Alginate gel microchip for real-time monitoring of intracellular processes in bacterial and yeast cells

A method of alginate-based hydrogel cell microchip manufacturing is proposed. The development of mild conditions for cell immobilization in microvolumes of non-toxic alginate gel allows extending the range of microorganisms used. Different approaches to cell analysis using microchip have been approved in pilot studies. By the example of Escherichia coli, Bordetella bronchiseptica and Saccharomyces cerevisiae it is shown that cell microchip can be successfully applied for monitoring of nucleic acid and protein synthesis in growing cells simultaneously using two fluorescent dyes. The influence of chloramphenicol on the nucleic acids and protein synthesis in five bacterial strains has been studied on the microchip. The microchip was also applied for the analysis of inducible fluorescent protein EGFP synthesis in E. coli cells, the correlation between the level of EGFP synthesis and concentration of the inductor in the medium has been established.     

Ozone-induced damage of Escherichia coli K-12

Escherichia coli K-12 transformed with pACYC184 plasmid DNA was exposed to ozone (O₃) in aqueous solution. The damage to the membrane, protein, plasmid DNA, and cell survival were investigated. Cell viability was unaffected by short-term O₃ exposure (1–5 min) but membrane permeability was compromised as indicated by protein and nucleic acid leakage and lipid oxidation. The intracellular components, protein and DNA, remained intact. With longer durations of O₃ exposure (up to 30 min) cell viability decreased with a more significant increase in lipid oxidation and protein and nucleic acid leakage. The proteins leaking out were further oxidized by O₃. The total intracellular proteins run on sodium dodecyl sulfate/polyacrylamide gel electrophoresis, and plasmid DNA run on agarose gel, showed progressive degradation corresponding to the decrease in cell viability. The data indicate that membrane components are the primary targets of O₃ damage with subsequent reactions involving the intracellular components, protein and DNA. Received: 18 Apirl 1996 / Received revision: 26 July 1996 / Accepted: 5 August 1996     

L-Lactic acid production from raw cassava starch in a circulating loop bioreactor with cells immobilized in loofa (Luffa cylindrica)

l-Lactic acid was produced from raw cassava starch, by simultaneous enzyme production, starch saccharification and fermentation in a circulating loop bioreactor with Aspergillus awamori and Lactococcus lactis spp. lactis immobilized in loofa sponge. A. awamori was immobilized directly in cylindrical loofa sponge while the L. lactis was immobilized in a loofa sponge alginate gel cube. In the loofa sponge alginate gel cube, the sponge serves as skeletal support for the gel with the cells. The alginate gel formed a hard outer layer covering the soft porous gel inside. By controlling the rate and frequency of broth circulation between the riser and downcomer columns, the riser could be maintained under aerobic condition while the downcomer was under anaerobic condition. Repeated fed-batch l-lactic acid production was performed for more than 400 h and the average lactic acid yield and productivity from raw cassava starch were 0.76 g lactic acid g^–1 starch and 1.6 g lactic acid l^–1 h^–1, respectively.     

Purification and Properties of a β-1,3-glucanase from Chaetomium sp. that is Involved in Mycoparasitism

A β-1,3-glucanase was detected, using laminarin as substrate, in the culture broth of Chaetomium sp. Major activity was associated with a 70 kDa protein band visualized on a polyacrylamide gel. β-1,3-Glucanase was purified by a one-step, native gel purification procedure. Optimal activity was observed at pH 6.0 and 30 °C (over 30 min). It could degrade cell walls of plant pathogens including Rhizoctonia solani, Gibberella zeae, Fusarium sp., Colletotrichum gloeosporioides and Phoma sp. The N-terminal amino acid residues of the purified β-1,3-glucanase are PYQLQTP, which do not exhibit homology to other fungal β-1,3-glucanases suggesting it may be a novel enzyme. Received 20 July 2005; Revisions requested 2 August 2005 and 27 September 2005; Revisions received 16 September 2005 and 3 November 2005; Accepted 6 November 2005     

Influence onEuglena gracilis of three types of inhibitors

Three groups of antibiotics were established according to their mechanism of action on the incorporation of¹⁴C-labelled precursors inEuglena gracilis:1. antibiotics markedly inhibiting nucleic acid synthesis and negligibly affecting protein synthesis and inducing permanently bleachedE. gracilis; 2. antibiotics markedly inhibiting protein synthesis and only moderately nucleic acid synthesis and not causing permanent bleaching ofE. gracilis; 3. compounds inhibiting both protein synthesis and nucleic acid synthesis to a similar degree, some of them bringing about permanent bleaching ofE. gracilis. Nitrofurantoin was comparable to compounds of the first group, sodium azide to those of the third group. Both exhibited 100 % bleaching ofE. gracilis, although with the latter this occurred only after a short-term increase of the incubation temperature from 25 to 37 °C.     

