Compositional Asymmetry Research Articles

The effects of light stimulation during incubation on indicators of stress susceptibility in broilers

Providing light during incubation has been shown to decrease bilateral physical asymmetry of broilers posthatch, which may indicate that early light stimulation reduces later stress susceptibility. This experiment evaluated the effects of lighting during embryogenesis on other measures of stress responsiveness in broilers. Cobb 500 eggs (n = 1,404) were incubated under 0L:24D, 1L:23D, 6L:18D, or 12L:12D; the light level was 550 lx. The broilers were then raised in floor pens under a 12L:12D lighting regimen, and various stress parameters were measured during wk 3 to 6 of age. There was an effect of incubation lighting regimen on posthatch stress responses. Following 1 h of crating, the change in corticosterone (CORT) concentration was less in the 12L:12D (−0.06 ng/mL, P < 0.05) treatment than all other treatments (pooled mean = 0.24 ng/mL); however, there were no treatment differences in CORT response to adrenocorticotropic hormone administration (pooled mean pre- vs. 1 h postadministration = 17.5 ng/mL, P > 0.05). Anti-keyhole limpet hemocyanin titers were higher in the 12L:12D birds (92,395 units/mL; P < 0.05) than all other treatments (pooled mean = 68,407 units/mL) on d 1 postcrating. Additionally, composite asymmetry scores were lower in the 12L:12D treatment (0.92 mm) than all other treatments (pooled mean = 1.14 mm, P < 0.05). These results demonstrate that providing 12 h of light per day during incubation can reduce the stress susceptibility of broilers posthatch.

The Molecular Mechanism of the Morphology Change in PS/PVME/Silica Blends Based on Rheology

The morphology change and the corresponding molecular mechanism of polystyrene (PS)/poly(vinyl methyl ether) (PVME) blends induced by hydrophilic or hydrophobic nanoparticles were studied. It was found that there was a threshold of hydrophilic silica loading for the occurrence of network–droplet morphological transition in PS/PVME blends. On the contrary, the viscoelastic network could sustain for a much longer time in the blends with higher loading of hydrophobic silica. Rheological measurements suggested that the networking of hydrophilic silica nanoparticles in the PVME-rich phase would significantly reduce the dynamic asymmetry of two phases and make the compositional asymmetry the dominant factor in controlling the morphology development during phase separation. However, adding the hydrophobic silica fillers would result in an increase of dynamic asymmetry and a decrease in compositional asymmetry because of their selective dispersion in the PS-rich phase, both stabilizing the continuous network stru...

Well-Organized Dense Arrays of Nanodomains in Thin Films of Poly(dimethylsiloxane)-b-poly(lactide) Diblock Copolymers

Thin films with well-organized arrays of densely packed nanodomains were fabricated from poly(dimethylsiloxane)-b-poly(dl-lactide) (DL) diblock copolymers. As a consequence of the unusually large Flory–Huggins interaction parameter between these repeat units, domains with sizes ∼10 nm are routinely generated using low molar mass diblock copolymers. Different morphologies are easily accessible by judiciously adjusting the block composition, garnering dot patterns (from spheres) and line patterns (from parallel cylinders) in a facile manner. The strong incompatibility also allows retention of order at relatively low molar mass even with high degrees of compositional asymmetry (e.g., fL ∼ 0.15). Block copolymers with various compositions are shown to form well-organized morphologies on various substrates and thermal annealing readily enhanced long-range order. All block copolymers were prepared on a >10 g scale, and the processing conditions are compatible with the current infrastructure of the microelectronics industry, demonstrating a strong potential for commercial relevance.

