Seeing is believing: Recent trends in the measurement of Ca2+ in subcellular domains and intracellular organelles

The role of Ca2+ in the regulation of the cell cycle has been investigated mostly in studies assessing global cytosolic free Ca2+. Recent studies, however, have used unique techniques to assess Ca2+ in subcellular organelles, such as mitochondria, and in discrete regions of the cytoplasm. These studies have used advanced fluorescence digital imaging techniques and Ca2+-sensitive fluorescence probes, and/or targeting of Ca2+-sensitive proteins to intracellular organelles. The present review describes the results of some of these studies and the techniques used. The novel techniques used to measure Ca2+ in microdomains and intracellular organelles are likely to be of great use in future investigations assessing Ca2+ homeostasis during the cell cycle.

Limitations of the widely used GAM42a and BET42a probes targeting bacteria in the Gammaproteobacteria radiation

The 23S rRNA-targeted probes GAM42a and BET42a provided equivocal results with the uncultured gammaproteobacterium 'Candidatus Competibacter phosphatis' where some cells bound GAM42a and other cells bound BET42a in fluorescence in situ hybridization (FISH) experiments. Probes GAM42a and BET42a span positions 1027-1043 in the 23S rRNAand differ from each other by one nucleotide at position 1033. Clone libraries were prepared from PCR products spanning the 16S rRNA genes, intergenic spacer region and 23S rRNA genes from two mixed cultures enriched in 'Candidatus C. phosphatis'. With individual clone inserts, the 16S rDNA portion was used to confirm the source organism as 'Candidatus C. phosphatis' and the 23S rDNA portion was used to determine the sequence of the GAM42a/BET42a probe target region. Of the 19 clones sequenced, 8 had the GAM42a probe target (T at position 1033) and 11 had G at position 1033, the only mismatch with GAM42a. However, none of the clones had the BET42a probe target (A at 1033). Non-canonical base-pairing between the 23S rRNA of 'Candidatus C. phosphatis' with G at position 1033 and GAM42a (G-A) or BET42a (G-T) is likely to explain the probing anomalies. A probe (GAM42_C1033) was optimized for use in FISH, targeting cells with G at position 1033, and was found to highlight not only some 'Candidatus C. phosphatis' cells, but also other bacteria. This demonstrates that there are bacteria in addition to 'Candidatus C. phosphatis' with the GAM42_C1033 probe target and not the BET42a or GAM42a probe target.

Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community

A denitrifying microbial consortium was enriched in an anoxically operated, methanol-fed sequencing batch reactor (SBR) fed with a mineral salts medium containing methanol as the sole carbon source and nitrate as the electron acceptor. The SBR was inoculated with sludge from a biological nutrient removal activated sludge plant exhibiting good denitrification. The SBR denitrification rate improved from less than 0.02 mg of NO3-.N mg of mixed-liquor volatile suspended solids (MLVSS)(-1) h(-1) to a steady-state value of 0.06 mg of NO3-.N mg of MLVSS-1 h(-1) over a 7-month operational period. At this time, the enriched microbial community was subjected to stable-isotope probing (SIP) with [C-13] methanol to biomark the DNA of the denitrifiers. The extracted [C-13]DNA and [C-12]DNA from the SIP experiment were separately subjected to full-cycle rRNA analysis. The dominant 16S rRNA gene phylotype (group A clones) in the [C-13]DNA clone library was closely related to those of the obligate methylotrophs Methylobacillus and Methylophilus in the order Methylophilales of the Betaproteobacteria (96 to 97% sequence identities), while the most abundant clone groups in the [C-12]DNA clone library mostly belonged to the family Saprospiraceae in the Bacteroidetes phylum. Oligonucleotide probes for use in fluorescence in situ hybridization (FISH) were designed to specifically target the group A clones and Methylophilales (probes DEN67 and MET1216, respectively) and the Saprospiraceae clones (probe SAP553). Application of these probes to the SBR biomass over the enrichment period demonstrated a strong correlation between the level of SBR denitrification and relative abundance of DEN67-targeted bacteria in the SBR community. By contrast, there was no correlation between the denitrification rate and the relative abundances of the well-known denitrifying genera Hyphomicrobium and Paracoccus or the Saprospiraceae clones visualized by FISH in the SBR biomass. FISH combined with microautoradiography independently confirmed that the DEN67-targeted cells were the dominant bacterial group capable of anoxic [C-14] methanol uptake in the enriched biomass. The well-known denitrification lag period in the methanol-fed SBR was shown to coincide with a lag phase in growth of the DEN67-targeted denitrifying population. We conclude that Methylophilales bacteria are the dominant denitrifiers in our SBR system and likely are important denitrifiers in full-scale methanol-fed denitrifying sludges.

