Characean actin bundles as a tool for stydying actomyosin-based motility

At the inner surface of the stagnant chloroplasts of Characeae cells, bundles of actin filaments having uniform polarity are anchored. These bundles are responsible for generating the motive force of cytoplasmic streaming. It is now possible to induce movement of either beads coated with foreign myosin or organelles associated with myosin along the characean actin bundles. The Ca²⁺ sensitivities of the reconstitued movements are consistent with those of the actin-activated myosin ATPases. The use of reconstituted systems is finding wide application in the detection of various myosins in materials from which myosin is not significantly purified. Furthermore, sliding velocities and the Ca²⁺ regulation of myosins bound to organelles are now being determined. Recipient of the Botanical Society Award for Young Scientists, 1987.     

Riboprints as a tool for rapid preliminary identification of sphingomonads

Fourtythree strains of the genus Sphingomonas and close relatives were subjected to riboprint analyses generated after digestion of genomic DNA with the restriction enzyme EcoRI and hybridization with E. coli rrnB operon. The majority of strains were characterized by a complex banding pattern in the riboprints. High degrees of similarities in the riboprints were only observed among strains of the same species such as S. yanoikuyae, S. aromaticivorans, S. subarctica and S. chlorophenolica. Strains of different species including close phylogenetic relatives such as S. asaccharolytica, S. mali and S. pruni were easily distinguished by the differences in the riboprints even after visual evaluation. Thus, our data demonstrate that riboprint analysis is useful for preliminary identification of new sphingomonad isolates at the species level.     

Polymer membrane ion-selective electrodes as a convenient tool for lipases and esterases assays

We have proposed a novel assay for lipases and esterases activity determination based on potentiometry with ion-selective electrodes (ISEs). Enzyme preparations, obtained from the living cells, are complex mixtures of various proteins, short peptides, lipids, carbohydrates, and other compounds. The most commonly used quantitative methods in enzyme studies are based on spectrophotometric or spectroflourimetric protocols which has significant limitations. They are not valid for samples that are turbid or strongly colored. To overcome those drawbacks we have proposed an assay based on potentiometry with ISEs for lipases and esterases activity determination. This electrochemical methodology represents an attractive tool for enzyme analysis, because of its low detection limit, independence from sample volume and from sample turbidity. The usefulness of this assay has been proven by the determination of the activity of various raw enzymes “acetone powders” isolated from animal tissues. Moreover, activities of fractions obtained during purification of one of those raw biocatalysts were also determined that way. The reliability of determination enzyme activity with ISE assay was proven by comparison with a classical spectrophotometric method.     

Bacterial assays for recombinagens.

Two principal strategies have been used for studying recombinagenic effects of chemicals and radiation in bacteria: (1) measurement of homologous recombination involving defined alleles in a partially diploid strain, and (2) measurement of the formation and loss of genetic duplications in the bacterial chromosome. In the former category, most methods involve one allele in the bacterial chromosome and another in a plasmid, but it is also possible to detect recombination between two chromosomal alleles or between two extrachromosomal alleles. This review summarizes methods that use each of these approaches for detecting recombination and tabulates data on agents that have been found to be recombinagenic in bacteria. The assays are discussed with respect to their effectiveness in testing for recombinagens and their potential for elucidating mechanisms underlying recombinagenic effects.     

Proteomics as a tool for tapping potential of entomopathogens as microbial insecticides

Biopesticides are collective pest control harnessing the knowledge of the target pest and its natural enemies that minimize the risks of synthetic pesticides. A subset of biopesticides; bioinsecticides, are specifically used in controlling insect pests. Entomopathogens (EPMs) are micro‐organisms sought after as subject for bioinsecticide development. However, lack of understanding of EPM mechanism of toxicity and pathogenicity slowed the progress of bioinsecticide development. Proteomics is a useful tool in elucidating the interaction of entomopathogenic fungi, entomopathogenic bacteria, and entomopathogenic virus with their target host. Collectively, proteomics shed light onto insect host response to EPM infection, mechanism of action of EPM’s toxic proteins and secondary metabolites besides characterizing secreted and membrane‐bound proteins of EPM that more precisely describe relevant proteins for host recognition and mediating pathogenesis. However, proteomics requires optimized protein extraction methods to maximize the number of proteins for analysis and availability of organism's genome for a more precise protein identification.     

