Mass-spectrometry based minisequencing method for the rapid detection of drug resistance in Mycobacterium tuberculosis

A MALDI TOF MS based minisequencing method has been developed and applied for the analysis of rifampin (RIF)- and isoniazid (INH)-resistant M. tuberculosis strains. Eight genetic markers of RIF resistance-nucleotide polymorphisms located in RRDR of rpoB gene, and three of INH resistance including codon 315 of katG gene and − 8 and − 15 positions of the promoter region of fabG1-inhA operon were worked out. Based on the analysis of 100 M. tuberculosis strains collected from the Moscow region in 1997–2005 we deduced that 91% of RIF-resistant and 94% of INH-resistant strains can be identified using the technique suggested. The approach is rapid, reliable and allows to reveal the drug resistance of M. tuberculosis strains within 12 h after sample isolation.     

The increase in mitochondrial DNA copy number in the tissues of gamma-irradiated mice

Changes in the number of mitochondrial DNA (mtDNA) copies in the brain and spleen tissues of gamma-irradiated (3 Gy) mice were studied by comparative analysis of the long-extension PCR products of mtDNA (15.9 kb) and a fragment of the cluster nuclear beta-globin gene (8.7 kb) amplified simultaneously in one and the same test-tube within total DNA. The analysis showed that, compared to the nuclear beta-globin gene, an increase in mtDNA copy number (polyploidization) took place in the brain and spleen cells of mice exposed to gamma-radiation. This data led to the suggestion that the major mechanism for maintenance of the mitochondrial genome, which is constantly damaged by endogenous ROS and easily affected by ionizing radiation or other exogenous factors, is the induction of synthesis of new mtDNA copies on intact or little affected mtDNA templates because the repair systems in the mitochondria function at a low level of efficiency.     

Temperature-dependent variations and intraspecies diversity of the structure of the lipopolysaccharide of Yersinia pestis

Yersinia pestis spread throughout the Americas in the early 20th century, and it occurs predominantly as a single clone within this part of the world. However, within Eurasia and parts of Africa there is significant diversity among Y. pestis strains, which can be classified into different biovars (bv.) and/or subspecies (ssp.), with bv. orientalis/ssp. pestis most closely related to the American clone. To determine one aspect of the relatedness of these different Y. pestis isolates, the structure of the lipopolysaccharide (LPS) of four wild-type and one LPS-mutant Eurasian/African strains of Y. pestis was determined, evaluating effects of growth at mammalian (37 degrees C) or flea (25 degrees C) temperatures on the structure and composition of the core oligosaccharide and lipid A. In the wild-type clones of ssp. pestis, a single major core glycoform was synthesized at 37 degrees C whereas multiple core oligosaccharide glycoforms were produced at 25 degrees C. Structural differences occurred primarily in the terminal monosaccharides. Only tetraacyl lipid A was made at 37 degrees C, whereas at 25 degrees C additional pentaacyl and hexaacyl lipid A structures were produced. 4-Amino-4-deoxyarabinose levels in lipid A increased with lower growth temperatures or when bacteria were cultured in the presence of polymyxin B. In Y. pestis ssp. caucasica, the LPS core lacked D-glycero-D-manno-heptose and the content of 4-amino-4-deoxyarabinose showed no dependence on growth temperature, whereas the degree of acylation of the lipid A and the structure of the oligosaccharide core were temperature dependent. A spontaneous deep-rough LPS mutant strain possessed only a disaccharide core and a slightly variant lipid A. The diversity and differences in the structure of the Y. pestis LPS suggest important contributions of these variations to the pathogenesis of this organism, potentially related to innate and acquired immune recognition of Y. pestis and epidemiologic means to detect, classify, control and respond to Y. pestis infections.     

The core structure of the lipopolysaccharide from the causative agent of plague, Yersinia pestis

The rough-type lipopolysaccharide (LPS) of the plague pathogen, Yersinia pestis, was studied after mild-acid and strong-alkaline degradations by chemical analyses, NMR spectroscopy and electrospray-ionization mass spectrometry, and the following structure of the core region was determined:where L-alpha-D-Hep stands for L-glycero-alpha-D-manno-heptose, Sug1 for either 3-deoxy-alpha-D-manno-oct-2-ulosonic acid (alpha-Kdo) or D-glycero-alpha-D-talo-oct-2-ulosonic acid (alpha-Ko), and Sug2 for either beta-D-galactose or D-glycero-alpha-D-manno-heptose. A minority of the LPS molecules lacks GlcNAc.     

