Depletion interaction in colloid/polymer mixtures: application of density functional theory

Insert-route density functional approach (IRDFT), modified fundamental measure theory (MFMT) and thermodynamic perturbation theory (TPT1 and TPT2) are combined to study the depletion force between colloidal particles in hard sphere/hard sphere chain mixtures which represent a model of systems containing colloids dispersed in an athermal polymer solution. The predicted results are compared to simulations showing the reliability of the method used which captures the main characteristics of depletion interaction between colloids induced by polymers. Results of TPT2 are slightly more repulsive and better than that of TPT1 especially when the inter-particle distance is small than the diameter of polymer segment indicating the essential influence of the three-body correlations. Effects of the polymer density, polymer chain length and size ratio of colloid to polymer segment on the depletion force are studied in detail. Due to a little deterioration of the prediction in the high density region, further improvement is anticipated to better balance the competition between the excluded-volume effect and the chain connectivity.     

Platelets induce reactive oxygen species-dependent growth of human skin fibroblasts

A growing amount of evidence suggests that reactive oxygen species (ROS), such as hydrogen peroxide and superoxide anion, regulate intracellular signalling and have a role in cell proliferation. In the present study, we show that platelets increase the mitogenic rate in human fibroblasts and that this effect was inhibited by the intracellular antioxidant N-acetyl-L-cysteine (NAC) and the NADPH-oxidase inhibitor diphenyleneiodonium chloride (DPI). The mitogenic effects of platelets were mimicked by the platelet factors platelet-derived growth factor BB-isoform (PDGF-BB), transforming growth factor beta1 (TGF-beta1) and sphingosine-1-phosphate (S1P). The sphingosine kinase inhibitor DL-threo-dihydrosphingosine (DL-dihydro) abrogated the platelet-induced growth, while antibodies directed against PDGF or TGF-beta had modest effects. Exposure of fibroblasts to platelets, PDGF-BB, TGF-beta1 or S1P caused an extensive intracellular ROS production, measured as changes in dichlorofluorescein fluorescence. This ROS production was totally inhibited by NAC, pyrrolidinethiocarbamate (PDTC), DPI and apocynin. In conclusion, the results presented are indicative of a crucial role of ROS in the platelet-mediated regulation of fibroblast proliferation.     

Using mixtures of biological samples as process controls for RNA-sequencing experiments

Background

Genome-scale “-omics” measurements are challenging to benchmark due to the enormous variety of unique biological molecules involved. Mixtures of previously-characterized samples can be used to benchmark repeatability and reproducibility using component proportions as truth for the measurement. We describe and evaluate experiments characterizing the performance of RNA-sequencing (RNA-Seq) measurements, and discuss cases where mixtures can serve as effective process controls.

Results

We apply a linear model to total RNA mixture samples in RNA-seq experiments. This model provides a context for performance benchmarking. The parameters of the model fit to experimental results can be evaluated to assess bias and variability of the measurement of a mixture. A linear model describes the behavior of mixture expression measures and provides a context for performance benchmarking. Residuals from fitting the model to experimental data can be used as a metric for evaluating the effect that an individual step in an experimental process has on the linear response function and precision of the underlying measurement while identifying signals affected by interference from other sources. Effective benchmarking requires well-defined mixtures, which for RNA-Seq requires knowledge of the post-enrichment ‘target RNA’ content of the individual total RNA components. We demonstrate and evaluate an experimental method suitable for use in genome-scale process control and lay out a method utilizing spike-in controls to determine enriched RNA content of total RNA in samples.

Conclusions

Genome-scale process controls can be derived from mixtures. These controls relate prior knowledge of individual components to a complex mixture, allowing assessment of measurement performance. The target RNA fraction accounts for differential selection of RNA out of variable total RNA samples. Spike-in controls can be utilized to measure this relationship between target RNA content and input total RNA. Our mixture analysis method also enables estimation of the proportions of an unknown mixture, even when component-specific markers are not previously known, whenever pure components are measured alongside the mixture.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1912-7) contains supplementary material, which is available to authorized users.     