Bacterial and archaeal flagella as prokaryotic motility organelles

The properties and molecular organization of flagella—the bacterial and archaeal motility organelles—are reviewed. The organization of these functional motility elements of prokaryotic organisms belonging to different kingdoms is compared. A mechanism for both in vivo and in vitro assembly of bacterial flagellum filaments (BFFs) is discussed, and similarity is supposed between flagellin and actin with regard to their polymeric forms (BFF and F-actin). Our own data on intracellular fixation of the Halobacterium salinarium flagellum are presented. Comparative characteristics of intracellular fixation of bacterial and archaeal flagella are also described.Translated from Biokhimiya, Vol. 69, No. 11, 2004, pp. 1477–1488.Original Russian Text Copyright © 2004 by Metlina.     

Evaluation of droplet-based microfluidic platforms as a convenient tool for lipases and esterases assays

Abstract

The accurate estimation of kinetic parameters is of fundamental importance for biochemical studies for research and industry. In this paper, we demonstrate the application of a modular microfluidic system for execution of enzyme assays that allow determining the kinetic parameters of the enzymatic reactions such as V_max – the maximum rate of reaction and K_M – the Michaelis constant. For experiments, the fluorogenic carbonate as a probe for a rapid determination of the kinetic parameters of hydrolases, such as lipases and esterases, was used. The microfluidic system together with the method described yields the kinetic constants calculated from the concentration of enzymatic product changes via a Michaelis–Menten model using the Lambert function W(x). This modular microfluidic system was validated on three selected enzymes (hydrolases).     

Wavelet transform as a potential tool for ECG analysis and compression

The recently introduced wavelet transform is a member of the class of time-frequency representations which include the Gabor short-time Fourier transform and Wigner-Ville distribution. Such techniques are of significance because of their ability to display the spectral content of a signal as time elapses. The value of the wavelet transform as a signal analysis tool has been demonstrated by its successful application to the study of turbulence and processing of speech and music. Since, in common with these subjects, both the time and frequency content of physiological signals are often of interest (the ECG being an obvious example), the wavelet transform represents a particularly relevant means of analysis. Following a brief introduction to the wavelet transform and its implementation, this paper describes a preliminary investigation into its application to the study of both ECG and heart rate variability data. In addition, the wavelet transform can be used to perform multiresolution signal decomposition. Since this process can be considered as a sub-band coding technique, it offers the opportunity for data compression, which can be implemented using efficient pyramidal algorithms. Results of the compression and reconstruction of ECG data are given which suggest that the wavelet transform is well suited to this task.     

Cyanobacteria inoculation as a potential tool for stabilization of burned soils

The practice of “cyanobacterization” (soil inoculation with cyanobacteria) has been shown to be effective in increasing soil fertility and physical stability in natural and agricultural soils, but little is known about its utility for the recovery of burned soils. To partly fill this knowledge gap, we inoculated two cyanobacterial species, Phormidium ambiguum and Scytonema javanicum, in two burned sterilized soils having contrasting properties, and incubated them under laboratory conditions for 45 days. The development of a cyanobacterial biocrust induced by the inoculum was evident and confirmed by the significant increase in chlorophyll a content compared to control soils. Hydrophobicity, surface penetration resistance, and exopolysaccharide content of the two soils were also evaluated. Cyanobacteria inoculation significantly decreased soil hydrophobicity, as assessed by the lower repellency index 15 days after the inoculation compared to the control soils. A significant increase in penetration resistance was recorded in the inoculated samples compared to control ones after 45 days of soil incubation. The effect of cyanobacteria inoculation depended on the characteristics of the burned soil, being more marked in the soil finer in texture, richer in organic carbon and nitrogen, and with lower initial soil hydrophobicity. In conclusion, this study points to the potential of cyanobacterization for the stabilization and recovery of soils in burned areas, which is one of the major concerns in postfire management to avoid net soil loss and major hydrogeological issues.     

Symptoms of somatization as a rapid screening tool for mitochondrial dysfunction in depression

Recent progress in neuroscience revealed diverse regions of the CNS which moderate autonomic and affective responses. The ventro-medial prefrontal cortex (vmPFC) plays a key role in these regulations. There is evidence that vmPFC activity is associated with cardiovascular changes during a motor task that are mediated by parasympathetic activity. Moreover, vmPFC activity makes important contributions to regulations of affective and stressful situations. This review selectively summarizes literature in which vmPFC activation was studied in healthy subjects as well as in patients with affective disorders. The reviewed literature suggests that vmPFC activity plays a pivotal role in biopsychosocial processes of disease. Activity in the vmPFC might link affective disorders, stressful environmental conditions, and immune function.     

