Schistosomiasis remains a major neglected tropical disease that afflicts over 200 million people globally. Schistosomes, the aetiological agent of schistosomiasis, are parasitic flatworms that propagate between molluscan and mammalian hosts. Inside the mammalian host, schistosomes rapidly grow over 100-fold in size and develop into a sexually mature male or female that thrives in the bloodstream for several decades. Recent work has identified schistosome stem cells as the source that drives parasite transmission, reproduction and longevity. Moreover, studies have begun to uncover molecular programmes deployed by stem cells that are essential for tissue development and maintenance, parasite survival and immune evasion. Such programmes are reminiscent of neoblast-driven development and regeneration of planarians, the free-living flatworm relative of schistosomes. Over the last few decades, research in planarians has employed modern functional genomic tools that significantly enhanced our understanding of stem cell-driven animal development and regeneration. In this review, we take a broad stroke overview of major flatworm organ systems at the cellular and molecular levels. We summarize recent advances on genetic regulators that play critical roles in differentiation and maintenance of flatworm cell types. Finally, we provide perspectives on how investigation of basic parasite biology is critical to discovering new approaches to battle schistosomiasis.

Helminth parasitology is an important discipline, which poses often unique technical challenges. One challenge is that helminth parasites, particularly those in humans, are often difficult to obtain alive and in sufficient quantities for study; another is the challenge of studying these organisms in vitro – no helminth parasite life cycle has been fully recapitulated outside of a host. Arguably, the key issue retarding progress in helminth parasitology has been a lack of experimental tools and resources, certainly relative to the riches that have driven many parasitologists to adopt free-living model organisms as surrogate systems. In response to these needs, the past 10–12 years have seen the beginnings of helminth parasitology's journey into the ‘omics’ era, with the release of abundant sequencing resources, and the functional genomics tools with which to test biological hypotheses. To reflect this progress, the 2019 Autumn Symposium of the British Society for Parasitology was held in Queen's University Belfast on the topic of ‘post-genomic progress in helminth parasitology’. This issue presents examples of the current state of play in the field, while this editorial summarizes how genomic datasets and functional genomic tools have stimulated impressive recent progress in our understanding of parasite biology.

Ocean warming and acidification are expected to influence the biology of the ecologically and economically important red king crab, Paralithodes camtschaticus. We investigated transcriptome responses of adult, larval and juvenile red king crab to assess sensitivity to reduced pH and elevated temperature. In adults, gill tissue (but not heart or cuticle) responded to reduced pH by differentially regulating many genes involved in metabolic, membrane and cuticular processes, but not ionic or acid/base regulation. In larval crabs, we found little evidence for a strong transcriptomic response to pH, but did observe large differences in the transcriptomes of newly hatched and one-week old larvae. In juvenile crabs, we found that there was a strong transcriptomic response to temperature across all pH conditions, but that only extreme low pH caused transcriptomic shifts. Most of the genes in juveniles that were differentially expressed were for cuticular and calcification processes. While inferences regarding the specific biological responses associated with changes in gene expression are likely to change as resources for red king crab genomics enabled studies continue to improve (i.e. better assemblies and annotation), our inferences about general sensitivities to temperature and pH across the life stages of red king crab are robust and unlikely to shift. Overall, our data suggest that red king crab are more sensitive to warming than acidification, and that responses to acidification at the transcriptomic level occur at different levels of pH across life stages, with juveniles being less pH sensitive than adults.

Many advances in disciplines such as chemistry, biochemistry, plant breeding, genetics, engineering, and others have been applied in a positive manner to improve knowledge in weed science. The emerging field of genomics is likely to have a similar positive effect on our understanding of weeds and their management in various plant agriculture systems. Genomics involves the large-scale use of molecular techniques for identification and functional analysis of complete or nearly complete genomic complements of genes. Commercial application of genomics has already occurred for improvement in certain crop input and output traits, including improved quality characteristics and herbicide and insect resistance. Additional commercial applications of genomics in weed science will be identification of genes involved in a crops' competitive ability. Genes controlling early crop shoot emergence, rapid early-season leaf and root development for fast canopy closure, production of allelochemicals for natural weed control, identification of novel herbicide target sites, resistance mechanisms, and genes for safening crops against specific herbicides can and will be identified. Successful crop improvement in these areas using the tools of genomics will dramatically affect weed–crop interactions and improve crop yields while reducing weed problems. In relation to improved basic knowledge of weeds and the resulting ability to improve our weed management techniques, genomics will offer the weed science community many new and exciting research opportunities. Scientists will be able to determine the genetic composition of weed populations and how it changes over time in relation to agricultural practices. Identification of genes contributing to weediness, perennial growth habit, herbicide resistance, seed and vegetative structure dormancy, plant architecture and morphology, plant reproductive characters (outcrossing and hybridization, introgression), and allelopathy will be identified and utilized with high-throughput DNA sequencing and other genomics-based technologies. Using genomics to improve our understanding of weed biology by determining which genes function to affect the fitness, competitiveness, and adaptation of weeds in agricultural environments will allow the development of improved management strategies. This review provides a summary of the various plant genomic research methods being used. Information is provided concerning the current state of molecular research in various areas of weed science and specific genomic research currently being conducted at Purdue University using transfer DNA (T-DNA) activation tagging to generate large populations of mutated plants that can be screened for genes of importance to weed science.

