Showing papers on "Lysis published in 1999"
TL;DR: In this article, the Activated Sludge Model No. 3 (ASM3) is proposed to predict oxygen consumption, sludge production, nitrification and denitrification of activated sludge systems.
2,108 citations
TL;DR: It is indicated 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.
Abstract: 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.
963 citations
TL;DR: The aim of the present investigation was to improve the extraction, purification, and quantification of DNA derived from as large a portion of the soil microbial community as possible, with special emphasis placed on obtaining DNA from gram-positive bacteria, which form structures that are difficult to disrupt.
Abstract: In recent years, several protocols based on the extraction of nucleic acids directly from the soil matrix after lysis treatment have been developed for the detection of microorganisms in soil. Extraction efficiency has often been evaluated based on the recovery of a specific gene sequence from an organism inoculated into the soil. The aim of the present investigation was to improve the extraction, purification, and quantification of DNA derived from as large a portion of the soil microbial community as possible, with special emphasis placed on obtaining DNA from gram-positive bacteria, which form structures that are difficult to disrupt. Furthermore, we wanted to identify and minimize the biases related to each step in the procedure. Six soils, covering a range of pHs, clay contents, and organic matter contents, were studied. Lysis was carried out by soil grinding, sonication, thermal shocks, and chemical treatments. DNA was extracted from the indigenous microflora as well as from inoculated bacterial cells, spores, and hyphae, and the quality and quantity of the DNA were determined by gel electrophoresis and dot blot hybridization. Lysis efficiency was also estimated by microscopy and viable cell counts. Grinding increased the extracellular DNA yield compared with the yield obtained without any lysis treatment, but none of the subsequent treatments clearly increased the DNA yield. Phage λ DNA was inoculated into the soils to mimic the fate of extracellular DNA. No more than 6% of this DNA could be recovered from the different soils. The clay content strongly influenced the recovery of DNA. The adsorption of DNA to clay particles decreased when the soil was pretreated with RNA in order to saturate the adsorption sites. We also investigated different purification techniques and optimized the PCR methods in order to develop a protocol based on hybridization of the PCR products and quantification by phosphorimaging.
523 citations
TL;DR: The results showed that analyzing wash waters is essential in quantifying biofilm EPS; the contribution of this step varied from 8-50% of the total carbohydrate yield, depending on the extraction method.
343 citations
TL;DR: Denaturing gradient gel electrophoresis analysis of DNA isolated using a range of lytic treatments revealed alterations in band patterns which might reflect differences in the efficiency of Lytic treatments.
294 citations
TL;DR: The experimental observation suggests that E. coli are also lysed by the pulsed electric field, and the means of using electric field lysing can greatly simplify purification steps for preparation of biological samples compared to conventional chemical methods.
Abstract: A new micromachined cell lysis device is developed. It is designed for miniature bio-analysis systems where cell lysing is needed to obtain intracellular materials for further analysis such as DNA identification. It consists of multi-electrode pairs to apply electric fields to cells. We adopt the means of using electric field lysing because it can greatly simplify purification steps for preparation of biological samples compared to conventional chemical methods. Yeast, Chinese cabbage, radish cells and Escherichia coli are tested with the device. The lysis of yeast, Chinese cabbage and radish cells is observed by a microscope. The experimental observation suggests that E. coli are also lysed by the pulsed electric field. The range of electric field for the lysis is on the order of 1 kV/cm to 10 kV/cm. The Teflon coated on the electrodes can protect the electrodes during the pulsing period. In addition, for practical reasons, we reduce the voltage required for lysing to less than 10 V by making the electrode gap on the order of microns.
220 citations
TL;DR: It is concluded that Hcs77 is dedicated to signaling cell wall Stress during vegetative growth and that Mid2 participates in this signaling, but its primary role is in signaling wall stress during pheromone-induced morphogenesis.
