Non-linear least squares analysis of phase diagrams for non-ideal binary mixtures of phospholipids

A computer program for non-linear least squares minimization has been applied to construct temperature-composition phase diagrams for several binary systems of different phospholipids based on their calorimetric data. The calculated phase diagram is guided to fit the calorimetric data with two adjustable parameters that describe the non-ideal mixing of lipid components in the gel and liquid-crystalline phases. The parameter estimation procedure is presented to show that the computer program can be used not only to generate phase diagrams with characteristic shapes but also to numerically estimate the lipid-lipid pair interactions between the mixed and the like pairs in the two-dimensional plane of the bilayer in both the gel and liquid-crystalline states. The binary lipid systems examined include dimyristoylphosphatidylcholine/1-palmitoyl-2-stearoylphosphatidylchol ine, 1-capryl-2-behenoylphosphatidylcholine/1-behenoyl-2-lauro ylphosphatidylcholine, and 1-stearoyl-2-caprylphosphatidylcholine/dimyristoylphosphatidylchol ine.     

The ocular skeleton through the eye of evo-devo

An evolutionary developmental (evo-devo) approach to understanding the evolution, homology, and development of structures has proved important for unraveling complex integrated skeletal systems through the use of modules, or modularity. An ocular skeleton, which consists of cartilage and sometimes bone, is present in many vertebrates; however, the origin of these two components remains elusive. Using both paleontological and developmental data, I propose that the vertebrate ocular skeleton is neural crest derived and that a single cranial neural crest module divided early in vertebrate evolution, possibly during the Ordovician, to give rise to an endoskeletal component and an exoskeletal component within the eye. These two components subsequently became uncoupled with respect to timing, placement within the sclera and inductive epithelia, enabling them to evolve independently and to diversify. In some extant groups, these two modules have become reassociated with one another. Furthermore, the data suggest that the endoskeletal component of the ocular skeleton was likely established and therefore evolved before the exoskeletal component. This study provides important insights into the evolution of the ocular skeleton, a region with a long evolutionary history among vertebrates.     

MONOPLASTIDIC CELL DIVISION IN LOWER LAND PLANTS

In many bryophytes and vascular cryptogams mitosis and/or meiosis takes place in cells containing a single plastid. In monoplastidic cell division plastid polarity assures that nuclear and plastid division are infallibly coordinated. The two major components of plastid polarity are morphogenetic plastid migration and microtubule organization at the plastids. Before nuclear division the plastid migrates to a position intersecting the future division plane. This morphogenetic migration is a reliable marker of division polarity in cells with and without a preprophase band of microtubules (PPB). The PPB, which predicts the future division plane before mitosis, is a characteristic feature of land plants and its insertion into the cytokinetic apparatus marks the evolution of a cortical microtubule system and a commitment to meristematic growth. Microtubule systems associated with plastid division, the axial microtubule system (AMS) in mitosis and the quadripolar microtubule system (QMS) in meiosis, contribute to predictive positioning of plastids and participate directly in spindle ontogeny. Division polarity in monoplastidic sporocytes is remarkable in that division sites are selected prior to the two successive nuclear divisions of meiosis. Plastid arrangement prior to meiosis determines the future spore domains in monoplastidic sporocytes, whereas in polyplastidic sporocytes the spore nuclei play a major role in claiming cytoplasmic domains. It is hypothesized that predivision microtubule systems associated with monoplastidic cell division are early forming components of the mitotic apparatus that serve to orient the spindle and insure equal apportionment of nucleus and plastids. “Can it be supposed that cytoplasm would be intrusted with so important a task as the preparation of a chloroplast for each of the four nuclei that are later to preside over the spores before there is any indication that such nuclear division is to take place?” Bradley Moore Davis, 1899     

Water interaction in paper cellulose fibres as investigated by NMR pulsed field gradient

In this paper, water diffusion coefficients were measured using NMR pulsed field gradient, on a variety of paper materials made from predominantly cellulose fibre and nanofibres, derived from wood, with different dimensions, internal porosity, and chemical composition. The moisture content ranged from 0.2 to 1.2 g of water/g of dry fibre. Diffusion measurements were made both in the plane and through the thickness of the sheet. All data was generally well fitted by a simple two component diffusion model. For moisture contents less than 0.55 and 0.85 g/g for measurements in the plane and through the thickness, respectively, it was found that both diffusion components increased approximately linearly with moisture content, with the faster diffusion coefficient being approximately five times larger than the smaller. The water appeared, within errors, to be evenly split between two components. The measured diffusion coefficients were not affected by fibre dimensions, internal structure or chemical composition, but were consistently higher when measured in the plane.     

