Progress in Biophysics and Molecular Biology

In atrial myocytes lacking t-tubules, action potential triggers junctional Ca(2+) releases in the cell periphery, which propagates into the cell interior. The present article describes growing evidence on atrial local Ca(2+) signaling and on the functions of inositol 1,4,5-trisphosphate receptors (IP(3)Rs) in atrial myocytes, and show our new findings on the role of IP(3)R subtype in the regulation of spontaneous focal Ca(2+) releases in the compartmentalized areas of atrial myocytes. The Ca(2+) sparks, representing focal Ca(2+) releases from the sarcoplasmic reticulum (SR) through the ryanodine receptor (RyR) clusters, occur most frequently at the peripheral junctions in isolated resting atrial cells. The Ca(2+) sparks that were darker and longer lasting than peripheral and non-junctional (central) sparks, were found at peri-nuclear sites in rat atrial myocytes. Peri-nuclear sparks occurred more frequently than central sparks. Atrial cells express larger amounts of IP(3)Rs compared with ventricular cells and possess significant levels of type 1 IP(3)R (IP(3)R1) and type 2 IP(3)R (IP(3)R2). Over the last decade the roles of atrial IP(3)R on the enhancement of Ca(2+)-induced Ca(2+) release and arrhythmic Ca(2+) releases under hormonal stimulations have been well documented. Using protein knock-down method and confocal Ca(2+) imaging in conjunction with immunocytochemistry in the adult atrial cell line HL-1, we could demonstrate a role of IP(3)R1 in the maintenance of peri-nuclear and non-junctional Ca(2+) sparks via stimulating a posttranslational organization of RyR clusters.

CellML 1.1 was released as a formal specification in February 2006 with the first release of a complete implementation of the CellML API following in December. The combination of these two developments paves the way for a powerful new paradigm in mathematically modeling cardiac cellular electrophysiology. In this article we explore the practical application of this paradigm using the example of integrating new mechanisms into a well known model of human ventricular myocyte electrophysiology. Through practical application of the CellML 1.1 paradigm we demonstrate the advantages inherent in such an approach and contrast them to more traditional methods of model description, exchange, and publication. This work has also provided the impetus for some recent developments in regard to CellML metadata specifications. The development of the tools and techniques used in this work has helped define some guidelines that should prove useful in future developments in this field. By following these guidelines model authors can increase the usability of their work by other scientists. This work presents the first attempt to utilize annotated CellML models to present not only the underlying mathematical models but also specify the numerical simulations and graphical outputs in an interchangeable, machine readable format. By doing so, all simulations are able to be duplicated by anyone with access to a capable tool. Similarly, identical graphical representations of the numerical simulation results can be produced.

Usage of magnetic resonance imaging (MRI) is continuously increasing due to its excellent soft-tissue contrast and improving diagnostic values. MRI also has the advantage that it operates without ionizing radiation. The main safety concerns are torque, acceleration by the static field, nerve stimulation by the gradient fields, and tissue heating by the radio-frequency (RF) fields. This paper investigates if children and fetuses are at higher risks than adults when the current RF regulations are applied. We analyzed and compared local absorption hotspots, i.e., the peak spatial specific absorption rate averaged over any 10 g (psSAR10g) for five adults, three children of ages 5, 11 and 14 years, and 1 pregnant female (36 weeks' gestation) in 10 different Z-positions (head to calves). In the First Level Operating Mode (4 W/kg whole-body averaged exposure), the psSAR10g values found for adults were as large as 60 W/kg in the trunk and 104 W/kg in the extremities. The corresponding values for children were 43 and 58 W/kg, respectively, and 14 W/kg for the unborn child. Modeling of worst case anatomical RF loops can substantially increase the psSAR10g values, i.e., by factor >2. The results suggest that local exposure for children and fetuses is smaller than for adults (15-75%), i.e., no special considerations for children and the unborn child are needed regarding psSAR10g due to RF. However, the local thermal load of the unborn may be significantly increased due to the high exposure average (up to 4 W/kg) of the non-perfused amniotic fluid.

The passive stiffness of cardiac muscle plays a critical role in ventricular filling during diastole and is determined by the extracellular matrix and the sarcomeric protein titin. Titin spans from the Z-disk to the M-band of the sarcomere and also contains a large extensible region that acts as a molecular spring and develops passive force during sarcomere stretch. This extensible segment is titin's I-band region, and its force-generating mechanical properties determine titin-based passive tension. The properties of titin's I-band region can be modulated by isoform splicing and post-translational modification and are intimately linked to diastolic function. This review discusses the physical origin of titin-based passive tension, the mechanisms that alter titin stiffness, and titin's role in stress-sensing signaling pathways.

