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Norcantharidin (NCTD) is currently used for anticancer therapy but the exact mechanism of action remains unknown. Pre-replicative complexes (pre-RCs) are essential for cell DNA replication and highly related to malignant proliferation. Here, we examined the inhibitory effect of NCTD on pre-RC components in HepG2 cells. We showed that NCTD induced degradation of Cdc6 and Mcm2 in a dose-dependent manner. Under 100 μM NCTD concentration, about 70% of Cdc6 and 50% of Mcm2 were degraded. In addition, the nuclear translocation of Mcm6 was inhibited by NCTD. Further studies aiming at G1 synchronous cells showed that, NCTD reduced the chromatin-bound Cdc6, Mcm2 and Mcm6. Moreover, the cells were blocked from entering the S phase and accumulated at the G1 phase when released synchronously into the cell cycle. Consistently, the DNA replication was inhibited by NCTD. Finally, the combination NCTD with Cdc6 depletion lead to more severe cytotoxicity (88%) than NCTD (52%) and Cdc6 depletion (39%) alone. A synergic cytotoxicity was observed between Cdc6 depletion and NCTD. In conclusion, our results demonstrate that NCTD inhibits pre-RC assembly; subsequently blocks the G1 to S transition; and inhibits DNA replication in HepG2 cells. Pre-RCs are an intriguing target for cancer therapy, which merits further investigations for anticancer development.

In this paper, we consider the transformation of a breather type soliton in DNA into its demodulated version due to the strong impact of proteins associated with some sequences of DNA chain. These proteins are, for example, RNA polymerase responsible for the formation of m-RNA or initiation protein complex indispensable for chromosome replication.

Single-molecule experiments revealed that the replication rate of T7 DNA polymerase has a peak value at tension of about 5.5 pN. However, the mechanism leading to this peak has only been partially investigated. Here, we present a two-state model to investigate the effect of mechanical tension on DNA polymerase activity. The model consists of polymerase and exonuclease. The polymerase's kinetic pathway has been simplified into Michaelis–Menten form with two steps. One is the conformational change from "open" to "close". The other is the base-stacking. The results are in good agreement with experimental observations. We also predict that the tension on template is beneficial to the fidelity of DNA replication.

A model that controls DNA replication and the cell cycle is derived in terms of manybody physics. It predicts a long range force F(φ) =-(κ/2)φ(1-φ/N) (2-φ/N) in the lattice of pre-replication complexes (pre-RCs) bound by the DNA duplex, φ being the number of pre-RCS, N the threshold number at which replication is initiated, and κ the compressibility modulus in the lattice which behaves like an elastically braced string. Initiation of replication is explained by a switch of sign of F, from attraction (-) and assembly in the G1 phase (0 <φ<N), to repulsion (+) and partial disassembly in the S phase (N<φ<2N), with concomitant release of licensing factors from pre-RCs and prevention of re-replication. Termination of replication is due to a vanishing of F at φ=2N, at which all primed replicons in DNA have been duplicated once, and F(0)=0 corresponds to a resting cell in absence of a driving force at φ=0. The switch of sign of F at φ=N similarly explains the dynamic instability in growing microtubules (MTs), as well as the switch mechanism in the interaction of interleukin-2 (IL2) with its receptor in late G1, at the R-point, after which a T cell proceeds to replication without further exposure to IL2. Shape, slope and scale of the response curves derived agree well with experimental data from dividing T cells and polymerizing MTs, the variable length of which is explained here by a nonlinear dependence of the growth amplitude on the initial concentrations of guanosine-triphosphate (GTP) and tubulin dimers.

Professor Roger D. Komberg — 2006 Nobel Prize in Chemistry.

In this paper, we perform an analysis of bacterial cell-cycle models implementing different strategies to coordinately regulate genome replication and cell growth dynamics. It has been shown that the problem of coupling these processes does not depend directly on the dynamics of cell volume expansion, but does depend on the type of cell growth law. Our analysis has distinguished two types of cell growth laws, "exponential" and "linear", each of which may include both exponential and linear patterns of cell growth. If a cell grows following a law of the "exponential" type, including the exponential V(t) = V₀exp(kt) and linear V(t) = V₀(1 + kt) dynamic patterns, then the cell encounters the problem of coupling growth rates and replication. It has been demonstrated that to solve the problem, it is sufficient for a cell to have a repressor mechanism to regulate DNA replication initiation. For a cell expanding its volume by a law of the "linear" type, including exponential V(t) = V₀ + V₁exp(kt) and linear V(t) = V₀ + kt dynamic patterns, the problem of coupling growth rates and replication does not exist. In other words, in the context of the coupling problem, a repressor mechanism to regulate DNA replication, and cell growth laws of the "linear" type displays the attributes of universality. The repressor-type mechanism allows a cell to follow any growth dynamic pattern, while the "linear" type growth law allows a cell to use any mechanism to regulate DNA replication.

