Use of ‘Omic’ Approaches in Unraveling Mechanisms of Gene-Environment Interactions

Pleiotropy, plasticity, and the evolution of plant abiotic stress tolerance

Progress in understanding the mechanisms of adaptive plant abiotic stress response has historically come from two separate fields. Molecular biologists employ mutagenic screens, experimental manipulations, and controlled stress treatment to identify genes that, when perturbed, have fairly large effects on phenotype. By contrast, quantitative and evolutionary geneticists generally study naturally occurring variants to inform multigenic models of trait architecture in an effort to predict, for example, the evolutionary response to selection. We discuss five emerging themes from the molecular study of osmotic stress response: the multigenic nature of adaptive response, the modular organization of response to specific cues, the pleiotropic effects of key signaling proteins, the integration of many environmental signals, and the abundant cross-talk between signaling pathways. We argue that these concepts can be incorporated into existing models of trait evolution and provide examples of what may constitute the molecular basis of plasticity and evolvability of abiotic stress response. We conclude by considering future directions in the study of the functional molecular evolution of abiotic stress response that may facilitate new discoveries in molecular biology, evolutionary studies, and plant breeding.

Genetics of autism spectrum disorders

Autism spectrum disorders (ASDs) are a clinically complex group of childhood disorders that have firm evidence of an underlying genetic etiology. Many techniques have been used to characterize the genetic bases of ASDs. Linkage studies have identified several replicated susceptibility loci, including 2q24-2q31, 7q, and 17q11-17q21. Association studies and mutation analysis of candidate genes have implicated the synaptic genes NRXN1, NLGN3, NLGN4, SHANK3, and CNTNAP2 in ASDs. Traditional cytogenetic approaches highlight the high frequency of large chromosomal abnormalities (3%-7% of patients), including the most frequently observed maternal 15q11-13 duplications (1%-3% of patients). Newly developed techniques include high-resolution DNA microarray technologies, which have discovered formerly undetectable submicroscopic copy number variants, and genomewide association studies, which allow simultaneous detection of multiple genes associated with ASDs. Although great progress has been made in autism genetics, the molecular bases of most ASDs remains enigmatic.

PTPRR protein tyrosine phosphatase isoforms and locomotion of vesicles and mice

Protein tyrosine phosphatases (PTPs) are central players in many different cellular processes and their aberrant activity is associated with multiple human pathologies. In this review, we present current knowledge on the PTPRR subfamily of classical PTPs that is expressed in neuronal cells and comprises receptor-type (PTPBR7, PTP-SL) as well as cytosolic (PTPPBSγ-37, PTPPBSγ-42) isoforms. The two receptor-type isoforms PTPBR7 and PTP-SL both localize in late endosomes and the Golgi area. PTPBR7, however, is additionally localized at the cell surface and on early endosomes. During cerebellar maturation, PTPBR7 expression in developing Purkinje cells ceases and is replaced by PTP-SL expression in the mature Purkinje cells. All PTPRR isoforms contain a kinase interacting motif that makes them mitogen-activated protein kinase phosphatases. The distinct subcellular localization of the different PTPRR isoforms may reflect differential roles in growth-factor-induced MAPK-mediated retrograde signaling cascades. Studies in PTPRR-deficient mice established that PTPRR isoforms are physiological regulators of MAPK phosphorylation levels. Surprisingly, PTPRR-deficient mice display defects in motor coordination and balancing skills, while cerebellar morphological abnormalities, which are often encountered in ataxic mouse models, are absent. This is reminiscent of the phenotype observed in a handful of mouse mutants that have alterations in cerebellar calcium ion homeostasis. Elucidation of the molecular mechanisms by which PTPRR deficiency imposes impairment of cerebellar neurons and motor coordination may provide candidate molecules for hereditary cerebellar ataxias that still await identification of the corresponding disease genes.

From information to understanding: the role of model organism databases in comparative and functional genomics

Data integration is key to functional and comparative genomics because integration allows diverse data types to be evaluated in new contexts. To achieve data integration in a scalable and sensible way, semantic standards are needed, both for naming things (standardized nomenclatures, use of key words) and also for knowledge representation. The Mouse Genome Informatics database and other model organism databases help to close the gap between information and understanding of biological processes because these resources enforce well-defined nomenclature and knowledge representation standards. Model organism databases have a critical role to play in ensuring that diverse kinds of data, especially genome-scale data sets and information, remain useful to the biological community in the long-term. The efforts of model organism database groups ensure not only that organism-specific data are integrated, curated and accessible but also that the information is structured in such a way that comparison of biological knowledge across model organisms is facilitated.

Genomics in environmental health research--opportunities and challenges

Environmental health research impacts both environmental health regulatory policy and the practice of medicine. However, this area of medical research has not garnered public support and attention of medical researchers because of its emphasis on prevention and public health. Also, the pervasiveness of a scientific culture wedded to old problems and outdated technologies and models systems has not been helpful in generating enthusiasm for the field. While the emphasis on prevention is both laudable and appropriate, the adoption of cutting-edge technologies to exploit the new scientific opportunities, made possible by the nation's investment in genomics, is essential if the discipline expects to be competitive with other highly deserving programs. The new 'omics' era of environmental health research, ushered in over the past decade, characterized by the linkage of genomics, proteomics and metabolomics to conventional toxicology and pathology databases, holds great promise for elucidating mechanisms of gene-environment interaction in human health and disease. These combined approaches will allow one to monitor multiple molecular events, pathways and interactive networks simultaneously-a requirement for elucidating toxic mechanisms. But, before embracing the 'omics' technologies as the 'be all-end all;' they need to be validated for their predictive capacities in large-scale multi-institutional studies, such as those described in this article.