Description of Nearly Completed Mitochondrial Genome Sequences of the Garden Chafer Polyphylla laticollis manchurica, Endangered in Korea (Insecta: Coleoptera)

In this study, we present the nearly complete mitogenome sequences of the garden chafer, Polyphylla laticollis manchurica, which is listed as an endangered species in Korea. The P. l. manchurica mitogenome, which includes unfinished whole A+T-rich region and a partial srRNA was 14,473-bp long, possessing typical sets of genes (13 PCGs, 22 tRNA genes, and 2 rRNA genes). Gene arrangement of the P. l. manchurica mitogenome was identical to the common one found in the majority of insects. The 5 bp-long motif sequence (TAGTA) that has been suggested to be the possible binding site for the transcription termination peptide for the major-strand was also found in the P. l. manchurica mitogenome between <TEX>$tRNA^{Ser}$</TEX>(UCN) and ND1. The start codon for COI gene and ATPase8 was designated as a typical TTG. All tRNAs of the P. l. manchurica showed a stable canonical clover-leaf structure of other mt tRNAs, except for <TEX>$tRNA^{Ser}$</TEX>(AGN), DHU arm of which could not form stable stemloop structure. As has been previously determined, the high A/T content was unanimously observed in P. l. manchurica in terms of A/T bias in the third codon position (73.5%) compared with the first (66.4%) and second codon position (66.2%). The PCGs encoded in major-strands are slightly T-skewed, whereas those of the minor-strand are A-skewed, indicating strand asymmetry in nucleotide composition in the Coleoptera including P. l. manchurica.

Layer-by-layer cell membrane assembly

Eukaryotic subcellular membrane systems, such as the nuclear envelope or endoplasmic reticulum, present a rich array of architecturally and compositionally complex supramolecular targets that are yet inaccessible. Here we describe layer-by-layer phospholipid membrane assembly on microfluidic droplets, a route to structures with defined compositional asymmetry and lamellarity. Starting with phospholipid-stabilized water-in-oil droplets trapped in a static droplet array, lipid monolayer deposition proceeds as oil/water phase boundaries pass over the droplets. Unilamellar vesicles assembled layer-by-layer support functional insertion of both purified and in situ expressed membrane proteins. Synthesis and chemical probing of asymmetric unilamellar and double bilayer vesicles demonstrate the programmability of both membrane lamellarity and lipid leaflet composition during assembly. The immobilized vesicle arrays are a pragmatic experimental platform for biophysical studies of membranes and their associated proteins, particularly complexes that assemble and function in multilamellar contexts in vivo.

Beyond Treatment and Impact

Discrimination remains integral to understanding both how inequality is produced and how it can be remedied in employment settings. Yet like many sociological concepts, the notion of discrimination involves an uneasy mapping of theory to practice. Traditional conceptualizations of discrimination as differential treatment are ill-fitted to the structural and relational nature of much discrimination in the contemporary era. The disparate impact doctrine, which recognizes policies or practices that systematically disadvantage protected groups, picks up some of the theoretical slack, but offers little in the way of conceptualizing individuals’ complex and entangled experiences with inequality at work. In this article, I provide a conceptual reorganization of theories of discrimination, underscoring recent calls to move beyond the confines of the current disparate treatment and disparate impact binary by recognizing the structurally and culturally embedded nature of bias and discrimination. Drawing on recent sociological research as well as my own analysis of legal records and interviews with plaintiffs involved in high-profile sex and race lawsuits settled in the past decade, I illustrate how differential treatment emerges in the context of and enabled by systems of vulnerability and privilege, workplace culture, and compositional asymmetries. I conclude with a discussion of the implications of this framework for antidiscrimination enforcement efforts.

Dynamic Balance Performance and Noncontact Lower Extremity Injury in College Football Players

