Bacteria can form interconnected microcolonies when a self-excreted product reduces their surface motility: evidence from individual-based model simulations

Recent experimental observations of Pseudomonas aeruginosa, a model bacterium in biofilm research, reveal that, under specific growth conditions, bacterial cells form patterns of interconnected microcolonies. In the present work, we use an individual-based model to assess the involvement of bacteria motility and self-produced extracellular substance in the formation of these patterns. In our simulations, the pattern of interconnected microcolonies appears only when bacteria motility is reduced by excreted extracellular macromolecules. Immotile bacteria form isolated microcolonies and constantly motile bacteria form flat biofilms. Based on experimental data and computer simulations, we suggest a mechanism that could be responsible for these interconnected microcolonies.     

Mathematical modelling of juxtacrine patterning

Spatial pattern formation is one of the key issues in developmental biology. Some patterns arising in early development have a very small spatial scale and a natural explanation is that they arise by direct cell—cell signalling in epithelia. This necessitates the use of a spatially discrete model, in contrast to the continuum-based approach of the widely studied Turing and mechanochemical models. In this work, we consider the pattern-forming potential of a model for juxtacrine communication, in which signalling molecules anchored in the cell membrane bind to and activate receptors on the surface of immediately neighbouring cells. The key assumption is that ligand and receptor production are both up-regulated by binding. By linear analysis, we show that conditions for pattern formation are dependent on the feedback functions of the model. We investigate the form of the pattern: specifically, we look at how the range of unstable wavenumbers varies with the parameter regime and find an estimate for the wavenumber associated with the fastest growing mode. A previous juxtacrine model for Delta-Notch signalling studied by Collier et al. (1996, J. Theor. Biol. 183, 429–446) only gives rise to patterning with a length scale of one or two cells, consistent with the fine-grained patterns seen in a number of developmental processes. However, there is evidence of longer range patterns in early development of the fruit fly Drosophila. The analysis we carry out predicts that patterns longer than one or two cell lengths are possible with our positive feedback mechanism, and numerical simulations confirm this. Our work shows that juxtacrine signalling provides a novel and robust mechanism for the generation of spatial patterns.     

Development of the cell covering in the dinoflagellate Scrippsiella hexapraecingula (Peridiniales, Dinophyceae)

The organization and development of cell coverings in two alternate phases of the life cycle in a marine dinoflagellate, Scrippsiella hexapraecingula Horiguchi et Chihara, were investigated by thin sectioning and freeze‐fracture electron microscopy. In one of these phases, the motile phase, cells have an outermost plasma membrane that is lined with flattened amphiesmal vesicles. Groups of microtubules lie beneath these vesicles. In mature motile cells, thecal plates are completely enclosed in individual amphiesmal vesicles. After settling, the cells enter the second, non‐motile phase. Here, ecdysis occurs, resulting in several steps including formation of the first pellicle layer (PI), fusion of the inner amphiesmal vesicle membranes to form the new plasma membrane, deposition of the second pellicle layer (PM) under PI, and the appearance and fusion of juvenile amphiesmal vesicles to form new territories, which eventually give rise to new thecal plates in the next motile phase. Thus, the pattern in which thecal plates are arranged in motile cells is determined at the time when the amphiesmal vesicles develop into non‐motile cells.     

Cellular events associated with lung branching morphogenesis including the deposition of collagen type IV

In this study mouse lung development was examined using an in vitro model system. The culture system permitted examination of a morphogenic process that eventually led to the formation of presumptive alveoli (terminal sacs). The observations included changes in epithelial cell morphology (transition from a columnar to a spindle shape), and evidence for motile activity on the part of primitive airway epithelial cells. The importance of Type IV collagen to the cellular events associated with branching morphogenesis was investigated by immunolocalization. In addition, we assessed the similarity of normal lung development to in vitro development by comparing cultured lungs with equivalent stages of embryonic and fetal mouse lungs. The results show that cultured embryonic lung explants proceed along a morphogenic pathway that parallels normal lung development; that primitive pulmonary epithelial cells engage in motile activity and transiently acquire an extended cell shape both in vitro and in vivo; that, as suggested by others, the pattern of late branching morphogenesis is not dichotomous, but irregular; and that short wisplike fibers of Type IV collagen are present in developing embryonic and fetal lung mesenchyme. Taken together, the results show that early and late lung branching patterns differ significantly, and suggest that later stages of lung branching involve distinct epithelial cell shape transitions. The immunofluorescence data suggest that fibrous Type IV collagen may be the extracellular matrix scaffold within which early epithelial cells accomplish lung branching morphogenesis.     

