Shapes thatEscherichia coliCells Can Achieve, as a Paradigm for Other Bacteria

Quantification of cell shape, intracellular flows and transport based on DIC object detection and tracking

Computational image analysis combined with label-free imaging has helped maintain its relevance for cell biology, despite the rapid technical improvements in fluorescence microscopy with the molecular specificity of tags. Here, we discuss some computational tools developed in our lab and their application to quantify cell shape, intracellular organelle movement and bead transport in vitro, using differential interference contrast (DIC) microscopy data as inputs. The focus of these methods is image filtering to enhance image gradients, and combining them with segmentation and single particle tracking (SPT). We demonstrate the application of these methods to Escherichia coli cell length estimation and tracking of densely packed lipid granules in Caenorhabditis elegans one-celled embryos, diffusing beads in solutions of different viscosities and kinesin-driven transport on microtubules. These approaches demonstrate how improvements to low-level image analysis methods can help obtain insights through quantitative cellular and subcellular microscopy.

Quantifying Nanoparticle Layer Topography: Theoretical Modeling and Atomic Force Microscopy Investigations

A comprehensive method consisting of theoretical modeling and experimental atomic force microscopy (AFM) measurements was developed for the quantitative analysis of nanoparticle layer topography. Analytical results were derived for particles of various shapes such as cylinders (rods), disks, ellipsoids, hemispheres (caps), etc. It was shown that for all particles, their root-mean-square (rms) parameter exhibited a maximum at the coverage about 0.5, whereas the skewness was a monotonically decreasing function of the coverage. This enabled a facile determination of the particle coverage in the layer, even if the shape and size were not known. The validity of the analytical results was confirmed by computer modeling and experimental data acquired by AFM measurements for polymer nanoparticle deposition on mica and silica. The topographical analysis developed in this work can be exploited for a quantitative characterization of self-assembled layers of nano- and bioparticles, e.g., carbon nanotubes, silica and noble metal particles, DNA fragments, proteins, vesicles, viruses, and bacteria at solid surfaces. The acquired results also enabled a proper calibration, in particular the determination of the measurement precision, of various electron and scanning probe microscopies, such as AFM.

QCM-D Investigations of Anisotropic Particle Deposition Kinetics: Evidences of the Hydrodynamic Slip Mechanisms

Deposition kinetics of positively charged polymer microparticles, characterized by prolate spheroid shape, at silica and gold sensors was investigated using the quartz microbalance (QCM) technique. Reference measurements were also performed for positively charged polymer particles of spherical shape and the same mass as the spheroids. Primarily, the frequency and bandwidth shifts for various overtones were measured as a function of time. It is shown that the ratio of these signals is close to unity for all overtones. These results were converted to the dependence of the frequency shift on the particle coverage, directly determined by atomic force microscopy and theoretically interpreted in terms of the hydrodynamic model. A quantitative agreement with experiments was attained considering particle slip relative to the ambient oscillating flow. In contrast, the theoretical results pertinent to the rigid contact model proved inadequate. The particle deposition kinetics derived from the QCM method was compared with theoretical modeling performed according to the random sequential adsorption approach. This allowed to assess the feasibility of the QCM technique to furnish proper deposition kinetics for anisotropic particles. It is argued that the hydrodynamic slip effect should be considered in the interpretation of QCM kinetic results acquired for bioparticles, especially viruses.

Pleiomorphism in Mycobacterium

Morphological variants in mycobacterial cultures under different growth conditions, including aging of the culture, have been shown to include fibrous aggregates, biofilms, coccoids, and spores. Here we discuss the diversity in shape and size changes demonstrated by bacterial cells with special reference to pleiomorphism observed in Mycobacterium spp. in response to nutritional and other environmental stresses. Inherent asymmetry in cell division and compartmentalization of cell interior under different growth conditions might contribute toward the observed pleiomorphism in mycobacteria. The regulatory genes comprising the bacterial signaling pathway responsible for initiating morphogenesis are speculated upon from bioinformatic identifications of genes for known sensors, kinases, and phosphatases existing in mycobacterial genomes as well as on the basis of what is known in other bacteria.