Abstract: Hcs77 is a putative cell surface sensor for cell integrity signaling in Saccharomyces cerevisiae. Its loss of function results in cell lysis during growth at elevated temperatures (e.g., 39°C) and impaired signaling to the Mpk1 mitogen-activated protein kinase in response to mild heat shock. We isolated the MID2 gene as a dosage suppressor of the cell lysis defect of an hcs77 null mutant. MID2 encodes a putative membrane protein whose function is required for survival of pheromone treatment. Mid2 possesses properties similar to those of Hcs77, including a single transmembrane domain and a long region that is rich in seryl and threonyl residues. We demonstrate that Mid2 is required for cell integrity signaling in response to pheromone. Additionally, we show that Mid2 and Hcs77 serve a redundant but essential function as cell surface sensors for cell integrity signaling during vegetative growth. Both proteins are uniformly distributed through the plasma membrane and are highly O-mannosylated on their extracellular domains. Finally, we identified a yeast homolog of MID2, designated MTL1, which provides a partially redundant function with MID2 for cell integrity signaling during vegetative growth at elevated temperature but not for survival of pheromone treatment. We conclude that Hcs77 is dedicated to signaling cell wall stress during vegetative growth and that Mid2 participates in this signaling, but its primary role is in signaling wall stress during pheromone-induced morphogenesis.
207 citations
TL;DR: Three different procedures for the solubilization of yeast (S. cerevisiae) cell proteins were compared on the basis of the obtained two‐dimensional (2‐D) polypeptide patterns and major emphasis was laid on minimizing handling steps, protein modification or degradation, and quantitative loss of high molecular mass proteins.
Abstract: Three different procedures for the solubilization of yeast (S. cerevisiae) cell proteins were compared on the basis of the obtained two-dimensional (2-D) polypeptide patterns. Major emphasis was laid on minimizing handling steps, protein modification or degradation, and quantitative loss of high molecular mass proteins. The procedures employed were sonication, followed by (i) protein solubilization with “standard” lysis buffer (9 M urea, 2% 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS)), 1% dithiothreitol (DTT), 2% v/v carrier ampholytes, (ii) presolubilization of proteins with sodium dodecyl sulfate (SDS) buffer, consisting of 1% SDS and 100 mM tris(hydroxymethyl)aminomethane (Tris)-HCl, pH 7.0, followed by dilution with “standard” lysis buffer, and (iii) boiling the sample with SDS during cell lysis, followed by dilution with thiourea/urea lysis buffer (2 M thiourea / 7 M urea, 4% w/v CHAPS, 1% w/v DTT, 2% v/v carrier ampholytes). All procedures tested were rapid and simple. However, with the first procedure (i), considerable degradation of high Mr proteins occurred. In contrast, protein degradation was minimized by boiling the sample in SDS buffer immediately after sonication (method ii). Protein disaggregation and solubilization of high Mr proteins were further improved by pre-boiling with SDS and using thiourea/urea lysis buffer instead of “standard” lysis buffer (procedure iii).
171 citations
TL;DR: The findings show that the tertiary structure of plasmid DNA can be severely affected by shear forces, and the interaction of shear with air-liquid interfaces shows the highest potential for damaging SC plasmids DNA during bioprocesses.