Risk analysis and management decisions for weed biological control agents: Ecological theory and modeling results

Biologically based control methods offer many advantages for the control of invasive plant species; however, these methods are not without risks to native species. Thus, there is a need for more effective and efficient methods of risk analysis for biological control agents. We show how the process of ecological risk assessment established by the United States’ Environmental Protection Agency may be adapted to improve assessment of the risks of proposed biological control agents. We discuss the risks posed by weed biological control agents, and present a simple individual-based model of herbivorous insect movement and oviposition on two species of host plant, a target invasive plant species and a non-target native species, in simulated landscapes. The model shows that risks of non-target impacts may be influenced by the details of the movement behavior of biological control agents in heterogeneous landscapes. The specific details of insect movement that appear to be relevant are readily measured in field trials and the general modeling approach is readily adapted to real landscapes. Current biological control risk assessments typically emphasize effects analysis at the expense of exposure analysis; the modeling approach presented here provides a simple and feasible way to incorporate exposure analyses. We conclude that models such as ours should be given serious consideration as part of a comprehensive strategy of risk assessment for proposed weed biological control agents.     

Improved dilute bicelle solutions for high-resolution NMR of biological macromolecules

Dissolving biological macromolecules in dilute bicelle solutions, which form oriented liquid crystals in the presence of a magnetic field, permits measurement of anisotropic spin interactions such as dipolar couplings [Tjandra, N. and Bax, A., Science, 278, 1111–1114]. However, the lifetimes and temperature ranges of orientation for these samples are critically dependent on sample composition and experimental conditions. This paper demonstrates that doping dilute bicelle solutions with small amounts of charged amphiphiles substantially improves the stability and degree of alignment, as well as extends the temperature range of orientation for these systems. An explanation of the dependence of bicelle aggregation on sample composition is proposed based on the DLVO theory of colloids.     

Mathematical modelling of engineered tissue growth using a multiphase porous flow mixture theory

This paper outlines the framework of a porous flow mixture theory for the mathematical modelling of in vitro tissue growth, and gives an application of this theory to an aspect of tissue engineering. The problem is formulated as a set of partial differential equations governing the space and time dependence of the amounts of each component of the tissue (phase), together with the physical stresses in each component. The theory requires constitutive relations to specify the material properties of each phase, and also requires relations to specify the stresses developed due to mechanical interactions, both within each phase and between different phases. An application of the theory is given to the study of the mobility and aggregation of a population of cells seeded into an artificial polymeric scaffold. Stability analysis techniques show that the interplay of the forces between the tissue constituents results in two different regimes: either the cells form aggregates or disperse through the scaffold.     

Investigation of growth phases for bottlenose dolphins using a Bayesian modeling approach

The Gompertz function is the most commonly used growth function for cetacean studies. However, this function cannot represent multiple phases of growth. In this study, we present a Bayesian framework fitting parameters of a triple-logistic growth function to describe multiple phases of growth for bottlenose dolphins ( Tursiops truncatus ), simultaneously fitting and comparing all growth parameters between South Carolina (SC), Mississippi Sound (MSS), and Indian River Lagoon (IRL) cohorts. The fitted functions indicated a preliminary early, rapid growth phase, followed by a second phase of slower growth, and then a moderate growth spurt later in life. Growth parameters between geographic cohorts did not show obvious differences, although asymptotic length for SC dolphins was lower than MSS and IRL dolphins and significantly lower between females from SC and the IRL. Growth rate velocities between the sexes showed females exceed males initially (<1 yr), followed by males gaining an advantage around the ages of 3–4 yr until the age of around 15 yr when growth rates for both sexes approached zero (asymptotic length). This study demonstrates age-related changes in growth rates between bottlenose dolphin sexes and evidence of at least some differences ( i.e. , asymptotic length) across geographic cohorts.     

