Detection of Phanerochaete chrysosporium in soil by PCR and restriction enzyme analysis.

A nonradioactive method to detect Phanerochaete chrysosporium grown in a soil matrix was developed. This method involved DNA extraction, PCR amplification, and restriction enzyme analysis. Amplification of ligninase H8 DNA from pure cultures of P. chrysosporium was not as sensitive as amplification of the internal transcribed spacer (ITS) of the highly repetitive nuclear ribosomal DNA. Amplified ITS DNA was digested with restriction enzymes for analysis. The restriction enzyme pattern of PCR-amplified ITS DNA of P. chrysosporium was unique compared with those of unrelated fungi. Two strains of Phanerochaete chrysosporium and two strains of Phanerochaete sordida were indistinguishable by restriction enzyme analysis, while a third strain of P. chrysosporium had an unique pattern. These results were confirmed by sequence information and indicate that species designations of Phanerochaete spp. should be reexamined. The restriction enzyme pattern of DNA extracted and PCR amplified from P. chrysosporium grown in soil was identical to that from P. chrysosporium grown in pure culture. The ITS sequence was detected in 14 ng of the 100 micrograms of total DNA extracted from 1 g of soil.     

The use of cetyltrimethylammonium bromide for the rapid isolation from Staphylococcus aureus of relaxable and non-relaxable plasmid DNA suitable for in vitro manipulation

Plasmid DNA was isolated from Staphylococcus aureus by a rapid method that depends on the precipitation of DNA from cleared lysates by cetyltrimethylammonium bromide at low salt concentrations. The method was validated by its ability to provide DNA for restriction analysis of a highly relaxable plasmid species that is not isolated by more traditional techniques. The DNA can be digested with restriction endonucleases and used for transformation without further purification. The method also provides the basis for analysing staphylococcal plasmids that display a high frequency of deletion after transfer. Simple modifications of the technique allow plasmid DNA to be isolated from other bacteria and the rapid purification of DNA samples before in vitro manipulation.     

The Use of DNA Fingerprinting in Ecological Studies of Phragmites australis (Cav.) Trin. ex Steudel

A number of reed populations (Phragmites australis) from natural locations on the shore of Lake Ammersee in the south of Bavaria as well as artificially grown reed plants were analyzed for restriction fragment length polymorphisms (RFLPs) in order to evaluate for further ecological studies the dynamics of the restriction pattern within the genome of plants which propagate themselves asexually. The artificially grown reed plants were raised in four ponds supplemented with different phosphate concentrations (8 μg, 16 μg, 50 μg, and 200 μg/l) from rhizomes taken from a neighbouring fish pond. The genomic DNA of 25 of these plants and the DNA from 37 plants out of 18 stands from the lakeshore was isolated and restricted with the enzyme EcoRI, EcoRV, XbaI and HindIII and hybridized to three probes from a shot-gun cloned reed plasmid library. The probes gave between 15 and 26 bands (DNA fingerprints) of high polymorphic frequency (68% ? 100%) after hybridization with repetitive sequences of restricted DNA. A cluster analysis based on the banding pattern as a measure of genetic similarity (GS) was performed with the two sets of reed plants. The plants from the lakeshore exhibited a clear formation of clusters with GS up to 100%; the 20 plants grown from rhizomes, in contrast, did not show any clear correlation among themselves, neither to the phosphate concentration they grew in, nor to the five plants tested from the pond their rhizomes came from. The value of genetical investigations of the plant genome in context with environmental impact on plants is being discussed.     

Structural changes in simian virus 40 chromatin as probed by restriction endonucleases.