Abstract: This study was designed to evaluate the effect of shear on the supercoiled circular (SC) form of plasmid DNA. The conditions chosen are representative of those occurring during the processing of plasmid-based genes for gene therapy and DNA vaccination. Controlled shear was generated using a capillary rheometer and a rotating disk shear device. Plasmid DNA was tested in a clarified alkaline lysate solution. This chemical environment is characteristic of the early stages of plasmid purification. Quantitative data is reported on shear degradation of three homologous recombinant plasmids of 13, 20 and 29 kb in size. Shear sensitivity increased dramatically with plasmid molecular weight. Ultrapure plasmid DNA redissolved in 10 mM Tris/HCl, 1 mM EDTA pH 8 (TE buffer) was subjected to shear using the capillary rheometer. The shear sensitivity of the three plasmids was similar to that observed for the same plasmids in the clarified alkaline lysate. Further experiments were carried out using the 20 kb plasmid and the rotating disk shear device. In contrast with the capillary rheometer data, ultrapure DNA redissolved in TE buffer was up to eight times more sensitive to shear compared to plasmid DNA in the clarified alkaline lysate. However, this enhanced sensitivity decreased when the ionic strength of the solution was raised by the addition of NaCl to 150 mM. In addition, shear damage was found to be independent of plasmid DNA concentration in the range from 0.2 μg/ml to 20 μg/ml. The combination of shear and air-liquid interfaces caused extensive degradation of the plasmid DNA. The damage was more evident at low ionic strength and low DNA concentration. These findings show that the tertiary structure of plasmid DNA can be severely affected by shear forces. The extent of damage was found to be critically dependent on plasmid size and the ionic strength of the environment. The interaction of shear with air-liquid interfaces shows the highest potential for damaging SC plasmid DNA during bioprocesses.
139 citations
TL;DR: This method combines mini-bead beating, which is most efficient in breaking bacterial aggregate flocs and cells, with protection of RNA with diethyl pyrocarbonate, and precipitation of impurities with ammonium acetate to allow simultaneous DNA and RNA extraction from activated sludge samples.
Abstract: DNA and RNA are usually extracted from activated sludge samples using two separate methods developed for soil and sediment samples However, activated sludge differs from soil and sediment in at least three aspects: high biomass density, low humic acid content, and the presence of bacterial aggregate flocs Taking these characteristics into consideration, we developed a simple and rapid method allowing simultaneous DNA and RNA extraction from activated sludge samples This method combines (i) mini-bead beating, which is most efficient in breaking bacterial aggregate flocs and cells, (ii) protection of RNA with diethyl pyrocarbonate, and (iii) precipitation of impurities with ammonium acetate Phenol/chloroform extraction and column purification are not necessary The resulting DNA and RNA are suitable for PCR and reverse transcriptase - PCR, respectively The efficiencies of cell lysis and nucleic acid recovery were high enough to permit detection by PCR of 102 cells/mL of mixed liquor By simultaneously
119 citations
TL;DR: Findings suggest that the bacterial envelope sites engaged in cell growth may represent preferential sites for the action and cytotoxic consequences of group IIA PLA2 attack against Gram-positive bacteria.
Abstract: We have shown previously that a group IIA phospholipase A2 (PLA2) is responsible for the potent bactericidal activity of inflammatory fluids against many Gram-positive bacteria. To exert its antibacterial activity, this PLA2 must first bind and traverse the bacterial cell wall to produce the extensive degradation of membrane phospholipids (PL) required for bacterial killing. In this study, we have examined the properties of the cell-wall that may determine the potency of group IIA PLA2 action. Inhibition of bacterial growth by nutrient deprivation or a bacteriostatic antibiotic reversibly increased bacterial resistance to PLA2-triggered PL degradation and killing. Conversely, pretreatment of Staphylococcus aureus or Enterococcus faecium with subinhibitory doses of β-lactam antibiotics increased the rate and extent of PL degradation and/or bacterial killing after addition of PLA2. Isogenic wild-type (lyt+) and autolysis-deficient (lyt–) strains of S. aureus were equally sensitive to the phospholipolytic action of PLA2, but killing and lysis was much greater in the lyt+ strain. Thus, changes in cell-wall cross-linking and/or autolytic activity can modulate PLA2 action either by affecting enzyme access to membrane PL or by the coupling of massive PL degradation to autolysin-dependent killing and bacterial lysis or both. Taken together, these findings suggest that the bacterial envelope sites engaged in cell growth may represent preferential sites for the action and cytotoxic consequences of group IIA PLA2 attack against Gram-positive bacteria.
J. Clin. Invest. 103:715–721 (1999)
TL;DR: The most consistent lysis and biodegradation results occurred at pH 10 and 60 °C after a 20-min incubation, and the biodegradability of the soluble fraction, both the immediate and the post-treatment carbon release, was investigated.