Bacterial endotoxins as potential antitumor agents

Natural and modified preparations of lipopolysaccharides and lipopolysaccharide-protein complexes isolated from the S- and R-form of Shigella dysenteriae serovar 1 were found to markedly inhibit the initial growth of mouse solid tumors derived from Németh-Kellner lymphoma, Gardner 6C3HED lymphoma, an ill-defined syngeneic lymphoma of DBA mice (Skalsky lymphoma) and LP-2 plasmacytoma. The biopreparations were given intraperitoneally, most frequently at a dose range from 50 to 200 micrograms per mouse; significant inhibitory effects on tumor growth were evidenced even in mice bearing tumors weighing 113 to 507 mg.     

Bacterial toxicity of cyclodextrins: Luminuous Escherichia coli as a model

The effect of various concentrations of natural and chemically modified cyclodextrins on the luminescence of an Escherichia coli suspension was investigated. All cyclodextrins were found to reduce, albeit to a varying degree, the luminescence level of the bacterial cells, thus suggesting a direct interaction between the cyclodextrins and cells. The inhibitory concentrations IC₂₀ and IC₅₀ of the various cyclodextrins were determined and taken to represent their toxicity effects upon the bacterial cells. Among the natural cyclodextrins, - and -CD interfered minimally with the bacterial luminescence and consequently were essentially non-toxic. The following descending order of toxicity was observed: -CD -CD > -CD. Among the chemically modified cyclodextrins, Dimeb was clearly toxic while Trimeb and the hydroxylated derivatives (hydroxypropyl-ga-CD, HPACD;--CD, HPBCD;--CD, HPGCD) were essentially non-toxic. The following descending order of toxicity was observed: Dimeb HPBCD > Trimeb > HPACD > HPGCD.     

Selective felling as a potential tool for maintaining biodiversity in managed forests

In Sweden one forestry method, the clear-cutting method, has been used all over the country despite differences in climate, topography etc. At present there is a growing interest in using alternative methods such as selective felling, which to a larger extent mimic natural disturbances. In this study we compare virgin forests with stands which have been cut with old selective felling (dimension felling), new selective felling (single tree selection felling), and clear-cutting with respect to frequency of characters important to biodiversity (mainly dead wood). The frequency of different types of dead wood decreases with increasing intensity of the cutting method in the following order: old selective felling, new selective felling, and clear-cutting. New selective felling had higher amounts and quality of dead wood compared to clear-cutting. New selective felling also showed less differences compared to virgin forests than clear-cutting. Dead wood in new selective felling compared to clear-cutting may offer substrate for different types of faunas because of the environment surrounding the dead wood. Even if the new selective felling method seems to provide higher amounts of dead wood compared to the clear-cutting method, further studies of organisms utilising the dead wood are needed. New selective felling does not seem to solve the problem of decreasing availability of dead wood in managed forests and there is still a need to preserve unmanaged forest patches in a landscape perspective in order to offer habitats with a high amount of dead wood.     

Quantum dots: a new tool for anti-malarial drug assays

Background

Malaria infects over 300 million people every year and one of the major obstacles for the eradication of the disease is parasite's resistance to current chemotherapy, thus new drugs are urgently needed. Quantum dot (QD) is a fluorescent nanocrystal that has been in the spotlight as a robust tool for visualization of live cell processes in real time. Here, a simple and efficient method using QD to directly label Plasmodium falciparum-infected erythrocytes (iRBCs) was searched in order to use the QD as a probe in an anti-malarial drug-screening assay.

Methods

A range of QDs with different chemical coatings were tested for their ability to specifically bind iRBCs by immunofluorescence assay (IFA). One QD was selected and used to detect parasite growth and drug sensitivity by flow cytometry.

Results

PEGylated-cationic QD (PCQD) was found to specifically label infected erythrocytes preferentially with late stage parasites. The detection of QD-labelled infected erythrocytes by flow cytometry was sensitive enough to monitor chloroquine anti-malarial toxicity with a drug incubation period as short as 24 h (EC₅₀ = 113nM). A comparison of our assay with another widely used anti-malarial drug screening assay, the pLDH assay, showed that PCQD-based assay had 50% improved sensitivity in detecting drug efficacy within a parasite life cycle. An excellent Z-factor of 0.8 shows that the QD assay is suitable for high-throughput screening.