The development of the immune system begins during embryogenesis, continues throughout fetal life, and completes its maturation during infancy. Exposure to immune-toxic compounds at levels producing limited/transient effects in adults, results in long-lasting or permanent immune deficits when it occurs during perinatal life. Potentially harmful radiofrequency (RF) exposure has been investigated mainly in adult animals or with cells from adult subjects, with most of the studies showing no effects. Is the developing immune system more susceptible to the effects of RF exposure? To address this question, newborn mice were exposed to WiFi signals at constant specific absorption rates (SAR) of 0.08 or 4 W/kg, 2h/day, 5 days/week, for 5 consecutive weeks, starting the day after birth. The experiments were performed with a blind procedure using sham-exposed groups as controls. No differences in body weight and development among the groups were found in mice of both sexes. For the immunological analyses, results on female and male newborn mice exposed during early post-natal life did not show any effects on all the investigated parameters with one exception: a reduced IFN-γ production in spleen cells from microwaves (MW)-exposed (SAR 4 W/kg) male (not in female) mice compared with sham-exposed mice. Altogether our findings do not support the hypothesis that early post-natal life exposure to WiFi signals induces detrimental effects on the developing immune system.

Decoding of the genome information in terms of regulation and function will be the next great challenge in the life sciences in this millennium and indeed, today we are experiencing a rapid explosion of technology for the high throughput expression analysis of genes and their products (functional genomics). In particular, the field of proteomics is booming as proteins are often the functional molecules and represent important targets for the pharmaceutical industry. The proteomic technology is complex, and comprises a plethora of state-of-the-art techniques to resolve, identify and detect their interacting partners, as well as to store and communicate protein information in comprehensive two-dimensional polyacrylamide gel electrophoresis (2D PAGE) databases. Besides annotating the genome, these databases will offer a global approach to the study of gene expression both in health and disease. Here, we review the current status of human 2D PAGE databases that we are systematically constructing for the study of bladder cancer and skin ageing.

Malignant hypertension is a rare but serious syndrome complicating 1% of essential hypertension and causing neurological, renal and cardiac complications. Despite improved anti-hypertensive medication, the incidence of this condition fails to decline. In the first part of this review, we discuss transgenic rat models of malignant hypertension, generated by over-expressing renin, to illustrate the role of the renin-angiotensin system in the development of systemic hypertensive vascular remodelling and hypertension. In the second part, we focus on the cerebrovascular response to hypertension and discuss new data using a conditional, transgenic model of malignant hypertension, the inducible hypertensive rat (IHR). Cerebral infarction associates strongly with hypertension in man and the mechanisms by which hypertension predisposes to different types of stroke remains poorly understood. Rats have similar cerebrovascular anatomy and structure to humans and as such provide a good experimental tool. To date, such models lack controllability and blood-pressure matched controls. Using the IHR, we have manipulated dietary salt and water intake to generate a novel, controllable stroke phenotype. Hypertensive small-vessel stroke develops over a predictable time period, permitting the study of developing cerebrovascular lesions. Systemic end-organ injury and hypertension are not affected. Dissociation of the systemic and central vascular responses in this way, will allow for comparative study of animals with equivalent hypertension, genetic background and systemic features of hypertension with or without stroke.

There is a paucity of knowledge on how mRNA transcripts in the spatially crowded, but molecularly organized bacterial cytoplasm contact the 30S ribosomal subunits. Does simple diffusion in the cytoplasm account for transcript-ribosome interactions given that a large number of ribosomes (e.g., about 72,000 in Escherichia coli during exponential growth) can be present in the cytoplasm? Or are undiscovered mechanisms present where specific transcripts are directed to specific ribosomes at specific cytoplasmic locations, while others are mobilized in a random manner? Moreover, is it possible that cytoplasmic mobilization occurs in bacteria, driven possibly by thermal infrared (IR) radiation and the generation of exclusion zone (EZ) water? These aspects will be discussed in this article and hypotheses presented.

The availability of high-quality crystals is crucial to the structure determination of proteins by X-ray diffraction. With the advent of structural genomics the pressure to produce crystals is greater than ever before. Finding favourable conditions for crystallisation is usually achieved by screening of the protein solution with numerous crystallising agents. Optimisation of the crystallisation conditions involves the manipulation of the crystallisation phase diagram with the aim of leading crystal growth in the direction that will produce the desired results. This article highlights recent advances in experimental methods for improving crystal size and quality by separating the nucleation and growth phases of crystallisation using the vapour diffusion and microbatch techniques.