Diversity and evolution of microsporogenesis in Bromeliaceae

In this study, we explore the features of microsporogenesis in Bromeliaceae and, in particular, the diversity and evolution of additional callose deposits. Cytokinesis type, cell wall formation, tetrad form and patterns of additional callose deposition after intersporal wall formation were studied in 12 species of Bromeliaceae (each from a different genus) presenting four different aperture patterns. Microsporogenesis is highly conserved, with successive cytokinesis, centrifugal cell plate formation and predominantly tetragonal and decussate tetrads, as in many monocots, but five different patterns of additional callose deposition were recorded. The optimization of patterns of additional callose deposition on the phylogeny of Bromeliaceae reveals convergences. Additional callose deposition is a variable and labile feature of microsporogenesis in Bromeliaceae and is linked, to some extent, to aperture pattern. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 36–45.     

Gene position within a long transcript as a determinant for stochastic switching in bacteria

How cultures of genetically identical cells bifurcate into distinct phenotypic subpopulations under uniform growth conditions is an important question in developmental biology of relevance even to relatively simple developmental systems, such as spore formation in bacteria. A growing Bacillus subtilis culture consists of either cells that are motile and can swim or cells that are non‐motile and are chained together. In this issue of Molecular Microbiology, Cozy and Kearns show that the probability of a cell to become motile depends on the position of the sigD gene within the long (27 kb) motility operon. sigD encodes the alternative sigma factor σ^D that, together with RNA polymerase, drives expression of genes required for cell separation and the assembly of flagella. sigD is the penultimate gene of the B. subtilis motility operon and, in the control strain approximately, 70% of the cells are motile. When sigD was moved upstream within the operon, a larger fraction of cells became motile (up to 100%). This study highlights that the position of a gene within an operon can have a large impact on the control of gene expression. Furthermore, it suggests that RNA polymerase processivity or mRNA turnover can play important roles as sources of noise in bacterial development, and that gene position might be an unrecognized and possibly widespread mechanism to regulate phenotypic variation.     

Spatial cues play a role in the development of Myxococcus xanthus

Intercellular signaling plays an important role in spatially regulated developmental processes. Myxococcus xanthus C signal transmission during fruiting body formation requires motile, densely packed, well aligned cells. tThe fruiting body consists of two domains: an outer domain which has densely packed, well aligned, motile cells: and an inner domain of more loosely packed, non-motile, sporulating cells. The two domains are characterized by different patterns of C-dependent gene expression, which begins in the outer domain where C-signaling is most efficient, and reaches its maximum in the inner domain. These domains may be maintained by a dynamic mechanism which relies on passive transport of the sporulating cells from the outer domain, where sporulation is initiated, to the inner domain by the motile cells in the outer domain.     

Pelagic-benthic transition of the harmful alga, Heterosigma akashiwo: Changes in swimming and implications for benthic cell distributions

