Biological features of <i>E. coli</i> cells used to describe our EABM agents.

*<p>Please note that the number of flagella can reach 20 due to the starvation and hypergravity conditions and that the length of flagella in the model is expressed in arbitrary and normalized units according to the formula for the average agent speed.</p

Culture growth and colony formation in conditions of normal gravity and hypergravity.

<p>Identical set of initial random seeds are used for the simulations at normal gravity and hypergravity. (a) Predicted character of movement in normal gravity (G = 1.0) at different time points as shown on the left. The dots correspond to individual cells. (b) Predicted character of movement in hypergravity (G = 1.5) at the different time points. The walls of the virtual Petri dish are shown on the X and the Y. (c) Predicted average cell speed in normal gravity (an empty square) and hypergravity (a full square). X-axis depicts the time rescaled from computer steps to hours. Y-axis shows the average cell speed in links per computer step (hours).</p

Average bacterial growth rate and nutrient availability at different gravity levels.

<p>The bacterial growth curves are shown with squares – at normal gravity, G = 1.0, empty squares; at hypergravity G = 1.5, full squares. Time dependent changes in nutrients amount on the lattice due to bacterial consumption is shown with empty circles for G = 1.0 and full circles for G = 1.5. Bacterial growth and nutrients availability is shown on the Y-axis. Maximum bacterial growth corresponds to ∼10⁸ cells and 0 corresponds to 1000 cells. Availability of nutrients on 85% of the lattice corresponds to the maximum nutrients availability. The X-axis depicts the time, rescaled from computer steps to hours. Domain A corresponds to the <i>lag</i> phase of the bacterial growth; domain B - <i>logarithmic</i> growth phase; domain C - long-term <i>stationary</i> phase.</p

Average time required for initiation of the <i>rpoS</i> gene expression.

<p>The predicted average time for initiation of <i>rpoS</i> gene expression in hypergravity conditions is shown with full squares; normal gravity - empty squares. The X-axis depicts the time, rescaled from computer steps to hours; Y axis - average interval after which the preservation <i>rpoS</i> gene is expressed.</p

Average speed characteristics.

<p>Average speed characteristics.</p

Changes of flagella under normal and hypergravity conditions.

<p>(a) The average number of flagella is plotted on the Y-axis. The X-axis depicts the time, rescaled from computer steps to hours. (b) Predicted time dependent change of the average length of flagella in the cell culture. The Y-axis shows the average flagella length in arbitrary units. The X-axis depicts the time rescaled from computer steps to hours. Empty squares correspond to normal gravity conditions; full squares correspond to hypergravity conditions.</p

Bile acid production in primary cultured human cumulus granulosa cells (CGC).

<p>Cholesterol entering granulosa cells may be used to form sex steroids or bile acids (Panel a). With increasing cholesterol concentration in media, CGC demonstrate dose-dependent bile acid content (Panel b).</p

Presence of bile acids synthesis enzymes in human ovarian follicle.

<p>Protein presence was analyzed with enzyme specific antibodies and immunofluorescence. Present - the enzyme is present at a protein level; absent - the enzyme is not present at a protein level.</p

Collective opening profiles of the collagen nonpromoter sequence calculated from the PBD Langevin dynamic simulations.

<p>(A) Probability for collective opening (vertical axis) of ten base pairs starting at specific nucleotide position within the collagen intron (horizontal axis), as a function of bubble amplitude [Å]. For comparison the profile of the collagen promoter is also presented (bottom panel). Probability values are colored to the same scale between the promoter and the intron sequences, as shown below the plots. Nucleotide positions in the collagen promoter are labeled relative to the TSS (+1). The sequence identity is shown at the top. (B) Probability for opening (vertical axis) of amplitude threshold (tr)≥1 Å, starting at specific nucleotide positions (horizontal axis), as a function of bubble length [bp]. Probability values are colored to the same scale, as shown below the plots. The sequence identity is shown at the top. (C) Average lifetimes of DNA collective openings of amplitude tr≥1 Å (vertical axis), starting at specific nucleotide positions (horizontal axis), as a function of length [bp]. The average lifetimes of collective openings for the collagen promoter are shown below. The TSS is marked with a vertical line. The color scale shown below the plots represents the average lifetimes [ps].</p

Core promoter sequences analyzed by PBD Langevin dynamics simulations.

<p>Experimentally verified transcriptional start sites (TSS) are shown in large letters. Common promoter sequence elements are indicated by colored boxes. For illustrative purposes, sequences that fit the element definitions but are not properly positioned relative to the TSS are also shown as colored letters. Deviations from the consensus sequence are indicated in gray. The sequences were obtained from the Eukaryotic Promoter Database (EPD, <a href="http://www.epd.isb-sib.ch/" target="_blank">http://www.epd.isb-sib.ch/</a>). The identity of each promoter is described in column 1, the sequence is shown in column 2, and the mode of regulation in column 3.</p