Quantitative Biology

The distributions of many proteins in rod-shaped bacteria are far from homogenous. Often they accumulate at the cell poles or in the cell center. At the same time, the copy number of proteins in a single cell is relatively small making the patterns noisy. To explore limits to protein patterns due to molecular noise, we studied a generic mechanism for spontaneous polar protein assemblies in rod-shaped bacteria, which is based on cooperative binding of proteins to the cytoplasmic membrane. For mono-polar assemblies, we find that the switching time between the two poles increases exponentially with the cell length and with the protein number.

Mathematical models of cardiac action potentials have become increasingly important in the study of heart disease and pharmacology, but concerns linger over their robustness during long periods of simulation, in particular due to issues such as model drift and non-unique steady states. Previous studies have linked these to violation of conservation laws, but only explored those issues with respect to charge conservation in specific models. Here, we propose a general and systematic method of identifying conservation laws hidden in models of cardiac electrophysiology by using bond graphs, and develop a bond graph model of the cardiac action potential to study long-term behaviour. Bond graphs provide an explicit energy-based framework for modelling physical systems, which makes them well-suited for examining conservation within electrophysiological models. We find that the charge conservation laws derived in previous studies are examples of the more general concept of a "conserved moiety". Conserved moieties explain model drift and non-unique steady states, generalising the results from previous studies. The bond graph approach provides a rigorous method to check for drift and non-unique steady states in a wide range of cardiac action potential models, and can be extended to examine behaviours of other excitable systems.

Bond rupture mechanism enables to explain in block asymmetry of elaxation, force-velocity curve and the path of energy dissipation in muscle

Reconstituted nicotinic acetylcholine receptors (nAChRs) exhibit significant gain-of-function upon addition of cholesterol to reconstitution mixtures, and cholesterol affects organization of nAChRs within domain-forming membranes, but whether nAChR partitions to cholesterol-rich liquid-ordered ("raft" or l o ) domains or cholesterol-poor liquid-disordered ( l do ) domains is unknown. We use coarse-grained molecular dynamics simulations to observe spontaneous interactions of cholesterol, saturated lipids, and polyunsaturated (PUFA) lipids with nAChRs. In binary Dipalmitoylphosphatidylcholine:Cholesterol (DPPC:CHOL) mixtures, both CHOL and DPPC acyl chains were observed spontaneously entering deep "non-annular" cavities in the nAChR TMD, particularly at the subunit interface and the β subunit center, facilitated by the low amino acid density in the cryo-EM structure of nAChR in a native membrane. Cholesterol was highly enriched in the annulus around the TMD, but this effect extended over (at most) 5-10Å. In domain-forming ternary mixtures containing PUFAs, the presence of a single receptor did not significantly affect the likelihood of domain formation. nAChR partitioned to any cholesterol-poor l do domain that was present, regardless of whether the l do or l o domain lipids had PC or PE headgroups. Enrichment of PUFAs among boundary lipids was positively correlated with their propensity for demixing from cholesterol-rich phases. Long n−3 chains (tested here with Docosahexaenoic Acid, DHA) were highly enriched in annular and non-annular embedded sites, partially displacing cholesterol and completely displacing DPPC, and occupying sites even deeper within the bundle. Shorter n−6 chains were far less effective at displacing cholesterol from non-annular sites.

Actin networks, acting as an engine pushing against an external load, are fundamentally important to cell motility. A measure of the effectiveness of an engine is the velocity the engine is able to produce at a given force, the force-velocity curve. One type of force-velocity curve, consisting of a concave region where velocity is insensitive to increasing force followed by a decrease in velocity, is indicative of an adaptive response. In contrast, an engine whose velocity rapidly decays as a convex curve in response to increasing force would indicate a lack of adaptive response. Even taken outside of a cellular context, branching actin networks have been observed to exhibit both concave and convex force-velocity curves. The exact mechanism that can explain both force-velocity curves is not yet known. We carried out an agent-based stochastic simulation to explore such a mechanism. Our results suggest that upon loading, branching actin networks are capable of remodeling by increasing the number filaments growing against the load. Our model provides a mechanism that can account for both convex and concave force-velocity relationships observed in branching actin networks. Finally, our model gives a potential explanation to the experimentally observed force history dependence for actin network velocity.

We scrutinize the temporally-resolved speed of active cargo transport in living cells, and show intermittent bursting motions. These nonlinear fluctuations follow a scaling law over several decades of time and space, the statistical regularities displaying a time-averaged shape that we interpret to reflect stress buildup followed by rapid release. The power law of scaling is the same as seen in driven jammed colloids, granular, and magnetic systems. The implied regulation of active transport with environmental obstruction extends the classical notion of molecular crowding.

