Taxonomic colouring of phylogenetic trees of protein sequences

BACKGROUND: Phylogenetic analyses of protein families are used to define the evolutionary relationships between homologous proteins. The interpretation of protein-sequence phylogenetic trees requires the examination of the taxonomic properties of the species associated to those sequences. However, there is no online tool to facilitate this interpretation, for example, by automatically attaching taxonomic information to the nodes of a tree, or by interactively colouring the branches of a tree according to any combination of taxonomic divisions. This is especially problematic if the tree contains on the order of hundreds of sequences, which, given the accelerated increase in the size of the protein sequence databases, is a situation that is becoming common. RESULTS: We have developed PhyloView, a web based tool for colouring phylogenetic trees upon arbitrary taxonomic properties of the species represented in a protein sequence phylogenetic tree. Provided that the tree contains SwissProt, SpTrembl, or GenBank protein identifiers, the tool retrieves the taxonomic information from the corresponding database. A colour picker displays a summary of the findings and allows the user to associate colours to the leaves of the tree according to any number of taxonomic partitions. Then, the colours are propagated to the branches of the tree. CONCLUSION: PhyloView can be used at . A tutorial, the software with documentation, and GPL licensed source code, can be accessed at the same web address

TreeVector: Scalable, Interactive, Phylogenetic Trees for the Web

Background: Phylogenetic trees are complex data forms that need to be graphically displayed to be human-readable. Traditional techniques of plotting phylogenetic trees focus on rendering a single static image, but increases in the production of biological data and large-scale analyses demand scalable, browsable, and interactive trees. Methodology/Principal Findings: We introduce TreeVector, a Scalable Vector Graphics–and Java-based method that allows trees to be integrated and viewed seamlessly in standard web browsers with no extra software required, and can be modified and linked using standard web technologies. There are now many bioinformatics servers and databases with a range of dynamic processes and updates to cope with the increasing volume of data. TreeVector is designed as a framework to integrate with these processes and produce user-customized phylogenies automatically. We also address the strengths of phylogenetic trees as part of a linked-in browsing process rather than an end graphic for print. Conclusions/Significance: TreeVector is fast and easy to use and is available to download precompiled, but is also open source. It can also be run from the web server listed below or the user’s own web server. It has already been deployed o

MixtureTree Annotator: A Program for Automatic Colorization and Visual Annotation of MixtureTree

abstract: The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information. In order to visualize the resulting output file, a modified version of FigTree is used. Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy. In addition to allowing the user to automatically color any given Newick tree by sequence name, the MixtureTree Annotator is the only method that allows the user to automatically annotate the resulting tree created by the MixtureTree program. The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.The article is published at http://journals.plos.org/plosone/article?id=10.1371/journal.pone.011889

Shedding light on the role of plant miRNAs in DNA damage response (DDR) and trans-kingdom transfer