Advances in food transformation have dramatically increased the diversity of products on the market and, consequently, exposed consumers to a complex spectrum of bioactive nutrients whose potential risks and benefits have mostly not been confidently demonstrated. Therefore, tools are needed to efficiently screen products for selected physiological properties before they enter the market. NutriChip is an interdisciplinary modular project funded by the Swiss programme Nano-Tera, which groups scientists from several areas of research with the aim of developing analytical strategies that will enable functional screening of foods. The project focuses on postprandial inflammatory stress, which potentially contributes to the development of chronic inflammatory diseases. The first module of the NutriChip project is composed of three in vitro biochemical steps that mimic the digestion process, intestinal absorption, and subsequent modulation of immune cells by the bioavailable nutrients. The second module is a miniaturised form of the first module (gut-on-a-chip) that integrates a microfluidic-based cell co-culture system and super-resolution imaging technologies to provide a physiologically relevant fluid flow environment and allows sensitive real-time analysis of the products screened in vitro. The third module aims at validating the in vitro screening model by assessing the nutritional properties of selected food products in humans. Because of the immunomodulatory properties of milk as well as its amenability to technological transformation, dairy products have been selected as model foods. The NutriChip project reflects the opening of food and nutrition sciences to state-of-the-art technologies, a key step in the translation of transdisciplinary knowledge into nutritional advice.

Draft genome sequences for Schistosoma mansoni and Schistosoma japonicum are now available. However, the identity and importance of most schistosome genes have yet to be determined. Recently, progress has been made towards the genetic manipulation and transgenesis of schistosomes. Both loss-of-function and gain-of-function approaches appear to be feasible in schistosomes based on findings described in the past 5 years. This review focuses on reports of schistosome transgenesis, specifically those dealing with the transformation of schistosomes with exogenous mobile genetic elements and/or their endogenous relatives for the genetic manipulation of schistosomes. Transgenesis mediated by mobile genetic elements offers a potentially tractable route to introduce foreign genes to schistosomes, a means to determine the importance of schistosome genes, including those that could be targeted in novel interventions and the potential to undertake large-scale forward genetics by insertional mutagenesis.

The aim of this study was to determine which Arabidopsis thaliana (L.) genes had significantly altered expression following 2–36 h of infestation by the aphid Myzus persicae (Sulzer). Six biological replicates were performed for both control and treatment at each time point, allowing rigorous statistical analysis of any changes. Only two genes showed altered expression after 2 h (one up- and one down-regulated) while two were down-regulated and twenty three were up-regulated at 36 h. The transcript annotation allowed classification of the significantly altered genes into a number of classes, including those involved in cell wall modification, carbon metabolism and signalling. Additionally, a number of genes were implicated in oxidative stress and defence against other pathogens. Five genes could not currently be assigned any function. The changes in gene expression are discussed in relation to current models of plant-insect interactions.

Résumé

La génomique de la volaille a bénéficié des avancements technologiques rapides acquis en génomique humaine et sur les organismes modèles. Certains outils et certains approches sont maintenant bien établis chez le poulet, y compris les cartes et marqueurs (génétiques comme physiques), mapping loci pour caractéres quantitatifs, mapping comparative, ressources expressed sequence tag et bacterial artificial chromosome, et mapping physique. De plus, la phase suivante de la découverte génétique, la génomique fonctionnelle, est en cours. Les progre`s dans le mapping de loci pour caracte`res quantitatifs de croissance et d'adiposité seront discutés pour illustrer ces nouvelles technologies et ces nouvelles approches dans l'étude de la génétique et de la physiologie avicole.

With the sequencing of the Arabidopsis thaliana genome, the field of plant biology has made a quantum leap. The sequence information available to the community has greatly facilitated the identification of genes responsible for mutant phenotypes and the large-scale analysis of gene expression in Arabidopsis. High-throughput laboratory tools for DNA sequencing (genomics), mutant analysis (functional genomics), mRNA quantification (transcriptomics) and protein analysis (proteomics) are being used to scrutinize this model plant. For seed physiologists, the challenge lies in translating this information into physiological processes in seeds from other plant species. Combining more traditional seed biology with the new high-throughput molecular tools should yield breakthroughs in seed science.

The improvement of quality and quantitative traits in industrial crops is among the most important goals in plant breeding. Many traits of interest are controlled by multiple genes and improvements have so far only been obtained through conventional breeding. The use of biotechnological tools to modify quantitative traits is highly challenging. CropDesign has developed TraitMill™, an automated plant evaluation platform allowing high-throughput testing of the effect of plant-based transgenes on agronomically valuable traits in crop plants. The focus of the platform is currently on rice, a good model for other important cereals such as maize and wheat. TraitMill™ offers a high-throughput prediction of gene function. Genes of validated function that confer trait improvement can then be transferred to other cereal crop species such as maize, but also to dicots, trees and ornamentals. TraitMill™ involves the following key components: (i) selection of candidate trait improvement genes among genes involved in signal transduction, cell cycle control, transcription, nutrient metabolism, etc.; (ii) a suite of validated constitutive or tissue-specific promoters from rice allowing for the selection of the most appropriate promoter–gene combination in view of the desired trait improvement; (iii) an industrialized plant transformation system generating tens of thousands of transgenic plants annually; and (iv) a robotized trait evaluation set-up for plant evaluation, proprietary image analysis software for measuring plant performance parameters and statistical analysis of results.