Tomography and static-mechanical properties of adherent cells

A tomography approach is used to reconstruct 3D cell shapes and, simultaneously, the shapes/positions of the nuclei within these cells. Subjecting the cells to well-defined microconfinements of various diameters allow for relating the steady-state shapes of cells to their static-mechanical properties. The observed shapes show striking regularities between different cell types and all fit to a model that takes into account the cell membrane, cortical actin, and the nucleus.

Lipid localization in bacterial cells through curvature-mediated microphase separation

Although many proteins are known to localize in bacterial cells, for the most part our understanding of how such localization takes place is limited. Recent evidence that the phospholipid cardiolipin localizes to the poles of rod-shaped bacteria suggests that targeting of some proteins may rely on the heterogeneous distribution of membrane lipids. Membrane curvature has been proposed as a factor in the polar localization of high-intrinsic-curvature lipids, but the small size of lipids compared to the dimensions of the cell means that single molecules cannot stably localize. At the other extreme, phase separation of the membrane energetically favors a single domain of such lipids at one pole. We have proposed a physical mechanism in which osmotic pinning of the membrane to the cell wall naturally produces microphase separation, i.e., lipid domains of finite size, whose aggregate sensitivity to cell curvature can support spontaneous and stable localization to both poles. Here, we demonstrate that variations in the strength of pinning of the membrane to the cell wall can also act as a strong localization mechanism, in agreement with observations of cardiolipin relocalization from the poles to the septum during sporulation in the bacterium Bacillus subtilis. In addition, we rigorously determine the relationship between localization and the domain-size distribution including the effects of entropy, and quantify the strength of domain-domain interactions. Our model predicts a critical concentration of cardiolipin below which domains will not form and hence polar localization will not take place. This observation is consistent with recent experiments showing that in Escherichia coli cells with reduced cardiolipin concentrations, cardiolipin and the osmoregulatory protein ProP fail to localize to the poles.

Multiple consecutive lavage samplings reveal greater burden of disease and provide direct access to the nontypeable Haemophilus influenzae biofilm in experimental otitis media

The typically recovered quantity of nontypeable Haemophilus influenzae (NTHi) bacteria in an ex vivo middle ear (ME) aspirate from the chinchilla model of experimental otitis media is insufficient for direct analysis of gene expression by microarray or of lipopolysaccharide glycoforms by mass spectrometry. This prompted us to investigate a strategy of multiple consecutive lavage samplings to increase ex vivo bacterial recovery. As multiple consecutive lavage samples significantly increased the total number of bacterial CFU collected during nasopharyngeal colonization or ME infection, this led us to evaluate whether bacteria sequentially acquired from consecutive lavages were similar. Comparative observation of complete ex vivo sample series by microscopy initially revealed ME inflammatory fluid consisting solely of planktonic-phase NTHi. In contrast, subsequent lavage samplings of the same infected ear revealed the existence of bacteria in two additional growth states, filamentous and biofilm encased. Gene expression analysis of such ex vivo samples was in accord with different bacterial growth phases in sequential lavage specimens. The existence of morphologically distinct NTHi subpopulations with varying levels of gene expression indicates that the pooling of specimens requires caution until methods for their separation are developed. This study based on multiple consecutive lavages is consistent with prior reports that NTHi forms a biofilm in vivo, describes the means to directly acquire ex vivo biofilm samples without sacrificing the animal, and has broad applicability for a study of mucosal infections. Moreover, this approach revealed that the actual burden of bacteria in experimental otitis media is significantly greater than was previously reported. Such findings may have direct implications for antibiotic treatment and vaccine development against NTHi.

The Exocytoskeleton

The murein or peptidoglycan wall enclosing most bacteria is essential for the life style of most organisms in the Domain of Bacteria. Only in special situations does it not play a role in the bacterial growth cycle. When life first appeared on this planet the cellular osmotic pressure was probably low and a sacculus was probably not relevant, but became necessary as bacterial life evolved from the complex and sophisticated cell called the Last Universal Ancestor. The construction of the murein wall outside of the cytoplasmic membrane is complex and requires elaborate special biochemistry. Growth of the sacculus in some parts of the surface and not in others is important for bacteria cells and allows them to divide and grow without becoming larger and larger and for their being able to maintain a shape characteristic of individual species.