Relevance of Rheological Properties of Sodium Alginate in Solution to Calcium Alginate Gel Properties

The purpose of this study is to determine whether sodium alginate solutions’ rheological parameters are meaningful relative to sodium alginate’s use in the formulation of calcium alginate gels. Calcium alginate gels were prepared from six different grades of sodium alginate (FMC Biopolymer), one of which was available in ten batches. Cylindrical gel samples were prepared from each of the gels and subjected to compression to fracture on an Instron Universal Testing Machine, equipped with a 1-kN load cell, at a cross-head speed of 120 mm/min. Among the grades with similar % G, (grades 1, 3, and 4), there is a significant correlation between deformation work (L _E) and apparent viscosity (η _app). However, the results for the partial correlation analysis for all six grades of sodium alginate show that L _E is significantly correlated with % G, but not with the rheological properties of the sodium alginate solutions. Studies of the ten batches of one grade of sodium alginate show that η _app of their solutions did not correlate with L _E while tan δ was significantly, but minimally, correlated to L _E. These results suggest that other factors—polydispersity and the randomness of guluronic acid sequencing—are likely to influence the mechanical properties of the resultant gels. In summary, the rheological properties of solutions for different grades of sodium alginate are not indicative of the resultant gel properties. Inter-batch differences in the rheological behavior for one specific grade of sodium alginate were insufficient to predict the corresponding calcium alginate gel’s mechanical properties.     

Nature of the ligand bound to uncoupling CSP310 protein

It was shown that, in preparations of winter rye (Secale cereale L.) and winter wheat (Triticum aestivum L.), in proteins immunochemically related to a cold shock protein CSP310, and also in purified CSP310 from winter rye and triticale (Triticosecale X.), nucleic acid was present. Treatments with DNase and RNase showed that this nucleic acid was RNA. This protein-bound RNA was detected in the preparation of constitutively synthesized but not stress-induced protein. Stress-induced CSP310 bound high-molecular RNA in vitro at both 26 and 0°C, but it did not bind DNA. The data obtained permit an assumption that, during low-temperature stress, constitutively synthesized CSP310 with a low uncoupling capacity releases RNA and transits to a stress-induced form with a high uncoupling capacity.Translated from Fiziologiya Rastenii, Vol. 52, No. 2, 2005, pp. 216–220.Original Russian Text Copyright © 2005 by Kolesnichenko, Tauson, Zykova, Klimenko, Grabelnykh, Pobezhimova.This revised version was published online in April 2005 with a corrected cover date.     

Isolation and characterization of an alginate lyase from Klebsiella aerogenes

The bacterium Klebsiella aerogenes (type 25) produced an inducible alginate lyase, whose major activity was located intracellularly during all growth phases. The enzyme was purified from the soluble fraction of sonicated cells by ammonium sulfate precipitation, anion- and cation-exchange chromatography and gel filtration. The apparent molecular weight of purified alginate lyase of 28,000 determined by gel filtration and of 31,600 determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicated that the active enzyme was composed of a single polypeptide. The alginate lyase displayed a pH optimum around 7.0 and a temperature optimum around 37°C. The purified enzyme depolymerized alginate by a lyase reaction in an endo manner releasing products which reacted in the thiobarbituric acid assay and absorbed strongly in the ultraviolet region at 235 nm. The alginate lyase was specific for guluronic acidrich alginate preparations. Propylene glycol esters of alginate and O-acetylated bacterial alginates were poorly degraded by the lyase compared with unmodified polysaccharide. The guluronate-specific lyase activity was applied in an enzymatic method to detect mannuronan C-5 epimerase in three different mucoid (alginate-synthesizing) strains of Pseudomonas aeruginosa. This enzyme which converts polymannuronate to alginate could not be demonstrated either extracellularly or intracellularly in all strains suggesting the absence of a polymannuronate-modifying enzyme in P. aeruginosa.Abbreviations poly(ManA) (1–4)--D-mannuronan - poly(GulA) (1–4)--L-guluronan - TBA 2-thiobarbituric acid     

Development and evaluation of a novel nano‐scale vector for siRNA

To synthesize a lipid‐cationic polymer (LCP) containing brassidic acid side chain and to investigate its transfection efficiency and characteristics as a siRNA gene vector. The LCP was chemically synthesized and its nucleic acid binding capacity was determined by gel electrophoresis. HeLa‐EGFP and TH1080‐EGFP cell lines were transfected with siRNA against enhanced green fluorescent protein (EGFP) gene using a LCP to investigate the transfection efficiency. An MTT assay was performed to evaluate the cellular toxicity of the LCP vector. Its degradability and stability under acidic conditions were also investigated. The LCP vector possessed high DNA binding capacity. More than 73% of the cellular fluorescence was inhibited by the LCP‐mediated transfection of siRNA against EGFP gene, indicating that vector had high transfection efficiency. Cellular viability was about 95% at the optimum transfection efficiency of LCP, suggesting that the cellular toxicity of LCP was very low. The LCP was also observed to be degradable; moreover, it could be easily stored at normal temperature. A gene vector used for the transfection of siRNA was successfully fabricated from synthesized LCP. Its numerous excellent properties entitle values for further scientific research. J. Cell. Biochem. 111: 881–888, 2010. © 2010 Wiley‐Liss, Inc.     