Background:Field expedient screening tools that can identify individuals at an elevated risk for injury are needed to minimize time loss in American football players. Previous research has suggested that poor dynamic balance may be associated with an elevated risk for injury in athletes; however, this has yet to be examined in college football players.Hypothesis:To determine if dynamic balance deficits are associated with an elevated risk of injury in collegiate football players. It was hypothesized that football players with lower performance and increased asymmetry in dynamic balance would be at an elevated risk for sustaining a noncontact lower extremity injury.Study Design:Prospective cohort study.Methods:Fifty-nine collegiate American football players volunteered for this study. Demographic information, injury history, and dynamic balance testing performance were collected, and noncontact lower extremity injuries were recorded over the course of the season. Receiver operator characteristic curves were calculated based on performance on the Star Excursion Balance Test (SEBT), including composite score and asymmetry, to determine the population-specific risk cut-off point. Relative risk was then calculated based on these variables, as well as previous injury.Results:A cut-off point of 89.6% composite score on the SEBT optimized the sensitivity (100%) and specificity (71.7%). A college football player who scored below 89.6% was 3.5 times more likely to get injured.Conclusion:Poor performance on the SEBT may be related to an increased risk for sustaining a noncontact lower extremity injury over the course of a competitive American football season.Clinical Relevance:College football players should be screened preseason using the SEBT to identify those at an elevated risk for injury based upon dynamic balance performance to implement injury mitigation strategies to this specific subgroup of athletes.

Factors Associated With Paraspinal Muscle Asymmetry in Size and Composition in a General Population Sample of Men

Paraspinal muscle asymmetry in cross-sectional area (CSA) and composition have been associated with low back pain and pathology. However, substantial multifidus muscle asymmetry also has been reported in men who were asymptomatic, and little is known about other factors influencing asymmetry. The goal of this study was to identify behavioral, environmental, and constitutional factors associated with paraspinal muscle asymmetry. A cross-sectional study of 202 adult male twins was conducted. Data were collected through a structured interview, physical examination, and magnetic resonance imaging. Measurements of multifidus and erector spinae muscle CSA and the ratio of fat-free CSA to total CSA were obtained from T2-weighted axial images at L3-L4 and L5-S1. In multivariable analyses, greater asymmetry in multifidus CSA at L3-L4 was associated with lower occupational physical demands and less disk height narrowing. Handedness was the only factor associated with multifidus muscle CSA asymmetry at L5-S1. For the erector spinae muscle, greater age, handedness, and disk height narrowing were associated with CSA asymmetry at L3-L4, and sports activity, handedness, disk height narrowing, and familial aggregation were associated with CSA asymmetry at L5-S1. In multivariable analyses of asymmetry in muscle composition, familial aggregation explained 7% to 20% of the variance in multifidus and erector spinae muscle side-to-side differences at both levels measured. In addition, handedness and pain severity entered the model for erector spinae muscle asymmetry at L5-S1, and disability, handedness, and disk height narrowing entered the model for multifidus muscle asymmetry at L5-S1. Reliance on participants' recall for low back pain history, occupation, and physical activity levels was a limitation of this study. Few of the factors investigated were associated with paraspinal muscle asymmetry, and associations were inconsistent and modest, explaining little of the variance in paraspinal muscle asymmetry.

Early postsurgical visualization of composite mesh used in ventral hernia repair by amide proton transfer MRI

The feasibility of noninvasive visualization of composite meshes used in ventral hernia repair by amide-proton transfer magnetic resonance imaging (APT-MRI) was explored. Magnetization transfer asymmetry ratio images of composite meshes were obtained in vitro and in vivo from fast-spin echo acquisitions with frequency saturation offsets of ±3.5 ppm with respect to water frequency and no saturation. Three rats were assessed with APT-MRI each week for 1 month after the intraperitoneal implantation of two meshes, one on each side of the incision. One mesh was coated with collagen and the other was not. In vitro, meshes were delineated with APT-MRI as a thin continuous linear hypersignal located on one side of the mesh. Unlike collagen-free meshes, collagen-coated meshes were easily identified in vivo with APT-MRI during the first 3 weeks postimplantation. The composite meshes magnetization transfer asymmetry ratio (8.7 ± 2.8%) were significantly different from the muscle magnetization transfer asymmetry ratio value (-0.9 ± 1.6%). After a month, the mesh value dropped down to 1.1 ± 3.9%. Muscle and mesh magnetization transfer asymmetry ratio values were not significantly different and mesh conspicuity was no longer possible. The results suggest that APT-MRI is a promising technique for noninvasive, early postsurgical visualization of composite meshes used in ventral hernia repair.

