Lysis efficiency of standard DNA extraction methods for Halococcus spp. in an organic rich environment

The extraction of nucleic acids from a given environment marks a crucial and essential starting point in any molecular investigation. Members of Halococcus spp. are known for their rigid cell walls, and are thus difficult to lyse and could potentially be overlooked in an environment. Furthermore, the lack of a suitable lysis method hinders subsequent molecular analysis. The effects of six different DNA extraction methods were tested on Halococcus hamelinensis, Halococcus saccharolyticus and Halobacterium salinarum NRC-1 as well as on an organic rich, highly carbonated sediment from stromatolites spiked with Halococcus hamelinensis. The methods tested were based on physical disruption (boiling and freeze/thawing), chemical lysis (Triton X-100, potassium ethyl xanthogenate (XS) buffer and CTAB) and on enzymatic lysis (lysozyme). Results showed that boiling and freeze/thawing had little effect on the lysis of both Halococcus strains. Methods based on chemical lysis (Triton X-100, XS-buffer, and CTAB) showed the best results, however, Triton X-100 treatment failed to produce visible DNA fragments. Using a combination of bead beating, chemical lysis with lysozyme, and thermal shock, lysis of cells was achieved however DNA was badly sheared. Lysis of cells and DNA extraction of samples from spiked sediment proved to be difficult, with the XS-buffer method indicating the best results. This study provides an evaluation of six commonly used methods of cell lysis and DNA extraction of Halococcus spp., and the suitability of the resulting DNA for molecular analysis.     

A rapid and simple method for DNA extraction from yeasts and fungi isolated from Agave fourcroydes

A simple and easy protocol for extracting high-quality DNA from different yeast and filamentous fungal species is described. This method involves two important steps: first, the disruption of cell walls by mechanical means and freezing; and second, the extraction, isolation, and precipitation of genomic DNA. The absorbance ratios (A₂₆₀/A₂₈₀) obtained ranged from 1.6 to 2.0. The main objective of this procedure is to extract pure DNA from yeast and filamentous fungi, including those with high contents of proteins, polysaccharides, and other complex compounds in their cell walls. The yield and quality of the DNAs obtained were suitable for micro/minisatellite primer-polymerase chain reaction (MSP-PCR) fingerprinting as well as for the sequence of the D1/D2 domain of the 26S rDNA.     

A simple method for extraction of DNA from fungi and yeasts with anhydrous hydrogen fluoride

A novel method is described for the extraction of DNAs from fungi and yeasts. Anhydrous hydrogen fluoride (HF) selectively cleaves their cell walls under mild conditions (for 5 min at 0°C), enabling the effective extraction of DNAs from organisms with a cell wall. A possible mechanism for this method concerning the selective cleavage of O-glycosidic linkages in cell walls has been described previously [(1977) Anal. Biochem. 82, 289–309]. The extracted DNA is intact: in fact, the yeast DNA is directly applicable for restriction analysis and transformation of Escherichia coli.     

DROUGHT STRESS RESPONSES OF MICROSERIS SPECIES DIFFERING IN NUCLEAR DNA CONTENT

Anatomical and physiological responses to drought stress were compared in two Microseris species differing in DNA content and originating from contrasting habitats relative to water availability (M. bigelovii, DNA = 2.6 pg nucleus^–1, more xeric; M. laciniata, DNA = 6.8 pg nucleus^–1, mesic). Leaf mesophyll cell volume was positively correlated with DNA content and negatively correlated with tissue elasticity, i.e., low ϵ̄ and thin cell walls. Drought stress increased leaf tissue elasticity (lower ϵ̄, thinner cell walls). Cell volume, cell wall thickness, cell number, and leaf area were decreased most by drought stress in M. laciniata. Osmotic adjustment with a 20% increase in total solutes (mostly amino acids) after stress was observed in both species, but their estimated contribution to the change in osmotic potential was larger in M. bigelovii. These findings indicate that the Microseris species studied respond to low water availability by maintaining turgor with 1) small cell volumes, 2) elastic tissues (low ϵ̄, thin cell walls), and 3) osmotic adjustment. Both enhanced tissue elasticity and small cell volume appear to be inherent characteristics in M. bigelovii and drought-induced responses in M. laciniata. These data are compatible with the hypothesis that natural selection may influence DNA content through differential sensitivity of cell growth to environmental stress.     