A breast cancer subtype classification scheme, PAM50, based on genetic information is widely accepted for clinical applications. On the other hands, experimental cancer biology studies have been successful in revealing the mechanisms of breast cancer and now the hallmarks of cancer have been determined to explain the core mechanisms of tumorigenesis. Thus, it is important to understand how the breast cancer subtypes are related to the cancer core mechanisms, but multiple studies are yet to address the hallmarks of breast cancer subtypes. Therefore, a new approach that can explain the differences among breast cancer subtypes in terms of cancer hallmarks is needed.

We developed an information theoretic sub-network mining algorithm, differentially expressed sub-network and pathway analysis (DeSPA), that retrieves tumor-related genes by mining a gene regulatory network (GRN) of transcription factors and miRNAs. With extensive experiments of the cancer genome atlas (TCGA) breast cancer sequencing data, we showed that our approach was able to select genes that belong to cancer core pathways such as DNA replication, cell cycle, p53 pathways while keeping the accuracy of breast cancer subtype classification comparable to that of PAM50. In addition, our method produces a regulatory network of TF, miRNA, and their target genes that distinguish breast cancer subtypes, which is confirmed by experimental studies in the literature.

We present a kinetic model describing the growth of eukaryotic cells or, more specifically, the dependence of the cell volume on time in terms of the global interplay of the mRNA and protein synthesis and degradation and lipid synthesis. Addressing two long-standing questions in this interdisciplinary field, we explain why the average protein concentration in growing cells is nearly constant and the growth can accurately be fitted by using a bilinear or exponential function.

DNA replication is a fundamental process that is tightly regulated during the cell cycle. In budding yeast it starts from multiple origins of replication and proceeds in a timely fashion according to a reproducible temporal program until the entire DNA is replicated exactly once per cell cycle. In this program an origin seems to have an inherent firing probability at a specific time in S-phase that is conserved over the population. However, what exactly determines the origin initiation time remains obscure. In this work, we analyze the gene content that clusters around replication origins following the assumption that inherent origin properties that determine staggered initiation times could potentially be mirrored in the close origin proximity. We perform a Gene Ontology term enrichment test and find that metabolic genes are significantly over-represented in the regions that are close to the starting points of DNA replication. Furthermore, functional analysis also reveals that catabolic genes cluster around early firing origins, whereas anabolic genes can rather be found in the proximity of late firing origins of replication. We speculate that, in budding yeast, gene function around replication origins correlates with their intrinsic probability to initiate DNA replication at a given point in S-phase.

The understanding of complex biological processes whose function requires the interaction of a large number of components is strongly improved by the construction of mathematical models able to capture the underlying regulatory wirings and to predict the dynamics of the process in a variety of conditions. Iterative rounds of simulations and experimental analysis generate models of increasing accuracy, what is called the systems biology approach. The cell cycle is one of the complex biological processes that benefit from this approach, and in particular budding yeast is an established model organism for these studies. The recent publication about the modeling of the G₁/S transition of the budding yeast cell cycle under a systems biology analysis has highlighted in particular the implications of the cell size determination that impinge the events driving DNA replication. During the life cycle of eukaryotic cells, DNA replication is restricted to a specific time window, called the S phase, and several control mechanisms ensure that each DNA sequence is replicated once, and only once, in the period from one cell division to the next. Here we extend the analysis of the G₁/S transition model by including additional aspects concerning the DNA replication process, in order to give a reasonable explanation to the experimental dynamics, as well as of specific cell cycle mutants. Moreover, we show the mathematical description of the critical cell mass (P_s) that cells have to reach to start DNA replication, which value is modulated depending on the different activation of the replication origins. The sensitivity analysis of the influence that the kinetic parameters of the G₁/S transition model have on the setting of the P_s value is also reported.

Our macroscopic world abounds in knotted and linked rings. But even at the nanoscopic scale, works in molecular topology have shown that Nature builds DNA molecules, which form actual knots and links between themselves. Qualitative similarities may be observed between forms of the microscopic world, as well as between those of the macroscopic world; and by extracting the structures, it is possible to study their dynamics thanks to topological methods and techniques. This chapter is aimed to show that knots and links are ubiquitous scale-independent objects carrying a tremendous amount of precious information on the emergence of new forms and structures especially in quantum physics and in living matter. In fact, knotting and unknotting are “universal” principles underlying these forms and structures. This study is focused at showing that differential geometry and topological knots theory can be used notably (a) to find invariants for closed 3-manifolds related to quantum field theory, and (b) to describe 3-dimensional structures of DNA and protein-DNA complexes.