Relaxation of variable chlorophyll fluorescence after illumination of dark-adapted barley leaves as influenced by the redox states of electron carriers

Kinetics of the dark relaxation of variable chlorophyll fluorescence, Fv, were studied after brief illumination of dark-adapted barley leaves in order to understand the rapid reversibility of pulse-induced fluorescence increases, which is observed even when fast linear electron transport to an external electron acceptor is not possible. Four kinetically distinct components were observed which reveal complexity in the oxidation of the reduced primary quinone acceptor of Photosystem II, Q_A ⁻: the slowest component accounted for 4–5% of maximal Fv and had a life-time of several seconds. It is suggested to represent a minor population of inactive Photosystem II centers. The other three components displayed first-order kinetics with half-time of 6–8 ms (`fast' component), 60–80 ms (`middle' component) and 650–680 ms (`slow' component). The fast component dominated Fv when methyl viologen or far-red light accelerated oxidation of plastohydroquinone. It shows rapid oxidation of Q_A ⁻ during electron flow to plastoquinone commensurate with maximum linear electron flow through the electron transport chain. The other two components were observed under conditions of restricted electron flow and excessive reduction of electron carriers. Unexpectedly, the slow component, which is interpreted to reflect the recombination between Q_A ⁻ and an intermediate on the oxidizing side of Photosystem II, saturated already at low irradiances of actinic light when plastoquinone was not yet strongly reduced suggesting that dark-adaptation of leaves results not only in the loss of activity of light-regulated enzymes of the carbon cycle but affects also electron flow from Q_A ⁻ to plastoquinone. KCN poisoning or high temperature treatment of leaves produced a nonexponential pattern of slow Fv relaxation. This effect was largely (heat treatment) or even completely (KCN) abolished by far-red light. This revised version was published online in August 2006 with corrections to the Cover Date.     

Photosynthetic apparatus in primary leaves of barley seedlings grown under blue or red light of very low photon flux densities

Chlorophyll (Chl) a and Chl b contents, rate of CO₂ gas exchange, quenching coefficients of chlorophyll fluorescence, and endogenous phytohormones have been studied in primary leaves of barley seedlings cultivated under blue (BL) or red (RL) light. Photon flux densities (PFD) were between 0.3 and 12 mol m^-2 s^-1. Plants grown at PFD of 0.3 mol m^-2 s^-1 demonstrated in BL tenfold and in RL threefold decreased Chl content compared to plants grown at 12 mol m^-2 s^-1. Chl a/b ratio increased from 2.3–2.5 to 4.4–4.5 in BL, not in RL, following the decrease in PFD at plant cultivation from 12 to 0.3 mol m^-2 s^-1. Plants cultivated at weak BL demonstrated severalfold decreased rate of photosynthetic CO₂ uptake, whereas decrease in PFD of RL from 12 to 0.3 mol m^-2 s^-1 caused only 20% de cline in the rate of photosynthesis. Decrease in PFD during a plant cultivation reduced the maximum quantum yield of photosynthesis in BL, not in RL leaves. Light response curves of non-photochemical and photochemical quenching of chlorophyll fluorescence calculated on the basis of absorbed quanta were not affected by PFD of RL during plant cultivation. On the contrary, both non-photochemical quenching and accumulation of Q_A ^-, reduced primary acceptor of Photosystem II, occurred at lower amounts of absorbed quanta in leaves of BL plants grown at 0.3 than at 12 mol m^-2 s^-1. Two photoregulatory reactions were suggested to exert the light control of the development of photosynthetic apparatus in the range of low PFDs. The photoregulatory reaction saturating by very low PFDs of RL was supposed to be mediated by phytochrome. Phytochrome was proposed to enhance (as related to other pigment-protein complexes of thylakoids) the accu mulation of chlorophyll- b-binding light-harvesting complex of Photosystem II (LHC II). It acts independently of the pigment mediating the second photoregulatory reaction, as evidenced by the results of experiments with plant growth under mixed blue plus red light. The contents of cytokinins and indole-3-acetic acid in a leaf were not significantly affected by either light quality and PFD thus indicating those phytohormones not to be involved into photoregulatory processes.     

Recognition of specific and nonspecific DNA by human lactoferrin

The general principles of recognition of nucleic acids by proteins are among the most exciting problems of molecular biology. Human lactoferrin (LF) is a remarkable protein possessing many independent biological functions, including interaction with DNA. In human milk, LF is a major DNase featuring two DNA‐binding sites with different affinities for DNA. The mechanism of DNA recognition by LF was studied here for the first time. Electrophoretic mobility shift assay and fluorescence measurements were used to probe for interactions of the high‐affinity DNA‐binding site of LF with a series of model‐specific and nonspecific DNA ligands, and the structural determinants of DNA recognition by LF were characterized quantitatively. The minimal ligands for this binding site were orthophosphate (K_i = 5 mM), deoxyribose 5'‐phosphate (K_i = 3 mM), and different dNMPs (K_i = 0.56–1.6 mM). LF interacted additionally with 9–12 nucleotides or nucleotide pairs of single‐ and double‐stranded ribo‐ and deoxyribooligonucleotides of different lengths and sequences, mainly through weak additive contacts with internucleoside phosphate groups. Such nonspecific interactions of LF with noncognate single‐ and double‐stranded d(pN)₁₀ provided ~6 to ~7.5 orders of magnitude of the enzyme affinity for any DNA. This corresponds to the Gibbs free energy of binding (ΔG⁰) of ?8.5 to ?10.0 kcal/mol. Formation of specific contacts between the LF and its cognate DNA results in an increase of the DNA affinity for the enzyme by approximately 1 order of magnitude (K_d = 10 nM; ΔG⁰ ≈ ?11.1 kcal/mol). A general function for the LF affinity for nonspecific d(pN)_n of different sequences and lengths was obtained, giving the K_d values comparable with the experimentally measured ones. A thermodynamic model was constructed to describe the interactions of LF with DNA. Copyright © 2013 John Wiley & Sons, Ltd.     

