Session X10: Virology and Medical Physics

Viral Disease Networks?

Viral infections induce multiple perturbations that spread along the links of the biological networks of the host cells. Understanding the impact of these cascading perturbations requires an exhaustive knowledge of the cellular machinery as well as a systems biology approach that reveals how individual components of the cellular system function together. Here we describe an integrative method that provides a new approach to studying virus-human interactions and its correlations with diseases. Our method involves the combined utilization of protein - protein interactions, protein -- DNA interactions, metabolomics and gene - disease associations to build a ``viraldiseasome''. By solely using high-throughput data, we map well-known viral associated diseases and predict new candidate viral diseases. We use microarray data of virus-infected tissues and patient medical history data to further test the implications of the viral diseasome. We apply this method to Epstein-Barr virus and Human Papillomavirus and shed light into molecular development of viral diseases and disease pathways.   

Thermodynamics of nano-spheres encapsulated in virus capsids

We investigate the thermodynamics of complexation of functionalized charged nano-spheres with viral proteins. The physics of this problem is governed by electrostatic interaction between the proteins and the nano-sphere cores (screened by salt ions), but also by configurational degrees of freedom of the charged protein N-tails. We approach the problem by constructing an appropriate complexation free energy functional. On the basis of both numerical and analytical studies of this functional we construct the phase diagram for the assembly which contains the information on the assembled structures that appear in the thermodynamical equilibrium, depending on the size and surface charge density of the nano-sphere cores. We show that both the nano-sphere core charge as well as its radius determine the size of the capsid around the core.   

Mechanical oscillations of a viral capsid

Viruses are sub-microscopic infectious agents that infect almost every living creature on Earth. They are unable to grow or reproduce outside of a host cell and are therefore parasitic in nature. A virus' internal genetic material is protected by an external protein coat (capsid). We developed a theoretical model which uses the interaction of light with a viral capsid to create large amplitude motions within the capsid. This work displays the results of the model on the tobacco mosaic virus (TMV) with attached RNA genome. The development of this model was motivated by the experimental work of Tsen et. al. [1] who used ultra-short laser pulses to inactivate viruses. [1] K-T. Tsen et al., J. of Physics -- Cond. Mat. 19, 472201 (2007).   

Coarse-grained computational studies of the assembly of viral capsids around a flexible polymer

During the replication of many viruses, hundreds to thousands of protein subunits assemble around the viral nucleic acid to form a protein shell called a capsid. Recent electron microscopy experiments on small ssRNA viruses have shown that their enclosed RNA adopts the icosahedral symmetry of the overall capsid structure. The process that leads to this ordered encapsulation of the RNA is unknown. In this talk, we will explore dynamical simulations of coarse grained models that represent capsid proteins assembling around a flexible polymer, which shed light on the mechanisms by which icosahedral order emerges. We will discuss geometric and kinetic factors that control assembly, including the limits on the length of RNA that can be efficiently packaged. We will also report on several forms of cooperative polymer-protein motions that contribute to efficient and robust assembly. Finally, we will discuss how the simulation predictions can be tested with imaging experiments, bulk assembly kinetics measurements, and recently developed single molecule techniques that monitor the assembly of individual capsids.   

Low-dimensional clustering reveals new influenza strains before they become dominant

Influenza A virus has been circulating in the human population and has caused three pandemics in the last century (1918 H1N1, 1957 H2N2, 1968 H3N2). The newly appeared 2009 A(H1N1) has been classified by the World Health Organization (WHO) as the fourth pandemic virus strain. We here consider an approach for early detection of new dominant strains. We first construct a network model and apply it to the evolution of the 2009 A(H1N1) virus. By clustering the sequence data, we found two main clusters. We then define a metric to detect the emergence of dominant strains. We show on historical H3N2 data that this method is able to find a cluster around an incipient dominant strain before it becomes dominant. For example, for H3N2 as of 30 March 2009, we see the cluster for the new A/BritishColumbia/RV1222/2009 strain. Turning to H1N1 and the 2009 A(H1N1), we do not see evidence for antigenically novel 2009 A(H1N1) strains as of August 2009. This strain detection tool combines a projection operator with a density estimation.   

Information Entropy Analysis of the H1N1 Genetic Code

During the current H1N1 pandemic, viral samples are being obtained from large numbers of infected people world-wide and are being sequenced on the NCBI Influenza Virus Resource Database. The information entropy of the sequences was computed from the probability of occurrence of each nucleotide base at every position of each set of sequences using Shannon's definition of information entropy, \[ H=\sum\limits_b {p_b \,\log _2 \left( {\frac{1}{p_b }} \right)} \] where H is the observed information entropy at each nucleotide position and p$_{b}$ is the probability of the base pair of the nucleotides {\{}A, C, G, U{\}}. Information entropy of the current H1N1 pandemic is compared to reference human and swine H1N1 entropy. As expected, the current H1N1 entropy is in a low entropy state and has a very large mutation potential. Using the entropy method in mature genes we can identify low entropy regions of nucleotides that generally correlate to critical protein function.   

