title: A new method to extract and purify DNA from allophanic soils and paleosols, and potential for paleoenvironmental reconstruction and other applications

authors: Huang, Yu-Tuan

subjects: Andisols; allophane; DNA extraction; DNA purification; paleopedology; tephra

abstract: Andisols, developed from late-Quaternary tephra (volcanic ash) deposits and dominated by the nanocrystalline aluminosilicate, allophane, contain large stores of organic matter and are potential reservoirs for DNA. However, DNA recovery from Andisols and other allophane-bearing soils has been difficult and inefficient because of strong chemical bonding between DNA and both allophane and organic matter, and also because much DNA can be encased and physically protected in nanopores in allophane nano/microaggregates. We have therefore developed a new two-step DNA isolation method for allophanic soils and buried paleosols, including those low in clay, which circumvents these problems. The method centres on (1) releasing mainly microbial DNA, and extracellular (unbound) DNA, using an alkaline phosphate buffer (“Rai’s lysis buffer”) that blocks re-adsorption sites on the allophanic materials, and (2) the novel application of acidified ammonium oxalate (Tamm’s reagent) to dissolve the allophane and to release DNA which had been chemically-bound and also which had been protected within nanopores. Ammonium oxalate has not previously been applied to soil DNA extraction. DNA yields up to 44.5 µg g-1 soil (oven-dry basis) were obtained from three field-moist natural allophanic soil samples from northern New Zealand using this two-step method. Following extraction, we evaluated different DNA purification methods. Gel electrophoresis of the extracted DNA followed by gel purification of the DNA from the agarose gel, despite some DNA loss, was the only purification method that removed sufficient humic material for successful DNA amplification using the polymerase chain reaction (PCR) of multiple gene regions. Sequencing of PCR products obtained from a buried allophanic paleosol at 2.2-m depth on a sandy Holocene tephra yielded endemic and exotic plants that differed from the European grasses growing currently on the soil’s surface. This difference suggests that the DNA extraction method is able to access (paleo)environmental DNA derived from previous vegetation cover. Our DNA extraction and purification method hence may be applied to Andisols and allophane-bearing paleosols, potentially offering a means to isolate paleoenvironmental DNA and thus facilitate reconstruction of past environments in volcanic landscapes, datable using tephrochronology, and also aid biodiversity understanding of andic soils and paleosols.

text: A new method to extract and purify DNA from allophanic soils and paleosols, and potential for paleoenvironmental reconstruction and other applications Andisols, developed from late-Quaternary tephra (volcanic ash) deposits and dominated by the nanocrystalline aluminosilicate, allophane, contain large stores of organic matter and are potential reservoirs for DNA. However, DNA recovery from Andisols and other allophane-bearing soils has been difficult and inefficient because of strong chemical bonding between DNA and both allophane and organic matter, and also because much DNA can be encased and physically protected in nanopores in allophane nano/microaggregates. We have therefore developed a new two-step DNA isolation method for allophanic soils and buried paleosols, including those low in clay, which circumvents these problems. The method centres on (1) releasing mainly microbial DNA, and extracellular (unbound) DNA, using an alkaline phosphate buffer (“Rai’s lysis buffer”) that blocks re-adsorption sites on the allophanic materials, and (2) the novel application of acidified ammonium oxalate (Tamm’s reagent) to dissolve the allophane and to release DNA which had been chemically-bound and also which had been protected within nanopores. Ammonium oxalate has not previously been applied to soil DNA extraction. DNA yields up to 44.5 µg g-1 soil (oven-dry basis) were obtained from three field-moist natural allophanic soil samples from northern New Zealand using this two-step method. Following extraction, we evaluated different DNA purification methods. Gel electrophoresis of the extracted DNA followed by gel purification of the DNA from the agarose gel, despite some DNA loss, was the only purification method that removed sufficient humic material for successful DNA amplification using the polymerase chain reaction (PCR) of multiple gene regions. Sequencing of PCR products obtained from a buried allophanic paleosol at 2.2-m depth on a sandy Holocene tephra yielded endemic and exotic plants that differed from the European grasses growing currently on the soil’s surface. This difference suggests that the DNA extraction method is able to access (paleo)environmental DNA derived from previous vegetation cover. Our DNA extraction and purification method hence may be applied to Andisols and allophane-bearing paleosols, potentially offering a means to isolate paleoenvironmental DNA and thus facilitate reconstruction of past environments in volcanic landscapes, datable using tephrochronology, and also aid biodiversity understanding of andic soils and paleosols.

year: 2016-07-15

title: Determining the characteristics of a passive linear electro-magnetic damper for a lightweight vehicle.

authors: Fow, Alista John

abstract: Previous research has shown that passive electromagnetic damping could be feasible for automotive applications, but there would be a severe weight penalty, particularly in light weight vehicles. With modern advances in permanent magnets the feasibility of passive electromagnetic dampers is re-examined. A model of a permanent magnet and coil system is developed and validated in small scale. This magnet model is used to model a dynamic damper system which is again tested. Finally this dynamic model is then scaled up to a two degree of freedom system to determine the damping for a quarter car model. Two damper designs are created. While both dampers could achieve practical real-world damping levels, but both are at least a factor heavier than a comparable commercial hydraulic damper. Keywords: Electromagnetic, magnetic, EM, damping.

text: Determining the characteristics of a passive linear electro-magnetic damper for a lightweight vehicle. Previous research has shown that passive electromagnetic damping could be feasible for automotive applications, but there would be a severe weight penalty, particularly in light weight vehicles. With modern advances in permanent magnets the feasibility of passive electromagnetic dampers is re-examined. A model of a permanent magnet and coil system is developed and validated in small scale. This magnet model is used to model a dynamic damper system which is again tested. Finally this dynamic model is then scaled up to a two degree of freedom system to determine the damping for a quarter car model. Two damper designs are created. While both dampers could achieve practical real-world damping levels, but both are at least a factor heavier than a comparable commercial hydraulic damper. Keywords: Electromagnetic, magnetic, EM, damping.

year: 2016-04-22

title: Voices of the land: Richard Nunns in conversation with Martin Lodge

authors: Nunns, Richard

abstract: Richard Nunns in conversation with Martin Lodge

text: Voices of the land: Richard Nunns in conversation with Martin Lodge Richard Nunns in conversation with Martin Lodge

year: 2008