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 speed characteristics.

<p>Average speed characteristics.</p

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

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

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

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

The TRS expansion has an effect on the DNA bubble spectrum.

<p>EPBD based LMD simulations have been conducted on the: a) (CAG.CTG)₄₅ repeats and healthy (CAG.CTG)₁₀ repeats with 30 bp flanking huntington gene sequence; b) (GAA.TTC)₁₂₀ and (GAA.TTC)₆ MRS that are embedded in 50 bp frataxin gene sequence; c) (CGG.GCC)₂₄₀ and (CGG.GCC)₂₀ repeats together with 50 bp FMR1 gene flanking sequence. The y-axis represents the length of the bubbles in bp; the x-axis represents the number of the base pairs; the color axis gives the bubble duration in psec. The brackets above the panels denote the repeated sequence; red arrows- the largest and long-lived base-pairs openings.</p

Accumulation of (GAA.TTC) repeats leads to changes in local DNA breathing.

<p>BAD criteria are used to describe and compare the local base pair breathing of DNA sequences with different numbers of (GAA.TTC) repeats embedded within the frataxin gene [B7] promoter sequence. a) BAD coordinates [Å] are calculated with EPBD based MCMC simulations for sequence inserts with different numbers of repeats: (GAA.TTC)₆-black line, (GAA.TTC)₄₅-red line, and (GAA.TTC)₁₂₀-blue line. The position of the flanking sequence (fl) is shown above the panel. b) BAD coordinates for a randomized sequence with the same number of base pairs and G+C content as the (GAA.TTC)₄₁ sequence. The random sequence (red line) is missing the synchronized average base pair openings behavior of the symmetric (GAA.TTC)₄₁ (blue line). The nucleotide position is shown on the horizontal. The BAD coordinates are shown on the vertical in [Å].</p

Fis binding site modifications, Langevin dynamics simulations of DNA breathing, and EMSA experiments, the second set.

<p>(A) Langevin dynamics simulations reinforcing the local DNA breathing dynamics in FIS2^m3 via three O6-methylguanine modifications in the bubble formation region of FIS2 (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002881#pcbi-1002881-t001" target="_blank">Table 1</a>). The direct points-of-contacts remain unchanged. (B) Polyacrylamide gel electrophoresis of dsDNA oligonucleotides sequences - FIS2, FIS2^m2, and FIS2^m3 - demonstrating gel migratory effects due to possible bubble formation (gel at 15%). (C) Langevin dynamics simulations demonstrating local disruption of the hydrogen bonds in the super-enhanced DNA local openings of the FIS1–FIS2 sequence (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002881#pcbi-1002881-t001" target="_blank">Table 1</a>) caused by the presence of five mismatches at the FIS1 bubble formation region. (D) EMSA demonstrating the lack in complex formation in FIS1–FIS2. Concentration of the FIS1 and FIS1–FIS2 oligomers were constant at 100 nM and Fis protein ranged from 0 to 0.75 µM. Sonicated salmon sperm DNA at 0.5–1 µg/µl was added to the binding reactions to eliminate non-specific binding. In Langevin dynamics simulations (panels A and C) the probability of bubble openings is represented by the same color map as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002881#pcbi-1002881-g005" target="_blank">Figure 5</a>; red denotes high probability and blue denotes low probability of opening. The probability is determined from the lifetimes of all open states with a given length (bp) and above amplitude of 1.0 (Å), normalized over the complete time of the simulation. The length of the transient bubbles, given in base pairs [bp], is shown along the vertical axis. The horizontal axis depicts base pair position; the bubble formation region is highlighted in blue while the points-of-contact are highlighted in yellow. The names of each of the sequences are shown in the panels while the complete nucleotide sequences could be found in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002881#pcbi-1002881-t001" target="_blank">Table 1</a>.</p

DNA oligomers investigated with EPBD Langevin dynamics.

<p>Bold capital letters indicate direct points-of-contact or positions of inclusion/exclusion rules, which are located at: <b>−7;−4;−3</b>, and <b>+7;+4+3</b> positions; the location of the Fis bubble formation region is between −2 and +2 positions; low case letters indicate base pair substitutions; italic capital letters indicate complementary strand mismatches; ^mG represents O6-methylguanine.</p