Many harmful algal blooming (HAB) species transition between a vegetative, motile phase in the water column and a dormant, non-motile resting phase in the sediments. These life history transitions potentially regulate the timing, location and persistence of bloom events. Motility promotes aggregation and influences vertical distributions in the water column. However, the contribution of this behavior to benthic distributions of resting cells is currently unknown. We used video-tracking techniques to test the hypothesis that algal cells use active down-swimming during pelagic-benthic transition to favorably influence benthic distributions. In an experimental water column, we monitored cell swimming trajectories of Heterosigma akashiwo for 14 days after cells were signaled to enter the benthic resting stage. Using the statistical characteristics of individual cell trajectories, we developed a video-based motion assay to assign each tracked Heterosigma cell to one of three cell states known to occur during pelagic-benthic transition: induced motile, transitional and resting. The primary swimming characteristic influencing benthic distribution, net vertical velocity, was essentially the same for all three cell states. Hence, we found no evidence that active down-swimming influences benthic distributions. Our data suggest that benthic distributions of Heterosigma resting cells are similar to distributions of slowly sedimenting passive particles. These observations suggest that Heterosigma benthic resting cell distributions can be predicted by modeling the effects of cell sedimentation rates combined with geophysical flow patterns.     

WIPF2 promotes Shigella flexneri actin‐based motility and cell‐to‐cell spread

Shigella flexneri is an intracellular pathogen that disseminates in colonic epithelial cells through actin‐based motility and formation of membrane protrusions at cell–cell contacts, that project into adjacent cells and resolve into vacuoles, from which the pathogen escapes, thereby achieving cell‐to‐cell spread. Actin nucleation at the bacterial pole relies on the recruitment of the nucleation‐promoting factor N‐WASP, which activates the actin nucleator ARP2/3. In cells, the vast majority of N‐WASP exists as a complex with WIP. The involvement of WIP in N‐WASP‐dependent actin‐based motility of various pathogens, including vaccinia virus and S. flexneri, has been highly controversial. Here, we show that WIPF2 was the only WIP family member expressed in the human colonic epithelial cell line HT‐29, and its depletion impaired S. flexneri dissemination. WIPF2 depletion increased the number of cytosolic bacteria lacking actin tails (non‐motile) and decreased the velocity of motile bacteria. This correlated with a decrease in the recruitment of N‐WASP to the bacterial pole, and among N‐WASP‐positive bacteria, a decrease in actin tail‐positive bacteria, suggesting that WIPF2 is required for N‐WASP recruitment and activation at the bacterial pole. In addition, when motile bacteria formed protrusions, WIPF2 depletion decreased the number of membrane protrusions that successfully resolved into vacuoles.     

Pyramidodinium atrofuscum gen. et sp. nov. (Dinophyceae), a new marine sand-dwelling coccoid dinoflagellate from tropical waters

A new marine sand‐dwelling coccoid dinoflagellate Pyramidodinium atrofuscum Horiguchi et Sukigara gen. et sp. nov. is described from Jellyfish Lake, Republic of Palau. The dinoflagellate alternates a non‐motile vegetative stage with a motile gymnodinioid stage within its life cycle. The non‐motile stage is dominant in the life cycle and the dinoflagellate reproduces itself by means of the production of two motile cells. The released motile cell swims only for a short period and is directly transformed into the non‐motile cell. The non‐motile cell is sessile, pyramidal in shape, with a single longitudinal ridge and a double transverse ridge. The surface of the cell wall is covered with many processes. The motile cell has a Gymnodinium‐like morphology, but no apical groove is present. An ultrastructural study revealed that the dinoflagellate possesses typical dinoflagellate organelles. Based on the unique morphology of the vegetative non‐motile stage, we propose a new genus Pyramidodinium for this dinoflagellate, with the type species Pyramidodinium atrofuscum Horiguchi et Sukigara, gen. et sp. nov.     

Pigment pattern formation in the larval salamander Ambystoma maculatum

As part of an ongoing comparative study of pigment patterns and their formation in embryos and larvae of ambystomatid salamanders, Ambystoma maculatum from two differnt populations, one in the northern (New York) and one in the central (Tennessee) United States, were investigated. Scanning electron microscopy was used to study early neural crest development. Light microscopy in combination with markers for the two pigment cell types (xanthophores and melanophores) made it possible to follow pigment cell migration before the pigment cells were fully differentiated. A bilateral pigment pattern consisting of two horizontal melanophore stripes surrounding an interstripe area populated by xanthophores formed in the larvae. In both populations, some variation was present in the form of a continuum ranging from clear horizontal stripes to extreme cases with a random pattern. Unlike the other ambystomatids that have been investigated, the neural crest cells in A. maculatum do not form aggregates and no vertical bars are formed. Instead, both the pattern and its formation are very similar to what has been reported for salamandrids. If pattern formation mechanisms can act as developmental constraints we would expect the A. maculatum pattern to be the primitive condition in the Ambystomatidae, using the Salamandridae as the outgroup. There is no strong support for this when aggregate formation is used as a character and mapped onto phylogenies for the group. The aggregate formation mechanism, and the pigment pattern that it leads to, have most likely been secondarily lost in A. maculatum. © 1993 Wiley-Liss, Inc.     