A method for direct soil extraction and PCR amplification of endomycorrhizal fungal DNA

 DNA from endomycorrhizal fungi was extracted directly from a weathered soil (alfisol) mixed with sand. Mycorrhizae were established in a greenhouse culture of Glomus clarum with Sudan grass (Sorghum vulgare var. sudanense) host plants. The extraction procedure included enzymatic digestion of cell walls, sodium dodecyl sulfate lysis of cells, polyvinylpolypyrrolidone absorption of organic compounds, and ethanol precipitation of the DNA. DNA in the extracts was amplified by the polymerase chain reaction using primers from the nuclear 17S rRNA sequence that were general to fungi or were specific to endomycorrhizae. Accepted: 17 July 1996     

Rapid and simple methodology for isolation of high quality genomic DNA from coniferous tissues (<Emphasis Type="Italic">Taxus baccata</Emphasis>)

Various investigations have been so far performed for extraction of genomic DNA from plant tissues, in which the extracted intact DNA can be exploited for a diverse range of biological studies. Extraction of high quality DNA from leathery plant tissues (e.g., coniferous organs) appears to be a critical stage. Moreover, for some species such as Taxus trees, bioprocess engineering and biosynthesis of secondary metabolites (e.g., paclitaxel) is a crucial step due to the restrictions associated with extinction of these species. However, extraction of intact genomic DNA from these plants still demands a rapid, easy and efficient protocol. To pursue such aim, in the current work, we report on the development of a simple and highly efficient method for the extraction of DNA from Taxus baccata. Based upon our protocol, interfering phenolic compounds were removed from extraction using polyvinylpyrrolidone and RNA contamination was resolved using LiCl. By employing this method, high quality genomic DNA was successfully extracted from leaves of T. baccata. The quality of extracted DNA was validated by various techniques such as RAPD marker, restriction digestions and pre-AFLP. Upon our findings, we propose this simple method to be considered for extraction of DNA from leathery plant tissues.     

Comparison of Various Procedures for Removing Proteins and Nucleic Acids from Cell Walls of Bacillus Subtilis

Several procedures were used i n an attempt to prepare clean cell walls from Bacillus subtilis. The results indicate that protein and nucleic acids are tightly bound tothe walls. cleanest wall preparations were found following trichloroacetic acid extraction at 60° or by extraction with 0.lN NaOH under a nitrogen atmosphere for 10 hrs. Protein denaturants, such as sodium dodecyl sulfate and concentrated guanidine hydrochloride were relatively ineffective in removing proteins and nucleic acids from the cell walls. Cell wall-bound DNA was biologically The active i n transformation assays.     

Attempted localization of a substrate for chitinases in plant cells reveals abundant N-acetyl-d-glucosamine residues in secondary walls

Ultrathin sections of healthy and fungus-infected plant tissue were treated with either wheat-germ agglutinin (WGA) ovomucoid-gold complex or microbial chitinase-gold complexes for localizing putative chitin-like macromolecules. Fungal cell walls, known to contain chitin, were labeled with both probes and were considered as positive controls. Plant secondary cell walls of both healthy and infected tissues were also intensely labeled whereas compound middle lamella-primary walls and cell cytoplasm were free of labeling. Enzymatic digestion of plant tissues with chitinase from Streptomyces griseus abolished the fungal cell wall labeling but did not interfere with that of plant secondary cell walls. This suggests that polymers analogous to fungal chitin are absent in plant cell walls. Tissue digestions with either proteinase K or lipase led to surprising results as far as the possible nature of N-acetylglucosamine-containing molecules is concerned. The loss of labeling over plant secondary walls following lipase digestion suggests that N-acetylglucosamine residues may be linked to lipids to form glycolipids. However, these results have to be viewed with caution since the possibility that peptides may be present but inacessible to proteinase K should be considered. The role of the detected N-acetylglucosamine containing molecules as possible substrates for plant chitinases is discussed.     