Compositional-asymmetry influenced non-linear optical processes of plasmonic nanoparticle dimers

The influences of compositional asymmetry on the two-photon photoluminescence and the second harmonic generation processes in weakly coupled plasmonic dimers were addressed. Au-Au homodimer and Au-Ag heterodimer arrays produced using electron-beam lithography were investigated using confocal nonlinear optical imaging and spectroscopy. Compared to the Au-Au homodimers, the Au-Ag dimers showed slightly broadened two-photon photoluminescence near the X symmetry point at the first Brillouin zone of Au, whilst that from the L symmetry point stayed the same. Additionally, weakly coupled Au-Ag heterodimers generated strong second harmonic signals which were invisible in the Au-Au homodimers. The observations highlighted the importance of compositional asymmetry in the non-linear optical studies of plasmonic dimers.

Atomistic Simulations of Functional Gold Nanoparticles Au144(Sr)60 Interacting with Membranes

Gold nanoparticles (AuNps) are used in nanomedicine in, e.g., drug delivery and bio-imaging. However, it is regrettable that the understanding of nanoparticle properties in cellular surroundings is incompletely understood. Here, we have complemented our previous studies [1] by performing extensive atomistic molecular dynamics simulations of lipid membranes interacting with charged gold nanoparticles. We have elucidated the action of these nanoparticles on membranes characterized by lipid compositional asymmetry in the two leaflets, thereby unraveling the interactions of AuNPs with both the extracellular and the cytosolic sides of plasma membranes of eukaryotic cells. We have found that there is an appealing interplay between AuNps and the two membrane leaflets, where both the membrane leaflet composition and the charged nature of the nanoparticle (cationic vs. anionic) play a role. Here we discuss the resulting effects from both structural and dynamical points of view, and highlight the role of electrostatics in nanoparticle-membrane interactions.Figure 1Visualization of (a) anionic AuNP with the extracellular and (b) cationic AuNP with the cytosolic leaflet.View Large Image | View Hi-Res Image | Download PowerPoint Slide[1] E. Heikkila, et al. 2012. J. Phys. Chem. C 116: 9805-9815.

A comparative analysis on the synonymous codon usage pattern in viral functional genes and their translational initiation region of ASFV

The synonymous codon usage pattern of African swine fever virus (ASFV), the similarity degree of the synonymous codon usage between this virus and some organisms and the synonymous codon usage bias for the translation initiation region of viral functional genes in the whole genome of ASFV have been investigated by some simply statistical analyses. Although both GC12% (the GC content at the first and second codon positions) and GC3% (the GC content at the third codon position) of viral functional genes have a large fluctuation, the significant correlations between GC12 and GC3% and between GC3% and the first principal axis of principle component analysis on the relative synonymous codon usage of the viral functional genes imply that mutation pressure of ASFV plays an important role in the synonymous codon usage pattern. Turning to the synonymous codon usage of this virus, the codons with U/A end predominate in the synonymous codon family for the same amino acid and a weak codon usage bias in both leading and lagging strands suggests that strand compositional asymmetry does not take part in the formation of codon usage in ASFV. The interaction between the absolute codon usage bias and GC3% suggests that other selections take part in the formation of codon usage, except for the mutation pressure. It is noted that the similarity degree of codon usage between ASFV and soft tick is higher than that between the virus and the pig, suggesting that the soft tick plays a more important role than the pig in the codon usage pattern of ASFV. The translational initiation region of the viral functional genes generally have a strong tendency to select some synonymous codons with low GC content, suggesting that the synonymous codon usage bias caused by translation selection from the host takes part in modulating the translation initiation efficiency of ASFV functional genes.

