Erin E. Gill

The immunology of host defence peptides: beyond antimicrobial activity

Host defence peptides (HDPs) are short, cationic amphipathic peptides with diverse sequences that are produced by various cells and tissues in all complex life forms. HDPs have important roles in the bodys response to infection and inflammation. This Review focuses on human HDPs and explores the diverse immunomodulatory effects of HDPs from a systems biology perspective, which highlights the interconnected nature of the effect (or effects) of HDPs on the host. Studies have demonstrated that HDPs are expressed throughout the body and mediate a broad range of activities, which explains their association with various inflammatory diseases and autoimmune disorders. The diverse actions of HDPs, such as their roles in wound healing and in the maintenance of the microbiota, are also explored, in addition to potential therapeutic applications.

NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data

Meta-analysis of gene expression data sets is increasingly performed to help identify robust molecular signatures and to gain insights into underlying biological processes. The complicated nature of such analyses requires both advanced statistics and innovative visualization strategies to support efficient data comparison, interpretation and hypothesis generation. NetworkAnalyst (http://www.networkanalyst.ca) is a comprehensive web-based tool designed to allow bench researchers to perform various common and complex meta-analyses of gene expression data via an intuitive web interface. By coupling well-established statistical procedures with state-of-the-art data visualization techniques, NetworkAnalyst allows researchers to easily navigate large complex gene expression data sets to determine important features, patterns, functions and connections, thus leading to the generation of new biological hypotheses. This protocol provides a step-wise description of how to effectively use NetworkAnalyst to perform network analysis and visualization from gene lists; to perform meta-analysis on gene expression data while taking into account multiple metadata parameters; and, finally, to perform a meta-analysis of multiple gene expression data sets. NetworkAnalyst is designed to be accessible to biologists rather than to specialist bioinformaticians. The complete protocol can be executed in ∼1.5 h. Compared with other similar web-based tools, NetworkAnalyst offers a unique visual analytics experience that enables data analysis within the context of protein-protein interaction networks, heatmaps or chord diagrams. All of these analysis methods provide the user with supporting statistical and functional evidence.

Antibiotic Adjuvants: Diverse Strategies for Controlling Drug‐Resistant Pathogens

The growing number of bacterial pathogens that are resistant to numerous antibiotics is a cause for concern around the globe. There have been no new broad‐spectrum antibiotics developed in the last 40 years, and the drugs we have currently are quickly becoming ineffective. In this article, we explore a range of therapeutic strategies that could be employed in conjunction with antibiotics and may help to prolong the life span of these life‐saving drugs. Discussed topics include antiresistance drugs, which are administered to potentiate the effects of current antimicrobials in bacteria where they are no longer (or never were) effective; antivirulence drugs, which are directed against bacterial virulence factors; host‐directed therapies, which modulate the hosts immune system to facilitate infection clearance; and alternative treatments, which include such therapies as oral rehydration for diarrhea, phage therapy, and probiotics. All of these avenues show promise for the treatment of bacterial infections and should be further investigated to explore their full potential in the face of a postantibiotic era.

Stripped-down DNA repair in a highly reduced parasite

BackgroundEncephalitozoon cuniculi is a member of a distinctive group of single-celled parasitic eukaryotes called microsporidia, which are closely related to fungi. Some of these organisms, including E. cuniculi, also have uniquely small genomes that are within the prokaryotic range. Thus, E. cuniculi has undergone a massive genome reduction which has resulted in a loss of genes from diverse biological pathways, including those that act in DNA repair.DNA repair is essential to any living cell. A loss of these mechanisms invariably results in accumulation of mutations and/or cell death. Six major pathways of DNA repair in eukaryotes include: non-homologous end joining (NHEJ), homologous recombination repair (HRR), mismatch repair (MMR), nucleotide excision repair (NER), base excision repair (BER) and methyltransferase repair. DNA polymerases are also critical players in DNA repair processes.Given the close relationship between microsporidia and fungi, the repair mechanisms present in E. cuniculi were compared to those of the yeast Saccharomyces cerevisiae to ascertain how the process of genome reduction has affected the DNA repair pathways.ResultsE. cuniculi lacks 16 (plus another 6 potential absences) of the 56 DNA repair genes sought via BLASTP and PSI-BLAST searches. Six of 14 DNA polymerases or polymerase subunits are also absent in E. cuniculi. All of these genes are relatively well conserved within eukaryotes. The absence of genes is not distributed equally among the different repair pathways; some pathways lack only one protein, while there is a striking absence of many proteins that are components of both double strand break repair pathways. All specialized repair polymerases are also absent.ConclusionGiven the large number of DNA repair genes that are absent from the double strand break repair pathways, E. cuniculi is a prime candidate for the study of double strand break repair with minimal machinery. Strikingly, all of the double strand break repair genes that have been retained by E. cuniculi participate in other biological pathways.