Immunocytochemical Localization of Cell Wall-Bound Thionins and Hydroxyproline-Rich Glycoproteins in Fusarium culmorum-Infected Wheat Spikes

Abstract In the present study, a rabbit polyclonal antiserum against cell wall‐bound thionins from barley leaf and a mouse monoclonal antibody against hydroxyproline‐rich glycoproteins (HRGP) from maize were used to investigate the subcellular localization of thionins and HRGP or extensins in Fusarium culmorum‐infected wheat spikes by means of the immunogold labelling technique. The proteins were localized in cell walls of different tissues including the lemma, ovary and rachis, while the cytoplasm and organelles in these tissues showed almost no labelling. However, accumulation of thionins and HRGP in infected wheat spikes of resistant wheat cultivars differed distinctly from those of susceptible cultivars. Compared with the healthy tissues, labelling densities for the two types of proteins in cell walls of the infected lemma, ovary and rachis increased only slightly in the susceptible cultivar Agent, while in cell walls of infected tissues of the resistant cultivar Arina labelling densities of thionins and HRGP increased markedly. These findings indicated that accumulation of thionins and HRGP in cell walls of infected resistant wheat spikes may be involved in defence responses to infection and in spreading of F. culmorum.     

Stomatal mechanics II*: material properties of guard cell walls

Abstract In this revised formulation of guard cell mechanics, the material properties of the walls are re-examined. The observed elastic anisotropy of guard cell walls can be explained by non-random orientation of the cellulose micellae in the unstrained state. This micellar network is assumed to be loosely embedded in the wall matrix causing a two phase elongation process. In the first phase, the micellar network is ‘loose’ resulting in the walls behaving as an isotropic polymer when stretched. As the volume of the cell expands beyond some threshold, the network becomes ‘tightened’ and a second phase of elongation is initiated. During this anisotropic phase of cell expansion, wall elasticity reflectes changes in the orientation of the network to reduce its load. Using the above theoretical analysis, a turgor-pressure versus lumen volume relationship is simulated for Vicia faba. The relationship between aperture and water potential for this species is also established. The simulated results agree with the experimental evidence reported for Vicia faba. The estimated shear modulus of elasticity for guard cell walls is 2 MPa (20 bars) which is well within the limits of reported values for other biological tissues.     

Structure and distribution of lignin in primary and secondary cell walls of maize coleoptiles analyzed by chemical and immunological probes

Lignin is an integral constituent of the primary cell walls of the dark-grown maize (Zea mays L.) coleoptile, a juvenile organ that is still in the developmental state of rapid cell extension. Coleoptile lignin was characterized by (i) conversion to lignothiolglycolate derivative, (ii) isolation of polymeric fragments after alkaline hydrolysis, (iii) reactivity to antibodies against dehydrogenative polymers prepared from monolignols, and (iv) identification of thioacidolysis products typical of lignins. Substantial amounts of lignin could be solubilized from the coleoptile cell walls by mild alkali treatments. Thioacidolysis analyses of cell walls from coleoptiles and various mesocotyl tissues demonstrated the presence of guaiacyl-, syringyl- and (traces of)p-hydroxyphenyl units besidesp-coumaric and ferulic acids. There are tissue-specific differences in amount and composition of lignins from different parts of the maize seedling. Electron-microscopic immunogold labeling of epitopes recognized by a specific anti-guaiacyl/syringyl antibody demonstrated the presence of lignin in all cell walls of the 4-d-old coleoptile. The primary walls of parenchyma and epidermis were more weakly labeled than the secondary wall thickenings of tracheary elements. No label was found in middle lamellae and cell corners. Lignin epitopes appeared first in the tracheary elements on day 2 and in the parenchyma on day 3 after sowing. Incubation of coleoptile segments in H₂O₂ increased the amount of extractable lignin and the abundance of lignin epitopes in the parenchyma cell walls. Lignin deposition was temporally and spatially correlated with the appearance of epitopes for prolinerich proteins, but not for hydroxyproline-rich proteins, in the cell walls. The lignin content of coleoptiles was increased by irradiating the seedlings with white or farred light, correlated with the inhibition of elongation growth, while growth promotion by auxin had no effect. It is concluded that wall stiffness, and thus extension growth, of the coleoptile can be controlled by lignification of the primary cell walls. Primary-wall lignin may represent part of an extended polysaccharide-polyphenol network that limits the extensibility of the cell walls.Abbreviations G, S, H guaiacyl, syringyl andp-hydroxyphenyl constituents of lignin - HRGP hydroxyproline-rich glycoprotein - LTGA lignothioglycolic acid - PRP proline-rich protein Dedicated to Professor Benno Parthier on occasion of his 65th birthdayDeceased 7 November 1996     

