‐ both with weak population structure (high gene flow) ‐ seemed influenced by location rather than by host genetic distance. Our results suggest that in sponge species with high population structure, the host genetic cluster influence the microbial community more than the geographic location. ; ACKNOWLEDGEMENTS This project has received funding from the European Union's Horizon 2020 Research and Innovation Programme under the Marie Skłodowska‐Curie Individual Fellowships Grant Agreement No. 796011 ('DeepSym'), and Grant Agreement No. 679849 ('SponGES'). We thank the team around Andre Franke at the Institute of Clinical Molecular Biology, Kiel, for sequencing support. We also want to thank Shaun Nielsen for support and guidance through data analysis. Finally, we ...

Abstract Background Ophiocordyceps unilateralis is an outstanding insect fungus for its biology to manipulate host ants' behavior and for its extreme host-specificity. Through the sequencing and annotation of Ophiocordyceps polyrhachis-furcata , a species in the O. unilateralis species complex specific to the ant Polyrhachis furcata , comparative analyses on genes involved in pathogenicity and virulence between this fungus and other fungi were undertaken in order to gain insights into its biology and the emergence of host specificity. Results O. polyrhachis-furcata possesses various genes implicated in pathogenicity and virulence common with other fungi. Overall, this fungus possesses protein-coding genes similar to those found on other insect fungi with available genomic resources ( Beauveria bassiana, Metarhizium robertsii (formerly classified as M. anisopliae s.l. ) , Metarhizium acridum, Cordyceps militaris, Ophiocordyceps sinensis ). Comparative analyses in regard of the host ranges of insect fungi showed a tendency toward contractions of various gene families for narrow host-range species, including cuticle-degrading genes (proteases, carbohydrate esterases) and some families of pathogen-host interaction (PHI) genes. For many families of genes, O. polyrhachis-furcata had the least number of genes found; some genes commonly found in other insect fungi are even absent (e.g. Class 1 hydrophobin). However, there are expansions of genes involved in 1) the production of bacterial-like toxins in O. polyrhachis-furcata , compared with other entomopathogenic fungi, and 2) retrotransposable elements. Conclusions The gain and loss of gene families helps us understand how fungal pathogenicity in insect hosts evolved . The loss of various genes involved throughout the pathogenesis for O. unilateralis would result in a reduced capacity to exploit larger ranges of hosts and therefore in the different level of host specificity, while the expansions of other gene families suggest an adaptation to particular environments with unexpected strategies like oral toxicity, through the production of bacterial-like toxins, or sophisticated mechanisms underlying pathogenicity through retrotransposons.

Abstract
The magnitude and duration of vertebrate viremia are critical determinants of arbovirus transmission, geographic spread, and disease severity—yet, mechanisms determining arbovirus viremia levels are poorly defined. Previous studies have drawn associations between in vitro virion-glycosaminoglycan (GAG) interactions and in vivo clearance kinetics of virions from blood circulation. From these observations, it is commonly hypothesized that GAG-binding virions are rapidly removed from circulation due to ubiquitous expression of GAGs by vascular endothelial cells, thereby limiting viremia. Using an in vivo model for viremia, we compared the vascular clearance of low and enhanced GAG-binding viral variants of chikungunya, eastern- (EEEV), and Venezuelan- (VEEV) equine encephalitis viruses. We find GAG-binding virions are more quickly removed from circulation than their non-GAG-binding variant; however individual clearance kinetics vary between GAG-binding viruses, from swift (VEEV) to slow removal from circulation (EEEV). Remarkably, we find phagocytes are required for efficient vascular clearance of some enhanced GAG-binding virions. Moreover, transient depletion of vascular heparan sulfate impedes vascular clearance of only some GAG-binding viral variants and in a phagocyte-dependent manner, implying phagocytes can mediate vascular GAG-virion interactions. Finally, in direct contrast to mice, we find enhanced GAG-binding EEEV is resistant to vascular clearance in avian hosts, suggesting the existence of species-specificity in virion-GAG interactions. In summary, these data support a role for GAG-mediated clearance of some viral particles from the blood circulation, illuminate the potential of blood-contacting phagocytes as a site for GAG-virion binding, and suggest a role for species-specific GAG structures in arbovirus ecology.

Novel dissimilatory perchlorate-reducing bacteria (DPRB) were isolated from enrichments conducted under conditions different from those of all previously described DPRB. Strain LT-1(T) was enriched using medium buffered at pH 6.6 with 2-(N-morpholino)ethanesulfonic acid (MES) and had only 95% 16S rRNA gene identity with its closest relative, Azonexus caeni. Strain MP(T) was enriched in the cathodic chamber of a perchlorate-reducing bioelectrical reactor (BER) and together with an additional strain, CR (99% 16S rRNA gene identity), had 97% 16S rRNA gene identity with Propionivibrio limicola. The use of perchlorate and other electron acceptors distinguished strains MP(T) and CR from P. limicola physiologically. Strain LT-1(T) had differences in electron donor utilization and optimum growth temperatures from A. caeni. Strains LT-1(T) and MP(T) are the first DPRB to be described in the Betaproteobacteria outside of the Dechloromonas and Azospira genera. On the basis of phylogenetic and physiological features, strain LT-1(T) represents a novel genus in the Rhodocyclaceae; strain MP(T) represents a novel species within the genus Propionivibrio. The names Dechlorobacter hydrogenophilus gen. nov., sp. nov and Propionivibrio militaris sp. nov. are proposed.

