Showing papers on "Lysis published in 2010"

Galectin-3, a marker for vacuole lysis by invasive pathogens.

Abstract: Shigella bacteria invade macrophages and epithelial cells and following internalization lyse the phagosome and escape to the cytoplasm. Galectin-3, an abundant protein in macrophages and epithelial cells, belongs to a family of beta-galactoside-binding proteins, the galectins, with many proposed functions in immune response, development, differentiation, cancer and infection. Galectins are synthesized as cytosolic proteins and following non-classical secretion bind extracellular beta-galactosides. Here we analysed the localization of galectin-3 following entry of Shigella into the cytosol and detected a striking phenomenon. Very shortly after bacterial invasion, intracellular galectin-3 accumulated in structures in vicinity to internalized bacteria. By using immuno-electron microscopy analysis we identified galectin-3 in membranes localized in the phagosome and in tubules and vesicles that derive from the endocytic pathway. We also demonstrated that the binding of galectin-3 to host N-acetyllactosamine-containing glycans, was required for forming the structures. Accumulation of the structures was a type three secretion system-dependent process. More specifically, existence of structures was strictly dependent upon lysis of the phagocytic vacuole and could be shown also by Gram-positive Listeria and Salmonella sifA mutant. We suggest that galectin-3-containing structures may serve as a potential novel tool to spot vacuole lysis.

Extraction of extracellular polymeric substances (EPS) from anaerobic granular sludges: comparison of chemical and physical extraction protocols

Abstract: The characteristics of the extracellular polymeric substances (EPS) extracted with nine different extraction protocols from four different types of anaerobic granular sludge were studied. The efficiency of four physical (sonication, heating, cationic exchange resin (CER), and CER associated with sonication) and four chemical (ethylenediaminetetraacetic acid, ethanol, formaldehyde combined with heating, or NaOH) EPS extraction methods was compared to a control extraction protocols (i.e., centrifugation). The nucleic acid content and the protein/polysaccharide ratio of the EPS extracted show that the extraction does not induce abnormal cellular lysis. Chemical extraction protocols give the highest EPS extraction yields (calculated by the mass ratio between sludges and EPS dry weight (DW)). Infrared analyses as well as an extraction yield over 100% or organic carbon content over 1 g g(-1) of DW revealed, nevertheless, a carry-over of the chemical extractants into the EPS extracts. The EPS of the anaerobic granular sludges investigated are predominantly composed of humic-like substances, proteins, and polysaccharides. The EPS content in each biochemical compound varies depending on the sludge type and extraction technique used. Some extraction techniques lead to a slightly preferential extraction of some EPS compounds, e.g., CER gives a higher protein yield.

Direct cellular lysis/protein extraction protocol for soil metaproteomics.

Abstract: We present a novel direct protocol for deep proteome characterization of microorganisms in soil. The method employs thermally assisted detergent-based cellular lysis (SDS) of soil samples, followed by TCA precipitation for proteome extraction/cleanup prior to liquid chromatography-mass spectrometric characterization. This approach was developed and optimized using different soils inoculated with genome-sequenced bacteria (Gram-negative Pseudomonas putida or Gram-positive Arthrobacter chlorophenolicus). Direct soil protein extraction was compared to protein extraction from cells isolated from the soil matrix prior to lysis (indirect method). Each approach resulted in identification of greater than 500 unique proteins, with a wide range in molecular mass and functional categories. To our knowledge, this SDS-TCA approach enables the deepest proteome characterizations of microbes in soil to date, without significant biases in protein size, localization, or functional category compared to pure cultures. This protocol should provide a powerful tool for ecological studies of soil microbial communities.