An improved protocol and a new grinding device for extraction of genomic DNA from microorganisms by a two-step extraction procedure

Current protocols to extract genomic DNA from microorganisms are still laborious, tedious and costly, especially for the species with thick cell walls. In order to improve the effectiveness of extracting DNA from microbial samples, a novel protocol, defined as two-step extraction method, along with an improved tissue-grinding device, was developed. The protocol included two steps, disruption of microbial cells or spores by grinding the sample together with silica sand in a new device and extraction of DNA with an effective buffer containing cell lysis chemicals. The device was prepared by using a commercial electric mini-grinder, adapted with a grinding stone, and a sample cup processed by lathing from a polytetrafluoroethylene rod. We tested the method with vegetative cells of four microbial species and two microbial spores that have thick cell walls and are therefore hard to process; these included Escherichia coli JM109, Bacillus subtilis WB600, Sacchromyces cerevisiae INVSc1, Trichoderma viride AS3.3711, and the spores of S. cerevisiae and T. viride, respectively, representing Gram-positive bacteria, Gram-negative bacteria, yeast, filamentous fungi. We found that this new method and device extracted usable quantities of genomic DNA from the samples. The DNA fragments that were extracted exceeded 23 kb. The target sequences up to about 5 kb were successfully and exclusively amplified by PCR using extracted DNA as the template. In addition, the DNA extraction was finalized within 1.5 h. Thus, we conclude that this two-step extraction method is an effective and improved protocol for extraction of genomic DNA from microbial samples.     

Rhamnogalacturonan‐I is a determinant of cell–cell adhesion in poplar wood

The molecular basis of cell–cell adhesion in woody tissues is not known. Xylem cells in wood particles of hybrid poplar (Populus tremula × P. alba cv. INRA 717‐1B4) were separated by oxidation of lignin with acidic sodium chlorite when combined with extraction of xylan and rhamnogalacturonan‐I (RG‐I) using either dilute alkali or a combination of xylanase and RG‐lyase. Acidic chlorite followed by dilute alkali treatment enables cell–cell separation by removing material from the compound middle lamellae between the primary walls. Although lignin is known to contribute to adhesion between wood cells, we found that removing lignin is a necessary but not sufficient condition to effect complete cell–cell separation in poplar lines with various ratios of syringyl:guaiacyl lignin. Transgenic poplar lines expressing an Arabidopsis thaliana gene encoding an RG‐lyase (AtRGIL6) showed enhanced cell–cell separation, increased accessibility of cellulose and xylan to hydrolytic enzyme activities, and increased fragmentation of intact wood particles into small cell clusters and single cells under mechanical stress. Our results indicate a novel function for RG‐I, and also for xylan, as determinants of cell–cell adhesion in poplar wood cell walls. Genetic control of RG‐I content provides a new strategy to increase catalyst accessibility and saccharification yields from woody biomass for biofuels and industrial chemicals.     