Abstract: To decrease activated sludge production, microbial cell lysis can be amplified to enhance cryptic growth (biomass growth on lysates). Cell breakage techniques (thermal, alkaline, acid) were studied to generate Alcaligenes eutrophus and sludge lysates and to evaluate their biodegradability. Gentle treatment conditions produced the best results. Complete cell deactivation was obtained for temperatures higher than 55 °C. The release kinetics were similar for temperatures varying from 60 °C to 100 °C. A 20-min incubation was suitable for reaching 80% of the maximum releasable carbon. In thermal-chemical hydrolysis, NaOH was the most efficient for inducing cell lysis. Carbon release was a two-step process. First an immediate release occurred, which was of the same order of magnitude for A. eutrophus and sludge [100–200 mg dissolved organic C (DOC) g total suspended solids (TSS)−1], followed by a post-treatment release. The second step was virtually equivalent to the first for sludge, and weaker for A. eutrophus (<50 mg DOC g TSS−1). The biodegradability of the soluble fraction, both the immediate and the post-treatment carbon release, was investigated. The optimal degradation yield, obtained with sludge cells, reached 55% after 48 h of incubation and 80% after 350 h. The most consistent lysis and biodegradation results occurred at pH 10 and 60 °C after a 20-min incubation.
TL;DR: In this paper, the results showed that the extraction with glutaraldehyde 3% (w/v) was the most suitable method, extracting great amounts of organic carbon without promoting cell lysis or permeabilization.
TL;DR: The results indicate that ultrasound- induced CD19 removal from R1 cells can occur without accompanying gross membrane loss, and indicate that the ultrasound-induced morphological change is associated with lethal membrane poration.
Abstract: The study objective was to gain insight into ultrasound-induced, sub-lytic cell surface modifications. Two primary hypotheses were tested by flow cytometric methods; viz ., sonication will: 1. remove all or part of a specific cell surface marker in lymphocytes surviving insonation, and 2. induce transient pores in the cell membranes of some surviving cells. RPMI 1788 human lymphocytes were exposed in vitro to 1-MHz, continuous-wave ultrasound (∼8 W/cm 2 I SP ) for 30 s, which lysed ∼50% of the cells. Insonation: 1. altered cell morphology, increasing the population of cells of reduced size but high structure (designated as population R2), many of which were nonviable, and diminishing the population of cells of large size and high structure (designated as population R1), most of which were viable, 2. diminished the fluorescence signal from the pan B lymphocyte marker CD19 in populations R1 and R2 to equivalent extents, and 3. increased by ∼7-fold the number of transiently permeabilized cells in R1, as evidenced by simultaneous uptake of propidium iodide and fluorescein diacetate. The results indicate that ultrasound-induced CD19 removal from R1 cells can occur without accompanying gross membrane loss. The cell morphology/mortality shifts indicate that the ultrasound-induced morphological change is associated with lethal membrane poration, suggesting that the diminished CD19 fluorescence signal from insonated R2 cells arises partly by simultaneous loss of membrane fragments, CD19 and cytoplasm.
TL;DR: Holben’s direct lysis method recovered significantly greater amounts of DNA than the other methods tested, while CsCl‐ethidium bromide density gradient ultracentrifugation was better than gel filtration at removing humic acid from crude DNA isolated from soil.
Abstract: Seven methods for bacterial DNA extraction and purification from soil samples were compared. Holben’s direct lysis method recovered significantly greater amounts of DNA than the other methods tested, while CsCl-ethidium bromide density gradient ultracentrifugation was better than gel filtration at removing humic acid from crude DNA isolated from soil. When both these methods were combined, 5·94 μg of DNA (A260/280 ratio around 1·754) was yielded g−1 oven-dried sandstone shale alluvial soil; similarly satisfactory yields were obtained from Taiwan clay, and sandstone shale and slate alluvial soil managed under different farming practices. DNA obtained by these methods was readily digested by EcoR I and Hind III. When soil samples were stored for 3 weeks at 4 °C, the fraction of high-molecular-weight DNA was reduced significantly. Thus, DNA extraction should be carried out as soon as possible after a soil sample has been collected from the field. When hyphae of Pythium aphanidermatum and Fusarium solani were subjected to the above lysis method, DNA could not be detected in the extract.
