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Bioinformatics meets virology: The European virus bioinformatics center's second annual meeting
(2018)
The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions. Approximately 120 researchers from around the world attended the Second Annual Meeting of the EVBC this year, including 15 renowned international speakers. This report presents an overview of new developments and novel research findings that emerged during the meeting.
Unity in defence: honeybee workers exhibit conserved molecular responses to diverse pathogens
(2017)
Background: Organisms typically face infection by diverse pathogens, and hosts are thought to have developed specific responses to each type of pathogen they encounter. The advent of transcriptomics now makes it possible to test this hypothesis and compare host gene expression responses to multiple pathogens at a genome-wide scale. Here, we performed a meta-analysis of multiple published and new transcriptomes using a newly developed bioinformatics approach that filters genes based on their expression profile across datasets. Thereby, we identified common and unique molecular responses of a model host species, the honey bee (Apis mellifera), to its major pathogens and parasites: the Microsporidia Nosema apis and Nosema ceranae, RNA viruses, and the ectoparasitic mite Varroa destructor, which transmits viruses.
Results: We identified a common suite of genes and conserved molecular pathways that respond to all investigated pathogens, a result that suggests a commonality in response mechanisms to diverse pathogens. We found that genes differentially expressed after infection exhibit a higher evolutionary rate than non-differentially expressed genes. Using our new bioinformatics approach, we unveiled additional pathogen-specific responses of honey bees; we found that apoptosis appeared to be an important response following microsporidian infection, while genes from the immune signalling pathways, Toll and Imd, were differentially expressed after Varroa/virus infection. Finally, we applied our bioinformatics approach and generated a gene co-expression network to identify highly connected (hub) genes that may represent important mediators and regulators of anti-pathogen responses.
Conclusions: Our meta-analysis generated a comprehensive overview of the host metabolic and other biological processes that mediate interactions between insects and their pathogens. We identified key host genes and pathways that respond to phylogenetically diverse pathogens, representing an important source for future functional studies as well as offering new routes to identify or generate pathogen resilient honey bee stocks. The statistical and bioinformatics approaches that were developed for this study are broadly applicable to synthesize information across transcriptomic datasets. These approaches will likely have utility in addressing a variety of biological questions.
Technetium- and Rhenium-Labelled Fatty Acids as Model Compounds for Myocardial Metabolism Imaging
(2002)
In an attempt to develop new technetium-based radiopharmaceuticals for the non-invasive diagnosis of oxidative myocardial metabolism, rhenium model compounds according to the 3+1' mixed ligand approach as well as the organometallic tricarbonyl-design were synthesized. The geometrical impact of different chelates on the integrity of the fatty acid head structure was determined by single crystal X-ray analyses. To evaluate the diagnostic potential of the analogous Technetium-99m compounds, fatty acid complexes of the 3+1' mixed ligand type were prepared on n.c.a.-level and studied in the isolated constant-flow-perfused guinea pig heart model; compared to established [123I]Iodine-labelled fatty acid radiotracers, the tested Technetium-99m derivatives showed a specific, however significantly lower myocardial extraction rate.
Background: Host–pathogen interactions can lead to dramatic changes in host feeding behaviour. One aspect of this includes self-medication, where infected individuals consume substances such as toxins or alter their macronutrient consumption to enhance immune competence. Another widely adopted animal response to infection is illness-induced anorexia, which is thought to assist host immunity directly or by limiting the nutritional resources available to pathogens. Here, we recorded macronutrient preferences of the global pest cockroach, Blatta orientalis to investigate how shifts in host macronutrient dietary preference and quantity of carbohydrate (C) and protein (P) interact with immunity following bacterial infection.
Results: We fnd that B. orientalis avoids diets enriched for P under normal conditions, and that high P diets reduce cockroach survival in the long term. However, following bacterial challenge, cockroaches signifcantly reduced their overall nutrient intake, particularly of carbohydrates, and increased the relative ratio of protein (P:C) consumed. Surprisingly, these behavioural shifts had a limited efect on cockroach immunity and survival, with minor changes to immune protein abundance and antimicrobial activity between individuals placed on diferent diets, regardless of infection status.
Conclusions: We show that cockroach feeding behaviour can be modulated by a pathogen, resulting in an illness-induced anorexia-like feeding response and a shift from a C-enriched to a more P:C equal diet. However, our results also indicate that such responses do not provide signifcant immune protection in B. orientalis, suggesting that the host’s dietary shift might also result from random rather than directed behaviour. The lack of an apparent beneft of the shift in feeding behaviour highlights a possible reduced importance of diet in immune regulation in these invasive animals, although further investigations employing pathogens with alternative infection strategies are warranted.
Honeybee symbionts, predominantly bacteria, play important roles in honeybee health, nutrition, and pathogen protection, thereby supporting colony health. On the other hand, fungi are often considered indicators of poor bee health, and honeybee microbiome studies generally exclude fungi and yeasts. We hypothesized that yeasts may be an important aspect of early honeybee biology, and if yeasts provide a mutual benefit to their hosts, then honeybees could provide a refuge during metamorphosis to ensure the presence of yeasts at emergence. We surveyed for yeast and fungi during pupal development and metamorphosis in worker bees using fungal-specific quantitative polymerase chain reaction (qPCR), next-generation sequencing, and standard microbiological culturing. On the basis of yeast presence in three distinct apiaries and multiple developmental stages, we conclude that yeasts can survive through metamorphosis and in naïve worker bees, albeit at relatively low levels. In comparison, known bacterial mutualists, like Gilliamella and Snodgrassella, were generally not found in pre-eclosed adult bees. Whether yeasts are actively retained as an important part of the bee microbiota or are passively propagating in the colony remains unknown. Our demonstration of the constancy of yeasts throughout development provides a framework to further understand the honeybee microbiota.
Synthesis of Li ion battery materials via ball milling has been a huge area of growth, leading to new high-capacity electrode materials, such as a number of promising disordered rocksalt (DRS) phases. In prior work, it was generally assumed that the synthesis was facilitated simply by local heating effects during the milling process. In this work, we show that ball milling Li2MoO4 leads to a phase transformation to the high pressure spinel polymorph and we report electrochemical data for this phase. This observation of the formation of a high pressure polymorph shows that local heating effects alone cannot explain the phase transformation observed (phenakite to spinel) and so indicates the importance of other effects. In particular, we propose that when the milling balls collide with the material, the resulting shockwaves exert a localised pressure effect, in addition to local heating. To provide further support for this, we additionally report ball milling results for a number of case studies (Li2MnO3, Li2SnO3, Nb2O5) which reinforces the conclusion that local heating alone cannot explain the phase transformations observed. The work presented thus provides greater fundamental understanding of milling as a synthetic pathway and suggests potential strategies to prepare such samples without milling (e.g., doping to create internal chemical pressure). In addition, we suggest that further research is needed into the effect of the use of milling as a route to smaller particles, since we believe that such milling may also be affecting the surface structure of the particles through the influence of the shockwaves generated.