Travelling Wave Solutions of Nonlinear Dynamical Equations in a Double-Chain Model of DNA

We consider the nonlinear dynamics in a double-chain model of DNA which consists of two long elastic homogeneous strands connected with each other by an elastic membrane. By using the method of dynamical systems, the bounded traveling wave solutions such as bell-shaped solitary waves and periodic waves for the coupled nonlinear dynamical equations of DNA model are obtained and simulated numerically. For the same wave speed, bell-shaped solitary waves of different heights are found to coexist

Dynamic Studies of Scaffold-dependent Mating Pathway in Yeast

The mating pathway in \emph{Saccharomyces cerevisiae} is one of the best understood signal transduction pathways in eukaryotes. It transmits the mating signal from plasma membrane into the nucleus through the G-protein coupled receptor and the mitogen-activated protein kinase (MAPK) cascade. According to the current understandings of the mating pathway, we construct a system of ordinary differential equations to describe the process. Our model is consistent with a wide range of experiments, indicating that it captures some main characteristics of the signal transduction along the pathway. Investigation with the model reveals that the shuttling of the scaffold protein and the dephosphorylation of kinases involved in the MAPK cascade cooperate to regulate the response upon pheromone induction and to help preserving the fidelity of the mating signaling. We explored factors affecting the dose-response curves of this pathway and found that both negative feedback and concentrations of the proteins involved in the MAPK cascade play crucial role. Contrary to some other MAPK systems where signaling sensitivity is being amplified successively along the cascade, here the mating signal is transmitted through the cascade in an almost linear fashion.Comment: 36 pages, 9 figure

Feature analysis of multidisciplinary scientific collaboration patterns based on PNAS

The features of collaboration patterns are often considered to be different from discipline to discipline. Meanwhile, collaborating among disciplines is an obvious feature emerged in modern scientific research, which incubates several interdisciplines. The features of collaborations in and among the disciplines of biological, physical and social sciences are analyzed based on 52,803 papers published in a multidisciplinary journal PNAS during 1999 to 2013. From those data, we found similar transitivity and assortativity of collaboration patterns as well as the identical distribution type of collaborators per author and that of papers per author, namely a mixture of generalized Poisson and power-law distributions. In addition, we found that interdisciplinary research is undertaken by a considerable fraction of authors, not just those with many collaborators or those with many papers. This case study provides a window for understanding aspects of multidisciplinary and interdisciplinary collaboration patterns

Direct Quantitative Analysis of Biomarkers using Mass Spectrometry

Point-of-care (POC) diagnostics describes a step in the medical treatment process where drugs can be monitored in a patient’s body on-site and in a timely fashion. Mass spectrometry (MS) can provide a quick, efficient, and highly accurate method of analysis of patient biofluids and tissues. Developing methods to bring this diagnostic mechanism to hospitals and clinics has the potential to improve patient care through, for example, personalized medicine. Our goal was to develop a way to effectively introduce internal standard (IS), a necessary chemical for the analytical process, to low-volume biofluid samples. Additionally, the effective direct quantitation of biomarkers with MS was demonstrated using a rat model of nicotine metabolism and the detection of 3-HPMA in urine. By pre-coating silica glass capillary tubes with a fixed volume with IS, biological samples, such as blood, can be obtained in the tube through capillary action and mixed with the IS before deposition for analysis. This method was applied to several different drugs and they were analyzed using a triple quadrupole mass spectrometer. It was optimized for the detection of the metabolite cotinine through a study of solvents and elution processes. Additionally, cotinine was quantified in rat’s blood using this method and the acrolein metabolite 3-HPMA was quantified in urine. Additional work is needed to expand this method for the rapid detection of other biomarkers. In the future, this can contribute to the expanded use of MS in clinical care and improved POC diagnostics