The structure of simian virus 40 (SV40) chromatin was probed by treatment with single- and multiple-site bacterial restriction endonucleases. Approximately the same fraction of the chromatin DNA was cleaved by each of three different single-site endonucleases, indicating that the nucleosomes do not have unique positions with regard to specific nucleotide sequences within the population of chromatin molecules. However, the extent of digestion was found to be strongly influenced by salt concentration. At 100 mM NaCl-5 mM MgCl2, only about 20% of the simian virus 40 (SV40) DNA I in chromatin was converted to linear SV40 DNA III. In contrast, at lower concentrations of NaCl (0.05 or 0.01 M), an additional 20 to 30% of the DNA was cleaved. These results suggest that at 100 mM NaCl only the DNA between nucleosomes was accessible to the restriction enzymes, whereas at the lower salt concentrations, DNA within the nucleosome regions became available for cleavage. Surprisingly, when SV40 chromatin was digested with multiple-site restriction enzymes, less than 2% of the DNA was digested to limit digest fragment, whereas only a small fraction (9 to 15%) received two or more cuts. Instead, the principal digest fragment was full-length linear SV40 DNA III. The failure to generate limit digest fragments was not a consequence of reduced enzyme activity in the reaction mixtures or of histone exchange. When the position of the principal cleavage site was mapped after HpaI digestion, it was found that this site was not unique. Nevertheless, all sites wree not cleaved with equal probability. An additional finding was that SV40 chromatin containing nicked-circular DNA II produced by random nicking of DNA I was also resistant to digestion by restriction enzymes. These results suggest that the initial cut which causes relaxation of topological constraint in SV40 chromatin DNA imparts resistance to further digestion by restriction enzymes. We propose that this may be accomplished by either "winding" of the internucleosomal DNA into the body of the nucleosome, or as suggested by others, by successive right-hand rotation of nucleosomes.     

REGULATION OF NaCl IN JAUMEA CARNOSA (ASTERACEAE), A SALT MARSH SPECIES,AND ITS EFFECT ON LEAF SUCCULENCE

A salt marsh species, Jaumea carnosa, was used in hydroponic experiments to test the effects of increasing NaCl concentrations on leaf succulence and plant accumulations of K, Ca, Mg, Na and Cl. A nested experimental design was used with four salinity levels. Plants were grown in full Hoagland's solution plus different amounts of NaCl (0.0–1.2 osmoles). Leaf succulence was measured as percent water content as well as vertical elongation of mesophyll cells. There were no corresponding increases in leaf succulence with increasing concentrations of NaCl in the root zone. Plants receiving aerosol spray (40 mg/dm²/day) did not show significant increases in leaf succulence. Leaf succulence was significantly increased when the plants were removed from the NaCl solutions and placed in non-salinized Hoagland's solution. Osmotic concentrations of cell sap in leaf tissues showed significant increases as NaCl concentrations increased in the root zone. The concentrations of K, Ca and Mg were higher in plants grown without NaCl than in those grown with NaCl. The accumulations of K in the root tissues were always higher than those of the shoot tissues. Although there was a two-fold difference in NaCl concentrations at the highest levels, the concentrations of Na in the shoot tissues were relatively similar. The results of the Cl analyses of shoot tissues showed a similar pattern of regulation of uptake. This regulation of salt uptake may be important in preventing injury by limiting accumulations of salt in plant tissues when growing in soils of high osmotic potentials.     

Random cleavage of superhelical SV 40 DNA S1 nuclease.

SV40 DNA FO I is randomly cleaved by S1 nuclease both at moderate (50 mM) and higher salt concentrations (250 mM NaC1). Full length linear S1 cleavage products of SV40 DNA when digested with various restriction endonucleases revealed fragments that were electrophoretically indistinguishable from the products found after digestion of superhelical SV40 DNA FO I with the corresponding enzyme. Concordingly, when the linear S1 generated duplexes were melted and renatured, circular duplexes were formed in addition to complex larger structures. This indicated that cleavage must have occurred at different sites. The double-strand-cleaving activity present in S1 nuclease preparations requires circular DNA as a substrate, as linear SV40 DNA is not cleaved. With regard to these properties S1 nuclease resembles some of the complex type I restriction nucleases from Escherichia coli which also cleave SV40 DNA only once, and, completely at random.     

CHARACTERIZATION OF THE NUCLEAR DNA OF HORDEUM VULGARE ROOT HAIRS: AMPLIFICATION DISAPPEARS UNDER SALT STRESS

In Hordeum vulgare L., the nucleus of differentiating root hairs contains amplified, extrachromosomal DNA sequences. Cytophotometry shows that the nuclei of trichoblasts and root hairs grown under normal conditions contain up to 50% more DNA than those grown in 200 mM salt. Although the root hairs develop and differentiate under salt stress, amplification of their nuclear DNA is suppressed. From this, we conclude that amplification is not necessary for differentiation at the cellular level. Characterization of the amplified nuclear DNA of the root hair is based on the physical/chemical nature of the DNA. The amplified sequences separate as a satellite band when total nucleic acids are centrifuged on CsCl gradients. Enzyme restriction of the satellite and main bands with Msp I and Hpa II followed by agarose gel electrophoresis shows that the satellite band is not more highly methylated than the main band. Restriction of the root hair DNA with EcoRI reveals repetitive DNA sequences not seen in similarly restricted whole root, leaf or salt-stressed root hair preparations. While these unique, repetitive sequences in the 2–6 kb region of the gel do not hybridize with ribosomal, chloroplast, or mitochondrial DNAs, RNA hybridization shows that some of them are transcribed. We believe that the amplified sequences are extrachromosomal based on their selective degradation during root hair senescence, their separation as a satellite band and their restriction patterns.     

