Evaluation and Optimization of DNA Extraction and Purification Procedures for Soil and Sediment Samples

We compared and statistically evaluated the effectiveness of nine DNA extraction procedures by using frozen and dried samples of two silt loam soils and a silt loam wetland sediment with different organic matter contents. The effects of different chemical extractants (sodium dodecyl sulfate [SDS], chloroform, phenol, Chelex 100, and guanadinium isothiocyanate), different physical disruption methods (bead mill homogenization and freeze-thaw lysis), and lysozyme digestion were evaluated based on the yield and molecular size of the recovered DNA. Pairwise comparisons of the nine extraction procedures revealed that bead mill homogenization with SDS combined with either chloroform or phenol optimized both the amount of DNA extracted and the molecular size of the DNA (maximum size, 16 to 20 kb). Neither lysozyme digestion before SDS treatment nor guanidine isothiocyanate treatment nor addition of Chelex 100 resin improved the DNA yields. Bead mill homogenization in a lysis mixture containing chloroform, SDS, NaCl, and phosphate-Tris buffer (pH 8) was found to be the best physical lysis technique when DNA yield and cell lysis efficiency were used as criteria. The bead mill homogenization conditions were also optimized for speed and duration with two different homogenizers. Recovery of high-molecular-weight DNA was greatest when we used lower speeds and shorter times (30 to 120 s). We evaluated four different DNA purification methods (silica-based DNA binding, agarose gel electrophoresis, ammonium acetate precipitation, and Sephadex G-200 gel filtration) for DNA recovery and removal of PCR inhibitors from crude extracts. Sephadex G-200 spin column purification was found to be the best method for removing PCR-inhibiting substances while minimizing DNA loss during purification. Our results indicate that for these types of samples, optimum DNA recovery requires brief, low-speed bead mill homogenization in the presence of a phosphate-buffered SDS-chloroform mixture, followed by Sephadex G-200 column purification.     

Anti-tumor Effect Induced by the DEPC-treated MH134 Cells in C3H Mouse

The mechanism of association of pectin by calcium ions was studied to elucidate the gelling process. The molecular weight and size were determined by light scattering measurements on samples of pectin demethylated in gradation (ELM-pectin) by pectinesterase from Aspergillus japonicus, acid demethylated pectin (CLM-pectin), and sodium polygalacturonic acid (PGA). The molecular size of ELM-pectin which was prepared from identical materials increased quantitatively as demethylation progressed. The molecular size of CLM-pectin and PGA was larger than ELM-pectin even though the methoxyl content was similar. This probably resulted from differences in molecular structure. When Ca²⁺ was added to ELM-pectin, as demethylation progressed, molecular weight increased due to cross-linking induced by Ca^{2 +} ; however, the increase was small, when Ca²⁺ was added to CLM-pectin, molecular weight increased greatly; however, the molecular size was small, and a slight contraction of molecular was caused by cross-linking, Ca²⁺ addition to PGA resulted in enhancement of phenomena observed with CLM-pectin.     

Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples.

We compared and statistically evaluated the effectiveness of nine DNA extraction procedures by using frozen and dried samples of two silt loam soils and a silt loam wetland sediment with different organic matter contents. The effects of different chemical extractants (sodium dodecyl sulfate [SDS], chloroform, phenol, Chelex 100, and guanadinium isothiocyanate), different physical disruption methods (bead mill homogenization and freeze-thaw lysis), and lysozyme digestion were evaluated based on the yield and molecular size of the recovered DNA. Pairwise comparisons of the nine extraction procedures revealed that bead mill homogenization with SDS combined with either chloroform or phenol optimized both the amount of DNA extracted and the molecular size of the DNA (maximum size, 16 to 20 kb). Neither lysozyme digestion before SDS treatment nor guanidine isothiocyanate treatment nor addition of Chelex 100 resin improved the DNA yields. Bead mill homogenization in a lysis mixture containing chloroform, SDS, NaCl, and phosphate-Tris buffer (pH 8) was found to be the best physical lysis technique when DNA yield and cell lysis efficiency were used as criteria. The bead mill homogenization conditions were also optimized for speed and duration with two different homogenizers. Recovery of high-molecular-weight DNA was greatest when we used lower speeds and shorter times (30 to 120 s). We evaluated four different DNA purification methods (silica-based DNA binding, agarose gel electrophoresis, ammonium acetate precipitation, and Sephadex G-200 gel filtration) for DNA recovery and removal of PCR inhibitors from crude extracts. Sephadex G-200 spin column purification was found to be the best method for removing PCR-inhibiting substances while minimizing DNA loss during purification. Our results indicate that for these types of samples, optimum DNA recovery requires brief, low-speed bead mill homogenization in the presence of a phosphate-buffered SDS-chloroform mixture, followed by Sephadex G-200 column purification.     

