Modifier genetics in neuropsychiatric disease: challenges and opportunities

A new study focuses attention on multigenic interactions influencing the risk of autism spectrum disorders.     

Perspectives and challenges in landscape genetics

A recent workshop held at the University of Grenoble gathered the leading experts in the field of landscape genetics and spatial statistics. Landscape genetics was only recently defined as an independent research field. It aims to understand the processes of gene flow and local adaptation by studying the interactions between genetic and spatial or environmental variation. This workshop discussed the perspectives and challenges of combining emerging molecular, spatial and statistical tools to unravel how landscape and environmental variables affect genetic variation.     

Osteochondral tissue engineering: Current strategies and challenges

Osteochondral defect management and repair remain a significant challenge in orthopedic surgery. Osteochondral defects contain damage to both the articular cartilage as well as the underlying subchondral bone. In order to repair an osteochondral defect the needs of the bone, cartilage and the bone-cartilage interface must be taken into account. Current clinical treatments for the repair of osteochondral defects have only been palliative, not curative. Tissue engineering has emerged as a potential alternative as it can be effectively used to regenerate bone, cartilage and the bone-cartilage interface. Several scaffold strategies, such as single phase, layered, and recently graded structures have been developed and evaluated for osteochondral defect repair. Also, as a potential cell source, tissue specific cells and progenitor cells are widely studied in cell culture models, as well with the osteochondral scaffolds in vitro and in vivo. Novel factor strategies being developed, including single factor, multi-factor, or controlled factor release in a graded fashion, not only assist bone and cartilage regeneration, but also establish osteochondral interface formation. The field of tissue engineering has made great strides, however further research needs to be carried out to make this strategy a clinical reality. In this review, we summarize current tissue engineering strategies, including scaffold design, bioreactor use, as well as cell and factor based approaches and recent developments for osteochondral defect repair. In addition, we discuss various challenges that need to be addressed in years to come.     

Complex-trait genetics: emergence of multivariate strategies

Complex traits, including many disease-related traits, are influenced by multiple genes. Bivariate approaches that associate one gene with one trait are yielding to multivariate methods to synthesize the effects of multiple genes, integrate results across independent studies, and aid in the identification of coordinated pathways and interactions between loci.     

Therapeutic siRNA: principles, challenges, and strategies

RNA interference (RNAi) is a remarkable endogenous regulatory pathway that can bring about sequence-specific gene silencing. If harnessed effectively, RNAi could result in a potent targeted therapeutic modality with applications ranging from viral diseases to cancer. The major barrier to realizing the full medicinal potential of RNAi is the difficulty of delivering effector molecules, such as small interfering RNAs (siRNAs), in vivo. An effective delivery strategy for siRNAs must address limitations that include poor stability and non-targeted biodistribution, while protecting against the stimulation of an undesirable innate immune response. The design of such a system requires rigorous understanding of all mechanisms involved. This article reviews the mechanistic principles of RNA interference, its potential, the greatest challenges for use in biomedical applications, and some of the work that has been done toward engineering delivery systems that overcome some of the hurdles facing siRNA-based therapeutics.     

Applications of landscape genetics in conservation biology: concepts and challenges

Landscape genetics plays an increasingly important role in the management and conservation of species. Here, we highlight some of the opportunities and challenges in using landscape genetic approaches in conservation biology. We first discuss challenges related to sampling design and introduce several recent methodological developments in landscape genetics (analyses based on pairwise relatedness, the application of Bayesian methods, inference from landscape resistance and a shift from population-based to individual-based analyses). We then show how simulations can foster the field of landscape genetics and, finally, elaborate on technical developments in sequencing techniques that will dramatically improve our ability to study genetic variation in wild species, opening up new and unprecedented avenues for genetic analysis in conservation biology.     

Training strategies for laboratory animal veterinarians: challenges and opportunities

The field of laboratory animal medicine is experiencing a serious shortage of appropriately trained veterinarians for both clinically related and research-oriented positions within academia, industry, and government. Recent outreach efforts sponsored by professional organizations have stimulated increased interest in the field. It is an opportune time to critically review and evaluate postgraduate training opportunities in the United States and Canada, including formal training programs, informal training, publicly accessible training resources and educational opportunities, and newly emerging training resources such as Internet-based learning aids. Challenges related to each of these training opportunities exist and include increasing enrollment in formal programs, securing adequate funding support, ensuring appropriate content between formal programs that may have diverse objectives, and accommodating the training needs of veterinarians who enter the field by the experience route. Current training opportunities and resources that exist for veterinarians who enter and are established within the field of laboratory animal science are examined. Strategies for improving formal laboratory animal medicine training programs and for developing alternative programs more suited to practicing clinical veterinarians are discussed. In addition, the resources for high-quality continuing education of experienced laboratory animal veterinarians are reviewed.     

Systems genetics: From GWAS to disease pathways

Most common diseases are complex, involving multiple genetic and environmental factors and their interactions. In the past decade, genome-wide association studies (GWAS) have successfully identified thousands of genetic variants underlying susceptibility to complex diseases. However, the results from these studies often do not provide evidence on how the variants affect downstream pathways and lead to the disease. Therefore, in the post-GWAS era the greatest challenge lies in combining GWAS findings with additional molecular data to functionally characterize the associations. The advances in various ~omics techniques have made it possible to investigate the effect of risk variants on intermediate molecular levels, such as gene expression, methylation, protein abundance or metabolite levels. As disease aetiology is complex, no single molecular analysis is expected to fully unravel the disease mechanism. Multiple molecular levels can interact and also show plasticity in different physiological conditions, cell types and disease stages. There is therefore a great need for new integrative approaches that can combine data from different molecular levels and can help construct the causal inference from genotype to phenotype. Systems genetics is such an approach; it is used to study genetic effects within the larger scope of systems biology by integrating genotype information with various ~omics datasets as well as with environmental and physiological variables. In this review, we describe this approach and discuss how it can help us unravel the molecular mechanisms through which genetic variation causes disease. This article is part of a Special Issue entitled: From Genome to Function.     