Resuscitation of Vibrio cholerae O1 strain TSI-4 from a viable but nonculturable state by heat shock

Abstract Vibrio cholerae strain TSI-4 was incubated in an M9 salt solution at 15 °C for more than 100 days. The plate counts showed no viable cells on day 30, but a broth culture from that day showed the growth of bacteria. However, after 35 days the bacteria entered the nonculturable state, based on the assessment of both the plate counts and broth culture. A portion of the culture was heated at 45 °C for 1 min in a water bath and subsequently plated onto a nutrient agar plate. More than 1000 colonies were recovered after this heat-shock treatment. The recovered cells showed the same chromosomal DNA pattern in the restriction map and the same outer membrane protein pattern in SDS-PAGE. Recovery of viable cells by heat-shock was achieved in cultures grown on M9 salt but not from cultures grown in phosphate-buffered saline. This suggests that the presence of NH₄Cl in the M9 salt solution may support the growth of the bacteria in a low nutrient medium, while also playing an important role in resuscitation.     

Production of sodium-chloride-tolerant Brassica juncea plants by in vitro selection at the somatic embryo level

Summary Somatic embryos, developed from hypocotyl segments of light-grown seedlings of Brassica juncea cv RLM198, were subjected to selection at varying concentrations of sodium chloride (NaCl). Plants were developed from proliferated somatic embryos selected on NaCl-containing medium. The selections were characterized for salt tolerance, esterase isozyme pattern, and proline accumulation. It has been found that: (i) selected tolerant lines showed better root growth, shoot growth, and fresh weight accumulation on salt-containing medium when compared to the control; (ii) salt tolerance was transmitted to the next generation in seed progeny of tolerant plants grown in the absence of exposure to salt; (iii) both the starting material and the tolerant selections accumulated proline, even when grown in salt-free medium. On salt-containing medium, however, the differences in accumulated proline between the control and tolerant lines became more pronounced, and (iv) the patterns of esterase isozymes of two tolerant selections were similar but distinctly different from that of the parental control.     

Degradation by Streptomyces viridosporus T7A of plant material grown under elevated CO2 conditions

The biodegradability of plant material derived from wheat grown under different concentrations of atmospheric CO2 was investigated using the lignocarbohydrate solubilising actinomycete, Streptomyces viridosporus. Growth of S. viridosporus and solubilisation of lignocarbohydrate were highest when wheat grown at ambient CO2 concentrations (350 ppm) was used as C-source. Growth of S. viridosporus and solubilisation were reduced when the plant material was derived from wheat grown at 645 ppm CO2. The results suggest that modifications in plant structure occur when wheat is grown under conditions of elevated atmospheric CO2 which make it more resistant to microbial digestion.     

UV-induced alleviation of K-specific restriction of bacteriophage lambda.

A partial release of K-specific restriction of phage lambda grown in Escherichia coli C was observed when E. coli K strains AB1157 (having wild-type repair of UV-produced DNA damage) and AB1886 (uvrA) were irradiated with UV light before infection. The effect occurred in AB1886 at lower UV fluences than it did in AB1157. Little or no release of restriction was observed when AB2463 (recA) or AB2494 (lex-1) was used. Such release of restriction appears to be another of the UV-induced phenomena associated with "SOS" repair.     

Evidence for tertiary structure in natural single stranded RNAs in solution.

Binding isotherms (20 degrees C) of ethidium bromide to a number of tRNA species at various ionic strengths indicate that i) the number ni of intercalation sites is high 7 to 11 per molecule, in the low salt form III, but small, 2 to 1, at high Mg2+ or Na+ when form I predominates. ii) modification of tRNA at strategic positions for 3D folding prevents full expression of intercalation restriction iii) maximal restriction is obtained at salt concentrations higher than needed for full conversion to form I. It is inferred that restriction, which is not observed with bihelical RNA (or DNA), requires the native tRNA 3D structure but also some physical coupling between the region of 3D folding and bihelical arms. Ribosomal RNAs, some viral RNAs, mRNA from sheep mammary gland as well as the random copolymers Poly UG, Poly AUG, Poly AUCG all exhibit intercalation restriction. Hence 3D folding of the polyribonucleotide chains appears to be a feature common to single-stranded RNAs when free in solution under physiological conditions.     