One of the challenges that living organisms face is to respond promptly to genotoxic stress to avoid DNA damage. To this purpose, they developed complex DNA damage response (DDR) mechanisms. These mechanisms are highly conserved among organisms, including plants, and need to be finely regulated to take place properly. In this scenario, microRNAs are emerging as active players, thus attracting the attention of the research community. The involvement of miRNAs in DDR has been investigated prominently in human cells wherease studies on plants are still scarce. In addition, recently, miRNAs started to be envisioned as trans-kingdom molecules able to exert regulatory functions in evolutionary distant organisms. Particularly, attention is drawn to plant miRNAs ingested with the diet; evidence is accumulating on their ability to regulate genes in organisms other than the one in which they were synthesized, including humans and pathogens.In the present PhD thesis, different bioinformatics approaches have been developed aiming at identifying plant miRNAs along with their endogenous and cross-kingdom targets to pinpoint conserved pathways between evolutionary distant species. Alonside model organisms, the developed pipeline may find application on any species of interest to address species-specific cross-kingdom interactions or to performe large-scale investigations involving several plant/animal species. The emergence of DDR-related miRNAs in plants and humans constitutes fundamental informations obtained from these approaches.To experimentally investigate the involvement of plant miRNAs in the regulation of DDR-associated pathways, an ad hoc system was developed, using the model legume Medicago truncatula. Specific treatments with camptothecin (CPT) and/or NSC120686 (NSC) targeting compoments of DDR, namely topoisomerase I (Top1) and tyrosyl-DNA phosphodiesterase 1 (Tdp1), were used. These treatments, imposed to M. truncatula seeds for a 7-day time period, do not influence the germination process, but result in inhibition of seedling development, causing an increase in cell death and accumulation of DNA damage. To demonstrate that the imposed treatments had an effect on DDR, the expression of SOG1 (suppressor of gamma response 1) master-regulator was investigated by qRT-PCR. Importantly, a phylogenetic study demonstrated that M. truncatula possessed a small SOG1 gene family, composed by MtSOG1A and MtSOG1B genes. The expression of both genes was significantly enhanced in treatment-specific manner. Additionally, the espression of multiple genes playing important roles in different DNA repair pathways, cell cycle regulation and chromatin remodelling, were differentially expressed in a treatment-specific manner. Subsequently, specific miRNAs identifyed from the bioinformatics approach as targeting genes involved in DDR processes, were investigated along side their targets, thus providing a first step in their function validation.To investigate plant miRNAs trans-kingdom potential, additional studies were conducted using apple (M. domestica) since it can be eaten raw and hence, can be a better system for feeding trials. As a proof of concept, artificial miRNAs (amiRNAs) were delivered to human colorectal adenocarcinoma cells and the expression of these microRNAs and their in silico predicted targets were evaluated by qRT-PCR. Specifically, amiRNAs mimicking mdm-miR482a-3p and mdm-miR858 were transfected into HT-29 cell lines. After 72 h, amiRNAs were clearly detected inside the cells and the performed qRT-PCR analysis showed a significant downregulation of the IL4R (Interleukin 4 Receptor) gene, involved in promoting Th2 differentiation, suggesting the possibility of apple miRNAs to regulate the activity of human genes in vitro. Taken together, the results presented in the current PhD thesis demonstrate the involvement of plant miRNAs in DDR-associated processes as well as present evidence on the plant miRNAs trans-kingdom potential.One of the challenges that living organisms face is to respond promptly to genotoxic stress to avoid DNA damage. To this purpose, they developed complex DNA damage response (DDR) mechanisms. These mechanisms are highly conserved among organisms, including plants, and need to be finely regulated to take place properly. In this scenario, microRNAs are emerging as active players, thus attracting the attention of the research community. The involvement of miRNAs in DDR has been investigated prominently in human cells wherease studies on plants are still scarce. In addition, recently, miRNAs started to be envisioned as trans-kingdom molecules able to exert regulatory functions in evolutionary distant organisms. Particularly, attention is drawn to plant miRNAs ingested with the diet; evidence is accumulating on their ability to regulate genes in organisms other than the one in which they were synthesized, including humans and pathogens.In the present PhD thesis, different bioinformatics approaches have been developed aiming at identifying plant miRNAs along with their endogenous and cross-kingdom targets to pinpoint conserved pathways between evolutionary distant species. Alonside model organisms, the developed pipeline may find application on any species of interest to address species-specific cross-kingdom interactions or to performe large-scale investigations involving several plant/animal species. The emergence of DDR-related miRNAs in plants and humans constitutes fundamental informations obtained from these approaches.To experimentally investigate the involvement of plant miRNAs in the regulation of DDR-associated pathways, an ad hoc system was developed, using the model legume Medicago truncatula. Specific treatments with camptothecin (CPT) and/or NSC120686 (NSC) targeting compoments of DDR, namely topoisomerase I (Top1) and tyrosyl-DNA phosphodiesterase 1 (Tdp1), were used. These treatments, imposed to M. truncatula seeds for a 7-day time period, do not influence the germination process, but result in inhibition of seedling development, causing an increase in cell death and accumulation of DNA damage. To demonstrate that the imposed treatments had an effect on DDR, the expression of SOG1 (suppressor of gamma response 1) master-regulator was investigated by qRT-PCR. Importantly, a phylogenetic study demonstrated that M. truncatula possessed a small SOG1 gene family, composed by MtSOG1A and MtSOG1B genes. The expression of both genes was significantly enhanced in treatment-specific manner. Additionally, the espression of multiple genes playing important roles in different DNA repair pathways, cell cycle regulation and chromatin remodelling, were differentially expressed in a treatment-specific manner. Subsequently, specific miRNAs identifyed from the bioinformatics approach as targeting genes involved in DDR processes, were investigated along side their targets, thus providing a first step in their function validation.To investigate plant miRNAs trans-kingdom potential, additional studies were conducted using apple (M. domestica) since it can be eaten raw and hence, can be a better system for feeding trials. As a proof of concept, artificial miRNAs (amiRNAs) were delivered to human colorectal adenocarcinoma cells and the expression of these microRNAs and their in silico predicted targets were evaluated by qRT-PCR. Specifically, amiRNAs mimicking mdm-miR482a-3p and mdm-miR858 were transfected into HT-29 cell lines. After 72 h, amiRNAs were clearly detected inside the cells and the performed qRT-PCR analysis showed a significant downregulation of the IL4R (Interleukin 4 Receptor) gene, involved in promoting Th2 differentiation, suggesting the possibility of apple miRNAs to regulate the activity of human genes in vitro. Taken together, the results presented in the current PhD thesis demonstrate the involvement of plant miRNAs in DDR-associated processes as well as present evidence on the plant miRNAs trans-kingdom potential