Measurements of the geometry and fibrous-sheet structure of the left and right ventricles of the pig heart are fitted with a finite element model. Mechanical changes during the heart cycle are computed by solving the equations of motion under specified ventricular boundary conditions and using experimentally defined constitutive laws for the active and passive material properties of myocardial tissue. The resulting patterns of deformation, such as axial torsion and changes in wall thickness and base-apex length, are consistent with experimental observations. The model can therefore be used to predict sarcomere length changes and other strain patterns throughout the myocardium and throughout the cardiac cycle. Here we present sarcomere length changes at a limited number of material points within the wall. Sarcomere length typically varies by 10% above and below the unloaded length; although under the boundary conditions imposed in the current model the midwall circumferentially oriented sarcomere lengths increased by up to 20% at end diastole. We provide web-access details for a downloadable software program designed to provide more extensive information on mechanical deformation, such as the principal strains and muscle fibre cross-sectional area changes during the cardiac cycle.

Membrane proteins play important roles in cell functions such as neurotransmission, muscle contraction, and hormone secretion, but their structures are mostly undetermined. Several techniques have been developed to elucidate the structure of macromolecules; X-ray or electron crystallography, nuclear magnetic resonance spectroscopy, and high-resolution electron microscopy. Electron microscopy-based single particle reconstruction, a computer-aided structure determination method, reconstructs a three-dimensional (3D) structure from projections of monodispersed protein. A large number of particle images are picked up from EM films, aligned and classified to generate two-dimensional (2D) averages, and, using the Euler angle of each 2D average, reconstructed into a 3D structure. This method is challenging due to the necessity for close collaboration between classical biochemistry and innovative information technology, including parallel computing. However, recent progress in electron microscopy, mathematical algorithms, and computational ability has greatly increased the subjects that are considered to be primarily addressable using single particle reconstruction. Membrane proteins are one of these targets to which the single particle reconstruction is successfully applied for understanding of their structures. In this paper, we will introduce recently reconstructed channel-related proteins and discuss the applicability of this technique in understanding molecular structures and their roles in pathology.

Ryanodine receptors (RyRs) are intracellular Ca(2+) release channels (CRCs) that play a pivotal role in cellular Ca(2+) signaling. In striated muscles, RyR-mediated Ca(2+) release from the sarcoplasmic reticulum (SR) induces elevation of cytosolic Ca(2+) concentration and subsequent muscle contraction. Evidence from various sources suggests that RyRs in homo-tetrameric conformation form a large conductance Ca(2+) permeable channel in the central pore and large cytoplasmic domains. RyRs form a large assembly with various cytosolic and luminal proteins. A number of papers have been published concerning the functions of RyRs and the regulation of the associated proteins, but the three dimensional (3D) structure of the assembly has not been addressed in detail. In this paper, we have attempted to establish a 3D-map for the assembly of RyRs by considering published cryo-EM data, available X-ray crystallographic information and molecular modeling methods.

Despite a vast amount of experimental and clinical data on the underlying ionic, cellular and tissue substrates, the mechanisms of common atrial arrhythmias (such as atrial fibrillation, AF) arising from the functional interactions at the whole atria level remain unclear. Computational modelling provides a quantitative framework for integrating such multi-scale data and understanding the arrhythmogenic behaviour that emerges from the collective spatio-temporal dynamics in all parts of the heart. In this study, we have developed a multi-scale hierarchy of biophysically detailed computational models for the human atria--the 3D virtual human atria. Primarily, diffusion tensor MRI reconstruction of the tissue geometry and fibre orientation in the human sinoatrial node (SAN) and surrounding atrial muscle was integrated into the 3D model of the whole atria dissected from the Visible Human dataset. The anatomical models were combined with the heterogeneous atrial action potential (AP) models, and used to simulate the AP conduction in the human atria under various conditions: SAN pacemaking and atrial activation in the normal rhythm, break-down of regular AP wave-fronts during rapid atrial pacing, and the genesis of multiple re-entrant wavelets characteristic of AF. Contributions of different properties of the tissue to mechanisms of the normal rhythm and arrhythmogenesis were investigated. Primarily, the simulations showed that tissue heterogeneity caused the break-down of the normal AP wave-fronts at rapid pacing rates, which initiated a pair of re-entrant spiral waves; and tissue anisotropy resulted in a further break-down of the spiral waves into multiple meandering wavelets characteristic of AF. The 3D virtual atria model itself was incorporated into the torso model to simulate the body surface ECG patterns in the normal and arrhythmic conditions. Therefore, a state-of-the-art computational platform has been developed, which can be used for studying multi-scale electrical phenomena during atrial conduction and AF arrhythmogenesis. Results of such simulations can be directly compared with electrophysiological and endocardial mapping data, as well as clinical ECG recordings. The virtual human atria can provide in-depth insights into 3D excitation propagation processes within atrial walls of a whole heart in vivo, which is beyond the current technical capabilities of experimental or clinical set-ups.

