The new COST Action European Venom Network (EUVEN)—synergy and future perspectives of modern venomics

Venom research is a highly multidisciplinary field that involves multiple subfields of biology, informatics, pharmacology, medicine, and other areas. These different research facets are often technologically challenging and pursued by different teams lacking connection with each other. This lack of coordination hampers the full development of venom investigation and applications. The COST Action CA19144–European Venom Network was recently launched to promote synergistic interactions among different stakeholders and foster venom research at the European level

Modern venomics – Current insights, novel methods and future perspectives in biological and applied animal venom research

Venoms have evolved >100 times in all major animal groups, and their components, known as toxins, have been fine-tuned over millions of years into highly effective biochemical weapons. There are many outstanding questions on the evolution of toxin arsenals, such as how venom genes originate, how venom contributes to the fitness of venomous species, and which modifications at the genomic, transcriptomic, and protein level drive their evolution. These questions have received particularly little attention outside of snakes, cone snails, spiders, and scorpions. Venom compounds have further become a source of inspiration for translational research using their diverse bioactivities for various applications. We highlight here recent advances and new strategies in modern venomics and discuss how recent technological innovations and multi-omic methods dramatically improve research on venomous animals. The study of genomes and their modifications through CRISPR and knockdown technologies will increase our understanding of how toxins evolve and which functions they have in the different ontogenetic stages during the development of venomous animals. Mass spectrometry imaging combined with spatial transcriptomics, in situ hybridization techniques, and modern computer tomography gives us further insights into the spatial distribution of toxins in the venom system and the function of the venom apparatus. All these evolutionary and biological insights contribute to more efficiently identify venom compounds, which can then be synthesized or produced in adapted expression systems to test their bioactivity. Finally, we critically discuss recent agrochemical, pharmaceutical, therapeutic, and diagnostic (so-called translational) aspects of venoms from which humans benefit

Isolation of Hox Cluster Genes from Insects Reveals an Accelerated Sequence Evolution Rate

Among gene families it is the Hox genes and among metazoan animals it is the insects (Hexapoda) that have attracted particular attention for studying the evolution of development. Surprisingly though, no Hox genes have been isolated from 26 out of 35 insect orders yet, and the existing sequences derive mainly from only two orders (61% from Hymenoptera and 22% from Diptera). We have designed insect specific primers and isolated 37 new partial homeobox sequences of Hox cluster genes (lab, pb, Hox3, ftz, Antp, Scr, abd-a, Abd-B, Dfd, and Ubx) from six insect orders, which are crucial to insect phylogenetics. These new gene sequences provide a first step towards comparative Hox gene studies in insects. Furthermore, comparative distance analyses of homeobox sequences reveal a correlation between gene divergence rate and species radiation success with insects showing the highest rate of homeobox sequence evolution

Potential pitfalls of modelling ribosomal RNA data in phylogenetic tree reconstruction: Evidence from case studies in the Metazoa

<p>Abstract</p> <p>Background</p> <p>Failure to account for covariation patterns in helical regions of ribosomal RNA (rRNA) genes has the potential to misdirect the estimation of the phylogenetic signal of the data. Furthermore, the extremes of length variation among taxa, combined with regional substitution rate variation can mislead the alignment of rRNA sequences and thus distort subsequent tree reconstructions. However, recent developments in phylogenetic methodology now allow a comprehensive integration of secondary structures in alignment and tree reconstruction analyses based on rRNA sequences, which has been shown to correct some of these problems. Here, we explore the potentials of RNA substitution models and the interactions of specific model setups with the inherent pattern of covariation in rRNA stems and substitution rate variation among loop regions.</p> <p>Results</p> <p>We found an explicit impact of RNA substitution models on tree reconstruction analyses. The application of specific RNA models in tree reconstructions is hampered by interaction between the appropriate modelling of covarying sites in stem regions, and excessive homoplasy in some loop regions. RNA models often failed to recover reasonable trees when single-stranded regions are excessively homoplastic, because these regions contribute a greater proportion of the data when covarying sites are essentially downweighted. In this context, the RNA6A model outperformed all other models, including the more parametrized RNA7 and RNA16 models.</p> <p>Conclusions</p> <p>Our results depict a trade-off between increased accuracy in estimation of interdependencies in helical regions with the risk of magnifying positions lacking phylogenetic signal. We can therefore conclude that caution is warranted when applying rRNA covariation models, and suggest that loop regions be independently screened for phylogenetic signal, and eliminated when they are indistinguishable from random noise. In addition to covariation and homoplasy, other factors, like non-stationarity of substitution rates and base compositional heterogeneity, can disrupt the signal of ribosomal RNA data. All these factors dictate sophisticated estimation of evolutionary pattern in rRNA data, just as other molecular data require similarly complicated (but different) corrections.</p

Toxins from scratch? Diverse, multimodal gene origins in the predatory robber fly Dasypogon diadema indicate a dynamic venom evolution in dipteran insects