Selective blotting of restriction DNA fragments on nitrocellulose membranes at low salt concentrations.

The pattern of restriction DNA fragments transferred from agarose gel to nitrocellulose membranes (Southern's technique) can be affected by the salt concentration of the transfer solvent.     

Estimation of taurindicine hybridization of American Zebu cattle in Brazil

Our objective was to estimate Bos primigenius taurus introgression in American Zebu cattle. One hundred and four American Zebu (Nellore) cattle were submitted to mtDNA, microsatellite and satellite analysis. Twenty-three alleles were detected in microsatellite analysis, averaging 4.6 ± 1.82/locus. Variance component comparisons of microsatellite allele sizes allowed the construction of two clusters separating taurus and indicus. No significant variation was observed when indicus and taurus mtDNA were compared. Three possible genotypes of 1711b satellite DNA were identified. All European animals showed the same restriction pattern, suggesting a Zebu-specific restriction pattern. The frequencies of B. primigenius indicus-specific microsatellite alleles and 1711b satellite DNA restriction patterns lead to an estimate of 14% taurine contribution in purebred Nellore.     

Mycoplasma restriction: identification of a new type of restriction specificity for DNA containing 5-methylcytosine.

Mycoplasma bacteriophage L51 single-stranded DNA and L2 double-stranded DNA are host cell modified and restricted when they transfect Acholeplasma laidlawii JA1 and K2 cells. The L51 genome has a single restriction endonuclease MboI site (recognition sequence GATC), which contains 5-methylcytosine when the DNA is isolated from L51 phage grown in K2 cells but is unmethylated when the DNA is from phage grown in JA1 cells. This GATC sequence is nonessential, since an L51 mutant in which the MboI site was deleted was still viable. DNA from this deletion mutant phage was not restricted during transfection of either strain K2 or JA1. Therefore, strain K2 restricts DNA containing the sequence GATC, and strain JA1 restricts DNA containing the sequence GAT 5-methylcytosine. We conclude that K2 cells have a restriction system specific for DNA containing the sequence GATC and protect their DNA by methylating cytosine in this sequence. In contrast, JA1 cells (which contain no methylated DNA bases) have a newly discovered type of restriction-modification system. From results of studies of the restriction of specifically methylated DNAs, we conclude that JA1 cells restrict DNA containing 5-methylcytosine, regardless of the nucleotide sequence containing 5-methylcytosine. This is the first report of a DNA restriction activity specific for a single (methylated) base. Modification in this system is the absence of cytosine methylating activity. A restriction-deficient variant of strain JA1, which retains the JA1 modification phenotype, was isolated, indicating that JA1 cells have a gene product with restriction specificity for DNA containing 5-methylcytosine.     

The concentration dependence of the right to left conformational transition in natural DNA identified by Raman spectroscopy

The classical and resonance Raman spectra of DNA from Chicken Erythrocytes have been obtained for different DNA concentrations in solution with low and high ionic strengths. The classical Raman spectra of 30 mg/ml DNA solutions were measured in varying the sodium chloride concentration from 0.1 to 4.5 M NaCl. An increase in the salt content of the solution leads to spectral changes in the 600-700 cm-1 region, indicating a C2' endo/anti to C3' endo/syn conformational transition of the purine residues. Other changes around 840 cm-1, due to the antisymmetrical stretching vibration of the PO2 group, are also detected: they were characteristic for the B----Z transition in model systems such as poly(dG-dC).poly(dG-dC). The resonance Raman spectra of low (1 mg/ml) and high (30 mg/ml) concentrated DNA solutions were obtained with low (0.1 M) and high (4.5 M) NaCl contents, in using a 284 nm excitation wavelength. No change was observed in the intensities and band positions in the low and high salt solutions of low concentrated DNA. Thus it is assumed that the DNA structure remains unchanged whatever the salt concentration for low concentrated DNA. In contrast, great modifications of the intensities and positions of some lines were found in the spectra of high DNA concentration solution when the NaCl content is increased up to 4.5 M: these changes resemble to some extent those observed in the study of B----Z transition of several polynucleotide model compounds. It is assumed that the right-handed to left-handed conformational transition may occur in certain sections of natural DNA, likely containing alternating purine-pyrimidine sequences, when the DNA concentration is sufficiently important.     

