Innovative Research Tools

Summary

Innovative tools and technologies are critical to a scientist’s ability to advance knowledge about microorganisms, plants, animals and humans. They enable researchers to isolate and identify specific genes, proteins, and small molecules. They make it possible for scientists to efficiently sort through enormous databases to find specific information needed for a particular project. And, they assist in the identification of molecules that may have evolutionary, biological or medical importance. Developing and perfecting innovative tools and technologies is an important area of research at BTI.

The Issue

People have 20,000 to 25,000 genes that direct the production of thousands of proteins essential for growth, health and reproduction. A fruit fly has about half as many genes as a human and a tomato plant has about 35,000. An organism’s full complement of genes is called its “genome.” When you consider the broad range of molecular biology research worldwide, it’s easy to understand the enormity of the genomic data scientists produce. To make this data usable it must be stored and organized in a way that makes each piece easily retrievable.

In addition to its genome, each organism is characterized by a “metabolome.” This is the complete array of small molecules that are involved in metabolism, which is the set of chemical reactions that occur in organisms to maintain life or carry out essential processes. Metabolites perform specialized functions, such as regulating the break down of food for energy, controlling immune responses, or fighting off competing organisms. Identifying the thousands of primary and secondary metabolites an organism produces and determining their function is a vast and important area of biological research.

To help with these important scientific pursuits, one BTI scientist is working on innovative tools to help organize and make the enormous amount of data generated in genomics easily available to researchers, while another is developing new analytical methods that are making it possible to identify small molecule metabolites in animals and humans and determine their function. Summaries of their research projects follow.

Potential Impacts

Genes, genes and more genes

Computers touch nearly every aspect of our lives, including the ability to explain life itself. When computerization is combined with mathematics, statistics and biology, it’s called “bioinformatics.” Bioinformatics is the technology that helps scientists at BTI and throughout the world organize, analyze, retrieve and use the vast array of genetic data science is producing.

At BTI, Zhangjun Fei, Ph.D., is developing databases to help scientists understand how genes work together and how they form functioning cells and organisms. He is also developing analytical and data-mining tools that allow scientists to efficiently access, identify and extract the biological information contained in the databases for use in their research.

In one project, Fei has developed a database that contains expression information on more than 10,000 tomato genes. The data includes the proteins tomatoes produce during various developmental processes and in response to different environmental stimuli, as well as information about the nutrition- and flavor-related metabolites of tomatoes. He has also developed a database – with tools for accessing it – that contains all the genomics information gathered to date for the cucurbit family of plants, which includes melons, cucumbers, watermelons and pumpkins among other fruits.

Work in Fei’s BTI laboratory is providing innovative tools and resources that organize all the data about an organism into a form scientists can easily use. His ultimate goal is to enable researchers in their quest for new biological insights. His contributions to bioinformatics will also help create a global perspective that will reveal unifying principles in biology never discovered before.

As the worm turns

Thanks to work in another area of technology at BTI, tiny worms, called nematodes, are giving up new information that’s important for human health. Scientist Frank Schroeder, Ph.D., identifies secondary metabolites produced by the worm that may advance our understanding of human health issues, such as bacterial infections, diabetes, cancer and, in particular, aging.

The worm used for these studies, called C. elegans, has much in common with humans in that many of its physiological functions are similar to ours. Just as the Arabidopsis plant is the “white mouse” of plant research, C. elegans is an important model system for learning about human disease and aging. Though all 20,000 genes in this nematode were identified more than 10 years ago, its metabolome (small molecules that, for example, regulate neurological functions, the immune system, development, and aging) remained largely unknown until the advent of new analytical methods developed by Schroeder.

His new methods are based on a technique called nuclear magnetic resonance spectroscopy (NMR), which is critical to researchers’ ability to identify the chemical structure of small molecules and to discover their biological functions. Using his new method, Schroeder and his research team recently identified several new compounds that influence a wide range of biological phenomena, from mating behavior to life span regulation.

Schroeder’s goal is to identify all of C. elegan’s secondary metabolites and their biological functions. This work will provide a much-needed knowledge base for medical researchers who are looking for new approaches to the treatment of human diseases such as diabetes, cancer, and the effects of aging.