A new precursor for the immobilization of enzymes inside sol-gel-derived hybrid silica nanocomposites containing polysaccharides

Tetrakis(2-hydroxyethyl) orthosilicate (THEOS) introduced by Hoffmann et al. (J. Phys. Chem. B., 106 (2002) 1528) was first used to prepare hybrid nanocomposites containing various polysaccharides and immobilize enzymes in these materials. Two different types of O-glycoside hydrolyses (EC3.2.1), 1-->3-beta-D-glucanase LIV from marine mollusk Spisula sacchalinensis and alpha-D-galactosidase from marine bacterium Pseudoalteromonas sp. KMM 701, were taken for the immobilization. To reveal whether the polysaccharide inside the hybrid material influences the enzyme entrapment and functioning, negatively charged xanthan, cationic derivative of hydroxyethylcellulose and uncharged locust bean gum were examined. The mechanical properties of these nanocomposites were characterized by a dynamic rheology and their structure by a scanning electron microscopy. It was found that 1-->3-beta-D-glucanase was usually immobilized without the loss of its activity, while the alpha-D-galactosidase activity in the immobilized state depended on the polysaccharide type of material. An important point is that the amount of immobilized enzymes was small, comparable to their content in the living cells. It was shown by the scanning electron microscopy that the hybrid nanocomposites are sufficiently porous that allows the enzymatic substrates and products to diffuse from an external aqueous solution to the enzymes, whereas protein molecules were immobilized firmly and not easily washed out of the silica matrix. A sharp increase of the enzyme lifetime (more than a hundred times) was observed after the immobilization. As established, the efficient entrapment of enzymes is caused by few advantages of new precursor over the currently used TEOS and TMOS: (i) organic solvents and catalysts are not needed owing to the complete solubility of THEOS in water and the catalytic effect of polysaccharides on the sol-gel processes; (ii) the entrapment of enzymes can be performed at any pH which is suitable for their structural integrity and functionality; (iii) a gel can be prepared at reduced concentrations of THEOS (1-2%) in the initial solution that excludes a notable heat release in the course of its hydrolysis.     

Accumulation of ferrous iron in Chlamydomonas reinhardtii. Influence of CO2 and anaerobic induction of the reversible hydrogenase

The green alga, Chlamydomonas reinhardtii, can photoproduce molecular H(2) via ferredoxin and the reversible [Fe]hydrogenase enzyme under anaerobic conditions. Recently, a novel approach for sustained H(2) gas photoproduction was discovered in cell cultures subjected to S-deprived conditions (A. Melis, L. Zhang, M. Forestier, M.L. Ghirardi, M. Seibert [2000] Plant Physiol 122: 127-135). The close relationship between S and Fe in the H(2)-production process is of interest because Fe-S clusters are constituents of both ferredoxin and hydrogenase. In this study, we used M?ssbauer spectroscopy to examine both the uptake of Fe by the alga at different CO(2) concentrations during growth and the influence of anaerobiosis on the accumulation of Fe. Algal cells grown in media with (57)Fe(III) at elevated (3%, v/v) CO(2) concentration exhibit elevated levels of Fe and have two comparable pools of the ion: (a) Fe(III) with M?ssbauer parameters of quadrupole splitting = 0.65 mm s(-1) and isomeric shift = 0.46 mm s(-1) and (b) Fe(II) with quadrupole splitting = 3.1 mm s(-1) and isomeric shift = 1.36 mm s(-1). Disruption of the cells and use of the specific Fe chelator, bathophenanthroline, have demonstrated that the Fe(II) pool is located inside the cell. The amount of Fe(III) in the cells increases with the age of the algal culture, whereas the amount of Fe(II) remains constant on a chlorophyll basis. Growing the algae under atmospheric CO(2) (limiting) conditions, compared with 3% (v/v) CO(2), resulted in a decrease in the intracellular Fe(II) content by a factor of 3. Incubating C. reinhardtii cells, grown at atmospheric CO(2) for 3 h in the dark under anaerobic conditions, not only induced hydrogenase activity but also increased the Fe(II) content in the cells up to the saturation level observed in cells grown aerobically at high CO(2). This result is novel and suggests a correlation between the amount of Fe(II) cations stored in the cells, the CO(2) concentration, and anaerobiosis. A comparison of Fe-uptake results with a cyanobacterium, yeast, and algae suggests that the intracellular Fe(II) pool in C. reinhardtii may reside in the cell vacuole.