Molecular dynamics study of the initial stages of catalyzed single-wall carbon nanotubes growth: force field development

Effective force fields for Ni-C interactions developed by Yamaguchi and Maruyama for the formation of metallofullerenes are modified to simulate the catalyzed growth of single-wall carbon nanotubes on Ni_n clusters with n >20, and the reactive empirical bond order Brenner potential for C-C interactions is also revised to include the effect of the metal atoms on such interactions. Figure Force field parameters for carbon-metal interactions obtained from DFT calculations in small clusters.     

Induction of transforming growth factor-beta 1 by androgen is mediated by reactive oxygen species in hair follicle dermal papilla cells

The progression of androgenetic alopecia is closely related to androgen-inducible transforming growth factor (TGF)-β1 secretion by hair follicle dermal papilla cells (DPCs) in bald scalp. Physiological levels of androgen exposure were reported to increase reactive oxygen species (ROS) generation. In this study, rat vibrissae dermal papilla cells (DP-6) transfected with androgen receptor showed increased ROS production following androgen treatment. We confirmed that TGF-β1 secretion is increased by androgen treatment in DP-6, whereas androgeninducible TGF-β1 was significantly suppressed by the ROSscavenger, N-acetyl cysteine. Therefore, we suggest that induction of TGF-β1 by androgen is mediated by ROS in hair follicle DPCs. [BMB Reports 2013; 46(9): 460-464]     

On the mechanochemical theory of biological pattern formation with application to vasculogenesis

We first describe the Murray-Oster mechanical theory of pattern formation, the biological basis of which is experimentally well documented. The model quantifies the interaction of cells and the extracellular matrix via the cell-generated forces. The model framework is described in quantitative detail. Vascular endothelial cells, when cultured on gelled basement membrane matrix, rapidly aggregate into clusters while deforming the matrix into a network of cord-like structures tessellating the planar culture. We apply the mechanical theory of pattern formation to this culture system and show that neither strain-biased anisotropic cell traction nor cell migration are necessary for pattern formation: isotropic, strain-stimulated cell traction is sufficient to form the observed patterns. Predictions from the model were confirmed experimentally.     

A contribution to the theory of biological staining based on the principles for structural organization of biological macromolecules

Biological staining is to a large degree explainable based on the principles governing folding and aggregation of macromolecules in aqueous solution. Most macromolecules are polyions, which, except for heteropolysaccharides, have a large proportion of nonpolar or only slightly polar residues. Because they are amphiphilic, they react in water by a complex set of hydrophobic interactions involving charged residues, nonpolar residues and water molecules. The hydrophobic interactions lead to complex folding systems or micelle-like structures. Dyes are amphiphilic molecules with a tendency to form micelles, but with limitations due to geometric constraints and charge repulsion. Macromolecules and dyes react with each other in aqueous solution following the same principles as for the structural organization of macromolecules, as in protein folding for example. Dye binding requires near contact between nonpolar groups in both the dye and macromolecule, and this is accomplished by choosing a pH at which the dye and macromolecule have opposite net charges. Charge attraction is insufficient for binding in most cases, but it is directive because it determines which macromolecules a given dye ion is able to contact. These considerations apply to the staining of globular (cytoplasmic) proteins and to nucleic acid staining. The staining mechanism is by hydrophobic interactions. Above approximately pH 3.5, DNA may also bind dyes by hydrophobic intercalation between the bases of the double helix; at lower pH the double helix opens and dye binding is as for RNA and globular proteins. Heteroglycans (mucins) have virtually no nonpolar groups, so nonpolar interactions are restricted to the dye molecules. Metachromatic staining of heteroglycans is due to hydrophobic bonding or micelle formation between the monovalent planar dye molecules aided by charge neutralization by the negatively charged heteroglycans. Alternatively, as the charge attraction increases with the number of closely placed charges, acidic heteroglycans may be stained by a polycation such as alcian blue or colloidal iron. For elastic fiber and collagen staining, actual hydrophobic interactions are less important and hydrogen bonding and simple nonpolar interactions play a major role. These macromolecules may therefore be stained using a nonaqueous alcoholic solution.     