Chromosomes of kinetoplastida

We have compared chromosome-sized DNA molecules (molecular karyotypes) of five genera (nine species) of kinetoplastida after cell lysis and deproteinization of DNA in agarose blocks and size fractionation of the intact DNA molecules by pulsed field gradient (PFG) gel electrophoresis. With the possible exception of Trypanosoma vivax and Crithidia fasciculata, all species have at least 20 chromosomes. There are large differences between species in molecular karyotype and in the chromosomal distribution of the genes for alpha- and beta-tubulin, rRNA and the common mini-exon sequence of kinetoplastid mRNAs. In all cases, the rRNA genes are in DNA that is larger than 500 kb. Whereas T. brucei has approximately 100 mini-chromosomes of 50-150 kb, only few are found in T. equiperdum; T. vivax has no DNA smaller than 2000 kb. As all three species exhibit antigenic variation, small chromosomes with telomeric variant surface glycoprotein genes cannot be vital to the mechanism of antigenic variation. The apparent plasticity of kinetoplastid genome composition makes PFG gel electrophoresis a potentially useful tool for taxonomic studies.     

Unexpected loss of genomic DNA from agarose gel plugs

Intact chromosomal DNAs are routinely prepared by embedding cells in agarose plugs before lysis. The large sizes of the genomic DNAs cause their retention while other macromolecules diffuse into and out of the gel matrix during lysis, washing and restriction cleavage incubations. However, in an analysis of agarose-embedded chromosomal DNAs cleaved with restriction enzymes, fragments larger than 30 kilobases were found to have eluted from the gel plugs. Since loss of fragments from gel plugs may affect qualitative and quantitative interpretations of electrophoretic patterns, an analysis of the diffusion of DNA segments from agarose plugs was performed. The two variables monitored were the time dependence and the DNA fragment size dependence of the diffusion process. The results indicate that small fragments (less than or equal to 2 kilobases) are quickly lost from 1% agarose gel plugs; moreover, significant amounts of large DNA segments (i.e., the 48.5-kilobase lambda phage chromosome) are also lost. In addition to urging caution in the analysis of restriction cleavage data, these observations suggest that intact small organelle genomes and extrachromosomal DNAs also may be lost from genomic DNAs prepared in agarose gel plugs.     

Extranuclear DNA of a Marine Chromophytic Alga : RESTRICTION ENDONUCLEASE ANALYSIS

Two extranuclear DNA species have been isolated from the marine alga Olisthodiscus luteus. Rapid lysis of cells followed by the immediate addition of CsCl to the lysate was critical to the preservation of these satellite DNA species. Restriction endonuclease analysis demonstrates a molecular weight of 99 × 10⁶ for chloroplast DNA and 23 × 10⁶ for a second satellite species. The origin of the second satellite is not known. However, this smaller satellite DNA which originates from a nonnuclear, DNAse insensitive cellular component, displays no sequence homology with ctDNA by hybridization experiments. Constancy of restriction endonuclease fragment patterns of chloroplast and second satellite species during all phases of the growth cycle, whether cultures were maintained synchronously or asynchronously, was demonstrated.     

Compaction agent protection of nucleic acids during mechanical lysis

Mechanical lysis is an efficient and widely used method of liberating the contents of microbial cells, but the sensitivity of large nucleic acids to shear damage has prevented the application of mechanical lysis to DNA purification. It is demonstrated that polycationic compaction agents can protect DNA from shear damage and allow chromosomal and plasmid DNA purification by mechanical lysis. In addition to being substantially protected during mechanical lysis, the compacted DNA can be separated with the insoluble cell debris, washed, and selectively resolubilized, yielding a substantially purified DNA product. An additional benefit of this method is that lysate viscosity is greatly reduced, allowing the use of much smaller processing volumes when compared with traditional lysis methods used in nucleic acid purification.     

Ribosomal genes not integrated into chromosomal DNA in Drosophila melanogaster

DNA obtained by a gentle lysis procedure from adult Drosophila melanogaster was analyzed by sucrose gradient sedimentation. The major portion of the DNA has an estimated weight of at least 5–10×10⁹ daltons. All of the ribosomal genes are present in this high molecular weight DNA in adult males with one nucleolus organizer or in adult females with two nucleolus organizers as shown by hybridizing fractions of the gradient with ribosomal RNA. In female adults with one nucleolus organizer instead of the usual two, 68% of the ribosomal genes are found in high molecular weight DNA and 32% are found in DNA of smaller size (3×10⁸ daltons). We propose that these latter genes are not integrated into the DNA of the chromosome.     

