Multiple axes of visual system diversity in Ithomiini, an ecologically diverse tribe of mimetic butterflies.

The striking structural variation seen in arthropod visual systems can be explained by the overall quantity and spatio-temporal structure of light within habitats coupled with developmental and physiological constraints. However, little is currently known about how fine-scale variation in visual structures arises across shorter evolutionary and ecological scales. In this study, we characterise patterns of interspecific (between species), intraspecific (between sexes) and intraindividual (between eye regions) variation in the visual system of four ithomiine butterfly species. These species are part of a diverse 26-million-year-old Neotropical radiation where changes in mimetic colouration are associated with fine-scale shifts in ecology, such as microhabitat preference. Using a combination of selection analyses on visual opsin sequences, in vivo ophthalmoscopy, micro-computed tomography (micro-CT), immunohistochemistry, confocal microscopy and neural tracing, we quantify and describe physiological, anatomical and molecular traits involved in visual processing. Using these data, we provide evidence of substantial variation within the visual systems of Ithomiini, including: (i) relaxed selection on visual opsins, perhaps mediated by habitat preference, (ii) interspecific shifts in visual system physiology and anatomy, and (iii) extensive sexual dimorphism, including the complete absence of a butterfly-specific optic neuropil in the males of some species. We conclude that considerable visual system variation can exist within diverse insect radiations, hinting at the evolutionary lability of these systems to rapidly develop specialisations to distinct visual ecologies, with selection acting at the perceptual, processing and molecular level.

Tumour Expression of Histone Deacetylases in Uveal Melanoma.

PURPOSE: To determine the expression of histone deacetylase enzymes in uveal melanoma tumour cells. PROCEDURES: This is an observational immunohistochemical study of 16 formalin-fixed, paraffin-embedded eyes enucleated for uveal melanoma between January 2001 and March 2002. Haematoxylin and eosin paraffin sections were reviewed for histopathological parameters according to the American Joint Committee on Cancer 7th edition. Sections were then immunohistochemically stained for histone deacetylases 1, 2, 3, 4 and 6 and sirtuin 2 using an automated Leica Bond II platform and Fast Red chromogen, then digitally scanned using Aperio software before assessment of staining. RESULTS: Nuclear expression of histone deacetylases 1, 2, 3, 4 and 6 and of sirtuin 2 was confirmed in uveal melanoma tumour cells. In addition, the tumour cells showed cytoplasmic expression of histone deacetylases 4 and 6 and sirtuin 2. Nuclear and cytoplasmic immunostaining was also seen in intraocular tissues uninvolved by the tumour. CONCLUSION: Uveal melanoma tumour cells express histone deacetylases 1, 2, 3, 4 and 6 and sirtuin 2, confirming potential tissue targets for histone deacetylase inhibitors.

STAble: a novel approach to de novo assembly of RNA-seq data and its application in a metabolic model network based metatranscriptomic workflow.

BACKGROUND: De novo assembly of RNA-seq data allows the study of transcriptome in absence of a reference genome either if data is obtained from a single organism or from a mixed sample as in metatranscriptomics studies. Given the high number of sequences obtained from NGS approaches, a critical step in any analysis workflow is the assembly of reads to reconstruct transcripts thus reducing the complexity of the analysis. Despite many available tools show a good sensitivity, there is a high percentage of false positives due to the high number of assemblies considered and it is likely that the high frequency of false positive is underestimated by currently used benchmarks. The reconstruction of not existing transcripts may false the biological interpretation of results as - for example - may overestimate the identification of "novel" transcripts. Moreover, benchmarks performed are usually based on RNA-seq data from annotated genomes and assembled transcripts are compared to annotations and genomes to identify putative good and wrong reconstructions, but these tests alone may lead to accept a particular type of false positive as true, as better described below. RESULTS: Here we present a novel methodology of de novo assembly, implemented in a software named STAble (Short-reads Transcriptome Assembler). The novel concept of this assembler is that the whole reads are used to determine possible alignments instead of using smaller k-mers, with the aim of reducing the number of chimeras produced. Furthermore, we applied a new set of benchmarks based on simulated data to better define the performance of assembly method and carefully identifying true reconstructions. STAble was also used to build a prototype workflow to analyse metatranscriptomics data in connection to a steady state metabolic modelling algorithm. This algorithm was used to produce high quality metabolic interpretations of small gene expression sets obtained from already published RNA-seq data that we assembled with STAble. CONCLUSIONS: The presented results, albeit preliminary, clearly suggest that with this approach is possible to identify informative reactions not directly revealed by raw transcriptomic data.