Circadian clocks: A cry in the dark?

Cryptochrome proteins are key components of the circadian systems of both Drosophila and mammals. In Drosophila, they appear to be responsible for the entrainment of the circadian clock by the light-dark cycle, while in mammals they perform an important role in rhythm generation itself.     

Optical Shading Induces an In‐Plane Potential Gradient in a Semiartificial Photosynthetic System Bringing Photoelectric Synergy

Semiartificial photosynthetic systems have opened up new avenues for harvesting solar energy using natural photosynthetic materials in combination with synthetic components. This work reports a new, semiartificial system for solar energy conversion that synergistically combines photoreactions in a purple bacterial photosynthetic membrane with those in three types of transition metal–semiconductor Schottky junctions. A transparent film of a common transition metal interfaced with an n‐doped silicon semiconductor exhibits an in‐plane potential gradient when a light‐penetration variance is established on its surface by optical shading of photoabsorbing photosynthetic membranes. The in‐plane potential gradients (0.08–0.3 V) enable a directional charge transport between the synthetic and natural photoelectric systems, which is further enhanced in a device setting by a biocompatible thixotropic gel electrolyte that permeates the membrane multilayer, facilitating a strong and steady photoelectric current as high as 1.3 mA cm^?2, the highest achieved so far with any anoxygenic photosynthetic system.     

Crocodiles don't focus underwater

Summary Crocodilians are amphibious reptiles which hunt prey both on land and in water. Previous refractive and anatomical studies have suggested that their eyes can focus objects in air and that their ability to refocus the eye underwater may be limited. Examination of the plane of focus of six species of crocodilians both in air and underwater has revealed that they are generally well focused in air for distant targets and severely defocused underwater. These results suggest that sensory systems other than vision must play an important role in prey capture underwater.Abbreviation D diopter     

Predictive models in spatially and temporally variable freshwater systems

Abstract This paper discusses the relationships between scaling and predictability in ecosystems. The logical basis of ecosystem modelling is explored using ideas first developed in complexity theory and analogies with the behaviour of complex adaptive systems. Any ecological model is a scale-dependent entity and both empirical and dynamic models of freshwater systems have their strengths and weaknesses. The logical basis of modelling using functional groups is explored. I conclude that such an approach can be justified and that such models have predictive power. Any predictive model of freshwater systems must take the major scales of external (atmospheric and catchment) forcing into account as well as the scales of key processes in the ecosystem itself. The importance of so-called ‘pink noise’ spectra, which arise both from external forcing and the internal dynamics of dynamic systems, is noted. The key scales of pattern and process in freshwater ecosystems are discussed in relation to the properties of the major functional groups. In order to have predictive power, I conclude that models of freshwater systems must include sediment exchanges and the properties of aquatic macrophytes as well as water column interactions and the pelagic components. When viewed at the scale of functional groups and the major biogeochemical processes, freshwater ecosystems may not be as complex as is often assumed.     

Accuracy and repeatability of joint angles measured using a single camera markerless motion capture system

Markerless motion capture systems have developed in an effort to evaluate human movement in a natural setting. However, the accuracy and reliability of these systems remain understudied. Therefore, the goals of this study were to quantify the accuracy and repeatability of joint angles using a single camera markerless motion capture system and to compare the markerless system performance with that of a marker-based system. A jig was placed in multiple static postures with marker trajectories collected using a ten camera motion analysis system. Depth and color image data were simultaneously collected from a single Microsoft Kinect camera, which was subsequently used to calculate virtual marker trajectories. A digital inclinometer provided a measure of ground-truth for sagittal and frontal plane joint angles. Joint angles were calculated with marker data from both motion capture systems using successive body-fixed rotations. The sagittal and frontal plane joint angles calculated from the marker-based and markerless system agreed with inclinometer measurements by <0.5°. The systems agreed with each other by <0.5° for sagittal and frontal plane joint angles and <2° for transverse plane rotation. Both systems showed a coefficient of reliability <0.5° for all angles. These results illustrate the feasibility of a single camera markerless motion capture system to accurately measure lower extremity kinematics and provide a first step in using this technology to discern clinically relevant differences in the joint kinematics of patient populations.     

Analysis of deformation and contraction in cylindrical crystals due to dispirations or dislocations.

