Generation of a highly attenuated strain of Pseudomonas aeruginosa for commercial production of alginate

Alginate is an important polysaccharide that is commonly used as a gelling agent in foods, cosmetics and healthcare products. Currently, all alginate used commercially is extracted from brown seaweed. However, with environmental changes such as increasing ocean temperature and the increasing number of biotechnological uses of alginates with specific properties, there is an emerging need for more reliable and customizable sources of alginate. An alternative to seaweed for alginate production is Pseudomonas aeruginosa, a common Gram-negative bacterium that can form alginate-containing biofilms. However, P. aeruginosa is an opportunistic pathogen that can cause life-threatening infections in immunocompromised patients. Therefore, we sought to engineer a non-pathogenic P. aeruginosa strain that is safe for commercial production of alginate. Using a homologous recombination strategy, we sequentially deleted five key pathogenicity genes from the P. aeruginosa chromosome, resulting in the marker-free strain PGN5. Intraperitoneal injection of mice with PGN5 resulted in 0% mortality, while injection with wild-type P. aeruginosa resulted in 95% mortality, providing evidence that the systemic virulence of PGN5 is highly attenuated. Importantly, PGN5 produces large amounts of alginate in response to overexpression of MucE, an activator of alginate biosynthesis. The alginate produced by PGN5 is structurally identical to alginate produced by wild-type P. aeruginosa, indicating that the alginate biosynthetic pathway remains functional in this modified strain. The genetic versatility of P. aeruginosa will allow us to further engineer PGN5 to produce alginates with specific chemical compositions and physical properties to meet different industrial and biomedical needs.     

Walking while Parasitized: Effects of a Naturally-Occurring Nematode on Locomotor Activity of Horned Passalus Beetles

Internal parasites typically are associated with a range of negative effects on their hosts, including reduced energy, which can manifest in behavioral alterations. With this in mind, we examined effects of a naturally-occurring nematode parasite, Chondronema passali, on locomotor activity level in horned passalus beetles, Odontotaenius disjunctus from Georgia, USA. This parasite is not well-studied but can number in the thousands in severely parasitized hosts. Prior study in our lab revealed that parasitized beetles actually consume more wood than unparasitized ones do, leading us to ask here, if parasitized beetles are also more physically active. Beetles were collected from nearby forests and housed individually in our lab. We created a simple tabletop arena to observe beetle locomotor activity, which was gridded and included small stones and paper objects. We allowed individual beetles to traverse the arena for 5 min and recorded the number of grid squares crossed. Then, beetles were dissected to determine parasite presence and level of infection (on a categorical scale). A total of 140 beetles were examined across three collections. Statistical analyses of locomotor activity revealed parasite severity predicted locomotor activity, but paradoxically, lightly-infected beetles were twice as active as those without this nematode. Activity diminished with increasing worm burdens thereafter, but even the group with the most severe burdens did not move less than those with no worms. From these results we conclude that this parasite does not result in overall reduction in activity, but rather it appears to come with heightened locomotion. Alternatively, this result could stem from the fact that more active beetles are simply more likely to contract the parasite.

     

Prototypes for automating product system model assembly

The International Journal of Life Cycle Assessment - The flexibility of life cycle inventory (LCI) background data selection is increasing with the increasing availability of data, but this comes...     

Improved Detection of Rare HIV-1 Variants using 454 Pyrosequencing

454 pyrosequencing, a massively parallel sequencing (MPS) technology, is often used to study HIV genetic variation. However, the substantial mismatch error rate of the PCR required to prepare HIV-containing samples for pyrosequencing has limited the detection of rare variants within viral populations to those present above ~1%. To improve detection of rare variants, we varied PCR enzymes and conditions to identify those that combined high sensitivity with a low error rate. Substitution errors were found to vary up to 3-fold between the different enzymes tested. The sensitivity of each enzyme, which impacts the number of templates amplified for pyrosequencing, was shown to vary, although not consistently across genes and different samples. We also describe an amplicon-based method to improve the consistency of read coverage over stretches of the HIV-1 genome. Twenty-two primers were designed to amplify 11 overlapping amplicons in the HIV-1 clade B gag-pol and env gp120 coding regions to encompass 4.7 kb of the viral genome per sample at sensitivities as low as 0.01-0.2%.