The ecological genetics of conditional strategies

We develop a quantitative genetic model for conditional strategies that incorporates the ecological realism of previous strategic models. Similar to strategic models, the results show that environmental heterogeneity, cue reliability, and environment-dependent fitness trade-offs for the alternative tactics of the conditional strategy interact to determine when conditional strategies will be favored and that conditional strategies should be a common form of adaptive variation in nature. The results also show that conditional and unconditional development can be maintained in one of two ways: by frequency-dependent selection or by the maintenance of genetic variation that exceeds the threshold for induction. We then modified the model to take into account variance in exposures to the environmental cue as well as variance in response to the cue, which allows a derivation of a dose-response curve. Here the results showed that increasing the genetic variance for response both flattens and shifts the dose-response curve. Finally, we modify the model to derive the dose-response curve for a population polymorphic for a gene that blocks expression of the conditional strategy. We illustrate the utility of the model by application to predator-induced defense in an intertidal barnacle and compare the results with phenotypic models of selection.     

Cellulosic ethanol production: Progress,challenges and strategies for solutions

Lignocellulosic biomass is a sustainable feedstock for fuel ethanol production, but it is characterized by low mass and energy densities, and distributed production with relatively small scales is more suitable for cellulosic ethanol, which can better balance cost for the feedstock logistics. Lignocellulosic biomass is recalcitrant to degradation, and pretreatment is needed, but more efficient pretreatment technologies should be developed based on an in-depth understanding of its biosynthesis and regulation for engineering plant cell walls with less recalcitrance. Simultaneous saccharification and co-fermentation has been developed for cellulosic ethanol production, but the concept has been mistakenly defined, since the saccharification and co-fermentation are by no means simultaneous. Lignin is unreactive, which not only occupies reactor spaces during the enzymatic hydrolysis of the cellulose component and ethanol fermentation thereafter, but also requires extra mixing, making high solid loading difficult for lignocellulosic biomass and ethanol titers substantially compromised, which consequently increases energy consumption for ethanol distillation and stillage discharge, presenting another challenge for cellulosic ethanol production. Pentose sugars released from the hydrolysis of hemicelluloses are not fermentable with Saccharomyces cerevisiae used for ethanol production from sugar- and starch-based feedstocks, and engineering the brewing yeast and other ethanologenic species such as Zymomonas mobilis with pentose metabolism has been performed within the past decades. However strategies for the simultaneous co-fermentation of pentose and hexose sugars that have been pursued overwhelmingly for strain development might be modified for robust ethanol production. Finally, unit integration and system optimization are needed to maximize economic and environmental benefits for cellulosic ethanol production. In this article, we critically reviewed updated progress, and highlighted challenges and strategies for solutions.     

Understanding the human condition: experimental strategies in mammalian genetics

Mice have become the mammalian model of choice for the application of genetics in biomedical research due to the evolutionary conservation of physiological systems and their attendant pathologies among all mammals as well as the exceptional power of genetic research technologies in the species. Beginning from aberrant phenotypes, a large number of mouse mutants and natural polymorphisms have been cloned, providing much information about the molecular basis of physiological processes. Additionally, the variable expression of these mutations in different inbred strain backgrounds has demonstrated the importance of modifier genes, which are also susceptible to cloning. Research efforts are keeping pace with these developments. In the area of gene discovery, large, government-funded mutagenesis programs now exist, and as a matter of great practical importance, recent evidence suggests that the same genes may be involved in the natural polymorphisms affecting disease in mice and humans. In parallel, dramatic advances are also being made in our ability to measure physiological processes in mice, and the advent of expression profiling promises revolutionary advances in understanding phenotype at the molecular level. Gene-driven approaches have relied on engineering the mouse genome, including adding, subtracting, and replacing genes and, most recently, the ability to control gene activity reversibly. Together, these multiple advances in our technical abilities have created extraordinary opportunities for future discovery.     

Nontypeable Haemophilus influenzae: challenges in developing a vaccine.

Nontypeable Haemophilus influenzae (NTHi) is a gram-negative coccobacillus that is one of the bacteria that form the commensal flora of the upper respiratory tract in humans. This bacterium is an important human pathogen causing a broad spectrum of disease in both adults and children, including invasive and localised infections. The challenges in developing a bacterial protein antigen into an effective vaccine are, firstly, understanding what factors constitute an effective protective immune response for the host, and secondly, to design an effective delivery system that can target and induce the required immune response in humans that will prevent the variety of infections caused by NTHi.     

Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges

Recent improvements in the speed, cost and accuracy of next generation sequencing are revolutionizing the discovery of single nucleotide polymorphisms (SNPs). SNPs are increasingly being used as an addition to the molecular ecology toolkit in nonmodel organisms, but their efficient use remains challenging. Here, we discuss common issues when employing SNP markers, including the high numbers of markers typically employed, the effects of ascertainment bias and the inclusion of nonneutral loci in a marker panel. We provide a critique of considerations specifically associated with the application and population genetic analysis of SNPs in nonmodel taxa, focusing specifically on some of the most commonly applied methods.