Single particle analysis and 3D reconstruction of molecules imaged by transmission electron microscopy have provided a wealth of medium to low resolution structures of biological molecules and macromolecular complexes, such as the ribosome, viruses, molecular chaperones and photosystem II. In this review, the principles of these techniques are introduced in a non-mathematical way, and single particle analysis is compared to other methods used for structural studies. In particular, the recent X-ray structures of the ribosome and of ribosomal subunits allow a critical comparison of single particle analysis and X-ray crystallography. This has emphasised the rapidity with which single particle analysis can produce medium resolution structures of complexes that are difficult to crystallise. Once crystals are available, X-ray crystallography can produce structures at a much higher resolution. The great similarities now seen between the structures obtained by the two techniques reinforce confidence in the use of single particle analysis and 3D reconstruction, and show that for electron cryo-microscopy structure distortion during sample preparation and imaging has not been a significant problem. The ability to analyse conformational flexibility and the ease with which time-resolved studies can be performed are significant advantages for single particle analysis. Future improvements in single particle analysis and electron microscopy should increase the attainable resolution. Combining single particle analysis of macromolecular complexes and electron tomography of subcellular structures with high-resolution X-ray structures may enable us to realise the ultimate dream of structural biology-a complete description of the macromolecular complexes of the cell in their different functional states.

All members of the inwardly rectifying potassium channels (Kir1-7) are regulated by the membrane phospholipid, phosphatidylinosital-4,5-bisphosphate (PIP(2)). Some are also modulated by other regulatory factors or ligands such as ATP and G-proteins, which give them their common names, such as the ATP sensitive potassium (K(ATP)) channel and the G-protein gated potassium channel. Other more non-specific regulators include polyamines, kinases, pH and Na(+) ions. Recent studies have demonstrated that PIP(2) acts cooperatively with other regulatory factors to modulate Kir channels. Here we review how PIP(2) and co-factors modulate channel activities in each subfamily of the Kir channels.

To characterize the effects of inhibition of Ryanodine receptor (RyR), TTX-sensitive neuronal Na+ current (iNa), "rapidly activating" delayed rectifier K+ current (iKr) and ultrarapid delayed rectifier potassium current (IKur) on the pacemaker activity of the sinoatrial node (SAN) and the atrioventricular node (AVN) in the mouse. The structure of mouse AVN was studied by histology and immunolabelling of Cx43 and hyperpolarization-activated, cyclic nucleotide-binding channels (HCN). The effects of Ryanodine, TTX, E-4031 and 4-AP on pacemaker activities recorded from mouse intact SAN and AVN preparations have been investigated. Immuno-histological characterization delineated the structure of the AVN showing the similar molecular phenotype of the SAN. The effects of these inhibitors on the cycle length (CL) of the spontaneous pacemaker activity of the SAN and the AVN were characterized. Inhibition of RyR by 0.2 and 2 microM Ryanodine prolonged CL by 42+/-12.3% and 64+/-18.1% in SAN preparations by 163+/-72.3% and 241+/-91.2% in AVN preparations. Inhibition of TTX-sensitive iNa by 100 nM TTX prolonged CL by 22+/-6.0% in SAN preparations and 53+/-13.6% in the AVN preparations. Block of iKr by E-4031 prolonged CL by 68+/-12.5% in SAN preparations and 28+/-3.4% in AVN preparations. Inhibition of iKur by 50 microM 4-AP prolonged CL by 20+/-3.4% in SAN preparations and 18+/-3.0% in AVN preparations. Mouse SAN and AVN showed distinct different response to the inhibition of RyR, TTX-sensitive INa, IKr and iKur, which reflects the variation in contribution of these currents to the pacemaker function of the cardiac nodes in the mouse. Our data provide valuable information for developing virtual tissue models of mouse SAN and AVN.

Connexins form a diverse and ubiquitous family of integral membrane proteins. Characteristically, connexins are assembled into intercellular channels that aggregate into discrete cell-cell contact areas termed gap junctions (GJ), allowing intercellular chemical communication, and are essential for propagation of electrical impulses in excitable tissues, including, prominently, myocardium, where connexin 43 (Cx43) is the most important isoform. Previous studies have shown that GJ-mediated communication has an important role in the cellular response to stress or ischemia. However, recent evidence suggests that connexins, and in particular Cx43, may have additional effects that may be important in cell death and survival by mechanisms independent of cell to cell communication. Connexin hemichannels, located at the plasma membrane, may be important in paracrine signaling that could influence intracellular calcium and cell survival by releasing intracellular mediators as ATP, NAD(+), or glutamate. In addition, recent studies have shown the presence of connexins in cell structures other than the plasma membrane, including the cell nucleus, where it has been suggested that Cx43 influences cell growth and differentiation. In addition, translocation of Cx43 to mitochondria appears to be important for certain forms of cardioprotection. These findings open a new field of research of previously unsuspected roles of Cx43 intracellular signaling.

