Nutrigenomics research for personalized nutrition and medicine

Current nutritional and genetic epidemiological methods yield 'risk factors' on the basis of population studies. Risk factors, however, are statistical estimates of the percentage reduction in disease in the population if the risk were to be avoided or the gene variant were not present. These measures are often assumed to apply to individuals who are likely to differ in genetic make-up, lifestyle, and dietary patterns than to the individuals in the study population. Developing individual risk factors in light of the genetic diversity of human populations, the complexity of foods, culture and lifestyle, and the variety of metabolic processes that lead to health or disease is a significant challenge for personalizing dietary advice for healthy or individuals with chronic disease.     

Cancer systems epidemiology: Overcoming misconceptions and integrating systems approaches into cancer research

Patricia Mabry and coauthors discuss application of systems approaches in cancer research.

Summary points

• While traditional epidemiological approaches have helped generate important insights about cancer prevention and treatment, they have important limitations and alone cannot bridge the gaps that continue to exist in cancer research and knowledge.
• One shortcoming is the failure to fully account for and characterize the complexity of various systems (e.g., biological, behavioral, social, environmental, and economic) that can lead to cancer and are affected by cancer.
• Systems approaches can help researchers, clinicians, and other decision makers better understand complex systems and address these systems at many levels, ranging from the cellular to the societal scale.
• Systems mapping can shed light on otherwise hidden mental models, and dynamic modeling can enable virtual experimentation—the systematic exploration of counterfactual scenarios not observable in the real world.
• We present and discuss 14 common misconceptions that will need to be overcome in order for systems epidemiology to realize its potential role in cancer prevention and control.
• Examples of systems approaches applied to cancer-related research topics are given to illustrate the utility of systems approaches to transform cancer epidemiology to cancer systems epidemiology.

     

Aggression and violence: perspectives on integrating animal and human research approaches

Aggression and violence are concerns that engage us across society as moral and cultural issues. They are also critical issues for mental health research--both for survivors and for understanding how such behaviors occur. Interpersonal violence often explodes in deliberate acts of physical force leaving survivors behind with a diminished sense of control that is often shadowed by persistent fear and anxiety. The treatment of the victims is a clear and immediate concern; from their perspectives the medical consequences require effective attention whether they suffered as a result of acts of nature, mental disease, ideology, or combinations of these. At the same time preventing violent behavior from happening in the first place is a compelling challenge for public health research.     

Focus: Nutrigenomics

Cover illustration: Nutrigenomics aims to identify the genes that influence the risk of diet-related diseases on a genomewide scale, and to understand the mechanisms that underlie these genetic predispositions. This BTJ special issue edited by Taesun Park features articles uncovering ‘dietary signatures’ associated with obesity and metabolic diseases. Images copyright: Yellow, green, and red bell peppers. © Photodisc, Microarray; © http://genomics.energy.gov     

A framework for integrating thermal biology into fragmentation research

Habitat fragmentation changes thermal conditions in remnant patches, and thermal conditions strongly influence organism morphology, distribution, and activity patterns. However, few studies explore temperature as a mechanism driving ecological responses to fragmentation. Here we offer a conceptual framework that integrates thermal biology into fragmentation research to better understand individual, species, community, and ecosystem‐level responses to fragmentation. Specifically, the framework addresses how fragmentation changes temperature and how the effects of those temperature changes spread through the ecosystem, from organism response via thermal sensitivity, to changes in species distribution and activity patterns, to shifts in community structure following species' responses, and ultimately to changes in ecosystem functions. We place a strong emphasis on future research directions by outlining “Critical gaps” for each step of the framework. Empirical efforts to apply and test this framework promise new understanding of fragmentation's ecological consequences and new strategies for conservation in an increasingly fragmented and warmer world.     

Nutrigenomics: goals and strategies

Nutrigenomics is the application of high-throughput genomics tools in nutrition research. Applied wisely, it will promote an increased understanding of how nutrition influences metabolic pathways and homeostatic control, how this regulation is disturbed in the early phase of a diet-related disease and to what extent individual sensitizing genotypes contribute to such diseases. Ultimately, nutrigenomics will allow effective dietary-intervention strategies to recover normal homeostasis and to prevent diet-related diseases.     

PRIME: a graphical interface for integrating genomic/proteomic databases

Data mining, finding and integration of information about proteins of interest, is an essential component in modern biological and biomedical research. Even when focusing on a single organism and only on a small number of proteins, there are often dozens fo data sources containing relevant information. We are developing PRIME, a protein information environment, to serve as a virtual central database which integrates distributed heterogeneous information about proteins (linked by common identifier). PRIME has powerful capabilities to visualize all kinds of protein annotation in specialized views. These views can be displayed side by side at the same time and can be synchronized in order to show simultaneously different aspects of identical proteins. These features allow a quick and comprehensive overview of properties of single proteins or protein sets.     