Batch production of propionic acid by immobilizedPropionibacterium sp

Whole cells ofPropionibacterium freudenreichii subsp.shermanii (two strains) were immobilized in a living state in 2 and 4% alginate gel and 2, 4 and 6% carrageenan gel. Production of propionic acid, acetic acid, and vitamin B₁₂ were examined. The best results were obtained in the fermentation with strains immobilized in 4% alginate gel when applied for the third time.     

Influence of immobilization parameters on growth and lactic acid production by <Emphasis Type="Italic">Streptococcus thermophilus</Emphasis> and <Emphasis Type="Italic">Lactobacillus bulgaricus</Emphasis> co-immobilized in calcium alginate gel beads

Streptococcus thermophilusand Lactobacillus bulgaricus were co-immobilized in different systems with varying calcium (0.1–1.5M) and alginate (1–2<><>, w/v) concentrations. Highest lactic acid production was 35 g l₁ when both bacteria were in high viscosity beads (1<><>, w/v alginate) hardened in 0.1 M CaCl₂ .The gel bead composition affected size and distribution of entrapped lactic acid bacteria.     

Effects of entrapment on nucleic acid content,cell morphology,cell surface property,and stress of pure cultures commonly found in biological wastewater treatment

The effects of cell entrapment on nucleic acid content, cell morphology, cell surface property, and stress of major groups of bacteria (betaproteobacteria and gammaproteobacteria) in biological municipal wastewater treatment were investigated. Three different entrapment media (alginate, carrageenan, and polyvinyl alcohol) were examined. Results indicated that the entrapment and type of entrapment media affected nucleic acid content, cell morphology, cell surface property, and stress of the three representative species (Alcaligenes faecalis, Comamonas testosteroni, and Pseudomonas putida) studied. The highest deoxyribonucleic acid and ribonucleic acid increases were observed with the alginate and polyvinyl alcohol (PVA) entrapment, respectively. A cell morphological change from bacilli to coccoidal was observed in the case of alginate entrapment while the PVA-entrapped cells had a slim morphology when compared to non-entrapped cells and formed putative nanowires. The entrapment increased or decreased the surface roughness of cells depending on the type of entrapment media. Expression of a nitrosative stress gene, which is linked to oxygen deprivation, was observed more in the alginate-entrapped cells. These research findings advance the fundamental understanding of the entrapped cell physiology which can lead to more efficient entrapped cell-based wastewater treatment.     

Why 3-D? Gel-based microarrays in proteomics

Gel-based microarrays (biochips) consisting of nanoliter and sub-nanoliter gel drops on hydrophobic substrate are a versatile technology platform for immobilization of proteins and other biopolymers. Biochips provide a highly hydrophilic environment, which stabilizes immobilized molecules and facilitates their interactions with analytes. The probes are immobilized simultaneously with gel polymerization, evenly distributed throughout individual elements, and are easily accessible because of large pores. Each element is an isolated nanotube. Applications of biochips in the studies of protein interactions with other proteins, nucleic acids, and glycans are described. In particular, biochips are compatible with MALDI-MS. Biochip-based assay of prostate-specific antigen became the first protein microarray approved for clinical use by a national regulatory agency. In this review, 3-D immobilization is compared with mainstream technologies based on surface immobilization.     

Dissociation and unfolding of inducible nitric oxide synthase oxygenase domain identifies structural role of tetrahydrobiopterin in modulating the heme environment

The oxygenase domain of the inducible nitric oxide synthase, Δ65 iNOSox is a dimer that binds heme, L-Arginine (L-Arg), and tetrahydrobiopterin (H₄B) and is the site for NO synthesis. The role of H₄B in iNOS structure-function is complex and its exact structural role is presently unknown. The present paper provides a simple mechanistic account of interaction of the cofactor tetrahydrobiopterin (H₄B) with the bacterially expressed Δ65 iNOSox protein. Transverse urea gradient gel electrophoresis studies indicated the presence of different conformers in the cofactor-incubated and cofactor-free Δ65 iNOSox protein. Dynamic Light Scattering (DLS) studies of cofactor-incubated and cofactor-free Δ65 iNOSox protein also showed two distinct populations of two different diameter ranges. Cofactor tetrahydrobiopterin (H₄B) shifted one population, with higher diameter, to the lower diameter ranges indicating conformational changes. The additional role played by the cofactor is to elevate the heme retaining capacity even in presence of denaturing stress. Together, these findings confirm that the H₄B is essential in modulating the iNOS heme environment and the protein environment in the dimeric iNOS oxygenase domain. (Mol Cell Boichem xxx: 1–10, 2005) Supported by Calcutta University Research Grants.     