The mitochondrial genome of Coridius chinensis (Hemiptera: Dinidoridae)

The nearly complete mitochondrial genome of Coridius chinensis (Dallas) is reported in this study. The mitogenome is a double-stranded circular molecule of more than 14,648 bp in length with an A+T content of 75.1%. It encoded 37 genes as in other insect mtDNAs, including 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and a control region (unsuccessful sequencing), and the gene order is the same as most other known heteropteran mitogenomes. All of the 22 transfer RNAs can be folded into the typical cloverleaf structure except tRNASer(AGN), which can only form a simple loop at the site of dihydrouridine (DHU) arm as known in other metazoans. The secondary structures of the large and small ribosomal RNAs of C. chinensis are similar to other presented insects. The rrnL consisted of six structural domains and 40 helices, and the rrnS consisted of three structural domains and 26 helices. Nine PCGs are initiated with the standard initiation codons (ATN), while ND6 and ND1 use GTG, and COI and ATP8 use TTG. All PCGs stopped with TAA/TAG termination codons except the COII terminated with a single T residue. Asymmetry in the nucleotide composition between J-strand and N-strand was observed in this mitogenome.

Linking the DNA strand asymmetry to the spatio-temporal replication program

In paper I, we addressed the impact of the spatio-temporal program on the DNA composition evolution in the case of time homogeneous and neighbor-independent substitution rates. But substitution rates do depend on the flanking nucleotides as exemplified in vertebrates where CpG sites are hypermutable so that the substitution rate C --> T depends dramatically (ten fold) on whether the cytosine belongs to a CG dinucleotide or not. With the specific goal to account for neighbor-dependence, we revisit our minimal modeling of neutral substitution rates in the human genome. When assuming that r = CpG --> TpG and its reverse complement r(c) = CpG --> CpA are (by far) the main neighbor-dependent substitution rates, we demonstrate, using perturbative analysis, that neighbor-dependence does not affect the decomposition of the compositional asymmetry into a transcription- and a replication-associated components, the former increases in magnitude with transcription rate and changes sign with gene orientation, whereas the latter is proportional to the replication fork polarity. Indeed the neighbor dependence case differs from the neighbor-independent model by an additional source term related to the CG dinucleotide content in both the transcription and replication-associated components. We finally discuss the case of time-dependent substitution rates confirming as a very general result the fact that the skew can still be decomposed into a transcription- and a replication-associated components.

High-tailing it to the apical surface. Focus on “Apical targeting of the P2Y4 receptor is directed by hydrophobic and basic residues in the cytoplasmic tail”

epithelial cell function requires the generation and maintenance of polarized apical and basolateral membrane domains with distinct protein and lipid compositions. This asymmetry in membrane composition is essential for myriad cell functions that include substratum adhesion, cell-cell communication

Linking the DNA strand asymmetry to the spatio-temporal replication program

Two key cellular processes, namely transcription and replication, require the opening of the DNA double helix and act differently on the two DNA strands, generating different mutational patterns (mutational asymmetry) that may result, after long evolutionary time, in different nucleotide compositions on the two DNA strands (compositional asymmetry). We elaborate on the simplest model of neutral substitution rates that takes into account the strand asymmetries generated by the transcription and replication processes. Using perturbation theory, we then solve the time evolution of the DNA composition under strand-asymmetric substitution rates. In our minimal model, the compositional and substitutional asymmetries are predicted to decompose into a transcription- and a replication-associated components. The transcription-associated asymmetry increases in magnitude with transcription rate and changes sign with gene orientation while the replication-associated asymmetry is proportional to the replication fork polarity. These results are confirmed experimentally in the human genome, using substitution rates obtained by aligning the human and chimpanzee genomes using macaca and orangutan as outgroups, and replication fork polarity determined in the HeLa cell line as estimated from the derivative of the mean replication timing. When further investigating the dynamics of compositional skew evolution, we show that it is not at equilibrium yet and that its evolution is an extremely slow process with characteristic time scales of several hundred Myrs.

