Assembly of Superparamagnetic Filaments in External Field

We present a theoretical and simulation study of anchored magneto-elastic filaments in external magnetic field. The filaments are composed of a mixture of superparamagnetic and nonmagnetic colloidal beads interlinked with elastic springs. We explore the steady-state structures of filaments with various composition and bending rigidity subject to external magnetic field parallel to the surface. The interplay of elastic and induced magnetic interactions results in a rich phase behavior with morphologies reminiscent of macromolecular folding: bent filaments, loops, sheets, helicoids, and other collapsed structures. Our results provide new insights into the design of hierarchically assembled supramolecular structures with controlled response to external stimuli

Crossover behavior in crowding factor.

<p>The crowding factor, Γ, as a function of average minimum attraction, <i>ϵ</i>, at different packing fraction, <i>ϕ</i>, for TPM. (b) Γ as a function of <i>ϵ</i> at different <i>ϕ</i>, for CBM. The horizontal solid line denotes ln Γ = 0.0. The vertical solid and dashed line respectively represents the fitting values of <i>ϵ</i> as well as <i>K</i> for crystallins, and the critical attraction at which ln Γ = 0.0 is achieved.</p

The influence of product shape on crowding factor of crystallins.

<p>The crowding factor, Γ, as a function of packing fraction, <i>ϕ</i>, at different value of asphericity parameter, λ, for (a) hard spheres, (b) TPM with <i>ϵ</i> = 13.9 and (c) CBM with <i>n</i>_<i>s</i> = 2 and <i>K</i> = 10.6.</p

The osmotic pressure, Π, as a function of protein concentration, c.

<p>(a) the Π − <i>c</i> relation for TPM at different <i>ϵ</i>. (b) best fitting Π − <i>c</i> curves for CBM with different combinations of <i>n</i>_<i>s</i> and <i>K</i>. Black symbols denote experimental results derived from the work of Tardieu <i>et</i>. <i>al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0151159#pone.0151159.ref015" target="_blank">15</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0151159#pone.0151159.ref037" target="_blank">37</a>]. In order to compare analytic with experimental results, we set <i>T</i> = 298.15<i>K</i>.</p

The activity coefficient and crowding factor for crystallins.

<p>(a) The activity coefficient, <i>γ</i>, and (b) the crowding factor, Γ, as a function of packing fraction, <i>ϕ</i>, for TPM with <i>ϵ</i> = 13.9 and CBM with different combinations of <i>n</i>_<i>s</i> and <i>K</i> that best fit the experimental data for osmotic pressure of crystallins.</p

Association of two crystallins in macromolecular crowding.

<p>Sketch of two crystallins as reactants polymerising into a dimer as product for (a) thermodynamic perturbation model (TPM), where blue spheres represent crystallins with isotropic intermolecular attraction, and (b) chemical binding model (CBM), where blue spheres and red points respectively represent crystallins with steric repulsion and binding sites with chemical attraction. The general shape of the product is a spherocylinder with asphericity λ.</p

The molecules of <i>tRNA^Ser(AGN)</i> and <i>tRNA^Lys</i> in plant bug mitochondrial genomes and the AGG codon reassignments.

<p>The <i>tRNA^Ser(AGN)</i> and <i>tRNA^Lys</i> anticodons in genus decoding as Ser or Lys, as well as the predicated translation of AGN and AAR mRNA-codons, were shown. IMGC, Invertebrate Mitochondrial Genetic Code. Anticodons were depicted in 3′ to 5′ sense, e.g., UUC in <i>tRNA^Lys</i> corresponded to the anticodon CUU in standard notation. The point mutations of anticodon in the genus <i>Adelphocoris</i> were highlighted by red color.</p

Species used in this study.

<p>*, nearly complete mt genome.</p

Phylogenetic relationships among five cimicomorphan families inferred from mitochondrial genome sequences.

<p>Numbers close to the branching points were Bayesian posterior probabilities and ML bootstrap support values. Numbers from left to right were from nt123RNA and RNA datasets respectively. To the right of the tree, the predicted translation of the AGG codon was shown for each taxon. The newly sequenced species were highlighted in bold.</p

Comparative Mitogenomics of Plant Bugs (Hemiptera: Miridae): Identifying the AGG Codon Reassignments between Serine and Lysine

<div><p>Insect mitochondrial genomes are very important to understand the molecular evolution as well as for phylogenetic and phylogeographic studies of the insects. The Miridae are the largest family of Heteroptera encompassing more than 11,000 described species and of great economic importance. For better understanding the diversity and the evolution of plant bugs, we sequence five new mitochondrial genomes and present the first comparative analysis of nine mitochondrial genomes of mirids available to date. Our result showed that gene content, gene arrangement, base composition and sequences of mitochondrial transcription termination factor were conserved in plant bugs. Intra-genus species shared more conserved genomic characteristics, such as nucleotide and amino acid composition of protein-coding genes, secondary structure and anticodon mutations of tRNAs, and non-coding sequences. Control region possessed several distinct characteristics, including: variable size, abundant tandem repetitions, and intra-genus conservation; and was useful in evolutionary and population genetic studies. The AGG codon reassignments were investigated between serine and lysine in the genera <i>Adelphocoris</i> and other cimicomorphans. Our analysis revealed correlated evolution between reassignments of the AGG codon and specific point mutations at the antidocons of <i>tRNA^Lys</i> and <i>tRNA^Ser(AGN)</i>. Phylogenetic analysis indicated that mitochondrial genome sequences were useful in resolving family level relationship of Cimicomorpha. Comparative evolutionary analysis of plant bug mitochondrial genomes allowed the identification of previously neglected coding genes or non-coding regions as potential molecular markers. The finding of the AGG codon reassignments between serine and lysine indicated the parallel evolution of the genetic code in Hemiptera mitochondrial genomes.</p></div