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Fujitani, H.

Publications and source records attributed to Fujitani, H..

3 recordsLinked to original sources

Environment-responsive individual cell growth behavior shapes stochastic and deterministic population establishment in ammonia-oxidizing bacteria

Many environmental bacteria do not readily grow under laboratory conditions and population establishment often occurs stochastically. Although the scout hypothesis has been proposed to explain stochastic population establishment in environmental bacteria, how stochastic population establishment is shaped by individual cell growth behaviors in environmental isolates remains unclear. In the present study, we focused on the ammonia-oxidizing bacterium Nitrosomonas sp. PY1 and showed that environmentally responsive individual cell growth behavior, incorporating time-dependent stochastic growth initiation, shapes both deterministic and stochastic population establishment dynamics. Using single-cell observation, we revealed that PY1 altered cell growth behavior in response to surrounding biomass production ({Delta}Vt). These {Delta}Vt-dependent changes in growth behavior were suppressed by the addition of its own cell-free supernatant (CFS), indicating the presence of a growth regulation mechanism via cell-cell communication. Replicate cultures under the same conditions showed that the population establishment of PY1 was stochastic, whereas the model strain Nitrosomonas europaea exhibited synchronized population establishment, consistent with previous reports. This stochasticity in PY1 was also eliminated by the addition of CFS. Finally, a simulation model based on {Delta}Vt-dependent cell growth behavior of PY1 successfully reproduced synchronized population establishment in the presence of CFS. By contrast, the stochastic population establishment observed in the absence of CFS was successfully reproduced by a model incorporating {Delta}Vt-independent growth initiation following a Weibull distribution. Such environmentally responsive changes in population establishment dynamics may contribute to the low isolation success of environmental bacteria and sudden blooms of the rare biosphere.

microbiology↗

High-throughput screening of high protein producer budding yeast using gel microdrop technology

The need for protein production has been growing over the years in various industries. We here present a high-throughput screening strategy to isolate high producer budding yeast clones from a mutagenized cell population using gel microdrop (GMD) technology. We use a microfluidic water-in-oil (W/O) emulsion method to produce monodisperse GMDs and a microfluidic cell sorter for damage-free sorting of GMDs by fluorescently quantifying secreted proteins. As a result, this high-throughput GMD screening method effectively selects high producer clones and improves protein production up to five-fold. We speculate that this screening strategy can be applied, in principle, to select any types of high producer cells (bacterial, fungal, mammalian, etc.) which produce arbitrary target protein as it does not depend on enzymes to be produced.

bioengineering↗

A new lipid force field (FUJI)

To explore inhomogeneous and anisotropic systems such as lipid bilayers, the Lennard-Jones particle mesh Ewald (LJ-PME) method was applied without a traditional isotropic dispersion correction. As the popular AMBER and CHARMM lipid force fields were developed using a cutoff scheme, their lipid bilayers unacceptably shrank when using LJ-PME method. A new lipid force field (FUJI) was developed on the basis of the AMBER force field scheme including the Lipid14 van der Waals parameters. Point charges were calculated by the restrained electrostatic potentials of many lipid conformers. The torsion energy profiles were calculated by high level ab initio molecular orbitals (LCCSD(T)/Aug-cc-pVTZ//LMP2/Aug-cc-pVTZ); then, the molecular mechanical dihedral parameters were derived by means of a fast Fourier transform. Incorporating these parameters into a new lipid force field without any fittings to experimental data, desirable lipid characteristics such as the area per lipid and lateral diffusion coefficients were obtained by GROMACS molecular dynamics simulations using the LJ-PME method and hydrogen virtual sites. The stability and structures of large membranes with undulatory fluctuations were studied by a multidrug efflux transporter (AcrABZ-TolC) with inner and outer membranes.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC=\"FIGDIR/small/373183_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (92K):\norg.highwire.dtl.DTLVardef@12cf574org.highwire.dtl.DTLVardef@a6cdbforg.highwire.dtl.DTLVardef@10dbd16org.highwire.dtl.DTLVardef@f8fd3a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