Classification and genetic characterization of pattern-forming Bacilli

One of the more natural but less commonly studied forms of colonial bacterial growth is pattern formation. This type of growth is characterized by bacterial populations behaving in an organized manner to generate readily identifiable geometric and predictable morphologies on solid and semi-solid surfaces. In our first attempt to study the molecular basis of pattern formation in Bacillus subtilis , we stumbled upon an enigma: some strains used to describe pattern formation in B. subtilis did not have the phenotypic or genotypic characteristics of B. subtilis . In this report, we show that these strains are actually not B. subtilis , but belong to a different class of Bacilli , group I. We show further that commonly used laboratory strains of B. subtilis can co-exist as mixed cultures with group I Bacilli , and that the latter go unnoticed when grown on frequently used laboratory substrates. However, when B. subtilis is grown under more stringent semiarid conditions, members of group I emerge in the form of complex patterns. When B. subtilis is grown under less stringent and more motile conditions, B. subtilis forms its own pattern, and members of group I remain unnoticed. These findings have led us to revise some of the mechanistic and evolutionary hypotheses that have been proposed to explain pattern growth in Bacilli .     

SUSCEPTIBILITY AND PROTECTIVE MECHANISMS OF MOTILE AND NON MOTILE CELLS OF HAEMATOCOCCUS PLUVIALIS (CHLOROPHYCEAE) TO PHOTOOXIDATIVE STRESS1

The life cycle of the unicellular green alga Haematococcus pluvialis consists of motile and nonmotile stages under typical growing conditions. In this study, we observed that motile cells were more susceptible than nonmotile cells to high light, resulting in a decrease in population density and photo‐bleaching. Using two Haematococcus strains, CCAP 34/12 (a motile cell dominated strain) and SAG 34/1b (a nonmotile cell dominated strain), as model systems we investigated the cause of cell death and the protective mechanisms of the cells that survived high light. The death of motile cells under high light was attributed to the generation of excess reactive oxygen species (ROS), which caused severe damage to the photosynthetic components and the membrane system. Motile cells were able to dissipate excess light energy by nonphotochemical quenching and to relax ROS production by a partially up‐regulated scavenging enzyme system. However, these strategies were not sufficient to protect the motile cells from high light stress. In contrast, nonmotile cells were able to cope with and survive under high light by (i) relaxing the over‐reduced photosynthetic electron transport chain (PETC), thereby effectively utilizing PETC‐generated NADPH to produce storage starch, neutral lipid, and astaxanthin, and thus preventing formation of excess ROS; (ii) down‐regulating the linear electron transport by decreasing the level of cytochrome f; and (iii) consuming excess electrons produced by PSII via a significantly enhanced plastid terminal oxidase pathway.     

Importance of region-specific epithelial rearrangements in mouse rugae development

Epithelial appendages on palatal rugae develop during mouse palatogenesis through epithelial thickening and pattern formation. Recently, the patterned formation of nine rugae was observed together with the specific expression patterns of Shh in rodents. However, no crucial evidence was found for a direct association between Shh expression and the distinct structural formation of rugae. In order to reveal possible relationships, we investigated the morphological changes of rugae and expression patterns of Shh directly by in vitro organ culture at embryonic day 13 (E13) for 2 days. To compare and examine the diverse growing aspects of the palate and rugae, we carefully observed the detailed morphogenesis, with cell proliferation of the rugae occurring between E13 and E14.5. After 2 days of cultivation at E13, DiI micro-injections revealed that the middle part of the palate, adjacent to the upper molar-forming region, contributed to the formation of the subsequent structure of rugae by extensive cell rearrangement and proliferation within the epithelium in the preferred anteroposterior direction. The results also defined the intimate relationship between Shh expression and rugae formation.     

