Simple Absorbance-Based Assays for Ultra-High Throughput Screening

Lavery, P.; Brown, Murray J. B.; Pope, Andrew J.

doi:10.1089/108705701750066971

Cited by 7 publications

(7 citation statements)

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“…The final structure of each duplex was produced from the 1,000 steps of minimized averaged structure of the last 800 ps of MD. Helix parameters were calculated with the program CURVES 5.3 [35]. All calculations were performed on a 2-CPU SGI Octane workstation.…”

Section: Methodsmentioning

confidence: 99%

Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations

et al. 2006

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Some structural insights into the conformations of the isonucleosides containing duplexes have been provided. Unrestrained molecular-dynamics simulations on 18-mer duplexes with isonucleosides incorporated at the 3'-end or in the center of one strand have been carried out with explicit solvent under periodic boundary conditions using the AMBER force field and the particle mesh Ewald method. The Watson-Crick hydrogen-bonding patterns of the duplexes studied remained intact throughout the simulation. For the modified duplexes, the changes observed in the inter-base pair parameters and backbone torsional angles were primarily localized at the isonucleoside-inserted area. All five structures studied remained in the B-form family. The decreased stacking abilities indicated by the large changes in inter-base pair parameters and the large changes in backbones made the modified duplexes show a minor thermal destabilization in comparison with native DNA. The MM_PBSA method for estimating binding free energies on two complementary strands was used. The results showed that the binding free energies of isonucleoside-incorporated DNA duplexes were lower than the native DNA duplex, which is in good agreement with experimental observations.

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Section: Methodsmentioning

confidence: 99%

Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations

et al. 2006

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“…This variety is a great source for finding more optimal, more characteristic production organisms. Knowledge on the pathways as described above enables specialized and high-throughput screening of culture collections (Lavery et al 2001 ; Smit et al 2004b ; Ingham et al 2007 ; van Hylckama Vlieg and Hugenholtz 2007 ; Pastink et al 2008 ). The large natural biodiversity could potentially offer specific traits for new products; some examples of using wild starter bacteria in products such as cheese have already been reported (Ayad et al 2003 ).…”

Section: Biodiversity Lysis Co-operationmentioning

confidence: 99%

Branched chain aldehydes: production and breakdown pathways and relevance for flavour in foods

Smit¹,

Engels

Smit

2009

Appl Microbiol Biotechnol

239

173

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Branched aldehydes, such as 2-methyl propanal and 2-and 3-methyl butanal, are important flavour compounds in many food products, both fermented and non-fermented (heat-treated) products. The production and degradation of these aldehydes from amino acids is described and reviewed extensively in literature. This paper reviews aspects influencing the formation of these aldehydes at the level of metabolic conversions, microbial and food composition. Special emphasis was on 3-methyl butanal and its presence in various food products. Knowledge gained about the generation pathways of these flavour compounds is essential for being able to control the formation of desired levels of these aldehydes.

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“…Many (HTS) enzyme assays are based on (indirect) colorimetric or fluorimetric measurements of product formation or substrate consumption during an in vitro reaction (Lavery et al. 2001; Cooper et al.…”

Section: Introductionmentioning

confidence: 99%

Development of a high throughput screening method to test flavour-forming capabilities of anaerobic micro-organisms

et al. 2004

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. Methods and Results:The method is based on the injection of a small headspace sample (100 ll) from culture vials (2 ml) in 96-well format directly into the mass spectrometry (MS). A special sample tray has been developed for liquid media, and anaerobically grown cultures. In principle, all volatile components can be measured, but a representative mass fragment has to be obtained in the MS. Representative masses for 3-methylbutanal, 2-methylpropanal and benzaldehyde are 58, 72 and 105, respectively. In 1 day over 1500 samples could be analysed and the coefficient of variation for the response was <5%. Conclusion: Screening of 72 strains belonging to the genus Lactococcus in quadruple on the production of the keyflavour compound 3-methylbutanal illustrated the effectiveness of the method. Furthermore, knowledge of the biochemistry and physiology of 3-methylbutanal formation was used to optimize the composition of the growth medium to enhance 3-methylbutanal production, and thereby improve the screening. Significance and Impact of the Study: A commonly used method to control flavour formation in fermented food products is the selection of bacterial strains, which are able to produce the desired flavour compounds. As large collections of strains are available for such screenings, studying biodiversity of micro-organisms on the level of metabolic routes is strongly facilitated by highly automated high throughput screening methods for measuring enzyme activities or production of metabolites. Therefore, this method will be a useful tool for selecting flavourproducing strains and for enhancing starter culture development.

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Simple Absorbance-Based Assays for Ultra-High Throughput Screening

Cited by 7 publications

References 0 publications

Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations

Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations

Branched chain aldehydes: production and breakdown pathways and relevance for flavour in foods

Development of a high throughput screening method to test flavour-forming capabilities of anaerobic micro-organisms

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