A contribution to the theory of biological staining based on the principles for structural organization of biological macromolecules

Biological staining is to a large degree explainable based on the principles governing folding and aggregation of macromolecules in aqueous solution. Most macromolecules are polyions, which, except for heteropolysaccharides, have a large proportion of nonpolar or only slightly polar residues. Because they are amphiphilic, they react in water by a complex set of hydrophobic interactions involving charged residues, nonpolar residues and water molecules. The hydrophobic interactions lead to complex folding systems or micelle-like structures. Dyes are amphiphilic molecules with a tendency to form micelles, but with limitations due to geometric constraints and charge repulsion. Macromolecules and dyes react with each other in aqueous solution following the same principles as for the structural organization of macromolecules, as in protein folding for example. Dye binding requires near contact between nonpolar groups in both the dye and macromolecule, and this is accomplished by choosing a pH at which the dye and macromolecule have opposite net charges. Charge attraction is insufficient for binding in most cases, but it is directive because it determines which macromolecules a given dye ion is able to contact. These considerations apply to the staining of globular (cytoplasmic) proteins and to nucleic acid staining. The staining mechanism is by hydrophobic interactions. Above approximately pH 3.5, DNA may also bind dyes by hydrophobic intercalation between the bases of the double helix; at lower pH the double helix opens and dye binding is as for RNA and globular proteins. Heteroglycans (mucins) have virtually no nonpolar groups, so nonpolar interactions are restricted to the dye molecules. Metachromatic staining of heteroglycans is due to hydrophobic bonding or micelle formation between the monovalent planar dye molecules aided by charge neutralization by the negatively charged heteroglycans. Alternatively, as the charge attraction increases with the number of closely placed charges, acidic heteroglycans may be stained by a polycation such as alcian blue or colloidal iron. For elastic fiber and collagen staining, actual hydrophobic interactions are less important and hydrogen bonding and simple nonpolar interactions play a major role. These macromolecules may therefore be stained using a nonaqueous alcoholic solution.     

A simple method to analyze the similarity of biological sequences based on the fuzzy theory

In this paper, we propose a simple method to analyze the similarity of biological sequences. By taking the average contents of biological sequences and their information entropies as the variables, the fuzzy method is used to cluster them. From the results of application, it finds that the method is relatively easy and rapid. Unlike other methods such as the graphical representation methods, which is usually very complex to compute some invariants of matric derived from graphical representation, our method pays more attention to the information of biological sequences themselves. Especially with the help of the software (SPSS), it seems to be very convenient. Therefore, it may be used to study the new biological sequences such as their evolution relationship and structures.     

A simple mathematical modeling of the growth of microorganism colonies

The growth rates of aspergillus, fusarium, and penicillium microorganism colonies in Czapex Dox Agar as a feed material, under room conditions, are observed to be linear. This phenomenon is mathematically modeled and exactly predicted on the basis of the exponential growth assumption of a single microorganism. The approach allows an easy determination of the multiplication constant of a had microorganisms been allowed to grow freely microorganism, in given conditions.     

Evidence for the acid-growth theory of fusicoccin action

Three predictions of the acid-growth theory of fusicoccin (FC) action in inducing cell elongation were reinvestigated using abraded segments of maize (Zea mays L.) coleoptiles. i) Quantitative comparison of segment elongation and medium-acidification kinetics measured in the same sample of tissue shows that these FC-induced processes are strictly correlated in time and respond coordinately to cations present in the medium. ii) Fusicoccin (1 mol l^-1) induces a rapid acidification of the cell-wall solution, reaching a final level of pH 3.8–4.0. Exogenous protons are able to substitute quantitatively for FC in causing segment elongation at pH 3.8–4.0. At pH 4, FC has no additional effect on cell elongation. iii) Neutral buffers (pH 7) completely abolish the FC-mediated growth response. iv) Cycloheximide (10 mg l^-1) inhibits both FC-induced and acid-buffer(pH 4)-induced elongation after a lag of 40–45 min, and FC-induced H⁺ excretion after a lag of 2 h. Under the same conditions, indole-3-acetic acid-induced elongation and H⁺ excretion are inhibited without detectable lag. It is concluded that these results are fully compatible with the acid-growth theory of FC action.Abbreviations IAA indole-3-acetic acid - CHI cycloheximide - FC fusicoccin     