Signaling networks are complex both in terms of the chemical and biophysical events that underlie them, and in the sheer number of interactions. Computer models are powerful tools to deal with both aspects of complexity, but their utility goes beyond simply replicating signaling events in silicon. Their great advantage is as a tool to understanding. The completeness of the description demanded by computer models highlights gaps in knowledge. The quantitative description in models facilitates a mapping between different kinds of analysis methods for complex systems. Systems analysis methods can highlight stable states of signaling networks and describe the transitions between them. Modeling also reveals functional similarities between signaling network properties and other well-understood systems such as electronic devices and neural networks. These suggest various metaphors as a tool to understanding. Based on such descriptions, it is possible to regard signaling networks as systems that decode complex inputs in time, space and chemistry into combinatorial output patterns of signaling activity. This would provide a natural interface to the combinatorial input patterns required by genetic circuits. Thus, a combination of computer modeling methods to capture the complexity and details, and useful abstractions revealed by these models, is necessary to achieve both rigorous description as well as human understanding.

Vitamin D, the sunshine vitamin, has been recognized for almost 100 years as being essential for bone health. Vitamin D provides an adequate amount of calcium and phosphorus for the normal development and mineralization of a healthy skeleton. Vitamin D made in the skin or ingested in the diet, however, is biologically inactive and requires obligate hydroxylations first in the liver to 25-hydroxyvitamin D, and then in the kidney to 1,25-dihydroxyvitamin D. 25-Hydroxyvitamin D is the major circulating form of vitamin D that is the best indicator of vitamin D status. 1,25-dihydroxyvitamin D is the biologically active form of vitamin D. This lipid-soluble hormone interacts with its specific nuclear receptor in the intestine and bone to regulate calcium metabolism. It is now recognized that the vitamin D receptor is also present in most tissues and cells in the body. 1,25-dihydroxyvitamin D, by interacting with its receptor in non-calcemic tissues, is able to elicit a wide variety of biologic responses. 1,25-dihydroxyvitamin D regulates cellular growth and influences the modulation of the immune system. There is compelling epidemiologic observations that suggest that living at higher latitudes is associated with increased risk of many common deadly cancers. Both prospective and retrospective studies help support the concept that it is vitamin D deficiency that is the driving force for increased risk of common cancers in people living at higher latitudes. Most tissues and cells not only have a vitamin D receptor, but also have the ability to make 1,25-dihydroxyvitamin D. It has been suggested that increasing vitamin D intake or sun exposure increases circulating concentrations of 25-hydroxyvitamin D, which in turn, is metabolized to 1,25-dihydroxyvitamin D(3) in prostate, colon, breast, etc. The local cellular production of 1,25-dihydroxyvitamin D acts in an autocrine fashion to regulate cell growth and decrease the risk of the cells becoming malignant. Therefore, measurement of 25-hydroxyvitamin D is important not only to monitor vitamin D status for bone health, but also for cancer prevention.

Three biological settings involving self-organization performed by the Turing-Child field inside a sphere and on its surface are considered. In the first setting the interior of a sphere made up of cells communicating via gap junctions is considered. It is suggested that the Turing-Child self-organization is the cause of radial polarization, the first differentiation of an early mammalian embryo. In the second setting, the Turing example of gastrulation of a hollow cellular sphere is considered. It is shown that Child's experimental patterns are predicted and explained by the Turing-Child theory. The third setting is the interior of a biological cell, and it is suggested that it is the self-organization of the Turing-Child field that causes the formation of the mitotic spindle.

The integrity of the bacterial cytoplasmic membrane is critical in maintaining the viability of cells and their metabolic functions, particularly under stress. Bacteria actively adjust membrane fluidity through changes in lipid composition in response to variations in temperature, pressure, ion concentrations, pH, nutrient availability, and xenobiotics. Fluorescence polarization methods are valuable for measuring bacterial cytoplasmic membrane fluidity. In this review we discuss the mechanisms of bacterial membrane adaptations and present data from research using 1,6-diphenyl-1,3,5-hexatirene (DPH) as a measure of membrane fluidity and phase transitions. We illustrate the range of fluidity in viable cells, extracted membranes, and liposomes under optimal and stressed physiological conditions.

