Optical biosensor technology continues to be the method of choice for label-free, real-time interaction analysis. But when it comes to improving the quality of the biosensor literature, education should be fundamental. Of the 1413 articles published in 2008, less than 30% would pass the requirements for high-school chemistry. To teach by example, we spotlight 10 papers that illustrate how to implement the technology properly. Then we grade every paper published in 2008 on a scale from A to F and outline what features make a biosensor article fabulous, middling or abysmal. To help improve the quality of published data, we focus on a few experimental, analysis and presentation mistakes that are alarmingly common. With the literature as a guide, we want to ensure that no user is left behind.

Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'.

High concentration ethanol production from corncob residues by fed-batch strategy.

This study investigated the development of fungal community composition in arable soil during the degradation of straw residue. We explored the short-term responses of the fungal community over 28 days of decomposition in soil using culture-independent polymerase chain reaction in combination with a clone library and denaturing gradient gel electrophoresis (DGGE). Fungal cellobiohydrolase I (cbhI) genes in the soil were also characterized, and their diversity suggested the existence of a different cellulose decomposer. The DGGE profiles based on fungal internal transcribed spacer analysis showed different successions of fungal populations during residue decomposition. Members of Lecythophora and Sordariales were dominant in the early succession, while Hypocrea and Engyodontium were better adapted in the late succession. The succession of fungal communities might be related to changes of residue quality during decomposition. Collectively, sequences assigned to Ascomycota members were dominant at different stages of the fungal succession during decomposition, revealing that they were key drivers responsible for residue degradation in the arable soil tested.

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Ascomycota members dominate fungal communities during straw residue decomposition in arable soil.

Despite intensive research, the mechanism of the rapid retardation in the rates of cellobiohydrolase (CBH) catalyzed cellulose hydrolysis is still not clear. Interpretation of the hydrolysis data has been complicated by the inability to measure the catalytic constants for CBH-s acting on cellulose. We developed a method for measuring the observed catalytic constant (k(obs)) for CBH catalyzed cellulose hydrolysis. It relies on in situ measurement of the concentration of CBH with the active site occupied by the cellulose chain. For that we followed the specific inhibition of the hydrolysis of para-nitrophenyl-beta-D-lactoside by cellulose. The method was applied to CBH-s TrCel7A from Trichoderma reesei and PcCel7D from Phanerochaete chrysosporium and their isolated catalytic domains. Bacterial microcrystalline cellulose, Avicel, amorphous cellulose, and lignocellulose were used as substrates. A rapid decrease of k(obs) in time was observed on all substrates. The k(obs) values for PcCel7D were about 1.5 times higher than those for TrCel7A. In case of both TrCel7A and PcCel7D, the k(obs) values for catalytic domains were similar to those for intact enzymes. A model where CBH action is limited by the average length of obstacle-free way on cellulose chain is proposed. Once formed, productive CBH-cellulose complex proceeds with a constant rate determined by the true catalytic constant. After encountering an obstacle CBH will "get stuck" and the rate of further cellulose hydrolysis will be governed by the dissociation rate constant (k(off)), which is low for processive CBH-s.

Mechanism of initial rapid rate retardation in cellobiohydrolase catalyzed cellulose hydrolysis.

Does change in accessibility with conversion depend on both the substrate and pretreatment technology

The enzymatic hydrolysis rate of cellulose decreases with irreversible adsorption of cellobiohydrolase I

In prokaryotes, the ribosome binding sequence (RBS), located in the 5' untranslated region (5' UTR) of an mRNA, plays a critical role in enhancing mRNA translation and stability. To evaluate the effect of the RBS on the sensitivity and signal intensity of an environmental whole-cell biosensor, three Escherichia coli-based biosensors that respond to benzene, toluene, ethylbenzene, and the xylenes (BTEX) were constructed; the three biosensors have the same Pu promoter and xylR regulator from the Pseudomonas putida TOL plasmid but differ in the engineered RBS in their reporter genes. The results from time and dose-dependent induction of luminescence activity by 2-chlorotoluene showed that the BTEX-SE and BTEX-SD biosensors with engineered RBS had signal intensities approximately 10-35 times higher than the primary BTEX-W biosensor. The limits of detection (LOD) of the BTEX-SE and BTEX-SD biosensors were also significantly lower than the LOD of the BTEX-W biosensor (20±5 μmol L �1 and 25± 5 μmol L �1 vs. 120±10 μmol L �1 ). Moreover, the BTEX- SE and BTEX-SD biosensors responded three times more rapidly to the analytes. These results suggest that rationally designed RBS in the 5' UTR of a reporter gene may be a promising strategy for increasing the sensitivity, signal intensity, and response speed of whole-cell biosensors.

Weifeng Liu

Papers

The enzymatic hydrolysis rate of cellulose decreases with irreversible adsorption of cellobiohydrolase I

An efficient design strategy for a whole-cell biosensor based on engineered ribosome binding sequences