TL;DR: It is proposed that polyP may have an effect on the ubiquitous bacterial cell division protein FtsZ, whose GTPase activity is known to be strictly dependent on divalent metal ions.
Abstract: We investigated the cellular mechanisms that led to growth inhibition, morphological changes, and lysis of Bacillus cereus WSBC 10030 when it was challenged with a long-chain polyphosphate (polyP). At a concentration of 0.1% or higher, polyP had a bacteriocidal effect on log-phase cells, in which it induced rapid lysis and reductions in viable cell counts of up to 3 log units. The cellular debris consisted of empty cell wall cylinders and polar caps, suggesting that polyP-induced lysis was spatially specific. This activity was strictly dependent on active growth and cell division, since polyP failed to induce lysis in cells treated with chloramphenicol and in stationary-phase cells, which were, however, bacteriostatically inhibited by polyP. Similar observations were made with B. cereus spores; 0.1% polyP inhibited spore germination and outgrowth, and a higher concentration (1.0%) was even sporocidal. Supplemental divalent metal ions (Mg2+ and Ca2+) could almost completely block and reverse the antimicrobial activity of polyP; i.e., they could immediately stop lysis and reinitiate rapid cell division and multiplication. Interestingly, a sublethal polyP concentration (0.05%) led to the formation of elongated cells (average length, 70 μm) after 4 h of incubation. While DNA replication and chromosome segregation were undisturbed, electron microscopy revealed a complete lack of septum formation within the filaments. Exposure to divalent cations resulted in instantaneous formation and growth of ring-shaped edges of invaginating septal walls. After approximately 30 min, septation was complete, and cell division resumed. We frequently observed a minicell-like phenotype and other septation defects, which were probably due to hyperdivision activity after cation supplementation. We propose that polyP may have an effect on the ubiquitous bacterial cell division protein FtsZ, whose GTPase activity is known to be strictly dependent on divalent metal ions. It is tempting to speculate that polyP, because of its metal ion-chelating nature, indirectly blocks the dynamic formation (polymerization) of the Z ring, which would explain the aseptate phenotype.
TL;DR: A mutation in the lambda pR promoter is described, which allows stringent repression of gene E expression at temperatures up to 36 degrees C, but still permits induction of cell lysis at 42 degrees C.
Abstract: Cell lysis of Gram-negative bacteria can be efficiently achieved by expression of the cloned lysis gene E of bacteriophage PhiX174. Gene E expression is tightly controlled by the rightward lambda pR promoter and the temperature-sensitive repressor cI857 on lysis plasmid pAW12. The resulting empty bacterial cell envelopes, called bacterial ghosts, are currently under investigation as candidate vaccines. Expression of gene E is stringently repressed at temperatures up to 30 degrees C, whereas gene E expression, and thus cell lysis, is induced at temperatures higher than 30 degrees C due to thermal inactivation of the cI857 repressor. As a consequence, the production of ghosts requires that bacteria have to be grown at 28 degrees C before the lysis process is induced. In order to reflect the growth temperature of pathogenic bacteria in vivo, it seemed favorable to extend the heat stability of the lambda pR promoter/cI857 repressor system, allowing pathogens to grow at 37 degrees C before induction of lysis. In this study we describe a mutation in the lambda pR promoter, which allows stringent repression of gene E expression at temperatures up to 36 degrees C, but still permits induction of cell lysis at 42 degrees C.
TL;DR: It is indicated that downstream processing times and costs can be considerably reduced without affecting plasmid purity, and several studies undertaken during the development of process flow‐sheets for the downstream processing of supercoiled plasmids are described.