γ-band oscillations are thought to play a crucial role in information processing in cortical networks. In addition to oscillatory activity between 30 and 60 Hz, current evidence from electro- and magnetoencephalography (EEG/MEG) and local-field potentials (LFPs) has consistently shown oscillations >60 Hz (high γ-band) whose function and generating mechanisms are unclear. In the present paper, we summarize data that highlights the importance of high γ-band activity for cortical computations through establishing correlations between the modulation of oscillations in the 60-200 Hz frequency and specific cognitive functions. Moreover, we will suggest that high γ-band activity is impaired in neuropsychiatric disorders, such as schizophrenia and epilepsy. In the final part of the paper, we will review physiological mechanisms underlying the generation of high γ-band oscillations and discuss the functional implications of low vs. high γ-band activity patterns in cortical networks.

In this review a description and an analysis are given of the interaction of antiarrhythmic drugs with their molecular target, i.e. ion channels and receptors. Our approach is based on the concept of vulnerable parameter, i.e. the electrophysiological property which plays a crucial role in the genesis of arrhythmias. To prevent or stop the arrhythmia a drug should modify the vulnerable parameter by its action on channel or receptor targets. In the first part, general aspects of the interaction between drugs channel molecules are considered. Drug binding depends on the state of the channel: rested, activated pre-open, activated open, or inactivated state. The change in channel behaviour with state is presented in the framework of the modulated-receptor hypothesis. Not only inhibition but also stimulation can be the result of drug binding. In the second part a detailed and systematic description and an analysis are given of the interaction of drugs with specific channels (Na+, Ca2+, K+, "pacemaker") and non-channel receptors. Emphasis is given to the type of state-dependent block involved (rested, activated and inactivated state block) and the change in channel kinetics. These properties vary and determine the voltage- and frequency-dependence of the change in ionic current. Finally, the question is asked as to whether the available drugs by their action on channels and receptors modify the vulnerable parameter in the desired way to stop or prevent arrhythmias.

The UVA (320-380 nm) component of sunlight has oxidizing properties which may be deleterious to skin cells and tissue but can also lead to the strong up-regulation of the heme-catabolizing enzyme, heme oxygenase-1. This enzyme has well-established antioxidant actions in cells as well as anti-inflammatory properties in mammals. There is also evidence from rodent models that this enzyme is responsible for the UVA-mediated protection against UVB-induced immunosuppression that occurs in skin. The relevance of these findings to acute and chronic effects of sunlight including skin carcinogenesis is currently under investigation as are the potential implications for sunlight protection in humans.

A hypothesis is proposed that the first cell(s) on the Earth assembled in a hydrogel environment. Gel environments are capable of retaining water, oily hydrocarbons, solutes, and gas bubbles, and are capable of carrying out many functions, even in the absence of a membrane. Thus, the gel-like environment may have conferred distinct advantages for the assembly of the first cell(s).

The major well-proven long-term health risks of excessive exposure to ultraviolet (UV) radiation relate to the skin. Premalignant skin lesions are seen very much earlier in white skinned populations exposed to excessive sunlight, and over time these same individuals develop larger numbers of all of the three major skin cancers than individuals who do not experience excessive UV exposure. These three skin cancers are squamous cell carcinoma (SCC), basal cell carcinoma (BCC), and malignant melanoma. In the case of SCC the major aetiological pattern is chronic long-term exposure, but for BCCs the pattern appears to be slightly different with short-term burning episodes being more important. In the case of melanomas, there is evidence that for the 4 main types of melanomas, the pattern of excess UV exposure which is most injurious varies.

Prediction of abdominal viscera and tumour positions during free breathing is a major challenge from which several medical applications could benefit. For instance, in radiotherapy it would reduce the healthy tissue irradiation. In this paper, we present a new approach to predict real-time abdominal viscera positions during free breathing. Our method needs an abdo-thoracic 3D preoperative CT or MR image, a second one limited to the diaphragmatic area, and a tracking of the patient's skin position. First, a physical analysis of the breathing motion shows it is possible to predict accurately abdominal viscera positions from the skin position and a modelling of the diaphragm motion. Secondly, a quantitative analysis of the skin and organ motion allows us to define the demands our real-time simulation has to fulfill. Then, we present in detail all the necessary steps of our original method to compute a deformation field from data extracted in both 3D preoperative image and skin surface tracking. Finally, experiments carried out with two human data show that our simulation model predicts abdominal viscera positions, such as liver, kidneys or spleen, at 50 Hz with an accuracy within 2-3 mm.