DNA-DNA interaction inside bacteriophage modulated by multivalent counterions

The problem of inhibiting viral DNA ejection from bacteriophages by multivalent counterions, especially Mg$^{+2}$ counterions, is studied. Experimentally, it is known that MgSO$_4$ salt has a strong and non-monotonic effect on the amount of DNA ejected. There exists an optimal concentration at which the least DNA is ejected from the virus. At lower or higher concentrations, more DNA is ejected from the capsid. We propose that this phenomenon is the result of DNA overcharging by Mg$^{+2}$ multivalent counterions. As Mg$^{+2}$ concentration increases from zero, DNA net charge changes from negative to positive. The optimal inhibition corresponds to the Mg$^{+2}$ concentration where DNA is neutral. At lower/higher concentrations, DNA genome is charged. It prefers to be in solution to lower its electrostatic self-energy, which consequently leads to an increase in DNA ejection. Our theory fits experimental data well. The strength of DNA - DNA short range attraction, mediated by Mg$^{+2}$, is found to be - 0.003 kBT per nucleotide base. Results from expanded ensemble Monte-Carlo simulation of hexagonal DNA bundles are discussed and are shown to be in good agreement with theoretical results.   

Chemically unassisted phototherapy: dose effects via real-time optical monitoring of cancer cells

Ultraviolet (UV) light and short wavelength visible (VIS) light have been used to kill pathogens for many years. Although the adverse effects of UV radiation on living cells have been extensively studied using biochemical and biomolecular techniques, most of the light therapies used for medical treatment are chemically assisted (i.e., photodynamic therapy). However, the use of light alone could prove both cost and therapeutically effective as an alternative treatment modality for localized diseases. In this study, real-time oblique incidence reflection (OIR) microscopy and image analysis were used to visualize and quantify the effects of chemically unassisted light therapy on untagged live cancer cells \textit{in vitro}. The incident radiation fluence (in mJ/cm$^{2})$ required to induce cell death was determined for selected quasi-monochromatic UV to VIS wavelengths ranging from 275nm to 460nm. A predictive mathematical equation quantifying the lethal fluence as a function of wavelength will be discussed.   

Biological Modeling Based Outcome Analysis (BMOA) in 3D Conformal Radiation Therapy (3DCRT) Treatments for Lung and Breast Cancers

3DCRT treatments are the most commonly used techniques in the treatment of lung and breast cancers. The purpose of this study was to perform the BMOA of the 3DCRT plans designed for the treatment of breast and lung cancers utilizing HART program (\textit{Med. Phys. 36, p.2547(2009)}). The BMOA parameters include normal tissue complication probability (NTCP), tumor control probability (TCP), and the complication-free tumor control probability (P+). The 3DCRT plans were designed for (i) the palliative treatment of 8 left lung cancer patients (CPs) at early stage (m=8), (ii) the curative treatment of 8 left lung CPs at stages II and III (k=8), and (iii) the curative treatment of 8 left breast CPs (n=8). The NTCPs were noticeably small ($<$2{\%}) for heart, lungs and cord in both types of treatments except for the esophagus in lung CPs (k=8). Assessments of the TCPs and P+s also indicated good improvements in local tumor control in all plans. Homogeneous target coverage and improved dose conformality were the major advantages of such techniques in the treatment of breast cancer. These achievements support the efficacy of the 3DCRT techniques for the efficient treatment of various types of cancer.   

Induction heating and controlled drug release from thermosensitive magnetic microgels

Poly-N-isopropyl acrylamide (PNIPAM) is a biocompatible thermosensitive polymer that exhibits reversible volume phase transition from a hydrophilic coil to hydrophobic globule at the lower critical solution temperature (LCST) of 32 $^{o}$C. To stimulate conformational change we introduced magnetite nanoparticles (size $\sim $12 nm) in the PNIPAM matrix. The PNIPAM/magnetite nanoparticles composite was then exposed to an alternating magnetic field at a frequency of 380 kHz to induce heating in the nanoparticles by Neel and Brownian relaxations. We report \textit{in vitro} controlled release of anti-cancer drug mitoxantrone which was loaded into PNIPAM/magnetite nanoparticles composite, driven solely by the heating induced by the external magnetic field. We found that the drug released reached 4{\%} in only 4 minutes of heating to 50 $^{o}$C. We also present results on dielectric and magnetic anomalies near the LCST of the PNIPAM-Fe$_{3}$O$_{4}$ composite.   

A mimic study on effects of fluoride on tooth enamel structures

Tooth enamel is the hardest tissue in human body, and this superior mechanical property is contributed by its unique microstructures, i.e., oriented growth of rod-like apatite crystals into basic structural units called the prisms Fluoride (F$^{-})$ has been recognized to have significant effects on the physical and chemical properties of tooth enamel. However, the role of F$^{-}$ on microstructures of apatite crystals is not well understood yet. Here we report a detailed investigation on the topic. Mimic \textit{in vitro} growth of tooth enamel structures is performed at the biophysical conditions in simulated body fluids, using belt-like hydroxyapatite crystals as substrates It shows that F$^{-}$ on the order of 0.1 mM will dramatically change the morphology of the grown crystals from irregular slabs to nano-needles, and the needles are aligned along the substrate with an average misorientation of $\sim $12\r{ }. Branched growth of bundles of nano-needles occurs with further increase of F$^{-}$, and finally, growth of highly porous structures as well as microspheres takes place when the F$^{-}$ concentration exceeds 5 mM. In comparison with real tooth enamel structures, the relationship between enamel microstructures and tooth caries as well as fluorosis is discussed.