Design, development, and use of molecular primers and probes for the detection of Gluconacetobacter species in the pink sugarcane mealybug

Molecular tools for the species-specific detection of Gluconacetobacter sacchari, Gluconacetobacter diazotrophicus, and Gluconacetobacter liquefaciens from the pink sugarcane mealybug (PSMB) Saccharicoccus sacchari Cockerell (Homiptera: Pseudococcidae) were developed and used in polymerase chain reactions (PCR) and in fluorescence in situ hybridizations (FISH) to better understand the microbial diversity and the numerical significance of the acetic acid bacteria in the PSMB microenvironment. The presence of these species in the PSMB occurred over a wide range of sites, but not in all sites in sugarcane-growing areas of Queensland, Australia, and was variable over time. Molecular probes for use in FISH were also designed for the three acetic acid bacterial species, and shown to be specific only for the target species. Use of these probes in FISH of squashed whole mealybugs indicated that these acetic acid bacteria species represent only a small proportion of the microbial population of the PSMB. Despite the detection of Glac. sacchari, Glac. diazotrophicus, and Glac. liquefaciens by PCR from different mealybugs isolated at various times and from various sugarcane-growing areas in Queensland, Australia, these bacteria do not appear to be significant commensals in the PSMB environment.

Discrepancies in the widely applied GAM42a fluorescence in situ hybridisation probe for Gammaproteobacteria

A bacterial culture collection of 104 strains was obtained from an activated sludge wastewater treatment plant to pursue studies into microbial flocculation. Characterisation of the culture collection using a polyphasic approach indicated seven isolates, phylogenetically affiliated with the deep-branching Xanthomonas group of the class Gammaproteobacteria, were unable to hybridise the GAM42a fluorescence in situ hybridisation (FISH) probe for Gammaproteobacteria. The sequence of the GAM42a probe target region in the 23S rRNA gene of these isolates was determined to have mismatches to GAM42a. Probes perfectly targeting the mismatches (GAM42a_TI038_G1031, and GAM42a_T1038 and GAM42a_A1041_A1040) were synthesised, and used in conjunction with GAM42a in FISH to,study the Gammaproteobacteria community structure in one full-scale activated sludge plant. Several bacteria in the activated sludge biomass bound the modified probes demonstrating their presence and the fact that these Gammaproteobacteria have been overlooked in community structure analyses of activated sludge. (C) 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.

Fluorescence in situ hybridization and spectral imaging of coral-associated bacterial communities

Microbial communities play important roles in the functioning of coral reef communities. However, extensive autofluorescence of coral tissues and endosymbionts limits the application of standard fluorescence in situ hybridization (FISH) techniques for the identification of the coral-associated bacterial communities. This study overcomes these limitations by combining FISH and spectral imaging.

Sequence variation can affect the performance of minor groove binder TaqMan probes in viral diagnostic assays

A minor groove binder (MGB) TaqMan real-time PCR assay was developed for the detection of respiratory syncytial virus (RSV) in clinical specimens. Upon evaluation of the assay, notable differences were observed in the overall fluorescent response obtained from RSV positive specimens, with some linear amplification curves deviating only slightly from baseline fluorescence. Sequencing of the probes targets in these RSV strains revealed single base mismatches with the MGB TaqMan probe. overall, these results highlight the usefulness of MGB TaqMan probes for the detection of mismatches, but suggest that MGB Taqman probes have limitations for routine screening for uncharacterised viral strains. (C) 2005 Elsevier B.V. All rights reserved.

Anomalous resonance fluorescence and dressed-state inversion by squeezed light in a Fabry-Perot microcavity

It has been suggested that phased atomic decay in a squeezed vacuum could be detected in the fluorescence spectrum emitted from a driven two-level atom in a cavity. Recently, the existence of other very distinctive features in the fluorescence spectra arising from the nonclassical features of the squeezed vacuum has been reported. In this paper, we investigate the possibility of experimental observation of these spectra. The main obstacle to the experimentalist is ensuring an effective squeezed-vacuum-atom coupling. To overcome this problem we propose the use of a Fabry-Perot microcavity. The analysis involves a consideration of the three-dimensional nature of the electromagnetic held, and the possibility of a mismatch between the squeezed and cavity modes. The problem of squeezing bandwidths is also addressed. We show that under experimentally realistic circumstances many of the spectral anomalies predicted in free space also occur in this environment. In addition, we report large population inversions in the dressed states of the two-level atom. [S1050-2947(98)02301-4].