We report for the first time abnormalities in cardiac ventricular electrophysiology in a genetically modified murine model lacking the Scn3b gene (Scn3b(-/-)). Scn3b(-/-) mice were created by homologous recombination in embryonic stem (ES) cells. RT-PCR analysis confirmed that Scn3b mRNA was expressed in the ventricles of wild-type (WT) hearts but was absent in the Scn3b(-/-) hearts. These hearts also showed increased expression levels of Scn1b mRNA in both ventricles and Scn5a mRNA in the right ventricles compared to findings in WT hearts. Scn1b and Scn5a mRNA was expressed at higher levels in the left than in the right ventricles of both Scn3b(-/-) and WT hearts. Bipolar electrogram and monophasic action potential recordings from the ventricles of Langendorff-perfused Scn3b(-/-) hearts demonstrated significantly shorter ventricular effective refractory periods (VERPs), larger ratios of electrogram duration obtained at the shortest and longest S(1)-S(2) intervals, and ventricular tachycardias (VTs) induced by programmed electrical stimulation. Such arrhythmogenesis took the form of either monomorphic or polymorphic VT. Despite shorter action potential durations (APDs) in both the endocardium and epicardium, Scn3b(-/-) hearts showed DeltaAPD(90) values that remained similar to those shown in WT hearts. The whole-cell patch-clamp technique applied to ventricular myocytes isolated from Scn3b(-/-) hearts demonstrated reduced peak Na(+) current densities and inactivation curves that were shifted in the negative direction, relative to those shown in WT myocytes. Together, these findings associate the lack of the Scn3b gene with arrhythmic tendencies in intact perfused hearts and electrophysiological features similar to those in Scn5a(+/-) hearts.

Amino acid side chains play fundamental roles in stabilising protein structures and in catalysing enzymatic reactions. These fields are increasingly investigated by infrared spectroscopy at the molecular level. To help the interpretation of the spectra, a review of the infrared absorption of amino acid side chains in H(2)O and 2H(2)O is given. The spectral region of 2600-900cm(-1) is covered.

The interaction of a dipole antenna with a human eye model in the presence of a metamaterial is investigated in this paper. The finite difference time domain (FDTD) method with convolutional perfectly matched layer (CPML) formulation have been used. A three-dimensional anatomical model of the human eye with resolution of 1.25mm × 1.25mm × 1.25mm was used in this study. The dipole antenna was driven by modulated Gaussian pulse and the numerical study is performed with dipole operating at 900 MHz. The analysis has been done by varying the size and value of electric permittivity of the metamaterial. By normalizing the peak SAR (1g and 10g) to 1 W for all examined cases, we observed how the SAR values are not affected by the different permittivity values with the size of the metamaterial kept fixed.

Systems biology is centrally engaged with computational modelling across multiple scales and at many levels of abstraction. Formal modelling, precise and formalised abstraction relationships, and computation also lie at the heart of computer science-and over the past decade a growing number of computer scientists have been bringing their discipline's core intellectual and computational tools to bear on biology in fascinating new ways. This paper explores some of the apparent points of contact between the two fields, in the context of a multi-disciplinary discussion on conceptual foundations of systems biology.

In his article of this issue, Denis Noble argues that causation can occur at and between any scales - rather than levels - in nature. I agree with this conclusion, but do not find his reasoning fully persuasive. I offer an independent but related argument for his position, which focuses on the role of the process of abstraction in identifying and understanding a phenomenon. My aim is to give the reader another way to think about causal talk within the framework of Systems Biology.

Experimentation is fundamental to the scientific method, whether for exploration, description or explanation. We argue that promoting the reuse of virtual experiments (the in silico analogues of wet-lab or field experiments) would vastly improve the usefulness and relevance of computational models, encouraging critical scrutiny of models and serving as a common language between modellers and experimentalists. We review the benefits of reusable virtual experiments: in specifying, assaying, and comparing the behavioural repertoires of models; as prerequisites for reproducible research; to guide model reuse and composition; and for quality assurance in the translational application of models. A key step towards achieving this is that models and experimental protocols should be represented separately, but annotated so as to facilitate the linking of models to experiments and data. Lastly, we outline how the rigorous, streamlined confrontation between experimental datasets and candidate models would enable a "continuous integration" of biological knowledge, transforming our approach to systems biology. Copyright © 2014. Published by Elsevier Ltd.

An acceleration of differentiation at the expense of proliferation is observed in our previous publications and in the literature after exposure of various biological models to low frequency and low amplitude electric and electromagnetic fields. This observation is related with a significant modification of genes expression. We observed and compared over time this modification. This study use microarray data obtained on epidermis cultures harvested from human abdominoplasty exposed to ELF electric fields. This protocol is repeated with samples collected on three different healthy patients. The sampling over time allows comparison of the effect of the stimulus at a given time with the evolution of control group. After four days, we observed a significant difference of the genes expression between control (D4C) and stimulated (D4S) (p < 0.05). On the control between day 4 and 7, we observed another group of genes with significant difference (p < 0.05) in their expression. We identify the common genes between these two groups and we select from them those expressing no difference between stimulate at four days (D4S) and control after seven days (D7C). The same analysis was performed with D4S-D4C-D12C and D7S-D7C-D12C. The lists of genes which follow this pattern show acceleration in their expressions under stimulation appearing on control at a later time. In this list, genes such as DKK1, SPRR3, NDRG4, and CHEK1 are involved in cell proliferation or differentiation. Numerous other genes are also playing a function in mitosis, cell cycle or in the DNA replication transcription and translation.