Comparative Genomic Analysis Indicates Strand Compositional Asymmetries as Regional Landmarks in Plasmid Evolution

Comparative Genomic Analysis Indicates Strand Compositional Asymmetries as Regional Landmarks in Plasmid Evolution

Ganglioside GM1 forces the redistribution of cholesterol in a biomimetic membrane

Neutron reflectivity has been applied to investigate different mixed asymmetric lipid systems, in the form of single “supported+floating” bilayers, made of phospholipids, cholesterol and GM1 ganglioside (Neu5Acα2-3(Galβ1-3GalNAcβ1-4)Galβ1-4Glcβ1Cer)) in bio-similar mole ratios. Bilayer preparation was carried out layer-by-layer with the Langmuir–Blodgett Langmuir–Schaefer techniques, allowing for compositional asymmetry in the system buildup. It is the first time that such a complex model membrane system is reported. Two important conclusions are drawn. First, it is experimentally shown that the presence of GM1 enforces an asymmetry in cholesterol distribution, opposite to what happens for a GM1-free membrane that, submitted to a similar procedure, results in a full symmetrization of cholesterol distribution. We underline that natural cholesterol has been used. Second, and most interesting, our results suggest that a preferential asymmetric distribution of GM1 and cholesterol is attained in a model membrane with biomimetic composition, revealing that a true coupling between the two molecular species occurs.

Validation of Bacterial Replication Termination Models Using Simulation of Genomic Mutations

In bacterial circular chromosomes and most plasmids, the replication is known to be terminated when either of the following occurs: the forks progressing in opposite directions meet at the distal end of the chromosome or the replication forks become trapped by Tus proteins bound to Ter sites. Most bacterial genomes have various polarities in their genomic structures. The most notable feature is polar genomic compositional asymmetry of the bases G and C in the leading and lagging strands, called GC skew. This asymmetry is caused by replication-associated mutation bias, and this “footprint" of the replication machinery suggests that, in contrast to the two known mechanisms, replication termination occurs near the chromosome dimer resolution site dif. To understand this difference between the known replication machinery and genomic compositional bias, we undertook a simulation study of genomic mutations, and we report here how different replication termination models contribute to the generation of replication-related genomic compositional asymmetry. Contrary to naive expectations, our results show that a single finite termination site at dif or at the GC skew shift point is not sufficient to reconstruct the genomic compositional bias as observed in published sequences. The results also show that the known replication mechanisms are sufficient to explain the position of the GC skew shift point.

Global variations of HDO and HDO/H2O ratios in the upper troposphere and lower stratosphere derived from ACE‐FTS satellite measurements

High‐quality satellite observations of water and deuterated water in the upper troposphere and lower stratosphere (UTLS) from the Atmospheric Chemistry Experiment Fourier transform spectrometer (ACE‐FTS) are used to map global climatological behavior. Spatial and temporal variability in these data suggest that convection plays a significant role in setting water vapor isotopic composition in these regions. In many instances, enhancements in HDO/H2O (i.e., δD) are closely tied to patterns of climatological deep convection and uncorrelated with water vapor, although convection appears to have different isotopic effects in different locations. The ACE‐FTS data reveal seasonal variations in the tropics and allow mapping of climatological regional structure. These data reveal strong regional isotopic enhancement associated with the North American summer monsoon but not the Asian monsoon or the western Pacific warm pool. We suggest that the isotopic effects of deep convection near the tropopause are moderated by the ambient relative humidity, which controls the amount of convective ice that evaporates. Local convective signals can in turn affect global behavior: the North America monsoon influence introduces a Northern Hemisphere–Southern Hemisphere asymmetry in water isotopic composition in the lower stratosphere that extends into the tropics and influences the apparent seasonal cycle in averaged tropical UTLS data. Seasonal variation in tropical lower stratospheric water isotopic composition extends up to ∼20 km in ACE retrievals, but in contrast to previous reports, there is no clear evidence of propagation beyond the lowermost stratosphere. The reliability of these observations is supported by the broad consistency of ACE‐FTS averaged tropical profiles with previous remote and in situ δD measurements.