ESTs from the microsporidian Edhazardia aedis

BackgroundMicrosporidia are a group of parasites related to fungi that infect a wide variety of animals and have gained recognition from the medical community in the past 20 years due to their ability to infect immuno-compromised humans. Microsporidian genomes range in size from 2.3 to 19.5 Mbp, but almost all of our knowledge comes from species that have small genomes (primarily from the human parasite Encephalitozoon cuniculi and the locust parasite Antonospora locustae). We have conducted an EST survey of the mosquito parasite Edhazardia aedis, which has an estimated genome size several times that of more well-studied species. The only other microsporidian EST project is from A. locustae, and serves as a basis for comparison with E. aedis.ResultsThe spore transcriptomes of A. locustae and E. aedis were compared and the numbers of unique transcripts that belong to each COG (Clusters of Orthologous Groups of proteins) category differ by at most 5%. The transcripts themselves have widely varying start sites and encode a number of proteins that have not been found in other microsporidia examined to date. However, E. aedis seems to lack the multi-gene transcripts present in A. locustae and E. cuniculi. We also present the first documented case of transcription of a transposable element in microsporidia.ConclusionAlthough E. aedis and A. locustae are distantly related, have very disparate life cycles and contain genomes estimated to be vastly different sizes, their patterns of transcription are similar. The architecture of the ancestral microsporidian genome is unknown, but the presence of genes in E. aedis that have not been found in other microsporidia suggests that extreme genome reduction and compaction is lineage specific and not typical of all microsporidia.

Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis.

Chlamydia trachomatis remains a leading cause of bacterial sexually transmitted infections and preventable blindness worldwide. There are, however, limited in vitro models to study the role of host genetics in the response of macrophages to this obligate human pathogen. Here, we describe an approach using macrophages derived from human induced pluripotent stem cells (iPSdMs) to study macrophage–Chlamydia interactions in vitro. We show that iPSdMs support the full infectious life cycle of C. trachomatis in a manner that mimics the infection of human blood-derived macrophages. Transcriptomic and proteomic profiling of the macrophage response to chlamydial infection highlighted the role of the type I interferon and interleukin 10-mediated responses. Using CRISPR/Cas9 technology, we generated biallelic knockout mutations in host genes encoding IRF5 and IL-10RA in iPSCs, and confirmed their roles in limiting chlamydial infection in macrophages. This model can potentially be extended to other pathogens and tissue systems to advance our understanding of host-pathogen interactions and the role of human genetics in influencing the outcome of infections.

MetaBridge: enabling network-based integrative analysis via direct protein interactors of metabolites

Summary Here, we present MetaBridge, a tool that collates protein interactors (curated metabolite-enzyme interactions) that influence the levels of specific metabolites including both biosynthetic and degradative enzymes. This enables network-based integrative analysis of metabolomics data with other omics data types. MetaBridge is designed to complement a systems-biology approach to analysis, pairing well with network analysis tools such as NetworkAnalyst.ca, but can be used in any bioinformatics workflow. Availability and implementation MetaBridge has been implemented as a web tool at https://www.metabridge.org, and the source code is available at https://github.com/samhinshaw/metabridge_shiny (GNU GPLv3).