Evaluating spatial constraints in cellular assembly processes using a Monte Carlo approach

Biomolecular behavior commonly involves complex sets of interacting components that are challenging to understand through solution-based chemical theories. Molecular assembly is especially intriguing in the cellular environment because of its links to cell structure in processes such as chemotaxis. We use a coarse-grained Monte Carlo simulation to elucidate the importance of spatial constraints in molecular assembly. We have performed a study of actin filament polymerization through this space-aware probabilistic lattice-based model. Quantitative results are compared with nonspatial models and show convergence over a wide parameter space, but marked divergence over realistic levels corresponding to macromolecular crowding inside cells and localized actin concentrations found at the leading edge during cell motility. These conclusions have direct implications for cell shape and structure, as well as tumor cell migration.     

Can the Red-Green Duochrome Test Be Used Prior to Correcting the Refractive Cylinder Component?

Purpose

A primary task of the eye care professional is determining the refraction, or optical correction, of a patient. The duochrome red-green test is a standard tool for verification of the final refraction. Traditionally, it is recommended for use both prior to and subsequent to determining the cylindrical or astigmatic component of the refraction. In order for it to be effective when used before correcting the cylinder it is necessary that the COLC (Circle of Least Confusion) be on the retina. This study examined whether it is necessarily true that the duochrome response in uncorrected astigmatism will be as trust-worthy as it is with corrected cylinders.

Methods

The red-green examination was performed monocularly under the following three conditions: a. fully corrected refraction for the subgroup of eyes that had spherical refractions and for the subgroup of eyes with sphero-cylindrical refractions. b. best sphere-only correction without cylinder correction in sphero-cylindrical eyes c. an induced cylinder error in spherical eyes. The interval between the last “red” response and the first “green” response for the right eyes as a group and separately for the physiological cylinder and induced cylinder correction sub-groups was calculated and compared using a paired, two-tailed t-test.

Results

The intervals between “red” and “green” responses were not significantly different in the population as a whole and in the uncorrected physiological cylinder and induced cylinder subgroups examined.

Conclusion

Based on the finding that the interval of red-green equality with fully corrected cylinder and without the cylindrical correction are not significantly different, the red-green duochrome test can indeed be used both before and after cylindrical correction.     

Oleic acid and adipokines synergize in inducing proliferation and inflammatory signalling in human vascular smooth muscle cells

In the context of obesity, perivascular fat produces various adipokines and releases free fatty acids, which may induce inflammation and proliferation in the vascular wall. In this study we investigated how adipokines, oleic acid (OA) and the combined treatment regulate human vascular smooth muscle cell (hVSMC) proliferation and migration and the underlying signalling pathways. Adipocyte‐conditioned media (CM) generated from human adipocytes induces a prominent proliferation and migration of hVSMC. Autocrine action of adiponectin totally abolishes CM‐induced proliferation. Furthermore, OA but not palmitic acid induces proliferation of hVSMC. CM itself does not contain fatty acids, but CM in combination with OA markedly enhances proliferation of hVSMC in a synergistic way. Both the nuclear factor (NF)‐κB and the mammalian target of rapamycin (mTOR) pathway were synergistically activated under these conditions and found to be essential for hVSMC proliferation. Expression of iNOS and production of nitric oxide was only enhanced by combined treatment inducing a marked release of VEGF. Combination of OA and VEGF induces an additive increase of hVSMC proliferation. We could show that the combination of CM and OA led to a synergistic proliferation of hVSMC. Expression of iNOS and production of nitric oxide were only enhanced under these conditions and were paralleled by a marked release of VEGF. These results suggest that the combined elevated release of fatty acids and adipokines by adipose tissue in obesity might be critically related to hVSMC dysfunction, vascular inflammation and the development of atherosclerosis.     

Unperturbing a non-helically perturbed bacterial flagellar filament: Salmonella typhimurium SJW23