Conclusions

This new assay can offer a rapid and robust platform to screen novel classes of anti-malarial drugs.

     

Dimethylsulfoxide as a potential tool for analysis of compartmentation in living plant cells

Data are presented which indicate that dimethylsulfoxide (DMSO) acts selectively on the plasma membrane of cultured tobacco cells, rendering it more permeable to small molecules, while having a far smaller effect on the permeability of the vacuolar membrane. The results which support this conclusion are: (a) DMSO (5 to 10%, by volume) causes complete release of [¹⁴C]tryptophan newly synthesized from [¹⁴C]indole while causing efflux of only about 20% of the total intracellular tryptophan pool; (b) similar concentrations of DMSO do not cause substantial release from these cells of phenolic compounds or preloaded neutral red, nor of β-cyanin from fresh beet discs; (c) kinetic studies of release of tryptophan and neutral sugars and of efflux of ⁸⁶Rb⁺ show that DMSO selectively promotes rapid release of a portion of the total pool, followed by a substantially slower release of the remaining pool; (d) when tobacco cell protoplasts are incubated in the presence of 7.5% (by volume) DMSO, rapid lysis is observed concomitant with the release of intact vacuoles. These data indicate that a procedure involving a brief treatment of intact plant cells or tissues with DMSO may be used to assess the distribution of metabolites between cytoplasmic and vacuolar compartments.     

Unusual phyletic distribution of peptidases as a tool for identifying potential drug targets

Profound changes in the phosphorylation state of many proteins occur during mitosis. It is well established that many of these mitotic phosphorylations are carried out by archetypal mitotic kinases that are activated only during mitosis, shifting the equilibrium of kinases and phosphatases towards phosphorylation. However, many studies have also detailed the phosphorylation of proteins at mitosis by kinases that are constitutively active throughout the cell cycle. In most cases, it is uncertain how kinases and phosphatases that appear to be constitutively active can induce phosphorylations specifically at mitosis. In this issue of the Biochemical Journal, Escargueil and Larsen provide evidence of an interesting alternative mechanism to attain specific mitotic phosphorylation. A mitosis-specific phosphorylation site in DNA topoisomerase IIalpha, which is recognized by the MPM-2 antibody, is phosphorylated by protein kinase CK2. The authors found that phosphorylation of this site is suppressed during interphase due to competing dephosphorylation by protein phosphatase 2A. Interestingly, protein phosphatase 2A is excluded from the nucleus during early mitosis, allowing CK2 to phosphorylate topoisomerase IIalpha. It is possible that similar mechanisms are used to regulate the phosphorylation of other proteins.     

Cytochrome P450 expression profile of the PICM-19H pig liver cell line: potential application to rapid liver toxicity assays

Liver in vitro models are needed to replace animal models for rapid assessment of drug biotransformation and toxicity. The PICM-19 pig liver stem cell line may fulfill this need since these cells have activities associated with xenobiotic phase I and II metabolism lacking in other liver cell lines. The objective of this study was to characterize phase I and II metabolic functions of a PICM-19 derivative cell line, PICM-19H, compared to the tumor-derived human HepG2 C3A cell line and primary cultures of adult porcine hepatocytes. Following exposure of PICM-19H cells to either 3-methylcholanthrene, rifampicin or phenobarbital, the induced activities of cytochrome P450 (CYP450) isozymes CYP-1A, -2, and-3A were assessed. Relative to adult porcine hepatocytes, PICM-19H cells exhibited 30% and 43%, respectively, of CYP1A and 3A activities, while HepG2 C3A cells exhibited 7% and 0% of those activities. Fluorescent metabolites were extensively conjugated, i.e., 52% and 96% of CYP450-1A and-3A metabolites were released from medium samples following treatment with β-glucuronidase/arylsulfatase. Rifampicin induction of CYP450 isozyme activities was confirmed by conversion of testosterone to 6β-OH-, 2α-OH- and 2β-OH-testosterone, as determined by mass spectrometry. Susceptibility of PICM-19H cells to acetaminophen toxicity was determined; CD₅₀ was calculated to be 14.9 ± 0.9 mM. Toxicity and bioactivation of aflatoxin B1 was determined in 3-methylcholanthrene-treated cultures and untreated controls; CD₅₀ were 1.59 μM and 31 μM, respectively. These results demonstrate the potential use of PICM-19H cells in drug biotransformation and toxicity testing and further support their use in extracorporeal artificial liver device technology.