BACKGROUND: Venoms and the toxins they contain represent molecular adaptations that have evolved on numerous occasions throughout the animal kingdom. However, the processes that shape venom protein evolution are poorly understood because of the scarcity of whole-genome data available for comparative analyses of venomous species. RESULTS: We performed a broad comparative toxicogenomic analysis to gain insight into the genomic mechanisms of venom evolution in robber flies (Asilidae). We first sequenced a high-quality draft genome of the hymenopteran hunting robber fly Dasypogon diadema, analysed its venom by a combined proteotranscriptomic approach, and compared our results with recently described robber fly venoms to assess the general composition and major components of asilid venom. We then applied a comparative genomics approach, based on 1 additional asilid genome, 10 high-quality dipteran genomes, and 2 lepidopteran outgroup genomes, to reveal the evolutionary mechanisms and origins of identified venom proteins in robber flies. CONCLUSIONS: While homologues were identified for 15 of 30 predominant venom protein in the non-asilid genomes, the remaining 15 highly expressed venom proteins appear to be unique to robber flies. Our results reveal that the venom of D. diadema likely evolves in a multimodal fashion comprising (i) neofunctionalization after gene duplication, (ii) expression-dependent co-option of proteins, and (iii) asilid lineage-specific orphan genes with enigmatic origin. The role of such orphan genes is currently being disputed in evolutionary genomics but has not been discussed in the context of toxin evolution. Our results display an unexpected dynamic venom evolution in asilid insects, which contrasts the findings of the only other insect toxicogenomic evolutionary analysis, in parasitoid wasps (Hymenoptera), where toxin evolution is dominated by single gene co-option. These findings underpin the significance of further genomic studies to cover more neglected lineages of venomous taxa and to understand the importance of orphan genes as possible drivers for venom evolution

Vegetation and environmental responses to climate forcing during the Last Glacial Maximum and deglaciation in the East Carpathians: attenuated response to maximum cooling and increased biomass burning

The Carpathian Mountains were one of the main mountain reserves of the boreal and cool temperate flora during the Last Glacial Maximum (LGM) in East-Central Europe. Previous studies demonstrated Lateglacial vegetation dynamics in this area; however, our knowledge on the LGM vegetation composition is very limited due to the scarcity of suitable sedimentary archives. Here we present a new record of vegetation, fire and lacustrine sedimentation from the youngest volcanic crater of the Carpathians (Lake St Anne, Lacul Sfanta Ana, Szent-Anna-to) to examine environmental change in this region during the LGM and the subsequent deglaciation. Our record indicates the persistence of boreal forest steppe vegetation (with Pinus, Betula, Salix, Populus and Picea) in the foreland and low mountain zone of the East Carpathians and Juniperus shrubland at higher elevation. We demonstrate attenuated response of the regional vegetation to maximum global cooling. Between similar to 22,870 and 19,150 cal yr BP we find increased regional biomass burning that is antagonistic with the global trend. Increased regional fire activity suggests extreme continentality likely with relatively warm and dry summers. We also demonstrate xerophytic steppe expansion directly after the LGM, from similar to 19,150 cal yr BP, and regional increase in boreal woodland cover with Pinus and Betula from 16,300 cal yr BP. Plant macrofossils indicate local (950 m a.s.1.) establishment of Betula nana and Betula pubescens at 15,150 cal yr BP, Pirzus sylvestris at 14,700 cal yr BP and Larix decidua at 12,870 cal yr BP. Pollen data furthermore support population genetic inferences regarding the regional presence of some temperate deciduous trees during the LGM (Fagus sylvatica, Coiylus avellana, Fraxinus excelsior). Our sedimentological data also demonstrate intensified aeolian dust accumulation between 26,000 and 20,000 cal yr BP. (C) 2014 Elsevier Ltd. All rights reserved

Response to comment on "Phylogenomics resolves the timing and pattern of insect evolution"

Tong et al. comment on the accuracy of the dating analysis presented in our work on the phylogeny of insects and provide a reanalysis of our data. They replace log-normal priors with uniform priors and add a “roachoid” fossil as a calibration point. Although the reanalysis provides an interesting alternative viewpoint, we maintain that our choices were appropriate.2 page(s

Ordering the archive in early modern Venice (1400-1650)

The Republic of Venice was renowned for gathering and preserving from very early on a huge and growing archive. This article analyses the ways in which records were created, stored, and ordered for both immediate and future use. The political system of Venice, at once aristocratic and republican, had an important impact on the production and preservation of large quantities of documents in unbound filze and bound registri. In turn, the volume of this paperwork required the development of strict criteria for the organization of the material. In particular, this article analyses how records were divided at the moment of production, thus enabling a pragmatic combination of chronological and thematic ordering criteria. The latter were reinforced by finding tools arranged by subject matter, in particular indexes inside each volume and more general indexes across several volumes, both known as rubriche. The article suggests that indexing must be seen as a historical process dependent on Venice’s political structures and tied to specific moments in the wider history of the Republic, respectively in the fifteenth, early sixteenth, and early seventeenth centuries. Finally, the article points to some unexpected interactions between political secrecy and indexing