Interaction and Modulation of Two Antagonistic Cell Wall Enzymes of Mycobacteria

Abstract: Bacterial cell growth and division require coordinated cell wall hydrolysis and synthesis, allowing for the removal and expansion of cell wall material. Without proper coordination, unchecked hydrolysis can result in cell lysis. How these opposing activities are simultaneously regulated is poorly understood. In Mycobacterium tuberculosis, the resuscitation-promoting factor B (RpfB), a lytic transglycosylase, interacts and synergizes with Rpf-interacting protein A (RipA), an endopeptidase, to hydrolyze peptidoglycan. However, it remains unclear what governs this synergy and how it is coordinated with cell wall synthesis. Here we identify the bifunctional peptidoglycan-synthesizing enzyme, penicillin binding protein 1 (PBP1), as a RipA-interacting protein. PBP1, like RipA, localizes both at the poles and septa of dividing cells. Depletion of the ponA1 gene, encoding PBP1 in M. smegmatis, results in a severe growth defect and abnormally shaped cells, indicating that PBP1 is necessary for viability and cell wall stability. Finally, PBP1 inhibits the synergistic hydrolysis of peptidoglycan by the RipA-RpfB complex in vitro. These data reveal a post-translational mechanism for regulating cell wall hydrolysis and synthesis through protein–protein interactions between enzymes with antagonistic functions.

A Vibrio Effector Protein Is an Inositol Phosphatase and Disrupts Host Cell Membrane Integrity

Abstract: The marine bacterium Vibrio parahaemolyticus causes gastroenteritis in humans and encodes the type III effector protein VPA0450, which contributes to host cell death caused by autophagy, cell rounding, and cell lysis. We found that VPA0450 is an inositol polyphosphate 5-phosphatase that hydrolyzed the D5 phosphate from the plasma membrane phospholipid phosphatidylinositol 4,5-bisphosphate. VPA0450 disrupted cytoskeletal binding sites on the inner surface of membranes of human cells and caused plasma membrane blebbing, which compromised membrane integrity and probably contributed to cell death by facilitating lysis. Thus, bacterial pathogens can disrupt adaptor protein-binding sites required for proper membrane and cytoskeleton dynamics by altering the homeostasis of membrane-bound inositol-signaling molecules.

Continuous differential impedance spectroscopy of single cells

Abstract: A device for continuous differential impedance analysis of single cells held by a hydrodynamic cell trapping is presented. Measurements are accomplished by recording the current from two closely-situated electrode pairs, one empty (reference) and one containing a cell. We demonstrate time-dependent measurement of single cell impedance produced in response to dynamic chemical perturbations. First, the system is used to assay the response of HeLa cells to the effects of the surfactant Tween, which reduces the impedance of the trapped cells in a concentration dependent way and is interpreted as gradual lysis of the cell membrane. Second, the effects of the bacterial pore-forming toxin, Streptolysin-O are measured: a transient exponential decay in the impedance is recorded as the cell membrane becomes increasingly permeable. The decay time constant is inversely proportional to toxin concentration (482, 150, and 30 s for 0.1, 1, and 10 kU/ml, respectively).

Continuous-flow electrical lysis device with integrated control by dielectrophoretic cell sorting

Abstract: We present a device capable of electrical cell lysis and evaluation of lysis efficiency in continuous flow using dielectrophoretic cell sorting. We use a combination of AC electrical fields and so-called liquid electrodes to avoid bubble creation at the electrode surface. The electrical field distribution is calculated in different electrode configurations by numerical simulations. Cell sorting shows high lysis efficiency, 99% of yeast cells sorted after lysis featuring dielectric properties similar to dead cells. A study of the potential device throughput is performed.

Detergent effects on membranes at subsolubilizing concentrations: transmembrane lipid motion, bilayer permeabilization, and vesicle lysis/reassembly are independent phenomena.

Abstract: Soluble amphiphiles, or detergents, are known to produce a number of structural and dynamic effects on membranes, even at concentrations below those causing membrane solubilization (i.e. in the so-called stage I of detergent-membrane interaction). The main subsolubilizing detergent effects on membranes are transmembrane lipid motion (flip-flop), breakdown of the membrane permeability barrier (leakage), and vesicle lysis/reassembly. For a proper understanding of membrane solubilization by detergents, it is important to assess whether the various effects seen at subsolubilizing surfactant concentrations occur independently from each other or are interconnected by cause-effect relationships so that they can be interpreted as necessary steps in the overall process of solubilization. To answer this question, we have explored the three above-mentioned effects (i.e., flip-flop, leakage, and lysis/reassembly) apart from solubilization in model (large unilamellar vesicles) and cell (erythrocyte) membranes. Five structurally different surfactants, namely, chlorpromazine, imipramine, Triton X-100, sodium dodecylsulfate, and sodium deoxycholate have been used. Each of them behaves in a unique way. Our results reveal that lipid flip-flop, vesicle leakage, and vesicle lysis/reassembly occur independently between them and with respect to bilayer solubilization so that they cannot be considered to be necessary parts of a higher-order unified process of membrane solubilization by detergents.