Validation and rapid extraction of nucleic acids from alcohol-preserved ticks

A method has been developed to extract DNA from alcohol-preserved ticks (Acari: Ixodidae and Argasidae). The method combines the lysing property of the chaotropic agent guanidinium thiocyanate (GuSCN) and the nucleic acid-binding property of diatomaceous earth (fossilized cell walls of unicellular algae). Debris from the tick is removed in several sequential washing steps. To monitor the efficiency of this method, a polymerase chain reaction (PCR) was designed to amplify the 16S mt rRNA gene of five tick genera (Dermacentor Fabricius, Haemaphysalis Koch, Rhipicephalus Koch, Argas Latreille and Ixodes Latreille). Detection of amplification products from this PCR indicated that DNA had been successfully extracted and that Taq-polymerase inhibitors were absent. The extraction method, therefore, enables purification of DNA such that enzymatic analysis is possible.     

Mineral nutrient supply, cell wall adjustment and the control of leaf growth

The possibility that changes in the plasticity of expanding cell walls are involved in regulating early leaf growth responses to nutrient deficiencies in monocot plants was investigated. Intact maize seedlings (Zea mays L.) which were hydroponically grown with their roots in low-nutrient solution (1 mol m^?3 CaCl₂) showed early inhibition of first-leaf growth, as compared with seedlings on complete nutrient solution. This early inhibition of leaf growth was not associated with reduced cell production. However, segmental elongation along the cell expansion zone at the base of the leaf and the lengths of mature epidermal cells were reduced by the low-nutrient treatment. Solute (osmotic) potentials in the expanding leaf tissues were unchanged. In contrast, low-nutrient treatments significantly altered leaf plasticity, i.e. the irreversible extension caused by applying a small force in the direction of leaf growth. For example, in vivo plasticity decreased, along with leaf growth, after transfer of seedlings from complete nutrient solution to low-nutrient solution for 15 h. Conversely, in vivo plasticity increased, along with leaf growth, after transfer of plants previously grown on low-nutrient solution to complete nutrient solution for 15 h. The nutrient treatments also induced similar changes in the in vitro plasticity of the expanding leaf cell walls. There were no consistent changes in elasticity. Thus, reductions in the plasticity of expanding leaf cell walls appear to be involved in controlling the early inhibition of maize leaf growth by root imposition of nutrient stress.     

Improved high-throughput sunflower and cotton genomic DNA extraction and PCR fidelity

The extraction of high-quality genomic DNA for PCR amplification from sunflower (Helianthus annuus) and cotton (Gossypium spp.) is challenging because of the presence of polysaccharides, secondary metabolites, and polyphenolics in the tissues. A high-throughput DNA extraction protocol was needed in our laboratory for simple sequence repeats (SSR)-marker screening and other molecular analyses that do not require organic extraction steps of phenol or chloroform. Here we describe 2 improved highthroughput protocols for DNA extraction and in-PCR modification that result in successful PCR amplification of sunflower and cotton. While the sunflower DNA extraction protocol uses reducing agents such as sodium metabisulfite and dithiothreitol (DTT), the cotton protocol uses polyvinylpyrrolidone (PVP) in PCR reactions and reducing agents in the DNA extraction procedure.     

Leaf‐shape remodeling: programmed cell death in fistular leaves of Allium fistulosum

Some species of Allium in Liliaceae have fistular leaves. The fistular lamina of Allium fistulosum undergoes a process from solid to hollow during development. The aims were to reveal the process of fistular leaf formation involved in programmed cell death (PCD) and to compare the cytological events in the execution of cell death to those in the unusual leaf perforations or plant aerenchyma formation. In this study, light and transmission electron microscopy were used to characterize the development of fistular leaves and cytological events. Terminal deoxynucleotidyl transferase‐mediated dUTP nick end labeling (TUNEL) assays and gel electrophoresis were used to determine nuclear DNA cleavage during the PCD. The cavity arises in the leaf blade by degradation of specialized cells, the designated pre‐cavity cells, in the center of the leaves. Nuclei of cells within the pre‐cavity site become TUNEL‐positive, indicating that DNA cleavage is an early event. Gel electrophoresis revealed that DNA internucleosomal cleavage occurred resulting in a characteristic DNA ladder. Ultrastructural analysis of cells at the different stages showed disrupted vacuoles, misshapen nuclei with condensed chromatin, degraded cytoplasm and organelles and emergence of secondary vacuoles. The cell walls degraded last, and residue of degraded cell walls aggregated together. These results revealed that PCD plays a critical role in the development of A. fistulosum fistular leaves. The continuous cavity in A. fistulosum leaves resemble the aerenchyma in the pith of some gramineous plants to improve gas exchange.     

