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A device for automated hydrodynamic shearing of genomic DNA.

ABSTRACT: We describe a device for automated fragmentation of genomic DNA by hydrodynamic shearing using a filter screen with uniform pores. Human genomic DNA can be fragmented reproducibly to a range of 2000-12,000 bp by using various fluid flow rates and screens with 0.5-10-microm pores. The utilization of disposable screens eliminates sample cross-contamination and the tendency of device clogging, commonly encountered in single-orifice shearing devices.

SUBMITTER: Joneja A

PROVIDER: S-EPMC2880395 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature

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A device for automated hydrodynamic shearing of genomic DNA.

Joneja Aric A Huang Xiaohua X

BioTechniques 20090601 7

We describe a device for automated fragmentation of genomic DNA by hydrodynamic shearing using a filter screen with uniform pores. Human genomic DNA can be fragmented reproducibly to a range of 2000-12,000 bp by using various fluid flow rates and screens with 0.5-10-microm pores. The utilization of disposable screens eliminates sample cross-contamination and the tendency of device clogging, commonly encountered in single-orifice shearing devices. ...[more]

PMID: 19594456

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Project description:Highlights • Vortex based hydrodynamic cavitation was shown to enhance rate of extraction from macroalgae by an order of magnitude.• Per-pass extraction factor was found to be proportional to the mass fraction of product in macroalgae.• Pressure drop of 200 kPa was found to exhibit maximum rate of extraction within the considered range (50–300 kPa)• Energetic productivity (kg of product/kJ) was found to decrease steeply with increase in number of passes beyond 100. Macroalgae have a tremendous potential to become an important renewable resource for valuable biomolecules and chemicals. New and improved ways of cell disruption and of enhancing rate as well as yield of extraction of valuable products from macroalgae are needed to fully realise this potential. In this work, hydrodynamic cavitation (HC) was used for intensifying rate and yield of extraction of phycoerythrin, proteins and carbohydrates from marine macroalgae Palmaria palmata. We use vortex-based HC devices which do not use small restrictions like orifice-based HC devices or moving parts like rotor–stator based HC devices. A bench scale setup with a nominal slurry flow rate of 20 LPM was established. Dried and powdered macroalgae was used. Influence of key operating parameters like pressure drop and number of passes on extraction performance (the rate and yield) was measured. A simple, yet effective model was developed and used for interpreting and describing experimental data. The results indicate that there exists an optimum pressure drop across the device at which extraction performance is maximum. The extraction performance with HC was found to be significantly better than the stirred vessels. HC has resulted in 2 to 20 times improvement in the rate of extraction of phycoerythrin (R-PE), proteins and carbohydrates. Based on the results obtained in this work, pressure drop of 200 kPa and number of passes through the HC devices of about 100 were found to be most effective for HC-assisted intensified extraction from macroalgae. The presented results and model will be useful for harnessing vortex-based HC devices for intensifying the extraction of valuable products from macroalgae.

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A device for automated hydrodynamic shearing of genomic DNA.

Publications

A device for automated hydrodynamic shearing of genomic DNA.

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