Cascading signaling pathways improve the fidelity of a stochastically and deterministically simulated molecular RS latch

<p>Abstract</p> <p>Background</p> <p>While biological systems have often been compared with digital systems, they differ by the strong effect of crosstalk between signals due to diffusivity in the medium, reaction kinetics and geometry. Memory elements have allowed the creation of autonomous digital systems and although biological systems have similar properties of autonomy, equivalent memory mechanisms remain elusive. Any such equivalent memory system, however, must silence the effect of crosstalk to maintain memory fidelity.</p> <p>Results</p> <p>Here, we present a system of enzymatic reactions that behaves like an RS latch (a simple memory element in digital systems). Using both a stochastic molecular simulator and ordinary differential equation simulator, we showed that crosstalk between two latches operating in the same spatial localization disrupts the memory fidelity of both latches. Crosstalk was reduced or silenced when simple reaction loops were replaced with multiple step or cascading reactions, showing that cascading signaling pathways are less susceptible to crosstalk.</p> <p>Conclusion</p> <p>Thus, the common biological theme of cascading signaling pathways is advantageous for maintaining the fidelity of a memory latch in the presence of crosstalk. The experimental implementation of such a latch system will lead to novel approaches to cell control using synthetic proteins and will contribute to our understanding of why cells behave differently even when given the same stimulus.</p

Inferring causal molecular networks: empirical assessment through a community-based effort.

It remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge, which focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. Using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective, and incorporating known biology was generally advantageous. Additional sub-challenges considered time-course prediction and visualization. Our results suggest that learning causal relationships may be feasible in complex settings such as disease states. Furthermore, our scoring approach provides a practical way to empirically assess inferred molecular networks in a causal sense

Injectable oxygenation therapeutics: evaluating the oxygen delivery efficacy of artificial oxygen carriers and kosmotropes in vitro

The aim of this paper was to utilise an existing in vitro setup to quantify the oxygen offloading capabilities of two different subsets of injectable oxygenation therapeutics: (1) artificial oxygen carriers (AOCs), which bind or dissolve oxygen and act as transport vectors, and (2) kosmotropes, which increase water hydrogen bonding and thereby decrease the resistance to oxygen movement caused by the blood plasma. Dodecafluoropentane emulsion (DDFPe) was chosen to represent the AOC subset while trans sodium crocetinate (TSC) was selected to represent the kosmotrope subset. PEG-Telomer-B (PTB), the surfactant utilised to encapsulate DDFP in emulsion form, was also tested to determine whether it affected the oxygen transport ability of DDFPe. The in vitro set-up was used to simulate a semi closed-loop circulatory system, in which oxygen could be delivered from the lungs to hypoxic tissues. Results of this study showed that (1) 0.5 ml of a PFC outperformed 6.25 ml of a kosmotrope in a controlled, in vitro setting and (2) that PTB and sucrose do not contribute to the overall oxygen transportation efficacy of DDFPe. These results could be therapeutically beneficial to ongoing and future pre-clinical and clinical studies involving various oxygenation agents

Ultrasound-mediated gene delivery of factor VIII plasmids for hemophilia A gene therapy in mice

Gene therapy offers great promises for a cure of hemophilia A resulting from factor VIII (FVIII) gene deficiency. We have developed and optimized a non-viral ultrasound-mediated gene delivery (UMGD) strategy. UMGD of reporter plasmids targeting mice livers achieved high levels of transgene expression predominantly in hepatocytes. Following UMGD of a plasmid encoding human FVIII driven by a hepatocyte-specific promoter/enhancer (pHP-hF8/N6) into the livers of hemophilia A mice, a partial phenotypic correction was achieved in treated mice. In order to achieve persistent and therapeutic FVIII gene expression, we adopted a plasmid (pHP-hF8-X10) encoding an FVIII variant with significantly increased FVIII secretion. By employing an optimized pulse-train ultrasound condition and immunomodulation, the treated hemophilia A mice achieved 25%–150% of FVIII gene expression on days 1–7 with very mild transient liver damage, as indicated by a small increase of transaminase levels that returned to normal within 3 days. Therapeutic levels of FVIII can be maintained persistently without the generation of inhibitors in mice. These results indicate that UMGD can significantly enhance the efficiency of plasmid DNA transfer into the liver. They also demonstrate the potential of this novel technology to safely and effectively treat hemophilia A