Introduction: integrating genetic and cultural evolutionary approaches to language

The papers in this special issue of Human Biology address recent research in the field of language evolution, both the genetic evolution of the language faculty and the cultural evolution of specific languages. While both of these areas have received increasing interest in recent years, there is also a need to integrate these somewhat separate efforts and explore the relevant gene-culture coevolutionary interactions. Here we summarize the individual contributions, set them in the context of the wider literature, and identify outstanding future research questions. The first set of papers concerns the comparative study of nonhuman communication in primates and birds from both a behavioral and neurobiological perspective, revealing evidence for several common language-related traits in various nonhuman species and providing clues as to the evolutionary origin and function of the human language faculty. The second set of papers discusses the consequences of viewing language as a culturally evolving system in its own right, including claims that this removes the need for strong genetic biases for language acquisition, and that phylogenetic evolutionary methods can be used to reconstruct language histories. We conclude by highlighting outstanding areas for future research, including identifying the precise selection pressures that gave rise to the language faculty in ancestral hominin species, and determining the strength, domain specificity, and origin of the cultural transmission biases that shape languages as they pass along successive generations of language learners.     

Cross-cultural,developmental psychology: integrating approaches and key insights

Like psychology more broadly, developmental psychology has long suffered from a narrow focus on children from WEIRD societies—or those that are Western, Educated, Industrialized, Rich, and Democratic. In this review, we discuss how developmental scientists have sought to correct this bias through two complementary approaches: one centered on detailed, ethnographic investigations of child development within populations (increasing the depth of our understanding) and one focused on larger, multi-site studies that test children on standardized tasks across populations (increasing breadth). We review key papers from each of these approaches, describe how they are currently practiced, and discuss their strengths and weaknesses. Next, we highlight exemplary papers from the adult literature that offer useful insights, namely the importance of formal modeling and a greater focus on studying variation at multiple levels of analysis. We end by outlining best practices for future waves of cross-cultural, developmental science. Overall, we argue that a more integrated perspective, combining the strengths of the breadth & depth approaches, can help better elucidate the developmental origins of human behavioral diversity.     

Genetic and genomic approaches to glomerulosclerosis

Chronic kidney disease (CKD) is common, progressive and expensive to manage. Although modifiable risk factors can be treated and outcomes improved, CKD remains a chronic disease with excessive morbidity and mortality. The completion of the human genome sequence and the advent of methodologies to define gene function provide new opportunities to manage and treat patients with CKD and other chronic diseases. Despite the lack of clear correspondence between genotype and phenotype and an obvious Mendelian inheritance pattern, CKD susceptibility has a genetic basis. In this review, we focus on recent studies of familial focal segmental glomerulosclerosis and the discoveries that have resulted from both genetic and genomic approaches used to understand its pathogenesis. Key slit diaphragm proteins were discovered using linkage analyses of these rare causes of glomerulosclerosis and subsequent work has characterized slit diaphragm function in health and disease. Podocyte dysfunction is now recognized as a key contributor to the functional and histologic derangements that characterize glomerular dysfunction in many common causes of CKD. In aggregate, these studies provide a paradigm for approaches to better define mechanisms of CKD and to identify novel therapeutic targets.     

Systems-biology approaches for predicting genomic evolution

Is evolution predictable at the molecular level? The ambitious goal to answer this question requires an understanding of the mutational effects that govern the complex relationship between genotype and phenotype. In practice, it involves integrating systems-biology modelling, microbial laboratory evolution experiments and large-scale mutational analyses - a feat that is made possible by the recent availability of the necessary computational tools and experimental techniques. This Review investigates recent progresses in mapping evolutionary trajectories and discusses the degree to which these predictions are realistic.     

Time to integrate biotechnological approaches into fish gut microbiome research

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Nutrimetabolomics: integrating metabolomics in nutrition to disentangle intake of animal-based foods

Food intake and metabolization of foods is a complex and multi-facetted process that encompasses the introduction of new metabolite compounds in our body, initiation or alterations in endogenous metabolic processes and biochemical pathways, and likely also involving the activity of the gut microbial community that we host. The explorative nature of metabolomics makes it a superior tool for examining the whole response to food intake in a more thorough way and has led to the introduction of the term nutrimetabolomics. Protein derived from animal sources constitutes an important part of our diet, and there is therefore an interest in understanding how these animal-derived dietary sources influence us metabolically. This review aims to illuminate how the introduction of nutrimetabolomics has contributed to gain novel insight into metabolic and nutritional aspects related to intake of animal-based foods.