Temporal regulation of growth cone lamellar protrusion and the influence of target tissue

Guided nerve fiber growth depends upon the activities of the neuronal growth cone lamellae and filopodia. Defining the dynamics of growth cone remodeling and the influences that act on it may lead to greater understanding of guided axonal growth. While there were differences in the remodeling of growth cones of nerve fibers extended from spinal cord explants and from dorsal root ganglia of Rana pipiens larvae, both types exhibited fluctuations in lamellar expanse over time to produce “lamellar cycles.” We now show that these cycles are characterized by the temporal regulation of lamellar protrusion rate, the percentage of the lamellar perimeter undergoing protrusion, and invariant lamellar retraction with respect to time. Since axotomies did not abolish the lamellar cycles, the mechanism underlying cycling appears to reside at the level of the nerve fiber terminus. The previously demonstrated effects of the target tissue on growth cone remodeling appear to be due to target tissue—released factors that bind to the culture substratum, as evidenced by experiments using target tissue—conditioned medium. Further, the target tissue attenuated the fluctuations in lamellar protrusion rate during cycling, which resulted in changes in growth cone remodeling and morphology. These alterations may be related to the chemokinetic and chemotropic effects of the target on the nerve fiber extension. Thus, the process of remodeling of growth cone lamellar structures is the result of intrinsically controlled modifications in lamellar protrusion and target-based influences. © 1997 John Wiley & Sons, Inc. J Neurobiol 33: 929–944, 1997     

Suppression of tan spot and plant growth promotion of wheat by synthetic and biological inducers under field conditions

Tan spot of wheat caused by Pyrenophora tritici‐repentis (Ptr) is a major leaf spot disease. No single control measure is likely to be successful in controlling tan spot and a fully integrated system of disease management is more likely to achieve a long‐term solution. Research to improve control efficacy has focused on fungicide improvement, resistant cultivars, the use of biological control agents (BCAs) mixtures and combinatorial approaches involving BCAs and plant resistance stimulants with complementary modes of action. Various biotic and abiotic agents can stimulate wheat defence mechanisms and so benefit resistance to Ptr infection. Among them, Trichoderma spp. have been widely used as antagonistic fungal agents against several pathogens as well as plant growth enhancers. Also, the synthetic agents acibenzolar‐S‐methyl (ASM) and thiamethoxam (TM) have provided broad‐spectrum disease and pest control as well as enhanced plant vigour against several fungal diseases. The aim of this research was to evaluate the effectiveness of two Trichoderma harzianum strains and two substances of synthetic origin (ASM and TM) on the suppression of tan spot and plant growth promotion of wheat plants. When BCAs, ASM and TM were applied to field plots on wheat cultivar Klein Escorpion, the severity of tan spot reduced and plant height, fresh weight, dry weight of shoots and dry weight of roots increased in comparison with the control. When applied prior to Ptr inoculation, ASM, TM and the strain Th1 of T. harzianum caused a reduction in necrotic lesions >50% compared to the control treatment. Seed treatment with TM resulted in a significant enhancement of plant height. Application of ASM significantly increased foliar fresh weight by 45% as compared to the control treatment, whereas foliar fresh weight increased 29% and 50% when TM and T. harzianum strain Th1 were applied as seed coating. Acibenzolar‐S‐methyl alone or combined with Th1 increased dry weight to >60%, whereas the effects of TM and Th1 on dry mass showed an increase that ranged from 57% to 25%. Plants treated with Th1 and both synthetic compounds achieved up to sixfold increment in root dry weight over the control.