Quantum trajectory simulations of the fluorescence intensity from a two-level atom driven by a multichromatic field

The quantum trajectories method is illustrated for the resonance fluorescence of a two-level atom driven by a multichromatic field. We discuss the method for the time evolution of the fluorescence intensity in the presence of bichromatic and trichromatic driving fields. We consider the special case wherein one multichromatic field component is strong and resonant with the atomic transition whereas the other components are much weaker and arbitrarily detuned from the atomic resonance. We find that the phase-dependent modulations of the Rabi oscillations, recently observed experimentally [Q. Wu, D. J. Gauthier, and T. W. Mossberg, Phys. Rev. A 49, R1519 (1994)] for the special case when the weaker component of a bichromatic driving field is detuned from the atomic resonance by the strong-field Rabi frequency, appear also for detunings close to the subharmonics of the Rabi frequency. Furthermore, we show that for the atom initially prepared in one of the dressed states of the strong field component the modulations are not sensitive to the phase. We extend the calculations to the case of a trichromatic driving field and find that apart from the modulations of the amplitude there is a modulation of the frequency of the Rabi oscillations. Moreover, the time evolution of the fluorescence intensity depends on the phase regardless of the initial conditions and a phase-dependent suppression of the Rabi oscillations can be observed when the sideband fields are tuned to the subharmonics of the strong-field Rabi frequency. [S1050-2947(98)03501-X].

Anomalous fluorescence spectra in an extremely weak, broadband squeezed vacuum under monochromatic and bichromatic excitation

We show that a two-level atom interacting with an extremely weak squeezed vacuum can display resonance fluorescence spectra that are qualitatively different to those that can be obtained using fields with a classical analogue. We consider first the free space situation with monochromatic excitation, and then discuss a bichromatically driven two-level atom in a cavity as a practical scenario for experimentally detecting the anomalous features predicted. We show that in the bad cavity limit, the anomalous spectral features appear for a weak squeezed vacuum and large frequency differences of the bichromatic field, conditions which are easily accessible in laboratories. The advantage of bichromatic, as opposed to monochromatic, excitation is that there is no coherent scattering at line centre which could obscure the observations. A scaling law is derived, N similar to Omega(4) which relates the squeezed photon number to the Rabi frequency at which the anomalous features appear. (C) 1998 Elsevier Science B.V.

Changes in three-dimensional architecture of microfilaments in cultured vascular smooth muscle cells during phenotypic modulation

To investigate changes in the three-dimensional microfilament architecture of vascular smooth muscle cells (SMC) during the process of phenotypic modulation, rabbit aortic SMCs cultured under different conditions and at different time points were either labelled with fluorescein-conjugated probes to cytoskeletal and contractile proteins for observation by confocal laser scanning microscopy, or extracted with Triton X-100 for scanning electron microscopy. Densely seeded SMCs in primary culture, which maintain a contractile phenotype, display prominent linear myofilament bundles (stress fibres) that are present throughout the cytoplasm with alpha-actin filaments predominant in the central part and beta-actin filaments in the periphery of the cell. Intermediate filaments form a meshed network interconnecting the stress fibres and linking directly to the nucleus. Moderately and sparsely seeded SMCs, which modulate toward the synthetic phenotype during the first 5 days of culture, undergo a gradual redistribution of intermediate filaments from the perinuclear region toward the peripheral cytoplasm and a partial disassembly of stress fibres in the central part of the upper cortex of the cytoplasm, with an obvious decrease in alpha-actin and myosin staining. These changes are reversed in moderately seeded SMCs by day 8 of culture when they have reached confluence. The results reveal two changes in microfilament architecture in SMCs as they undergo a change in phenotype: the redistribution of intermediate filaments probably due to an increase in synthetic organelles in the perinuclear area, and the partial disassembly of stress fibres which may reflect a degradation of contractile components.

Shift of the subharmonic resonances and suppression of fluorescence in a two-level atom driven by a bichromatic field

We study the behavior of a two-level atom that is driven by a bichromatic field consisting of a strong resonant component and a weaker tunable component. In addition to the splitting of the energy levels (the multiphoton AC Stark effect), we find that the weaker component also shifts the subharmonic resonances, an effect we attribute to a dynamic Stark shift. When the weaker component is tuned to a shifted resonance, no fluorescence occurs at either the frequency of the strong component or the three-photon mixing frequency. Results are obtained with numerical techniques and explained in terms of the dressed-atom model of the system. (C) 1998 Optical Society of America [S0740-3224(98)01508-2] OCIS codes: 270.4180, 270.6620, 270.0270.

Resonance fluorescence spectrum in a weak squeezed field with an arbitrary bandwidth

We analyze the linewidth narrowing in the fluorescence spectrum of a two-level atom driven by a squeezed vacuum field of a finite bandwidth. It is found that the fluorescence spectrum in a low-intensity squeezed field can exhibit a (omega - omega(0))(-6) frequency dependence in the wings. We show that this fast fall-off behavior is intimately related to the properties of a narrow-bandwidth squeezed field and does not extend into the region of broadband excitation. We apply the Linear response model and find that the narrowing results from a convolution of the atom response with the spectrum of the incident field. On the experimental side, we emphasize that the linewidth narrowing is not sensitive to the solid angle of the squeezed modes coupled to the atom. We also compare the fluorescence spectrum with the quadrature-noise spectrum and find that the fluorescence spectrum for an off-resonance excitation does not reveal the noise spectrum. We show that this difference arises from the competing three-photon scattering processes. [S1050-2947(98)04308-X].