The island rule: made to be broken?

The island rule is a hypothesis whereby small mammals evolve larger size on islands while large insular mammals dwarf. The rule is believed to emanate from small mammals growing larger to control more resources and enhance metabolic efficiency, while large mammals evolve smaller size to reduce resource requirements and increase reproductive output. We show that there is no evidence for the existence of the island rule when phylogenetic comparative methods are applied to a large, high-quality dataset. Rather, there are just a few clade-specific patterns: carnivores; heteromyid rodents; and artiodactyls typically evolve smaller size on islands whereas murid rodents usually grow larger. The island rule is probably an artefact of comparing distantly related groups showing clade-specific responses to insularity. Instead of a rule, size evolution on islands is likely to be governed by the biotic and abiotic characteristics of different islands, the biology of the species in question and contingency.     

Plasmid size can affect the ability of Escherichia coli to produce high-quality plasmids

Large molecular weight plasmids are often used in gene therapy and DNA vaccines. To investigate the effect of plasmid size on the performance of Escherichia coli host strains during plasmid preparation, we employed E. coli JM109 and TOP10 cells to prepare four plasmids ranging from 4.7 to 16.8?kb in size. Each plasmid was extracted from JM109 and TOP10 cells using an alkaline lysis mini-preparation method. However, when commercial kits were used to extract the same plasmids from JM109 cells, the large molecular weight plasmids substantially degraded, compared with their smaller counterparts. No degradation was observed when the four plasmids were extracted from E. coli TOP10 cells using the same commercial kit. We conclude, therefore, that the performance of E. coli in high quality plasmid preparations can be affected by plasmid size.     

DNA recovery from soils of diverse composition.

A simple, rapid method for bacterial lysis and direct extraction of DNA from soils with minimal shearing was developed to address the risk of chimera formation from small template DNA during subsequent PCR. The method was based on lysis with a high-salt extraction buffer (1.5 M NaCl) and extended heating (2 to 3 h) of the soil suspension in the presence of sodium dodecyl sulfate (SDS), hexadecyltrimethylammonium bromide, and proteinase K. The extraction method required 6 h and was tested on eight soils differing in organic carbon, clay content, and pH, including ones from which DNA extraction is difficult. The DNA fragment size in crude extracts from all soils was > 23 kb. Preliminary trials indicated that DNA recovery from two soils seeded with gram-negative bacteria was 92 to 99%. When the method was tested on all eight unseeded soils, microscopic examination of indigenous bacteria in soil pellets before and after extraction showed variable cell lysis efficiency (26 to 92%). Crude DNA yields from the eight soils ranged from 2.5 to 26.9 micrograms of DNA g-1, and these were positively correlated with the organic carbon content in the soil (r = 0.73). DNA yields from gram-positive bacteria from pure cultures were two to six times higher when the high-salt-SDS-heat method was combined with mortar-and-pestle grinding and freeze-thawing, and most DNA recovered was of high molecular weight. Four methods for purifying crude DNA were also evaluated for percent recovery, fragment size, speed, enzyme restriction, PCR amplification, and DNA-DNA hybridization. In general, all methods produced DNA pure enough for PCR amplification. Since soil type and microbial community characteristics will influence DNA recovery, this study provides guidance for choosing appropriate extraction and purification methods on the basis of experimental goals.     

Plasmids of serogroup 1 strains ofLegionella pneumophila

Twelve strains ofLegionella pneumophila were tested for the presence of plasmid DNA. Three strains, belonging to serogroup 1, had large plasmids of 83.8×10⁶ daltons, as determined by electron microscopy. A fourth strain, also from serogroup 1, had a similar large plasmid in addition to a smaller plasmid. Restriction analysis of plasmid DNA isolated from the strains with a single size plasmid indicated that the plasmids were structurally very similar. The biologic functions of these plasmids are yet to be determined.     

Mass characteristics of DNA obtained from chromosomes of a human carcinoma cell line

Sedimentation studies of DNA from chromosomes extracted from human mitotic cells showed that highmolecular-weight DNA can be obtained if cell hypotonic treatments and prolonged metaphase blocks are avoided. Two types of large double-stranded DNA were observed. One of these (M _r = 2.5×10⁸) appeared as a size class with characteristics reminiscent of the chromosomal DNA subunit hypothesis. However, this DNA is the decay product of larger molecules, whose minimum molecular weight is 6×10⁸.     