We demonstrate that endonuclease deficient Clustered Regularly Interspaced Short Palindromic Repeats CRISPR-associated Cas9 protein (dCas9) fused to the photo-convertible fluorescence protein monomeric mEos3.1 (dCas9-mEos3) can be used to resolve sub-diffraction limited features of repetitive gene elements, thus providing a new route to investigate high-order chromatin organization at these sites.

Background: A fundamental problem in cancer research is identifying the cell type that is capable of sustaining neoplastic growth and its origin from normal tissue cells. Recent investigations of a variety of tumor types have shown that phenotypically identifiable and isolable subfractions of cells possess the tumor-forming ability. In the present paper, using two lineage-related human melanoma cell lines, primary melanoma line IGR39 and its metastatic derivative line IGR37, two main observations are reported. The first one is the first phenotypic evidence to support the origin of melanoma cancer stem cells (CSCs) from mutated tissue-specific stem cells; and the second one is the identification of a more aggressive subpopulation of CSCs in melanoma that are CXCR6+. Conclusions/Significance: The association of a more aggressive tumor phenotype with asymmetric self-renewal phenotype reveals a previously unrecognized aspect of tumor cell physiology. Namely, the retention of some tissue-specific stem cell attributes, like the ability to asymmetrically self-renew, impacts the natural history of human tumor development. Knowledge of this new aspect of tumor development and progression may provide new targets for cancer prevention and treatment.

Ketamine is widely used in veterinary medicine and in medicine. Ketamine is metabolized to its active metabolite norketamine principally by liver CYP3A. Drug metabolism alterations during aging have severe consequences particularly in anesthesiology and very few studies on older animals were conducted for ketamine. The objective of the present study is to assess the influence of aging on CYP3A metabolism of ketamine. Liver S9 fractions from 3, 6, 12 and 18 month old male Sprague Dawley rats were prepared and Michaelis-Menten parameters were determined for primary metabolic pathways. The derived maximum enzyme velocity (i.e. Vmax) suggests a rapid saturation of the CYP3A enzyme active sites in liver S9 fractions of 18-month old rats. Observed Vmax for Liver S9 fractions from 3, 6 and 12 month old male Sprague Dawley rats were 2.39 (+-0.23), 2.61 (+-0.18), and 2.07 (+-0.07) respectively compared to 0.68 (+-0.02) for Liver S9 fractions from 18 month old male Sprague Dawley rats. Interestingly, we observed a 6 to 7 fold change in the derived Km when comparing Liver S9 fractions from 18 month old male Sprague Dawley rats with Liver S9 fractions from younger rats. Our results suggest that rat CYP3A enzyme undergoes conformational changes with age particularly in our geriatric group (e.g. 18 month rats) leading significant decrease in the rate of formation of norketamine. Moreover, our results strongly suggest a severe impairment of CYP3A ketamine mediated metabolism.

Calcium (Ca2+) plays a central role in mediating both contractile function and hypertrophic signalling in ventricular cardiomyocytes. L-type Ca2+ channels trigger release of Ca2+ from ryanodine receptors (RyRs) for cellular contraction, while signalling downstream of Gq coupled receptors stimulates Ca2+ release via inositol 1,4,5-trisphosphate receptors (IP3Rs), engaging hypertrophic signalling pathways. Modulation of the amplitude, duration, and duty cycle of the cytosolic Ca2+ contraction signal, and spatial localisation, have all been proposed to encode this hypertrophic signal. Given current knowledge of IP3Rs, we develop a model describing the effect of functional interaction (cross-talk) between RyR and IP3R channels on the Ca2+ transient, and examine the sensitivity of the Ca2+ transient shape to properties of IP3R activation. A key result of our study is that IP3R activation increases Ca2+ transient duration for a broad range of IP3R properties, but the effect of IP3R activation on Ca2+ transient amplitude is dependent on IP3 concentration. Furthermore we demonstrate that IP3-mediated Ca2+ release in the cytosol increases the duty cycle of the Ca2+ transient, the fraction of the cycle for which [Ca2+] is elevated, across a broad range of parameter values and IP3 concentrations. When coupled to a model of downstream transcription factor (NFAT) activation, we demonstrate that there is a high correspondence between the Ca transient duty cycle and the proportion of activated NFAT in the nucleus. These findings suggest increased cytosolic Ca2+ duty cycle as a plausible mechanism for IP3-dependent hypertrophic signalling via Ca2+-sensitive transcription factors such as NFAT in ventricular cardiomyocytes.