Natural products from plants are still important sources for the development of drugs, despite their recent neglect in pharmaceutical discovery programmes. The rapidly dwindling number of species endangers the availability of these natural compounds, which are characterized by the immense chemical and functional diversity ultimately responsible for their pharmaceutical activity. Although many steps in the drug discovery process have been continuously modified during recent years, a common dilemma is still unresolved, i.e. the supply crisis for hits discovered in rare wild plants due to their inaccessibility or lack of reproducibility. New technology, combining tissue culture, functional genomics and metabolomics, shows promise to overcome these problems and even to supply a greater chemical diversity of compounds.

Tick saliva, a fluid once believed to be only relevant for lubrication of mouthparts and water balance, is now well known to be a cocktail of potent anti-haemostatic, anti-inflammatory and immunomodulatory molecules that helps these arthropods obtain a blood meal from their vertebrate hosts. The repertoire of pharmacologically active components in this cocktail is impressive as well as the number of targets they specifically affect. These salivary components change the physiology of the host at the bite site and, consequently, some pathogens transmitted by ticks take advantage of this change and become more infective. Tick salivary proteins have therefore become an attractive target to control tick-borne diseases. Recent advances in molecular biology, protein chemistry and computational biology are accelerating the isolation, sequencing and analysis of a large number of transcripts and proteins from the saliva of different ticks. Many of these newly isolated genes code for proteins with homologies to known proteins allowing identification or prediction of their function. However, most of these genes code for proteins with unknown functions therefore opening the road to functional genomic approaches to identify their biological activities and roles in blood feeding and hence, vaccine development to control tick-borne diseases.

Progress in the selection of production traits in the poultry industry has been dramatic over the past 75 years. Genetic progress has its biological limits and these may be reached in the next 20 years. The poultry industry will need to adapt with more emphasis on the needs of the consumer (e.g. product quality, health and animal welfare), as well as the needs of the breeders/producers (e.g. lower feed costs and higher fertility). These new traits are difficult and costly to measure by conventional genetic selection methods - the application of genomics is a possible solution. Poultry genomics has benefited from the rapid technological advances in the genetics of model organisms and human. A number of resources and approaches are now well established, including genetic markers and maps (both genetic and physical), QTL mapping, comparative mapping, EST and BAC resources. In addition, the next phase of gene discovery - Functional Genomics is underway. How the poultry industry can benefit and get access to these new technologies is discussed.

The three trypanosomatid genome projects have employed common strategies which include: analysis of pulsed-field gel electrophoretic chromosomal karyotypes; physical mapping using big DNA (cosmid, pacmid P1, bacterial artificial chromosome, yeast artificial chromosome) libraries; partial cDNA sequence analysis to develop sets of expressed sequence tags (ESTs) for gene discovery and use as markers in physical mapping; genomic sequencing; dissemination of information through development of web-sites and ACeDB-based fully integrated databases; and establishment of functional genomics programmes to maximize useful application of genome data. Highlights of the projects to date have been the demonstration that, despite extensive chromosomal size polymorphisms for diploid homologues within Africa trypanosomes, T. cruzi or Leishmania, the physical linkage groups for markers on each chromosome are retained across all isolates/species studied within each group. For African trypanosomes, detailed analysis of chromosome 1 has demonstrated that repetitive sequences and the two retroposon-like elements RIME and INGI are localized to a defined region at one end of the chromosome, with the bulk of the central region of the chromosome containing genes coding for expressed proteins. Comparative mapping shows that, although subtelomeric changes account for a large proportion of the polymorphism in chromosome size in African trypanosomes, there are significant expansions and contractions in regions across the entire chromosome. The highlight of the genomic sequencing projects has been the demonstration of just 2 putative transcriptional units of chromosome 1 of Leishmania major, extending on opposite strands from a point in the central region of the chromosome. A similar observation made on 93·4 kb of contiguous sequence for T. cruzi chromosome 3 suggests the presence of promoter and regulatory elements at the junctions of large polycistronic transcriptional units. All data obtained from the genome projects are made available through the public domain, which has prompted changing philosophies in how we approach analysis of the biology of these organisms, and strategies that we can employ now in the search for new therapies and vaccines.

GRASS (Graphical Representation and Analysis of Structures Server), a new web-based server, is described. GRASS exploits many of the features of the GRASP program and is designed to provide interactive molecular graphics and quantitative analysis tools with a simple interface over the World-Wide Web. Using GRASS, it is now possible to view many surface features of biological macromolecules on either standard workstations used in macromolecular analysis or personal computers. The result is a World-Wide Web-based, platform-independent, easily used tool for macromolecular visualization and structure analysis.