Abstract: Human clinical trial of gene therapy with nonviral vectors demands large amounts of pharmaceutical-grade plasmid DNA. Since standard molecular biology methods cannot be used for this purpose, there is a need for the development of processing methodologies for the large-scale production and purification of plasmids. This work describes several studies that were undertaken during the development of process flow-sheets for the downstream processing of supercoiled plasmids. Anion-exchange HPLC was used as a routine technique for monitoring plasmid purity in process streams. The use of RNase or high temperatures during alkaline lysis was proved unnecessary. Instead, RNA could be completely removed by performing sequentially clarification with a chaotropic salt, concentration with PEG, and ion-exchange and size-exclusion chromatography. Also, clarification of streams by precipitation was independent of the chaotropic salt used. Furthermore, by proceeding directly from cell lysis to chromatography it was possible to obtain plasmid with purity/quality identical to that of the one obtained when clarification and concentration were included in the process. This strategy has the advantage of increasing the overall process yield to 38%. The plasmid thus purified was depleted of RNA, chromosomal DNA, and proteins. Additionally, no animal-derived enzymes, alcohols, or toxic solvents were used, rendering validation potentially easier. The results described in this report also indicate that downstream processing times and costs can be considerably reduced without affecting plasmid purity.
TL;DR: Non-covalently attached or soluble cell wall proteins of Saccharomyces cerevisiae were extracted using a high pH/2-mercaptoethanol procedure and were separated for peptide sequencing using 2D-PAGE and transmission immunoelectron microscopy showed enolase to be present in the cell wall.
Abstract: Non-covalently attached or soluble cell wall proteins of Saccharomyces cerevisiae were extracted using a high pH/2-mercaptoethanol procedure and were separated for peptide sequencing using 2D-PAGE. A partial N- terminal sequence of a major protein spot was obtained and showed high identity with enolase gene products. Western blotting with an anti-enolase antibody confirmed that enolase was present in the cell wall extract. Biotinylation of cells prior to protein extraction with a membrane impermeable biotinylating agent confirmed that the detection was not owing to cell lysis during extraction. Transmission immunoelectron microscopy showed enolase to be present in the cell wall. Enolase contains no known secretion signal that would localize it to the cell wall. Thus S. cerevisiae must have further mechanisms for targeting proteins to the cell wall.
TL;DR: The industrially scaleable unit operations employed in this process are: optimized alkaline lysis; bag filtration; expanded bed anion exchange chromatography; ultrafiltration, and size exclusion chromatography which are scaleable alternatives to current approaches to plasmid DNA isolation.
Abstract: We describe a process for the commercial manufacture of therapeutic grade plasmid DNA. The industrially scaleable unit operations employed in this process are: (i) optimized alkaline lysis; (ii) bag filtration; (iii) expanded bed anion exchange chromatography; (iv) ultrafiltration, and (v) size exclusion chromatography. These steps are scaleable alternatives to current approaches to plasmid DNA isolation such as high speed centrifugation for feedstock clarification and solvent precipitation for plasmid concentration, and an efficient alternative to conventional low through-put packed bed chromatography.
TL;DR: CwlH produced in Escherichia coli harboring a cwlH plasmid is an N-acetylmuramoyl-L-alanine amidase and exhibited an optimum pH of 7.0 and high-level binding to the B. subtilis cell wall.
Abstract: Bacillus subtilis produces a 30-kDa peptidoglycan hydrolase, CwlH, during the late sporulation phase. Disruption of yqeE led to a complete loss of CwlH formation, indicating the identity of yqeE with cwlH. Northern blot analysis of cwlH revealed a 0.8-kb transcript after 6 to 7.5 h for the wild-type strain but not for the ςF, ςE, ςG, and ςK mutants. Expression of the ςK-dependent cwlH gene depended on gerE. Primer extension analysis also suggested that cwlH is transcribed by EςK RNA polymerase. CwlH produced in Escherichia coli harboring a cwlH plasmid is an N-acetylmuramoyl-l-alanine amidase (EC 3.5.1.28) and exhibited an optimum pH of 7.0 and high-level binding to the B. subtilis cell wall. A cwlC cwlH double mutation led to a lack of mother cell lysis even after 7 days of incubation in DSM medium, but the single mutations led to mother cell lysis after 24 h.
