Here’s the first of our winning essays! Congratulations to Stephanie Weldon, one of our second place winners.
The inherent connectedness of biological information makes research on the web of life naturally suited to Web 2.0. I study insect-bacterium-virus symbioses, where the lateral transfer of both infectious bacteria and their virus passengers’ genetic material requires me to cross-reference very diverse data sets, a circumstance that makes NextBio’s search apps very appealing.
Maternally inherited bacterial symbionts are quite common in insects. However, research in the past decade or so has shifted from focusing on these “obligate” symbionts that are essential to a host’s survival to include ‘facultative’ symbionts that are not required for an insect to survive, but provide perks like protection from pathogenic fungi or parasites.
The divide between a facultative symbiont and a pathogen is a slim one. Since these bacteria are not obliged to squeeze into the narrow niches offered by a single tissue in one host, they can carry larger genetic baggage when they transfer between insect hosts or invade novel tissues. This allows their genomes to retain pathogenic mechanisms not always seen in obligate symbionts, and also host other mobile genetic elements like bacteriophage.
I work with pea aphids, a group of insects that have created alliances with both symbiotic bacteria (H.defensa) and their bacteriophage APSE, which collectively help the aphids resist attack by a parasitic wasp. The phage APSE carries one of several toxins that protect the pea aphid from the endoparasitic wasp by killing the wasp’s eggs; the precise mechanisms of this process are still being studied.
Bacteriophage carrying effector molecules that can influence their hosts were first studied in human pathogens. While I love working with the most diverse class of animals in the biosphere, researching insects means I lack a personal background into literature on vertebrate pathogens. One of the phage variants that I am characterizing carries a Shiga-like toxin: NextBio’s QuickView provides me immediate insights on the functions of Shiga toxins in pathogenic bacteria and their impact on gene expression in human cells.
Ranked results allow researchers to view large amounts of data without artificially limiting the potential for productive cross-fertilization from more distant sources. Another form of the APSE phage carries a homolog to the B-subunit of the cytolethal distending holotoxin. I am currently working on characterizing bacteriophage phylogenies and the phenotypic effects of mutations in the cdtB gene in this variant phage. As with the Shiga-like toxin, NextBio’s literature app provides me with easy access to information that would otherwise be time-consuming to parse. The user-friendly sentence-matching allows me to jump to the relevant portions quickly, and the inline links to informational pop-ups are also immensely handy when wading into a foreign literature. Best, though, is the tag cloud: it provides, in addition to ease of navigation, moments of unexpected serendipity when a tag suggests an avenue I never would have otherwise considered.
While I have focused primarily on data mining for projects I am running independently, in the future I hope to use NextBio to facilitate the human-interactive side of science; I am rather looking forward to finding a way to bring the genome browser into the classroom when I am teaching introductory biology in the fall. The graphical user interface makes exploring a chromosome and selecting a feature sufficiently intuitive and entertaining that a student may actually be willing to read up on features not directly related to their course work.
Heightened recognition of the importance of lateral gene transfer and symbiosis in evolution has led some scientists to suggest that the tree of life, particularly the unicellular branches, might be better depicted as a web. The combination of nested hierarchies and web-like interaction provided by NextBio makes it an unusually appropriate platform for biological research, particularly for those of us actively investigating life’s web-like qualities by delving into bacterial-eukaryotic symbioses and mobile genetic elements.