Cylindrical crystal structures are common in biology. The shape changes and movements of cylindrical crystals are basic to the understanding of the contractile mechanisms in biological systems such as tobacco mosaic viruses and the tail sheath of T-even bacteriophages. It has been suggested that the concept of defects in crystal physics can be applied to study these contractile mechanisms. The defect believed to be responsible for the shape changes of cylindrical crystals is known as a dispiration. Dispirations are characterized by the shear displacement on the slip plane through a screw symmetry operation. The elastic field of a dispiration can be decomposed into its translational (dislocation) and rotational (disclination) components. The magnitude of the translational and rotational displacements in a cylindrical crystal has been related to the crystal structural parameters. The passage of a dispiration along a helical plane in a cylindrical crystal can induce one of two types of shape changes. In one type, only the disclination component of the dispiration contributes to contraction, whereas in the other type, both the disclination and dislocation components are responsible for the shape change. Estimates of the magnitude of contraction are made in terms of the dimensional and structural parameters of the cylindrical crystal. The reversal of the direction of helical slip results in extension instead of contraction of the cylindrical crystal. The local elastic deformation of a dispiration dipole situated on the helical plane of a cylindrical crystal is examined. It has been shown that, for the first type of deformation mentioned above, closed form solutions of the stress field can be obtained by superposing the stress fields of two dispiration dipoles with slip planes parallel and normal to the cylinder axis, respectively. The approximations of shallow shell theory are adopted in the analysis. Future problems of biological interests are identified.     

Magnetorotational instability of a weakly ionized accretion disk with vertical and azimuthal magnetic fields

Magnetorotational instability of a weakly ionized accretion disk with an admixture of charged dust grains in a magnetic field with the axial and toroidal components is analyzed. The dispersion relation for perturbations perpendicular to the disk plane is derived with allowance for both the Hall current and the finite transverse plasma conductivity. It is shown that dust grains play an important role in the disk magnetic dynamics. Due to the effect of dust grains, the Hall current can reverse its direction as compared to the case of electron-ion plasma. As a result, the instability threshold shifts toward the short-wavelength range. Under certain conditions, electromagnetic fluctuations of any length can become unstable. It is established that the instability criterion for waves of any scale length is satisfied within a finite interval of the density ratio between the dust and electron plasma components. The width of this interval and the instability growth rate as functions of the plasma parameters and the configuration of the magnetic field in the disk are analyzed.     

Combination chemical genetics

Predicting the behavior of living organisms is an enormous challenge given their vast complexity. Efforts to model biological systems require large datasets generated by physical binding experiments and perturbation studies. Genetic perturbations have proven important and are greatly facilitated by the advent of comprehensive mutant libraries in model organisms. Small-molecule chemical perturbagens provide a complementary approach, especially for systems that lack mutant libraries, and can easily probe the function of essential genes. Though single chemical or genetic perturbations provide crucial information associating individual components (for example, genes, proteins or small molecules) with pathways or phenotypes, functional relationships between pathways and modules of components are most effectively obtained from combined perturbation experiments. Here we review the current state of and discuss some future directions for 'combination chemical genetics', the systematic application of multiple chemical or mixed chemical and genetic perturbations, both to gain insight into biological systems and to facilitate medical discoveries.     

Principles of membrane stability and phase behavior under extreme conditions

Biological membranes consist of a complex assortment of lipids and proteins. The arrangement of the components, particularly in regard to their lateral disposition in the plane of the membrane under physiological conditions, is dependent on the phase behavior of the different membrane lipids and the way that this behavior is modified by interaction with other membrane components and electrolytes in the aqueous medium. Irreversible phase separation of components within the membrane may result from exposure to extreme environmental conditions including temperature, pressure, or electrolyte concentration. The principles underlying the phase-mixing behavior of model membrane systems can be used to provide useful information about the factors that determine the stability of biomembranes under physiological and non-physiological conditions. These data are reviewed and used to predict events that take place when membranes are exposed to environmental stress.     

