Genome-environment interactions and prospective technology assessment: evolution from pharmacogenomics to nutrigenomics and ecogenomics

Omics as a Window To Unravel the Dynamic Changes of Egg Components during Chicken Embryonic Development

Chicken egg, as a completely aseptic and self-sufficient biological entity, contains all of the components required for embryonic development. As such, it constitutes not only an excellent model to study the mechanisms of early embryo nutrition and disease origin but can also be used to develop egg-based products with specific applications. Different omics disciplines, like transcriptomics, proteomics, and metabolomics, represent promising approaches to assess nutritional and functional molecules in eggs under development. However, these individual molecules do not act in isolation during the dynamic embryogenic process (e.g., migration, transportation, and absorption). Unless we integrate the information from all of these omics disciplines, there will remain an unbridged gap in the systematic and holistic assessment of the information from one omics level to the other. This integrative review of the dynamic molecular processes of the different chicken egg components involved in embryo development describes the critical interplay between the egg components and their implications in immunity, hematopoiesis, organ formation, and nutrient transport functions during the embryonic process.

Lipidomics Insights in Health and Nutritional Intervention Studies

Lipids are among the major components of food and constitute the principal structural biomolecules of human body together with proteins and carbohydrates. Lipidomics encompasses the investigation of the lipidome, defined as the entire spectrum of lipids in a biological system at a given time. Among metabolomics technologies, lipidomics has evolved due to the relevance of lipids in nutrition and their well-recognized roles in health. Mass spectrometry advances have greatly facilitated lipidomics, but owing to the complexity and diversity of the lipids, lipidome purification and analysis are still challenging. This review focuses on lipidomics strategies, applications, and achievements of studies related to nutrition and health research.

Ayurnutrigenomics: Ayurveda-inspired personalized nutrition from inception to evidence

Ayurveda proclaims food and drugs are intersecting concepts that are vital for human survival and for the prevention and mitigation of diseases. Food interferes with the molecular mechanisms of an organism's “physiome”. It is consumed in large amounts compared to any drug. Hence, research on its effect and interaction with genome is highly relevant toward understanding diseases and their therapies. Ayurgenomics presents a personalized approach in the predictive, preventive, and curative aspects of stratified medicine with molecular variability, which embodies the study of interindividual variability due to genetic variability in humans for assessing susceptibility, and establishing diagnosis and prognosis, mainly on the basis of the constitution type of a person's Prakriti. Ayurnutrigenomics is an emerging field of interest pervading Ayurveda systems biology, where the selection of a suitable dietary, therapeutic, and lifestyle regime is made on the basis of clinical assessment of an individual maintaining one's Prakriti. This Ayurveda-inspired concept of personalized nutrition is a novel concept of nutrigenomic research for developing personalized functional foods and nutraceuticals suitable for one's genetic makeup with the help of Ayurveda. Here, we propose and present this novel concept of Ayurnutrigenomics and its emerging areas of research, which may unfold future possibilities toward smart yet safe therapeutics.

Unraveling the Complexities of Life Sciences Data

The life sciences have entered into the realm of big data and data-enabled science, where data can either empower or overwhelm. These data bring the challenges of the 5 Vs of big data: volume, veracity, velocity, variety, and value. Both independently and through our involvement with DELSA Global (Data-Enabled Life Sciences Alliance, DELSAglobal.org), the Kolker Lab ( kolkerlab.org ) is creating partnerships that identify data challenges and solve community needs. We specialize in solutions to complex biological data challenges, as exemplified by the community resource of MOPED (Model Organism Protein Expression Database, MOPED.proteinspire.org ) and the analysis pipeline of SPIRE (Systematic Protein Investigative Research Environment, PROTEINSPIRE.org ). Our collaborative work extends into the computationally intensive tasks of analysis and visualization of millions of protein sequences through innovative implementations of sequence alignment algorithms and creation of the Protein Sequence Universe tool (PSU). Pushing into the future together with our collaborators, our lab is pursuing integration of multi-omics data and exploration of biological pathways, as well as assigning function to proteins and porting solutions to the cloud. Big data have come to the life sciences; discovering the knowledge in the data will bring breakthroughs and benefits.

Nanoplatforms for constructing new approaches to cancer treatment, imaging, and drug delivery: what should be the policy?