Effects of bisphenol A and 4-nonylphenol on cellular responses through the different induction of LPA receptors in liver epithelial WB-F344 cells

Abstract

Lysophosphatidic acid (LPA) signaling via G protein-coupled transmembrane LPA receptors (LPA₁ to LPA₆) mediates a variety of cellular functions, including cell proliferation, migration, morphogenesis, and differentiation. Recently, we demonstrated that the different induction of LPA receptors by estrogens regulates cell motile activity of rat liver epithelial WB-F344 cells. In the present study, to assess whether endocrine disruptors (EDs) are involved in cellular functions through LPA signaling, we measured cell motile activity and LPA receptor expressions in WB-F344 cells treated with bisphenol A (BPA) and 4-nonylphenol (4-NP). Using quantitative real time RT-PCR analysis, the Lpar1 expression was elevated in BPA-treated cells, whereas the Lpar3 expression was decreased. In contrast, 4-NP increased the Lpar3 expression, but not the Lpar1 and Lpar2. For cell motility assay with a Cell Culture Insert, cell motile activity of BPA-treated cells was significantly lower than that of untreated cells. In contrast, 4-NP markedly enhanced cell motile activity. The effects of BPA and 4-NP on cell motility were inhibited by the Lpar1 or Lpar3 knockdown. These results suggest that BPA and 4-NP may regulate cell motile activity through the different induction of LPA receptors in WB-F344 cells.     

Pyramidodinium spinulosum sp. nov. (Dinophyceae), a sand‐dwelling non‐motile dinoflagellate from the seafloor (36 m deep) off Mageshima Island,Kagoshima, Japan

A new species of benthic marine dinoflagellate, Pyramidodinium spinulosum Horiguchi, Moriya, Pinto & Terada is described from the deep (36 m) seafloor off Mageshima Island, Kagoshima Prefecture, Japan in the subtropical region of the northwest Pacific. The life cycle of the dinoflagellate consists of a dominant, attached, dome‐shaped, vegetative form and short‐lasting, motile cell. Asexual reproduction takes place by the formation of two motile cells within each non‐motile cell. The released motile cells swim only for a short period and transform directly into the dome‐shaped vegetative form. The duration of the cell cycle varies and can be extremely long, ranging 5–38 days under culture conditions. The non‐motile cell is enclosed by a cell wall and its surface is covered with many (80 – 130) spines of various length. The dinoflagellate is photosynthetic and contains many (more than 50) discoidal chloroplasts. Phylogenetic analysis reveals that the dinoflagellate is closely related to the type species of the genus Pyramidodinium, P. atrofuscum which also possesses a dominant, attached, non‐motile form. However, P. spinulosum can be clearly distinguished from P. atrofuscum by the cell shape (dome‐shaped vs. pyramid‐shaped) and surface ornamentation (spines vs. wart‐like processes) of the non‐motile form. Based on these morphological differences together with molecular evidence, it was concluded that this organism from a deep water sand sample should be described as a second species of the genus Pyramidodinium, P. spinulosum.     

Involvement of extracellular cAMP-specific phosphodiesterase in the control of motile activity of <Emphasis Type="Italic">Physarum polycephalum</Emphasis> plasmodium

Possible involvement of extracellular cAMP-specific phosphodiesterase in the control of cell motile behavior has been investigated in Physarum polycephalum plasmodium, a multinuclear amoeboid cell with the autooscillatory mode of motility. It was found that the rate of the hydrolysis of 10 mM cAMP by a partially purified preparation of cAMP-specific phosphodiesterase secreted by the plasmodium in the course of migration decreases 20–30 times under the action of 1 mM dithiothreitol. In the presence of 1–5 mM of this strong reducing agent, the onset of the plasmodium spreading and the transition to the stage of migration were delayed in a concentration-dependent manner. In accordance with the morphological pattern of motile behavior, the duration of the maintenance of high frequency autooscillations, which normally precede the increase in the rate of the spreading and appear also in response to the application of attractants at spatially uniform concentrations, strongly increased by the action of dithiothreitol. The results obtained suggest that the autocrine production of cAMP and extracellular cAMP-specific phosphodiesterase is an important constituent of the mechanism controlling the motile behavior of the Physarum polycephalum plasmodium.     