The Ocular Skeleton Through The Eye of Evo-devo

An evolutionary developmental (evo-devo) approach to understanding the evolution, homology and development of structures has proved important for unraveling complex integrated skeletal systems through the use of modules, or modularity. An ocular skeleton, which consists of cartilage and sometimes bone, is present in many vertebrates; however the origin of these two components remains elusive. Using both palaeontological and developmental data, I propose that the vertebrate ocular skeleton is neural crest derived and that a single cranial neural crest module divided early in vertebrate evolution, possibly during the Ordovician, to give rise to an endoskeletal component and an exoskeletal component within the eye. These two components subsequently became uncoupled with respect to timing, placement within the sclera and inductive epithelia, enabling them to evolve independently and to diversify. In some extant groups, these two modules have become reassociated with one another. Furthermore, the data suggests that the endoskeletal component of the ocular skeleton was likely established and therefore evolved before the exoskeletal component. This study provides important insights into the evolution of the ocular skeleton, a region with a long evolutionary history amongst vertebrates. J. Exp. Zool. (Mol. Dev. Evol.) 9999B: 1-9, 2012. ? 2012 Wiley Periodicals, Inc.     

Classification using functional data analysis for temporal gene expression data

MOTIVATION: Temporal gene expression profiles provide an important characterization of gene function, as biological systems are predominantly developmental and dynamic. We propose a method of classifying collections of temporal gene expression curves in which individual expression profiles are modeled as independent realizations of a stochastic process. The method uses a recently developed functional logistic regression tool based on functional principal components, aimed at classifying gene expression curves into known gene groups. The number of eigenfunctions in the classifier can be chosen by leave-one-out cross-validation with the aim of minimizing the classification error. RESULTS: We demonstrate that this methodology provides low-error-rate classification for both yeast cell-cycle gene expression profiles and Dictyostelium cell-type specific gene expression patterns. It also works well in simulations. We compare our functional principal components approach with a B-spline implementation of functional discriminant analysis for the yeast cell-cycle data and simulations. This indicates comparative advantages of our approach which uses fewer eigenfunctions/base functions. The proposed methodology is promising for the analysis of temporal gene expression data and beyond. AVAILABILITY: MATLAB programs are available upon request.     

Decrease in 2,2,6,6-tetramethyl-piperidine-1-oxyl (TEMPO) EPR signal in ozone-treated erythrocyte membranes

In ozone-treated erythrocyte membrane suspension a slow decrease occurs in the EPR signal of 2,2,6,6-tetramethyl-piperidine-1-oxyl (TEMPO). Because of the absence of such a phenomenon in control membranes and ozonized buffer, this effect must be caused by reaction of nitroxide radicals with products of ozone reactions with membrane components. To find out which components are responsible for the decrease in EPR signal we studied this effect in simple model systems. The same phenomenon was observed both in lipid and protein systems treated by ozone. For unsaturated fatty acids, the correlation between the rate of decrease in EPR signal and the number of double bonds in the lipid molecule was very strong. This suggests that the observed decrease in the nitroxide radical TEMPO EPR signal in ozone-treated erythrocyte membranes is a complex process, but probably the most important reaction is recombination of nitroxide radicals with organic free radicals produced both in the process of lipid peroxidation and ozonolysis of double bonds.     

Decrease in 2,2,6,6-tetramethyl-piperidine-1-oxyl (TEMPO) EPR signal in ozone-treated erythrocyte membranes

In ozone-treated erythrocyte membrane suspension a slow decrease occurs in the EPR signal of 2,2,6,6-tetramethyl-piperidine-1-oxyl (TEMPO). Because of the absence of such a phenomenon in control membranes and ozonized buffer, this effect must be caused by reaction of nitroxide radicals with products of ozone reactions with membrane components. To find out which components are responsible for the decrease in EPR signal we studied this effect in simple model systems. The same phenomenon was observed both in lipid and protein systems treated by ozone. For unsaturated fatty acids, the correlation between the rate of decrease in EPR signal and the number of double bonds in the lipid molecule was very strong. This suggests that the observed decrease in the nitroxide radical TEMPO EPR signal in ozone-treated erythrocyte membranes is a complex process, but probably the most important reaction is recombination of nitroxide radicals with organic free radicals produced both in the process of lipid peroxidation and ozonolysis of double bonds.     

His-Asp phosphorelay signaling: a communication avenue between plants and their environment

His-Asp phosphorelay systems have been recently discovered in plants and have emerged as some of the most important signaling systems. The phosphorelay systems in plants include components with sensor (His-protein kinase) domains, His-containing phosphotransfer (HPt) domains, and receiver (response regulator) domains. Recent studies implicate phosphorelay systems in sensing and propagating signals from a wide variety of external and/or internal stimuli such as ethylene, cytokinin, and osmolarity. In maize and Arabidopsis, some response regulators are up-regulated by both cytokinins and nitrate. These findings imply that the His-Asp phosphorelay may operate in an inorganic nitrogen-signaling pathway mediated by cytokinin in plants.