Salmonella typhimurium SJW23 has a right-handed, non-helically perturbed filament of serotype gt with a unique surface pattern. Non-helical perturbations involve symmetry reduction along the five-start helical lines resulting in layer lines of fractional Bessel orders and a consequent seam. The flagellin gene, fliC₂₃, which we sequenced, differs from the sequence of the canonic, plain SJW1655 flagellin, fliC₁₆₅₅. We modified discrete components of fliC₂₃ in order to localize, in the expressed filament, the submolecular site responsible for the non-helical perturbation. These modifications include (i) deleting the outermost domain  D3₂₃, (ii) replacing D3₂₃ with D3₁₆₅₅, (iii) substituting a hydrophilic α-helix at the interface between the neighboring domains D1 and D2 with a hydrophobic one from fliC₁₆₅₅, and (iv) substituting a serine/glycine pair in the loop connecting the modified α-helix to its neighbor; these modifications were made in the presence and absence of D3₂₃. We used S. typhimurium SJW1655 both as a reference and as a source for ‘spare parts’. The symmetry of the constructs was assessed from the power spectra through changes in the layer lines at a height of 〈1/105〉 and 〈1/35〉 Å^? 1 , unique to the non-helical perturbation. Deleting D3₂₃, either alone or in combination with various substitutions, or replacing it with D3₁₆₅₅ transforms the non-helically perturbed filament into a plain one as judged by the disappearance of the typical layer lines from the power spectra. We conclude that the non-helical perturbation is a product of unique interactions in the D3₂₃ density shell. Whereas other minor structural changes may occur at the filaments interior, they are all helically symmetric.     

Genome methylation patterns across castes and generations in a parasitoid wasp

Environmental influences shape phenotypes within and across generations, often through DNA methylations that modify gene expression. Methylations were proposed to mediate caste and task allocation in some eusocial insects, but how an insect's environment affects DNA methylation in its offspring is yet unknown. We characterized parental effects on methylation profiles in the polyembryonic parasitoid wasp Copidosoma koehleri, as well as methylation patterns associated with its simple caste system. We used methylation‐sensitive amplified fragment length polymorphism (MS‐AFLP) to compare methylation patterns, among (1) reproductive and soldier larvae; and (2) offspring (larvae, pupae, and adults) of wasps that were reared at either high or low larval density and mated in the four possible combinations. Methylation frequencies were similar across castes, but the profiles of methylated fragments differed significantly. Parental rearing density did not affect methylation frequencies in the offspring at any developmental stage. Principal coordinate analysis indicated no significant differences in methylation profiles among the four crossbreeding groups and the three developmental stages. Nevertheless, a clustering analysis, performed on a subset of the fragments, revealed similar methylation patterns in larvae, pupae, and adults in two of the four parental crosses. Nine fragments were methylated at two cytosine sites in all larvae, and five others were methylated at two sites in all adults. Thus, DNA methylations correlate with within‐generation phenotypic plasticity due to caste. However, their association with developmental stage and with transgenerational epigenetic effects is not clearly supported.     

Factors Affecting the Design of Slow Release Formulations of Herbicides Based on Clay-Surfactant Systems. A Methodological Approach

A search for clay-surfactant based formulations with high percentage of the active ingredient, which can yield slow release of active molecules is described. The active ingredients were the herbicides metribuzin (MZ), mesotrione (MS) and flurtamone (FL), whose solubilities were examined in the presence of four commercial surfactants; (i) neutral: two berols (B048, B266) and an alkylpolyglucoside (AG6202); (ii) cationic: an ethoxylated amine (ET/15). Significant percent of active ingredient (a.i.) in the clay/surfactant/herbicide formulations could be achieved only when most of the surfactant was added as micelles. MZ and FL were well solubilized by berols, whereas MS by ET/15. Sorption of surfactants on the clay mineral sepiolite occurred mostly by sorption of micelles, and the loadings exceeded the CEC. Higher loadings were determined for B266 and ET/15. The sorption of surfactants was modeled by using the Langmuir-Scatchard equation which permitted the determination of binding coefficients that could be used for further predictions of the sorbed amounts of surfactants under a wide range of clay/surfactant ratios. A possibility was tested of designing clay-surfactant based formulations of certain herbicides by assuming the same ratio between herbicides and surfactants in the formulations as for herbicides incorporated in micelles in solution. Calculations indicated that satisfactory FL formulations could not be synthesized. The experimental fractions of herbicides in the formulations were in agreement with the predicted ones for MS and MZ. The validity of this approach was confirmed in in vitro release tests that showed a slowing down of the release of a.i. from the designed formulations relative to the technical products. Soil dissipation studies with MS formulations also showed improved bioactivity of the clay-surfactant formulation relative to the commercial one. This methodological approach can be extended to other clay-surfactant systems for encapsulation and slow release of target molecules of interest.     

Isolation of Mycoplasma Membranes by Digitonin

The cell membrane of Mycoplasma hominis was isolated by lysing the cells with digitonin. Electron microscopy and chemical, density gradient, and electrophoretic analyses of the membrane proteins showed the membranes so obtained, like those isolated by osmotic lysis, to be relatively free of cytoplasmic contaminants. Sensitivity to digitonin lysis depended on temperature but was not affected by Mg(2+) ions and was only slightly affected by the age of the culture. Accordingly, it seems that digitonin may be used for the isolation of cell membranes from sterol-requiring mycoplasmas that tend to be fairly resistant to osmotic lysis.