Differential Association of F′ Plasmid and R Plasmid Deoxyribonucleic Acid with a Rapidly Sedimenting Fraction of a Proteus mirabilis Lysate

We have examined the association of an F' plasmid and an R plasmid in Proteus mirabilis with a rapidly sedimenting material that is generated by sodium dodecyl sulfate lysis and low speed centrifugation. Virtually all of the chromosomal deoxyribonucleic acid (DNA) and the F' plasmid DNA are associated with the rapidly sedimenting material after gentle lysis and centrifugation. A portion of R plasmid NR1 DNA (usually 5 to 25%) is not bound to the rapidly sedimenting material and is recovered in the supernatant fraction. This difference in binding is not related to the size of the plasmid DNA, since F' plasmids and R plasmids of different molecular weights showed the same behavior. R plasmid DNA labeled by a brief pulse of [(3)H]thymine is recovered in the supernatant fraction to a lower extent than the total R plasmid DNA. It would appear that R plasmid replication takes place in association with the rapidly sedimenting material. With prolongation of the [(3)H]thymine pulse, the [(3)H]thymine-labeled R plasmid DNA is recovered in the supernatant fraction with the same probability as the total R plasmid DNA. This finding indicates that a change in R plasmid attachment to the rapidly sedimenting material occurs some time after its replication. The differences observed in the replication of F' plasmids and R plasmids in P. mirabilis may be related to their different modes of association with the rapidly sedimenting material.     

Mechanical properties of vesicles. II. A model for osmotic swelling and lysis.

Vesicle polydispersity and leakage of solutes from the vesicle lumen influence the measurement and analysis of osmotically induced vesicle swelling and lysis, but their effects have not been considered in previous studies of these processes. In this study, a model is developed which expressly includes polydispersity and leakage effects. The companion paper demonstrated the preparation and characterization of large unilamellar lipid vesicles. A dye release technique was employed to indicate the leakage of solutes from the vesicles during osmotic swelling. Changes in vesicle size were monitored by dynamic light scattering (DLS). In explaining the results, the model identifies three stages. The first phase involves differential increases in membrane tension with strain increasing in larger vesicles before smaller ones. In the second phase, the yield point for lysis (leakage) is reached sequentially from large sizes to small sizes. In the final phase, the lumen contents and the external medium partially equilibrate under conditions of constant membrane tension. When fit to the data, the model yields information on polydispersity-corrected values for membrane area compressibility, Young's modulus, and yield point for lysis.     

Ontogeny of cellular immunity: size and turnover of rat thymocytes responsive to in vitro stimulation

Velocity sedimentation of thymus cell suspensions prepared from Wistar rats of different ages has been used to separate cells mainly on the basis of size. Large cells, many in division, sediment faster than the major population of small thymocytes and can be separated from them on this basis. In vitro responsiveness to mitogens has been found to be associated with the minor populations of larger cells, particularly the medium-large cells (230–270 μm³). The mitogen-responsive populations also contain cells which show a high autonomous DNA synthesis.The size distribution of thymus cells in neonatal animals is more varied than in adults and there is frequently a higher proportion of large cells. The mitogen-responsive cells were again found among the fast sedimenting large cells and the highest responses were seen with the very largest cells (approximately 450 μm³).The cells in both adult and neonatal animals which have the capacity to respond to mitogens in vitro are probably larger in size than the normal peripheral recirculating thoracic duct cells. The major population of normal small thymocytes showed a much lower spontaneous uptake of ³H-thymidine and did not respond to mitogens.     

Optimization of a high-throughput CTAB-based protocol for the extraction of qPCR-grade DNA from rumen fluid, plant and bacterial pure cultures

The quality and yield of extracted DNA are critical for the majority of downstream applications in molecular biology. Moreover, molecular techniques such as quantitative real-time PCR (qPCR) are becoming increasingly widespread; thus, validation and cross-laboratory comparison of data require standardization of upstream experimental procedures. DNA extraction methods depend on the type and size of starting material(s) used. As such, the extraction of template DNA is arguably the most significant variable when cross-comparing data from different laboratories. Here, we describe a reliable, inexpensive and rapid method of DNA purification that is equally applicable to small or large scale or high-throughput purification of DNA. The protocol relies on a CTAB-based buffer for cell lysis and further purification of DNA with phenol : chloroform : isoamyl alcohol. The protocol has been used successfully for DNA purification from rumen fluid and plant cells. Moreover, after slight alterations, the same protocol was used for large-scale extraction of DNA from pure cultures of Gram-positive and Gram-negative bacteria. The yield of the DNA obtained with this method exceeded that from the same samples using commercial kits, and the quality was confirmed by successful qPCR applications.     