The in-vivo mechanical response of neural tissue during impact loading of the head is simulated using geometrically accurate finite element (FE) head models. However, current FE models do not account for the anisotropic elastic material behaviour of brain tissue. In soft biological tissue, there is a correlation between internal microscopic structure and macroscopic mechanical properties. Therefore, constitutive equations are important for the numerical analysis of the soft biological tissues. By exploiting diffusion tensor techniques the anisotropic orientation of neural tissue is incorporated into a non-linear viscoelastic material model for brain tissue and implemented in an explicit FE analysis. The viscoelastic material parameters are derived from published data and the viscoelastic model is used to describe the mechanical response of brain tissue. The model is formulated in terms of a large strain viscoelastic framework and considers non-linear viscous deformations in combination with non-linear elastic behaviour. The constitutive model was applied in the University College Dublin brain trauma model (UCDBTM) (i.e. three-dimensional finite element head model) to predict the mechanical response of the intra-cranial contents due to rotational injury.

Mechanical forces such as shear stress can modulate gene and protein expressions and hence cellular functions by activating membrane sensors and intracellular signaling. Using cultured endothelial cells, we have shown that laminar shear stress causes a transient increase in monocyte chemotactic protein-1 (MCP-1) expression, which involves the Ras-MAP kinase signaling pathway. We have demonstrated that integrins and the vascular endothelial growth factor receptor Flk-1 can sense shear stress, with integrins being upstream to Flk-1. Other possible membrane components involved in the sensing of shear stress include G-protein coupled receptors, intercellular junction proteins, membrane glycocalyx, and the lipid bilayer. Mechano-transduction involves the participation of a multitude of sensors, signaling molecules, and genes. Microarray analysis has demonstrated that shear stress can upregulate and downregulate different genes. Sustained shear stress downregulates atherogenic genes (e.g., MCP-1 and the genes that facilitate lipid accumulation) and upregulates growth-arrest genes. In contrast, disturbed flow observed at branch points and simulated in step-flow channels causes sustained activation of MCP-1 and the genes facilitating cell turnover and lipid accumulation. These findings provide a molecular basis for the explanation of the preferential localization of atherosclerotic lesions at regions of disturbed flow, such as the arterial branch points. The combination of mechanics and biology (from molecules-cells to organs-systems) can help to elucidate the physiological processes of mechano-chemical transduction and improving the methods of the management of important clinical conditions such as coronary artery disease.

Statistical shape models (SSM) are widely used in medical image analysis to represent variability in organ shape. However, representing subject-specific soft-tissue motion using this technique is problematic for applications where imaging organ changes in an individual is not possible or impractical. One solution is to synthesise training data by using biomechanical modelling. However, for many clinical applications, generating a biomechanical model of the organ(s) of interest is a non-trivial task that requires a significant amount of user-interaction to segment an image and create a finite element mesh. In this study, we investigate the impact of reducing the effort required to generate SSMs and the accuracy with which such models can predict tissue displacements within the prostate gland due to transrectal ultrasound probe pressure. In this approach, the finite element mesh is based on a simplified geometric representation of the organs. For example, the pelvic bone is represented by planar surfaces, or the number of distinct tissue compartments is reduced. Such representations are much easier to generate from images than a geometrically accurate mesh. The difference in the median root-mean-square displacement error between different SSMs of prostate was <0.2 mm. We conclude that reducing the geometric complexity of the training model in this way made little difference to the absolute accuracy of SSMs to recover tissue displacements. The implication is that SSMs of organ motion based on simulated training data may be generated using simplified geometric representations, which are much more compatible with the time constraints of clinical workflows.

Chemotactic cells of eukaryotic organisms are able to accurately sense shallow chemical concentration gradients using cell-surface receptors. This sensing ability is remarkable as cells must be able to spatially resolve small fractional differences in the numbers of particles randomly arriving at cell-surface receptors by diffusion. An additional challenge and source of uncertainty is that particles, once bound and released, may rebind the same or a different receptor, which adds to noise without providing any new information about the environment. We recently derived the fundamental physical limits of gradient sensing using a simple spherical-cell model, but not including explicit particle-receptor kinetics. Here, we use a method based on the fluctuation-dissipation theorem (FDT) to calculate the accuracy of gradient sensing by realistic receptors. We derive analytical results for two receptors, as well as two coaxial rings of receptors, e.g. one at each cell pole. For realistic receptors, we find that particle rebinding lowers the accuracy of gradient sensing, in line with our previous results.