hands-on science learning from the ground up

The Need for Hands-On Education – Our Current Challenge

Many of today's students view science as a dull, unchanging arena where all the interesting questions have been answered and very little remains to be discovered. This perception is definitely not true in modern biotechnology and genomics, where the pace of discovery is increasing at a breathtaking speed. Unfortunately, descriptions of these exciting new areas do not appear on the pages of science textbooks until many years after their discovery. In addition, the lack of inquiry-based approaches (where students are immersed in the active process of experimental scientific research), leaves high school and undergraduate biology students lagging behind, unaware of cutting-edge findings that make biology so exciting to researchers.

HudsonAlpha's Response to this Challenge

Using our life-science expertise and extensive educational collaborations, the HudsonAlpha Institute for Biotechnology is working to excite students about science and inspire them to seek careers in biotechnology and related fields. By partnering with educators, policy makers and civic groups to develop appropriate school curricula and interactive student experiences, we connect academic learning with real-world application.

HudsonAlpha offers area high school and undergraduate students the opportunity to be part of an in-depth internship experience known as BioTrain. Currently, the interns work either with the educational outreach team, a HudsonAlpha associate company or HudsonAlpha researcher. All summer BioTrain interns participate in “Biotech Bootcamp”, a one-week skills development session at the beginning of the program. Student interest in the program has been amazing – nearly 300 applications were received this spring for 24 summer internship slots. Such a response indicates a clear need for additional student biotechnology experiences.

The Sample to Sequence Experience

Gaining a broad understanding of the types of microbes (microscopic living organisms) present in a population is the first step in a metagenomics project. One of the most common approaches is based on a technique known as rRNA phylotyping. In a nutshell, this method determines the DNA sequence of a ribosomal RNA, or rRNA, gene common to all microbes. Ribosomal RNA genes are crucial to all life and serve as a historical marker for an organisms lineage and metabolism. The specific DNA sequence for these rRNA genes exhibits a great deal of variation across microbial species. Identifying the specific DNA variants from this gene provides a rough catalog of the range of microbes present in the sample. This methodology is one of the most rapid and cost-effective methods to assess bacterial diversity and abundance.

Students in the Sample to Sequence program will obtain a soil or water sample and perform rRNA phylotyping to determine which microbes are present in that habitat (see the workflow of this process to the right).

Throughout the experience, students will generate web-based portfolios to document the methods, results and implications. These portfolio pages will be hosted by the HudsonAlpha educational outreach program allowing students to cite the work as part of a career portfolio documenting their research skills to potential employers or institutes of higher education.

What samples will be analyzed?

Because microbial communities live virtually everywhere, and we are largely ignorant of their inhabitants and functions, there are literally millions of potential metagenomics projects available. One straightforward option is to analyze a soil sample obtained from a field on the HudsonAlpha biotechnology campus.

A second, very compelling option involves a collaboration with a local environmental analysis company examining brownfield sites identified by the Environmental Protection Agency (EPA). Brownfields are generally defined as abandoned or underused industrial or commercial properties where redevelopment is complicated by actual or perceived environmental contamination. In general, brownfield properties have relatively low levels of contamination that can be successfully addressed using standard environmental cleanup practices, but are stigmatized based on their past use.

We are setting up a collaboration with an environmental monitoring company. Such a partnership would allow students to link the molecular findings describing the microbial populations present at the brownfield site with geographical and historical information as well as a host of detailed soil analyses (e.g. soil pH, composition, metals and toxins present). This clearly connects student learning to real-world application, fulfilling a key goal for our educational efforts. In addition, students would receive training in proper sample analysis and receive access to specialized equipment at no additional cost to HudsonAlpha.

What students can participate in Sample to Sequence?

HudsonAlpha is working to add Sample to Sequence as an approved seminar course or independent study offering at both UAHuntsville and Athens State University. As the program matures, it will be possible to expand to other educational groups as well.

Near-term expectations
In addition to honing the skills needed to participate in the Sample to Sequence project, students will benefit from other relevant aspects of the program including:

• Improving science literacy.
• Understanding the scientific process as being a continuous building endeavor where foundations are established upon which knowledge systems develop.
• Connecting science content from other courses with hands-on methods.
• Exposure to data collection, analysis and the comparison to existing bioinformatics databases.

Long-term opportunities
The basic design of the Sample to Sequence program inherently promotes its continued development. As expertise is acquired and as access to newly developed techniques occurs, the program will continuously evolve. Specific areas that we see potentially developing within the program in the immediate future include :

• Examining a site across several months as natural and man-made conditions vary.
• Follow up of novel microbes with more detailed DNA analysis.
• Introduction to additional metagenomic technologies, such as microarray analysis, next-generation sequencing technologies, and so-called shotgun whole-genome sequencing to more fully characterize microbes within a specific community.