Nanotechnology is the design and assembly of submicroscopic devices called nanoparticles, which are 1-100 nm in diameter. Nanomedicine is the application of nanotechnology for the diagnosis and treatment of human disease. Disease-specific receptors on the surface of cells provide useful targets for nanoparticles. Because nanoparticles can be engineered from components that (1) recognize disease at the cellular level, (2) are visible on imaging studies, and (3) deliver therapeutic compounds, nanotechnology is well suited for the diagnosis and treatment of a variety of diseases. Nanotechnology will enable earlier detection and treatment of diseases that are best treated in their initial stages, such as cancer. Advances in nanotechnology will also spur the discovery of new methods for delivery of therapeutic compounds, including genes and proteins, to diseased tissue. A myriad of nanostructured drugs with effective site-targeting can be developed by combining a diverse selection of targeting, diagnostic, and therapeutic components. Incorporating immune target specificity with nanostructures introduces a new type of treatment modality, nano-immunochemotherapy, for patients with cancer. In this review, we will discuss the development and potential applications of nanoscale platforms in medical diagnosis and treatment. To impact the care of patients with neurological diseases, advances in nanotechnology will require accelerated translation to the fields of brain mapping, CNS imaging, and nanoneurosurgery. Advances in nanoplatform, nano-imaging, and nano-drug delivery will drive the future development of nanomedicine, personalized medicine, and targeted therapy. We believe that the formation of a science, technology, medicine law-healthcare policy (STML) hub/center, which encourages collaboration among universities, medical centers, US government, industry, patient advocacy groups, charitable foundations, and philanthropists, could significantly facilitate such advancements and contribute to the translation of nanotechnology across medical disciplines.

Environmental influences on development of type 2 diabetes and obesity: challenges in personalizing prevention and management

Recent epidemic increases in the U.S. prevalence of obesity and diabetes are a consequence of widespread environmental changes affecting energy balance and its regulation. These environmental changes range from exposure to endocrine disrupting pollutants to shortened sleep duration to physical inactivity to excess caloric intake. Overall, we need a better understanding of the factors affecting individual susceptibility and resistance to adverse exposures and behaviors and of determinants of individual response to treatment. Obesity and diabetes prevention will require responding to two primary behavioral risk factors: excess energy intake and insufficient energy expenditure. Adverse food environments (external, nonphysiological influences on eating behaviors) contribute to excess caloric intake but can be countered through behavioral and economic approaches. Adverse built environments, which can be modified to foster more physical activity, are promising venues for community-level intervention. Techniques to help people to modulate energy intake and increase energy expenditure must address their personal situations: health literacy, psychological factors, and social relationships. Behaviorally oriented translational research can help in developing useful interventions and environmental modifications that are tailored to individual needs.

Risk assessment and communication tools for genotype associations with multifactorial phenotypes: the concept of "edge effect" and cultivating an ethical bridge between omics innovations and society

Applications of omics technologies in the postgenomics era swiftly expanded from rare monogenic disorders to multifactorial common complex diseases, pharmacogenomics, and personalized medicine. Already, there are signposts indicative of further omics technology investment in nutritional sciences (nutrigenomics), environmental health/ecology (ecogenomics), and agriculture (agrigenomics). Genotype-phenotype association studies are a centerpiece of translational research in omics science. Yet scientific and ethical standards and ways to assess and communicate risk information obtained from association studies have been neglected to date. This is a significant gap because association studies decisively influence which genetic loci become genetic tests in the clinic or products in the genetic test marketplace. A growing challenge concerns the interpretation of large overlap typically observed in distribution of quantitative traits in a genetic association study with a polygenic/multifactorial phenotype. To remedy the shortage of risk assessment and communication tools for association studies, this paper presents the concept of edge effect. That is, the shift in population edges of a multifactorial quantitative phenotype is a more sensitive measure (than population averages) to gauge the population level impact and by extension, policy significance of an omics marker. Empirical application of the edge effect concept is illustrated using an original analysis of warfarin pharmacogenomics and the VKORC1 genetic variation in a Brazilian population sample. These edge effect analyses are examined in relation to regulatory guidance development for association studies. We explain that omics science transcends the conventional laboratory bench space and includes a highly heterogeneous cast of stakeholders in society who have a plurality of interests that are often in conflict. Hence, communication of risk information in diagnostic medicine also demands attention to processes involved in production of knowledge and human values embedded in scientific practice, for example, why, how, by whom, and to what ends association studies are conducted, and standards are developed (or not). To ensure sustainability of omics innovations and forecast their trajectory, we need interventions to bridge the gap between omics laboratory and society. Appreciation of scholarship in history of omics science is one remedy to responsibly learn from the past to ensure a sustainable future in omics fields, both emerging (nutrigenomics, ecogenomics), and those that are more established (pharmacogenomics). Another measure to build public trust and sustainability of omics fields could be legislative initiatives to create a multidisciplinary oversight body, at arm's length from conflict of interests, to carry out independent, impartial, and transparent innovation analyses and prospective technology assessment.