BeeSpace: An interactive environment for analyzing nature and nurture, 2006-2010

Adapted from a report to NIH FIBR:

One of the most important questions in biology is the origin of behaviors: nature or nurture? The study of behavior can be liberated from this dichotomy by viewing it as the result of inherited and environmental influences acting on the same substrate, the genome. The environment (“nurture”), including other individuals, impacts an inherited genome (“nature”) by controlling gene expression during an individual’s life. Our research moves to the frontier of contemporary biology, where biotechnology enables expression analysis and bioinformatics enables functional analysis unconstrained by pre-existing categories.

Honey bee genome

BeeSpace used the honey bee to elucidate the relationship between genes and life in an animal society on a whole-genome scale. Honey bees live in complex societies organized on the basis of division of labor among workers; instead of performing one role for the duration of her life a worker assumes many roles, influenced by heredity and the environment. The bee genome has been sequenced, and normal behavior can be molecularly analyzed via microarray recording from field-captured bees.

We developed an interactive computer environment to support integration of molecular description with information from ecology, evolution, behavioral science, and physiology. A functional analysis of all the roles of a worker honey bee within her society was done by combining microarray analysis, large-scale brain in situ hybridization, and a novel approach to informatics that links all sources from current genome databases to the existing scientific and natural history literatures on honey bees. BeeSpace enables biologists studying bee genes to place knowledge into an integrative biological context.

Interdisciplinary research

Our Biology Research has developed a master list of societal roles and collected honey bees from natural settings in the field for each such role. A bee microarray from the complete sequence has been fabricated and the first experiments are being processed to analyze the discriminating gene expressions. We investigated the heredity and environment influences on the transition from working in the hive to foraging in the field. This involved different genetic strains of bees, treatments with a variety of neuroactive chemicals, manipulations to change the social environment, and careful collection of bees engaged in different aspects of foraging behavior, such as nectar foragers, pollen foragers, and scout bees.

Our Informatics Research developed a prototype of the interactive environment for functional analysis. Specialized collections from Biosis and Medline represent different viewpoints such as model (honey bee, fruit fly) or behavior (social, territorial). These collections are semantically indexed to produce conceptual relationships between document phrases. Our users can navigate from concept to related concept across collections. Documents within collections can be summarized, by clustering documents into functional groups or by generating structured descriptions of contained genes.

Users

We actively worked with a small user community of molecular behavioral biologists to develop effective navigation for hypothesis testing. The BeeSpace environment was tested in 15 laboratories studying honey bees and related organisms.

BeeSpace was used for teaching science at Campus Middle School for Girls (Champaign), a field biology course using BeeSpace at the University Laboratory High School, and middle school students taught by Wake Forest freshmen trained in a newly developed bioinformatics course.