High temperature enhances cytotoxicity of mercury (HgCl2) on Hela S3 cells

The combined effect of mercury (HgCl₂) and high temperature on the growth and synthesis of nucleic acid and protein, and on the cell cycle of HeLa S₃ cells was investigated. The subsequent growth of the cells was dose-dependently inhibited by mercury at 37.2° and 41.2°C. The inhibitory effect of mercury on subsequent growth was enhanced at the higher temperature. IC₅₀ values for DNA and RNA synthesis but not protein synthesis, at 41.2°C, were significantly lower than those at 37.2°C (P<0.05,P<0.01, respectively). Flow cytometric analysis using synchronous cells indicated the possibility of blocking of cell cycle progression in the early part of S phase by the combined treatment. These results suggest that the cytotoxicity of mercury to cell growth was enhanced at the higher temperature and that this enhancement is related to the increased inhibitory effect of mercury on DNA and RNA synthesis and on the cell cycle at high temperatures.     

Purification and partial characterization of an extracellular alginate lyase from <Emphasis Type="Italic">Aspergillus oryzae</Emphasis> isolated from brown seaweed

The extracellular enzyme alginate lyase produced from marine fungus Aspergillus oryzae isolated from brown alga Dictyota dichotoma was purified, partially characterized, and evaluated for its sodium alginate depolymerization abilities. The enzyme characterization studies have revealed that alginate lyase consisted of two polypeptides with about 45 and 50 kDa each on 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis and showed 140-fold higher activity than crude enzyme under optimized pH (6.5) and temperature (35°C) conditions. Zn²⁺, Mn²⁺, Cu²⁺, Mg²⁺, Co²⁺ and NaCl were found to enhance the enzyme activity while (Ca²⁺, Cd²⁺, Fe²⁺, Hg²⁺, Sr²⁺, Ni²⁺), glutathione, and metal chelators (ethylenediaminetetraacetic acid and ethylene glycol tetraacetic acid) suppressed the activity. Fourier transform infrared and thin-layer chromatography analysis of depolymerized sodium alginate indicated the enzyme specificity for cleaving at the β-1,4 glycosidic bond between polyM and polyG blocks of sodium alginate and therefore resulted in estimation of relatively higher polyM content than polyG. Comparison of chemical shifts in ¹³C nuclear magnetic resonance spectra of both polyM and polyG from that of sodium alginate also showed further evidence for enzymatic depolymerization of sodium alginate.     

Enhancement of plasmid stability and enzymatic expression by immobilising recombinant Saccharomyces cerevisiae

Immobilisation of cells in a calcium alginate gel improved plasmid stability (up to 50%) and enzymatic expression (up to 57%) of a recombinant Saccharomyces cerevisiaeover-expressing the homologous gene EXG1. The rate of segregational loss in the free cells was 14-fold higher than that of the immobilised cells. Recombinant protein synthesis requires reduced cofactors, which affect the redox balance of the cell.     

Relations between DNA, RNA and Protein Synthesis, and the Cellular Basis of the Growth Response in Gibberellic acid-Treated Pea Internodes

1. A study was made of the influence of gibberellic acid (GA₂)on nucleic acid, protein, and cell-wall synthesis in pea internodesin vivo. 2. GA₃-treated fifth internodes finally contained more thantwice as much total RNA and protein as comparable untreatedones, and the contents of RNA and protein were closely relatedto the length of internode cortical cells. 3. Cell elongation, RNA, protein, and cell-wall synthesis werestimulated 24–48 h before there was any demonstrable GA₃effect on DNA synthesis and cell division. 4. Treated fifth internodes finally contained twice as manycortical cells as control internodes, a response that was matchedby a proportionate increase in the amount of DNA. 5. Internodes treated with actinomycin D or cycloheximide failedto elongate in response to GA₃ treatment, indicating that bothRNA and protein synthesis are essential for gibberellin-stimulatedcell elongation to occur in this tissue. 6. 5-fluorodeoxyuridine at concentrations which completely blockcell division did not prevent cells from elongating in the presenceof GA₃. 7. With the possible exception of pectic substances there wasno change in the relative proportions of each of the major cell-wallconstituents in treated, as compared to control internodes.