TL;DR: A rapid and convenient procedure for DNA damage determination in cell suspensions and solid tissues on single microplates was developed based on the ability of commercially available fluorochromes to interact preferentially with dsDNA in the presence of ssDNA, RNA, and proteins at high pH (>12.0), allowing direct measurements of DNA denaturation without sample handling or stepwise DNA separations.
TL;DR: The proposed protocols were highly efficient for DNA extraction, yielding about 50 mg DNA g−1 volatile suspended solids, and allowed PCR amplification of 16S rDNA.
Abstract: To optimize the cell lysis step for DNA extraction from activated sludge samples, two floc dispersion methods (sonication versus stirring with a cation exchange resin), and three cell lysis treatments (lysozyme + SDS, sonication in a water bath, and thermal shock) were tested. For dispersion, stirring with cation exchange resin was more efficient than sonication. The cell lysis procedures were applied in two sequences, and DNA was quantified after each cell lysis treatment. Lysozyme + SDS was the most effective step in the cell lysis procedures. The cell lysis treatment sequences giving the highest DNA yields were not the same for all the sludges. The differences in sludge microbial compositions and floc structures required specifically adapted cell lysis protocols. The proposed protocols were highly efficient for DNA extraction, yielding about 50 mg DNA g−1 volatile suspended solids, and allowed PCR amplification of 16S rDNA.
TL;DR: A chitinase gene (vChti-1) encoded by the Chlorella virus CVK2 was cloned and characterized and the protein produced in virus-infected cells showed chit inase activity on zymogram assays.
TL;DR: A plausible explanation for the mechanism by which components of the earthworm's immune system destroy non-self components is suggested, which can be activated by thiol groups and is inhibited by sphingomyelin.
Abstract: The cytolytic protein Eiseniapore (38 kDa) from coelomic fluid of the earthworm Eisenia fetida functionally requires sphingomyelin as revealed by using mammalian erythrocytes and phospholipid vesicles. The effects of ions, glycoproteins and phospholipids were investigated for the two-step Eiseniapore action mode, binding and pore formation in different assays. Eiseniapore lysis is activated by thiol groups but inhibited by metal ions. Eiseniapore binding to target membranes is inhibited by Eiseniapore-regulating factor, vitronectin, heparin and lysophosphatidylcholine. Ca2+ and Mg2+ were found to be not necessary for membrane binding or lytic activity. Sphingomyelin was essential for Eiseniapore-induced leakage of liposomes. We describe a cytolytic protein/toxin in Eiseniapore which differs from the established classification; it can be activated by thiol groups and is inhibited by sphingomyelin. Electron microscopy of erythrocyte membranes confirmed ring-shaped structures (pores) with a central channel with outer (10 nm) and inner (3 nm) diameters as shown previously [Lange, S., Nusler, F., Kauschke, E., Lutsch, G., Cooper, E.L. & Herrmann, A. (1997) J. Biol. Chem.272, 20 884–20 892] using artificial membranes. Functional evidence of pore formation by Eiseniapore was revealed as protection of lysis by carbohydrates occurred at an effective diameter above 3 nm. From these results, we suggest a plausible explanation for the mechanism by which components of the earthworm’s immune system destroy non-self components.
Patent•
06 Dec 1999
TL;DR: In this article, a method for isolating nucleic acids, in particular DNA, from optional complex starting materials with using the formulations according to the invention which is characterized by the lysis of the starting material, binding of nucleic acid to a carrier, washing of the nucleic acyclic acid bound to the carrier and elution of nucleical acids.
