However, CN is sufficient, but not necessary for the initiation of looping (Movie S4).
In zebrafish, it is known that the initial broad expression of bmp4 and versican become restricted to the myocardium at the level of the AVC during initiation of looping [27], [28].
The lag represents slow loop initiation and recycling of dissociated motors.
The FJC model predicts more unfavorable free energy for loop initiation, Δ G°37,FJC, as the number of unpaired nucleotides increases.
Previously published data for enthalpy changes for multibranch loop initiation, Δ H°MBL init, have been fit to (44) Similar to eqs 24, 25, and 26 for predicting free energy for multibranch loop initiation, the data can also be fit to a "universal" model, a model for three-way multibranch loops, and a model for four-way multibranch loops, eqs 29, 30, and 31, respectively.
Those with both poor perfusion and congestion have the worst overall risk for short- and long-term mortality as well as worsened renal function after the initiation of intravenous loop diuretics.
Linear regressions were used to derive parameters for eqs 29, 30, and 31 from the adjusted data excluding systems omitted from the regression of multibranch loop initiation free energy and using Δ H° from 1/ TM vs ln CT/4) for all sequences, including G_CG_G/C_C.
As in the previous work, the various Δ G parameters above are from the Turner nearest-neighbor rules [ 11], while a, b, and c are from the following estimate of the standard free energy change for multibranch loop initiation: (22) Δ G 0 = a + bn + ch Here n is the number of unpaired nucleotides and h is the number of branching helices [ 21].
According to the standard model of cpDNA replication, which is based on electron microscopic studies of pea and maize cpDNA molecules, replication starts at two displacement loop initiation sites located about 7-kb apart on opposite strands (Kolodner and Tewari 1975).
The entropy change for multibranch loop initiation, Δ S°MBL init, can be calculated from Δ H°MBL init and Δ G°37,MBL init, because The values of aS, bS, cS, dS, and Δ S°strain for the model similar to eqs 24, 25, and 26 are listed in Table 7. Essentially identical values are obtained if the entropy data is fit separately to an equation with the same terms as eqs 24, 25, and 26.