不同能源柳无性系对NaCl胁迫的生理响应

为了探索不同能源柳无性系的耐盐潜力,在盆栽条件下,对1年生能源柳无性系2、4、C、E扦插苗设置NaCl盐分梯度,使其土壤含盐量保持在0、0.2%、0.4%、0.6%、0.8%,并以乡土旱柳为对照,胁迫45d后,对5个无性系的气体交换参数、保护酶活性和有机渗透调节物质进行测定。研究发现:(1)在低浓度盐胁迫下(土壤含盐量0 0.4%),导致各能源柳光合速率降低的是气孔因素;在高浓度盐胁迫下(土壤含盐量大于0.4%),导致各能源柳无性系光合速率下降的主要是非气孔因素。(2)随着土壤盐浓度的增加,各能源柳无性系的过氧化氢酶(CAT)活性逐渐减小,过氧化物酶(POD)活性先增加后减小,而超氧化物歧化酶(SOD)活性呈现增加的趋势,并且4个能源柳无性系在盐胁迫条件下保护酶活性强于旱柳。(3)在土壤含盐量小于0.6%时,4个能源柳无性系的可溶性蛋白含量始终大于旱柳;在整个胁迫过程中,能源柳C的脯氨酸含量始终大于旱柳。(4)与旱柳相比,4个能源柳无性系在土壤含盐量0 0.4%的土壤中都能良好生长,其中能源柳C的耐盐潜力更大,可在土壤含盐量为0.6%的土壤中正常生长。这说明,4个能源柳无性系均可在天津轻、中度盐渍化地区栽培。     

Interaction of nitrogen nutrition and salinity in Grey poplar (Populus tremula x alba)

Salinity represents an increasing environmental problem in managed ecosystems. Populus spp. is widely used for wood production by short-rotation forestry in fertilized plantations and can be grown on saline soil. Because N fertilization plays an important role in salt tolerance, we analysed Grey poplar (Populus tremula x alba, syn. Populus canescens) grown with either 1 mM nitrate or ammonium subjected to moderate 75 mM NaCl. The impact of N nutrition on amelioration of salt tolerance was analysed on different levels of N metabolism such as N uptake, assimilation and N (total N, proteins and amino compounds) accumulation. Na concentration increased in all tissues over time of salt exposure. The N nutrition-dependent effects of salt exposure were more intensive in roots than in leaves. Application of salt reduced root increment as well as stem height increase and, at the same time, increased the concentration of total amino compounds more intensively in roots of ammonium-fed plants. In leaves, salt treatment increased concentrations of total N more intensively in nitrate-fed plants and concentrations of amino compounds independently of N nutrition. The major changes in N metabolism of Grey poplar exposed to moderate salt concentrations were detected in the significant increase of amino acid concentrations. The present results indicate that N metabolism of Grey poplar exposed to salt performed better when the plants were fed with nitrate instead of ammonium as sole N source. Therefore, nitrate fertilization of poplar plantations grown on saline soil should be preferred.     

Behaviour of antioxidant defense system in the adaptive response to salt stress in Helianthus annuus L. cells

A relationship between the antioxidant defense system and salt tolerance in two types of sunflower calli differing in salt sensitivity was studied. No reduction in growth occurred in the NaCl-salt-adapted cell line (T) when grown on 175 mM NaCl but growth of the salt-stressed cell line (S) was reduced by 83%. Lipid peroxidation and protein oxidation increased during acute stress of salt stressed cells at 14 and 28 d of the experiment, while salt-adapted calli (T) remained similar to non-shocked (C) values. The antioxidant defense system of callus adapted to growth under NaCl responded differently to 175 mM of salt compared with the corresponding controls under shock treatment. Salt-adapted and salt-stressed calli showed a similar pattern in GSH content at day 14 but at day 28 in S calli, GSH content was increased 100% over the non-shocked calli, while T calli returned to the initial values. In the salt-stressed calli, a general decrease in all the antioxidant enzymes studied (except for glutathione reductase and dehydroascorbate reductase activities) was observed at day 28. Except for catalase, the antioxidant enzymes were elevated constitutively in adapted calli as compared to stressed cells, when both were grown in the absence of NaCl (time 0), and remained unaltered until 28 d after the beginning of the experiment. These results suggest the involvement of an enzymatic antioxidant defense system in the adaptive response to salt stress in Helianthus annuus L. cells.