Mutual mate choice by mountain pine beetles: size‐dependence but not size‐assortative mating

1. Mutual mate choice may be rare, occurring when both sexes invest heavily in reproduction, mating opportunities are abundant, and individuals differ in quality. 2. Mountain pine beetles, Dendroctonus ponderosae (Curculionidae: Scolytinae) appear to meet the conditions for mutual mate choice. We introduced males to females in breeding sites and observed the occurrence and speed of a male entering a female's gallery. We tested for consequences of mutual mate choice, namely condition‐dependent choosiness and assortative mating. 3. Males were more likely to enter a female's gallery when the gallery was in a smaller tree with less resin production and when the gallery was larger. Female body size and condition did not influence the probability of entry. Larger males were less likely to enter a gallery than were smaller males, probably because of size‐dependent choosiness rather than physical limitations. 4. Small males took longer to enter galleries of large females than of small females, whereas large males entered as quickly into galleries of large females as small females. This suggests size‐dependent choosiness by females. 5. No assortative mating by body size was detected, probably because males appeared to choose on the basis of female‐associated resources rather than on female traits.     

The mechanism of wheat germ agglutinin mediated cytolysis of murine mastocytoma cells

The present study was undertaken to test whether cytolysis by wheat germ agglutinin requires lateral mobility of membranal lectin receptor sites into caps.Preincubation of interphase murine mastocytoma cells with 100 μg/ml trypsin promoted cap formation by the agglutinin in about 30% of the cells, followed by cytolysis of these cells. Pretreatment of the cells with NaN₃, low temperature or glutaraldehyde decreased degree of capping and to some extent decreased the degree of cytolusis, while the addition of antibodies to the agglutinin increased the degree of capping and lysis. A linear relationship with a high correlation coefficient exists between the degree of capping and the degree of cytolysis, suggesting that lateral mobility of membrane wheat germ agglutinin receptors is required for cytolysis by the lectin. Further studies have shown the restricted small hole damage followed by osmotic lysis is responsible for the damage induced by the agglutinin of trypsin-treated mastocytoma cells. This was demonstrated (a) by markers of low molecular weight (⁸⁶Rb) which were released from the cells before those of high molecular weight (⁵¹Cr-protein) and (b) by protecting the cells from lysis through incubating them in non-penetrating solutes, such as Dextrans of high molecular weight. It has been calculated the the initial size of the lytic lesion induced by wheat germ agglutinin is $\text{≈ 32}\text{A}\text{?}$.     

Neutral sucrose sedimentation of very large DNA from Bacillus subtilis. I. Effect of random double-strand breaks and centrifuge speed on sedimentation

A method is presented for preparing very large DNA from Bacillus subtilis protoplasts. When the DNA is characterized by sedimentation in neutral sucrose gradients, a fast-sedimenting component is found whose sedimentation coefficient varies with centrifuge speed. By use of [³H]thymine label for the DNA and a ¹⁴C-labeled amino acid, it is shown that less than 5% cellular material other than DNA is associated with this component. Irradiation of this DNA in solution with gamma rays forms a slower component, called the “main peak”, whose sedimentation coefficient also depends on centrifuge speed. More irradiation breaks down this main peak into even slower-sedimenting DNA; it is shown that for low doses, double-strand breaks are formed in both the B. subtilis DNA and in bacteriophage T2 DNA at the same rate linear in dose, 0.018 double-strand breaks per kilorad per mass equal to that of T2 DNA.The speed dependence of the DNA sedimenting at the main peak is compared with an approximate theory of the speed dependence of the sedimentation coefficient of linear DNA by B. H. Zimm (unpublished calculations). The comparison suggests that for sufficiently high centripedal acceleration, DNA molecules larger than a critical mass will sediment at much the same velocity. The theory, and data on the break-up of the DNA with gamma rays, are used to estimate that the DNA extracted is at least 13 times the mass of T2 DNA, and possibly larger.In the Appendix, data from the literature are put together with data taken during this work to make plausible the assumption that the usual theory for the sedimentation of DNA molecules, experimentally tested in salt solutions, may also be applied to sucrose solutions. If, in neutral sucrose gradients, the distance sedimented is proportional to a power α of the mass, the best value of α = 0.38.