A PCR reactor with an integrated alumina membrane for nucleic acid isolation.

Abstract: Recently, there has been a growing interest in point-of-care devices capable of detecting nucleic acids (NA) in clinical and environmental samples. Nucleic acid detection requires, however, various sample preparation steps that complicate device operation. An attractive remedy is to integrate many, if not all, sample preparation operations and nucleic acid amplification into a single reaction chamber. A microfluidic chip that integrates, in a single chamber, polymerase chain reaction (PCR) amplification with solid-phase extraction of nucleic acids using a nanoporous, aluminium oxide membrane (AOM) is described. Samples suspected of containing target bacteria and/or viruses are mixed with lysis agents and a chaotropic salt and loaded into a plastic chip housing a nanoporous, aluminium oxide membrane. The nucleic acids in the lysate bind to the membrane. The membrane is then washed, the chamber is filled with the PCR reaction reagents, and the chamber's temperature is cycled to amplify the captured nucleic acids and produce detectable products. Both DNA and RNA (with reverse-transcription) isolation and amplification are demonstrated. Due to the dry membrane's high resistance to liquid flow, a specialized flow control system was devised to facilitate sample introduction and membrane washing.

Degradation of fungal cell walls of phytopathogenic fungi by lytic enzyme of Streptomyces griseus.

Abstract: In vitro tests of interactions between Streptomyces griseus strains and some soil-borne plant pathogens (Fusarium oxysporum, Alternaria alternate, Rhizoctonia solani and Fusarium solani) and 2 isolates of Aspergillus flavus were studied on PDA medium. Strains tested produced a metabolite that inhibited growth of plant pathogenic fungi on PDA medium (dual culture test). When grown in liquid medium having fungal cell walls as sole carbon source, S. griseus produced chitinase enzyme in the medium. Higher levels of this enzyme were induced by cell wall ofAspergillus flavus and the crude chitinase enzyme extracted showed zone of inhibition on all pathogens inoculated PDA plates at all tested concentrations. When lytic enzyme produced by S. griseus was incubated with hyphal wall of the test fungi treated with 2 M NaOH and chloropharm: Methanol, the release of glucose and N acetyl glucosamine significantly increased relative to the untreated one. This result suggests that proteins in the cell walls of pathogens may make these walls more resistant to degradation by the extracellular lytic enzymes. Ionic strength of NaOH on lytic activity was tested, where as the enzymes lysed fungal cell wall best at ionic concentration of 2 M treatment. Pretreatment with alkali or proteolytic enzyme increases their susceptibility for lysis. In vitro lytic activity provides an appropriate condition and the effect of biocontrol organism in field level treatment. Key words: Chitinase enzyme, dual culture test, plant pathogenic fungi, NaOH treatment and Ionic strength.

Handheld mechanical cell lysis chip with ultra-sharp silicon nano-blade arrays for rapid intracellular protein extraction

Abstract: This paper presents a handheld mechanical cell lysis chip with ultra-sharp nano-blade arrays fabricated by simple and cost effective crystalline wet etching of (110) silicon. The ultra-sharp nano-blade array is simply formed by the undercutting of (110) silicon during the crystalline wet etching process. Cells can be easily disrupted by the silicon nano-blade array without the help of additional reagents or electrical sources. Based on the bench-top test of the proposed device, a handheld mechanical cell lysis chip with the nano-blade arrays is designed and fabricated for direct connection to a commercial syringe. The direct connection to a syringe provides rapid cell lysis, easy handling, and minimization of the lysate dead volume. The protein concentration in the cell lysate obtained by the proposed lysis chip is quantitatively comparable to the one prepared by a conventional chemical lysis method.