ISWI proteins participate in the genome‐wide nucleosome distribution in Arabidopsis

Chromatin is a highly organized structure with repetitive nucleosome subunits. Nucleosome distribution patterns, which contain information on epigenetic controls, are dynamically affected by ATP‐dependent chromatin remodeling factors (remodelers). However, whether plants have specific nucleosome distribution patterns and how plant remodelers contribute to the pattern formation are not clear. In this study we used the micrococcal nuclease digestion followed by deep sequencing (MNase‐seq) assay to show the genome‐wide nucleosome pattern in Arabidopsis thaliana. We demonstrated that the nucleosome distribution patterns of Arabidopsis are associated with the gene expression level, and have several specific characteristics that are different from those of animals and yeast. In addition, we found that remodelers in the A. thaliana imitation switch (AtISWI) subfamily are important for the formation of the nucleosome distribution pattern. Double mutations in the AtISWI genes, CHROMATIN REMODELING 11 (CHR11) and CHR17, resulted in the loss of the evenly spaced nucleosome pattern in gene bodies, but did not affect nucleosome density, supporting a previous idea that the primary role of ISWI is to slide nucleosomes in gene bodies for pattern formation.     

Formation,collective motion,and merging of macroscopic bacterial aggregates

Chemotactic bacteria form emergent spatial patterns of variable cell density within cultures that are initially spatially uniform. These patterns are the result of chemical gradients that are created from the directed movement and metabolic activity of billions of cells. A recent study on pattern formation in wild bacterial isolates has revealed unique collective behaviors of the bacteria Enterobacter cloacae. As in other bacterial species, Enterobacter cloacae form macroscopic aggregates. Once formed, these bacterial clusters can migrate several millimeters, sometimes resulting in the merging of two or more clusters. To better understand these phenomena, we examine the formation and dynamics of thousands of bacterial clusters that form within a 22 cm square culture dish filled with soft agar over two days. At the macroscale, the aggregates display spatial order at short length scales, and the migration of cell clusters is superdiffusive, with a merging acceleration that is correlated with aggregate size. At the microscale, aggregates are composed of immotile cells surrounded by low density regions of motile cells. The collective movement of the aggregates is the result of an asymmetric flux of bacteria at the boundary. An agent-based model is developed to examine how these phenomena are the result of both chemotactic movement and a change in motility at high cell density. These results identify and characterize a new mechanism for collective bacterial motility driven by a transient, density-dependent change in motility.     

The biology of coral metamorphosis: molecular responses of larvae to inducers of settlement and metamorphosis

Like many other cnidarians, corals undergo metamorphosis from a motile planula larva to a sedentary polyp. In some sea anemones such as Nematostella this process is a smooth transition requiring no extrinsic stimuli, but in many corals it is more complex and is cue-driven. To better understand the molecular events underlying coral metamorphosis, competent larvae were treated with either a natural inducer of settlement (crustose coralline algae chips/extract) or LWamide, which bypasses the settlement phase and drives larvae directly into metamorphosis. Microarrays featuring > 8000 Acropora unigenes were used to follow gene expression changes during the 12 h period after these treatments, and the expression patterns of specific genes, selected on the basis of the array experiments, were investigated by in situ hybridization. Three patterns of expression were common—an aboral pattern restricted to the searching/settlement phase, a second phase of aboral expression corresponding to the beginning of the development of the calicoblastic ectoderm and continuing after metamorphosis, and a later orally-restricted pattern.