The lipid content of cell walls obtained from juvenile,yeast-like and filamentous cells ofCandida albicans

Purified cell walls ofCandida albicans obtained from juvenile cells, mature yeast-like cells and filamentous cells were analyzed for their lipid components. Chloroform: methanol (2:1 v v) extraction of the acetone-treated dried cell walls indicated the total lipid content to be 2.1% of the dry weight of the juvenile cell walls, 1.8% of the mature yeast-like cell walls and 4.5% of the filamentous cell walls. Separation of the chloroform: methanol extractable fraction through a silicie acid column and quantitative determination of the fractions showed significant amounts of sterol esters, triglycerides, sterols, free fatty acids, and phospholipids in these extracts. Following acetone extraction sterols were shown to constitute a greater percentage of the cell wall of juvenile cells than mature cells. Thin-layer chromatography separated the acetone-extractable lipids into at least four components. Diethyl ether extracts of the cell walls indicated the presence of small amounts of glycerol phospholipids in the cell walls of juvenile and mature yeast cells. Boiling 95% ethanol also removed a small lipid fraction from the cell walls of both juvenile and mature yeast which could include sphingosine phosphatides or glycosides.     

CELL WALL CONFORMATION IN DRY SEEDS IN RELATION TO THE PRESERVATION OF STRUCTURAL INTEGRITY DURING DESICCATION

Internal tissues of mature air-dry seeds, prepared anhydrously for observation with the scanning electron microscope, exhibit cell wall structure which is different from that observed in aqueously fixed (hydrated) seed tissues. In a wide range of dry seeds observed (six members of the Cucurbitaceae, two species of Yucca, Hibiscus esculentus, Phaseolus vulgaris, and Helianthus annuus) cell walls exhibit a unique collapsed structure. The manner of cell wall collapse is characteristic for a given species and ranges from a highly regular folding pattern in the Cucurbitaceae to random wrinkling of the walls in Hibiscus. Evidence suggests that the regular patterns of wall folding may result from a mechanism located in the cell wall. Wall collapse in dry seeds is explained as a means of coordinating wall and protoplasmic shrinkage during desiccation and is thought to be essential for preserving the structural integrity of the tissue by conserving intercellular communication and plasmalemma-cell wall association. Implications of these observations may relate to retention of viability in seeds.     

An assessment of the efficiency of fungal DNA extraction methods for maximizing the detection of medically important fungi using PCR

To date, no single reported DNA extraction method is suitable for the efficient extraction of DNA from all fungal species. The efficiency of extraction is of particular importance in PCR-based medical diagnostic applications where the quantity of fungus in a tissue biopsy may be limited. We subjected 16 medically relevant fungi to physical, chemical and enzymatic cell wall disruption methods which constitutes the first step in extracting DNA. Examination by light microscopy showed that grinding with mortar and pestle was the most efficient means of disrupting the rigid fungal cell walls of hyphae and conidia. We then trialled several published DNA isolation protocols to ascertain the most efficient method of extraction. Optimal extraction was achieved by incorporating a lyticase and proteinase K enzymatic digestion step and adapting a DNA extraction procedure from a commercial kit (MO BIO) to generate high yields of high quality DNA from all 16 species. DNA quality was confirmed by the successful PCR amplification of the conserved region of the fungal 18S small-subunit rRNA multicopy gene.