Deficiency in l-Serine Deaminase Interferes with One-Carbon Metabolism and Cell Wall Synthesis in Escherichia coli K-12

Abstract: Escherichia coli K-12 provided with glucose and a mixture of amino acids depletes L-serine more quickly than any other amino acid even in the presence of ammonium sulfate. A mutant without three 4Fe4S L-serine deaminases (SdaA, SdaB, and TdcG) of E. coli K-12 is unable to do this. The high level of L-serine that accumulates when such a mutant is exposed to amino acid mixtures starves the cells for C(1) units and interferes with cell wall synthesis. We suggest that at high concentrations, L-serine decreases synthesis of UDP-N-acetylmuramate-L-alanine by the murC-encoded ligase, weakening the cell wall and producing misshapen cells and lysis. The inhibition by high L-serine is overcome in several ways: by a large concentration of L-alanine, by overproducing MurC together with a low concentration of L-alanine, and by overproducing FtsW, thus promoting septal assembly and also by overexpression of the glycine cleavage operon. S-Adenosylmethionine reduces lysis and allows an extensive increase in biomass without improving cell division. This suggests that E. coli has a metabolic trigger for cell division. Without that reaction, if no other inhibition occurs, other metabolic functions can continue and cells can elongate and replicate their DNA, reaching at least 180 times their usual length, but cannot divide.

Disruption of cultured cells by nitrogen cavitation.

Abstract: Cell disruption by nitrogen decompression from a pressurized vessel is a rapid and effective way to homogenize cells and tissues, to release intact organelles, and to prepare cell membranes. Cells are placed in a pressure vessel and large quantities of oxygen-free nitrogen are dissolved in the cells under high pressure (~5500 kilopascals [kPa], equivalent to 800 pounds per square inch [psi]). When the pressure is released suddenly, the nitrogen bubbles out of solution, rupturing the cell membrane and releasing the cell contents. Nitrogen cavitation is well suited for mammalian and plant cells and fragile bacteria, but is less effective with yeast, fungi, spores, or other cell types with tough cell walls. The chemical and physical stresses imposed by nitrogen cavitation on enzymes and subcellular compartments are minimized compared with ultrasonic and mechanical homogenizing methods. Unlike lysis methods relying on shear stresses and friction, there is no heat damage to proteins and organelles during nitrogen cavitation. Indeed, the method is accompanied by an adiabatic expansion that cools the sample instead. Also, labile cell components are protected from oxidation by the inert nitrogen gas. Furthermore, nitrogen does not alter the pH of the suspending medium. The process is fast and uniform because the same disruptive forces are applied within each cell and throughout the sample, ensuring reproducible cell-free homogenates. Finally, variable sample sizes (e.g., from ~1 mL to 1 L or more) can be accommodated with most commercial systems.

A rapid method for isolation of total DNA from pathogenic filamentous plant fungi.

Abstract: DNA isolation from some fungal organisms of agronomic importance is difficult because they have cell walls or capsules that are relatively unsusceptible to lysis. We have developed a fast DNA isolation protocol for Fusarium oxysporum, which causes fusarium wilt disease in more than 100 plant species, and for Pyrenochaeta terrestris, which causes pink root in onions. This protocol was based on the sodium dodecyl sulfate/phenol method, without beta-mercaptoethanol and without maceration in liquid nitrogen; it uses phenol/chloroform extraction to remove proteins and co-precipitated polysaccharides. The A(260/280) absorbance ratios of isolated DNA were around 1.9, suggesting that the DNA fraction was pure and may be used for further analysis. Additionally, the A(260/230) values were higher than 1.8, suggesting negligible contamination by polysaccharides. The DNA isolated by this protocol is of sufficient quality for molecular applications; this technique could be applied to other organisms that have similar substances that hinder DNA extraction.

Wireless induction heating in a microfluidic device for cell lysis

Abstract: A wireless induction heating system in a microfluidic device was devised for cell lysis to extract DNA and RNA from Escherichia coli. The thermal responses of nickel, iron and copper heating units were studied by applying an alternating magnetic field as a function of geometry of unit, strength of magnetic field, and kind of metal. Heating units were prepared by cutting metal film using a fiber laser, and the units were integrated into a microchannel system using a soft lithographic process. Variation and distribution of temperature on the surface of the heating units was observed using a thermographic camera and temperature labels. The amount of protein released from E. coli by thermal lysis was determined by protein concentration measurement. Hemoglobin released from red blood cells was observed using colorimetric intensity measurement. Extracted DNA was quantified by real-time polymerase chain reaction, and the profile was compared with that of a positive control of ultrasonically disrupted E. coli. The stability of RNA extracted by induction heating was quantified by the measurement of 23S/16S rRNA ratio and comparison with that by normal RNA extraction kit as a gold standard. A solid-shaped nickel structure was selected as the induction heating element in the microfluidic device because of the relatively small influence of geometries and faster thermal response. The amount of protein extracted from E. coli and hemoglobin released from red blood cells by induction heating of the nickel unit in the microfluidic device was proportional to the strength of the applied magnetic field. The lysis of E. coli by induction heating was as effective as lysis of DNA by the ultrasonication method because the threshold cycle values of the sample were compatible with those of the positive control as measured by ultrasonication. Thermal lysis of E. coli by induction heating represents a reasonable alternative to a commercial RNA extraction method as shown by the comparative ratio of 23S/16S obtained. In this study, wireless induction heating in a microfluidic device achieved convenience, portability, and economic efficiency by wireless operation, easy fabrication, disposability, and treatment of a large number of cells.