Abstract: The subject of the invention are formulations not containing chaotropic components for isolating nucleic acids with binding to a solid phase, in particular of DNA, from optional complex starting materials and quantities containing a lysis/binding buffer system which comprises at least one antichaotropic salt component, a solid phase and wash and elution buffers known as such. The lysis/binding buffer system may be an aqueous solution or a solid formulation in reaction vessels ready for use. All carriers used for isolation by means of chaotropic reagents, preferably glass fiber mats, glass membranes, silica carriers, ceramics, zeolites or materials showing negatively functionalised surfaces or chemically modified surfaces which may be converted to a negative charge potential may serve as a solid phase. Furthermore, the subject of the invention is a method for isolating nucleic acids, in particular DNA, from optional complex starting materials with using the formulations according to the invention which is characterized by the lysis of the starting material, binding of nucleic acids to a carrier, washing of the nucleic acids bound to the carrier and elution of nucleic acids.
TL;DR: The disruption of recombinant E. coli cells containing a 76.8 kb plasmid DNA was achieved by the chemical lysis method in a coaxial cylinder rheometer which allowed in situ measurements of rheological changes to be carried out as the lysis reaction proceeded.
TL;DR: OPA reacts strongly with primary amines and stabilizes, to some extent, the outer membrane and cell walls of vegetative organisms and this probably accounts for part, but not necessarily all, of its lethal action.
Abstract: The reaction of ortho-phthalaldehyde (OPA) with amino acids and proteins was investigated as a possible mode of action. Bacterial pellets (obtained by centrifugation) changed colour after exposure to OPA. These colours were more intense at alkaline than acidic pH. Acidic and alkaline OPA reacted with primary amino acids to form coloured products. The reaction rate accelerated with increasing pH. OPA increased the optical density of bacterial cell suspensions (an indication of protein coagulation or microbial surface or other changes in the opacity of cell constituents). The inhibition of ethylenediaminetetraacetic acid- and sodium lauryl sulphate-induced lysis was not as great as for glutaraldehyde (GTA), possibly indicating less cross-linking of amines. Interactions with primary amino groups of the outer envelope or cell wall probably play a part in the action of OPA but the level of cross-linking associated with the outer membrane does not appear to be as extensive as that of GTA. The aromatic component might allow OPA to penetrate the outer layers of cells, thus helping to explain the very high activity of OPA against Gram-negative vegetative organisms even though the degree of cross-linking seems to be less than that seen with GTA. Thus, OPA reacts strongly with primary amines and stabilizes, to some extent, the outer membrane and cell walls of vegetative organisms and this probably accounts for part, but not necessarily all, of its lethal action.
TL;DR: In this article, a modified procedure for extraction of high-quality genomic DNA that is rapid, simple, biologically nonhazardous, and generally applicable to pathogenic bacteria was reported, where bacterial cells were pretreated with 70% ethanol prior to enzymatic digestion with lysozyme.
TL;DR: Interference with the adsorption of phages to imm-, sp- or 5ts1-mutant-infected cells, in a variety of contexts, inhibits premature lysis-inhibition collapse.
Abstract: Lysis inhibition is a mechanism of latent-period extension and burst-size increase that is induced by the T4 bacteriophage adsorption of T4-infected cells. Mutants of T4 genes imm, sp and 5 (specifically the ts1 mutant of 5) display some lysis inhibition. However, these mutants experience lysis-inhibition collapse, the lysis of lysis-inhibited cells, earlier than wild-type-infected cells (i.e. their collapse occurs prematurely). Lysis from without is a lysis induced by excessive T4 adsorption. Gp5 is an inducer of lysis from without while gpimm and gpsp effect resistance to lysis from without. This paper shows that interfering with the adsorption of phages to imm-, sp- or 5ts1-mutant-infected cells, in a variety of contexts, inhibits premature lysis-inhibition collapse. From these data it is inferred that wild-type T4-infected cells display resistance to lysis-inhibition collapse by a mechanism resembling resistance to lysis from without.