The samurai wasp, Trissolcus japonicus, is the primary natural enemy of the invasive brown marmorated stink bug, Halyomorpha halys, in its native range of Asia. Laboratory tests have found that the wasp can parasitize numerous native pentatomid species in North America, yet many potentially influential factors involved with T. japonicus host acceptance and host suitability are understudied. In this study we evaluated the effects of host related semiochemicals and parental host species on T. japonicus host foraging behavior and host parasitism. To address possible influences of parental host species, separate parasitoid lines were established using H. halys and native predatory pentatomid Podisus maculiventris eggs as hosts. Female T. japonicus from both host types were exposed to soybean (Glycine max) leaf surfaces contaminated by adult kairomones of either host species in behavioral assays. Females from each host type were also subject to no-choice tests in which they were exposed to either H. halys or P. maculiventris egg masses in large mesh cages. Each female used in the no-choice tests was weighed and their right hind tibiae were measured to identify possible phenotypic plasticity. Results from the behavioral assays suggest that T. japonicus exhibits some degree of host fidelity while searching for hosts. Females which emerged from P. maculiventris eggs resided for equal amounts of time on leaves contaminated with kairomones from either stink bug species. Differences in no-choice test performance were not found between the two host types, as parasitism rates and host suitability were determined to be dependent on exposed host species and not the parasitoid parental host species. T. japonicus which emerged from H. halys possessed longer right hind tibiae and weighed roughly twice as much as wasps which emerged from P. maculiventris. ; USDAARS Cooperative AgreementUnited States Department of Agriculture (USDA)USDA Agricultural Research Service [58-8010-5-012] ; We thank Kathleen Tatman and Patricia Stout for their technical assistance, and Dr. Douglas Tallamy for comments on an earlier version of the manuscript. We would also like to thank the Xinqiao Jia research group at the University of Delaware for providing equipment to acquire our parasitoid weight data. This research was supported by the USDAARS Cooperative Agreement #58-8010-5-012. ; Public domain authored by a U.S. government employee

SUMO belongs to the ubiquitin-like family (UbL) of protein modifiers. SUMO is conserved among eukaryotes and is essential for the regulation of processes such as DNA damage repair, transcription, DNA replication and mitosis. UbL modification of proteins occurs via a specific enzymatic cascade formed by the crosstalk between the E1-activating enzyme, the E2-conjugating enzyme and the E3-ligase. An essential discrimination step in all UbL modifiers corresponds to the interaction between E1 and E2 enzymes, which is mediated by the recruitment of the E2 to the UFD domain (Ubiquitin-Fold Domain) of the E1 enzyme. To gain insights in the properties of this interface, we have compared the structures of the complexes between E1 UFD domain and E2 in human and yeast, revealing two alternative UFD platforms that interact with a conserved E2. Comparative sequence analysis of the E1 UFD domain indicates that the E2 binding region has been conserved across phylogenetic closely related species, in which higher sequence conservation can be found in the E2 binding region than in the entire UFD domain. These distinctive strategies for E1-E2 interactions through the UFD domain might be the consequence of a high selective pressure to ensure specificity of each modifier conjugation system. ; This work was supported by grants from the Ministerio de Economia y Competitividad BFU2015-66417-P (MINECO/FEDER) to DR, and from the Generalitat de Catalunya (2009SGR 09626) and from the European Commission (ERC-2014-PoC-671839) to LML. B.L. acknowledges his scholarship to the China Scholarship Council program from the Chinese government. ; Peer reviewed

We provide experimental and theoretical understanding on fundamental processes taking place at room temperature when a fluorinated fullerene dopant gets close to a metal surface. By employing scanning tunneling microscopy and photoelectron spectroscopies, we demonstrate that the on-surface integrity of C60F48 depends on the interaction with the particular metal it approaches. Whereas on Au(111) the molecule preserves its chemical structure, on more reactive surfaces such as Cu(111) and Ni(111), molecules interacting with the bare metal surface lose the halogen atoms and transform to C60. Though fluorine–metal bonding can be detected depending on the molecular surface density, no ordered fluorine structures are observed. We show the implications of the metal-dependent de-fluorination in the electronic structure of the molecules and the energy alignment at the molecule–metal interface. Molecular dynamics simulations with ReaxFF reactive force field corroborate the experimental facts and provide a detailed mechanistic picture of the surface-induced de-fluorination, which involves the rotation of the molecule on the surface. Outstandingly, a thermodynamic analysis indicates that the effect of the metal surface is lowering and diminishing the energy barrier for C–F cleave, demonstrating the catalytic role of the surface. The present study contributes to in-depth knowledge of the mechanisms that affect the degree of stability of chemical species on surfaces, which is essential to advance our understanding of the chemical reactivity of metals and their role in on-surface chemical reactions. ; This work has been supported by the Spanish Government under projects PID2019-110907GB-I00, MAT2016-77852-C2-1-R (AEI/FEDER, UE), RTI2018-096273-B-I00, the "Severo Ochoa" Program for Centers of Excellence in R&D (SEV-2015-0496) and the Generalitat de Catalunya 2017-SGR668. R. P. R. has been developing this work as part of his doctorate in Materials Science at the Universitat Autònoma de Barcelona (UAB). D. C. M. is supported by the European Union's Horizon 2020 Research and Innovation Programme under Marie Sklodowska-Curie grant agreement No. 6655919. O. S. is grateful for the support by the Center for Absorption in Science of the Ministry of Immigrant Absorption and the Committee for Planning and Budgeting of the Council for Higher Education in Israel under the framework of the KAMEA Program. We thank CESGA Supercomputing center for technical support and computer time at the supercomputer Finisterrae II. We are indebted to G. Sauthier from the ICN2 Photoemission Spectroscopy Facility. We are grateful to M. Paradinas and A. Mugarza from ICN2 for providing the Ni(111) crystal. ; Peer reviewed