Integrated electrical concentration and lysis of cells in a microfluidic chip

Abstract: Lysing cells is an important step in the analysis of intracellular contents. Concentrating cells is often required in order to acquire adequate cells for lysis. This work presents an integrated concentration and lysis of mammalian cells in a constriction microchannel using dc-biased ac electric fields. By adjusting the dc component, the electrokinetic cell motion can be precisely controlled, leading to an easy switch between concentration and lysis of red blood cells in the channel constriction. These two operations are also used in conjunction to demonstrate a continuous concentration and separation of leukemia cells from red blood cells in the same microchannel. The observed cell behaviors agree reasonably with the simulation results.

Electrochemical cell lysis device for DNA extraction

Abstract: We present a novel electrochemical cell lysis device to prepare DNA samples for lab-on-a-chip (LOC) applications. It utilizes the electrolysis of saline solution to generate hydroxide ions (OH(-)) at the cathode as alkaline lytic agents. Cathode and anode chambers are separated by a negatively-charged ion exchangeable polymer diaphragm to maintain the high pH level for efficient cell lysis in the cathode chamber, to prevent inflow of PCR-amplification inhibitors from the anode chamber, and to minimize binding of DNA molecules. Electric current flow and pH maintenance, which depended on the device design, were two important parameters of the device performance. After optimizing the design and visually confirming cell lysis of Chinese hamster ovary (CHO) cells in a very short amount of time, we directly electrolyzed four bacterial cell types suspended in saline solution. Real-time PCR (qPCR) analysis showed that our device could lyse both gram-positive and gram-negative bacterial cells with higher efficiency than other common methods and could detect DNA on the microlitre scale. Our data demonstrate several advantages of the proposed device: absence of cell lysis chemicals and heating; no adverse effects on PCR amplification; low DNA loss; low voltage and power consumption; and rapid processing. The device could potentially be applied as an on-chip DNA extraction component.

An inexpensive method for extraction of genomic DNA from fungal mycelia

Abstract: A rapid and efficient protocol for the extraction of genomic DNA from plant pathogenic fungi was developed. Key features of the protocol include the SDS-assisted lysis of fungal mycelium with inclusion of a glass bead to help break hyphal walls, followed by isopropanol precipitation of the DNA. The protocol was used to extract genomic DNA from a collection of 26 fungal species, representing many important plant pathogens. Yield of DNA ranged from 2.1–4.9 μg per 20 mg of mycelium or 0.4–0.6 μg per 20 mg of spores. The DNA was of sufficient purity to be digested by restriction enzymes, to serve as a template in the PCR-amplification of genomic fragments as large as 4.9 kb, and to be used in dot-blot hybridization for the detection of multiple- and single-copy genes.

Lysis of Cultured Cells for Immunoprecipitation

Abstract: Cell lysis with mild detergent is commonly used with cultured animal cells. If low detergent concentrations are sufficient to cause cell lysis (e.g., 1% Nonidet P-40 [NP-40] or 1% Triton X-100), this method can be gentler to the protein of interest than mechanical homogenization methods. The choice of detergent must be tailored to the nature of the epitope recognized by the immunoprecipitating antibody. If the antibody recognizes a linear peptide epitope (e.g., a synthetic peptide), then use a harsh denaturing lysis buffer (e.g., RIPA buffer). On the other hand, if the antibody is directed toward a conformational epitope, use NP-40 lysis buffer (or 1% Triton X-100). This protocol presents separate methods for lysing cells grown as monolayer cultures and for cells grown in suspension.