Optimization of Multi-Omic Genome-Scale Models: Methodologies, Hands-on Tutorial, and Perspectives.

Genome-scale metabolic models are valuable tools for assessing the metabolic potential of living organisms. Being downstream of gene expression, metabolism is increasingly being used as an indicator of the phenotypic outcome for drugs and therapies. We here present a review of the principal methods used for constraint-based modelling in systems biology, and explore how the integration of multi-omic data can be used to improve phenotypic predictions of genome-scale metabolic models. We believe that the large-scale comparison of the metabolic response of an organism to different environmental conditions will be an important challenge for genome-scale models. Therefore, within the context of multi-omic methods, we describe a tutorial for multi-objective optimization using the metabolic and transcriptomics adaptation estimator (METRADE), implemented in MATLAB. METRADE uses microarray and codon usage data to model bacterial metabolic response to environmental conditions (e.g., antibiotics, temperatures, heat shock). Finally, we discuss key considerations for the integration of multi-omic networks into metabolic models, towards automatically extracting knowledge from such models.

Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling.

Metabolic modelling has entered a mature phase with dozens of methods and software implementations available to the practitioner and the theoretician. It is not easy for a modeller to be able to see the wood (or the forest) for the trees. Driven by this analogy, we here present a 'forest' of principal methods used for constraint-based modelling in systems biology. This provides a tree-based view of methods available to prospective modellers, also available in interactive version at http://modellingmetabolism.net, where it will be kept updated with new methods after the publication of the present manuscript. Our updated classification of existing methods and tools highlights the most promising in the different branches, with the aim to develop a vision of how existing methods could hybridize and become more complex. We then provide the first hands-on tutorial for multi-objective optimization of metabolic models in R. We finally discuss the implementation of multi-view machine learning approaches in poly-omic integration. Throughout this work, we demonstrate the optimization of trade-offs between multiple metabolic objectives, with a focus on omic data integration through machine learning. We anticipate that the combination of a survey, a perspective on multi-view machine learning and a step-by-step R tutorial should be of interest for both the beginner and the advanced user.

Transcriptome and proteome analysis of Salmonella enterica serovar Typhimurium systemic infection of wild type and immune-deficient mice.

Salmonella enterica are a threat to public health. Current vaccines are not fully effective. The ability to grow in infected tissues within phagocytes is required for S. enterica virulence in systemic disease. As the infection progresses the bacteria are exposed to a complex host immune response. Consequently, in order to continue growing in the tissues, S. enterica requires the coordinated regulation of fitness genes. Bacterial gene regulation has so far been investigated largely using exposure to artificial environmental conditions or to in vitro cultured cells, and little information is available on how S. enterica adapts in vivo to sustain cell division and survival. We have studied the transcriptome, proteome and metabolic flux of Salmonella, and the transcriptome of the host during infection of wild type C57BL/6 and immune-deficient gp91-/-phox mice. Our analyses advance the understanding of how S. enterica and the host behaves during infection to a more sophisticated level than has previously been reported.

Multiplex methods provide effective integration of multi-omic data in genome-scale models.

BACKGROUND: Genomic, transcriptomic, and metabolic variations shape the complex adaptation landscape of bacteria to varying environmental conditions. Elucidating the genotype-phenotype relation paves the way for the prediction of such effects, but methods for characterizing the relationship between multiple environmental factors are still lacking. Here, we tackle the problem of extracting network-level information from collections of environmental conditions, by integrating the multiple omic levels at which the bacterial response is measured. RESULTS: To this end, we model a large compendium of growth conditions as a multiplex network consisting of transcriptomic and fluxomic layers, and we propose a multi-omic network approach to infer similarity of growth conditions by integrating layers of the multiplex network. Each node of the network represents a single condition, while edges are similarities between conditions, as measured by phenotypic and transcriptomic properties on different layers of the network. We then fuse these layers into one network, therefore capturing a global network of conditions and the associated similarities across two omic levels. We apply this multi-omic fusion to an updated genome-scale reconstruction of Escherichia coli that includes underground metabolism and new gene-protein-reaction associations. CONCLUSIONS: Our method can be readily used to evaluate and cross-compare different collections of conditions among different species. Acquiring multi-omic information on the topology of the space of experimental conditions makes it possible to infer the position and to build condition-specific models of untested or incomplete profiles for which experimental data is not available. Our weighted network fusion method for genome-scale models is freely available at https://github.com/maxconway/SNFtool .