Critical-layer structures and mechanisms in elastoinertial turbulence

Simulations of elastoinertial turbulence (EIT) of a polymer solution at low Reynolds number are shown to display localized polymer stretch fluctuations. These are very similar to structures arising from linear stability (Tollmien-Schlichting (TS) modes) and resolvent analyses: i.e., critical-layer structures localized where the mean fluid velocity equals the wavespeed. Computation of self-sustained nonlinear TS waves reveals that the critical layer exhibits stagnation points that generate sheets of large polymer stretch. These kinematics may be the genesis of similar structures in EIT.Comment: 5 pages, 4 figures; Accepted in Physical Review Letter

IView: introgression library visualization and query tool

<p>Abstract</p> <p>Background</p> <p>An introgression library is a family of near-isogenic lines in a common genetic background, each of which carries one or more genomic regions contributed by a donor genome. Near-isogenic lines are powerful genetic resources for the analysis of phenotypic variation and are important for map-base cloning genes underlying mutations and traits. With many thousands of distinct genotypes, querying introgression libraries for lines of interest is an issue. </p> <p>Results</p> <p>We have created IView, a tool to graphically display and query near-isogenic line libraries for specific introgressions. This tool incorporates a web interface for displaying the location and extent of introgressions. Each genetic marker is associated with a position on a reference map. Users can search for introgressions using marker names, or chromosome number and map positions. This search results in a display of lines carrying an introgression at the specified position. Upon selecting one of the lines, color-coded introgressions on all chromosomes of the line are displayed graphically.</p> <p>The source code for IView can be downloaded from <url>http://xrl.us/iview</url>. </p> <p>Conclusions</p> <p>IView will be useful for those wanting to make introgression data from their stock of germplasm searchable. </p

Self-sustained elastoinertial Tollmien-Schlichting waves

Direct simulations of two-dimensional plane channel flow of a viscoelastic fluid at Reynolds number Re = 3000 reveal the existence of a family of attractors whose structure closely resembles the linear Tollmien–Schlichting (TS) mode, and in particular exhibits strongly localized stress fluctuations at the critical layer position of the TS mode. At the parameter values chosen, this solution branch is not connected to the nonlinear TS solution branch found for Newtonian flow, and thus represents a solution family that is nonlinearly self-sustained by viscoelasticity. The ratio between stress and velocity fluctuations is in quantitative agreement for the attractor and the linear TS mode, and increases strongly with Weissenberg number, Wi. For the latter, there is a transition in the scaling of this ratio as Wi increases, and the Wi at which the nonlinear solution family comes into existence is just above this transition. Finally, evidence indicates that this branch is connected through an unstable solution branch to two-dimensional elastoinertial turbulence (EIT). These results suggest that, in the parameter range considered here, the bypass transition leading to EIT is mediated by nonlinear amplification and self-sustenance of perturbations that excite the TS mode

Using Association Mapping in Teosinte to Investigate the Function of Maize Selection-Candidate Genes

BACKGROUND:Large-scale screens of the maize genome identified 48 genes that show the putative signature of artificial selection during maize domestication or improvement. These selection-candidate genes may act as quantitative trait loci (QTL) that control the phenotypic differences between maize and its progenitor, teosinte. The selection-candidate genes appear to be located closer in the genome to domestication QTL than expected by chance. METHODS AND FINDINGS:As a step toward defining the traits controlled by these genes, we performed phenotype-genotype association mapping in teosinte for 32 of the 48 plus three other selection-candidate genes. Our analyses assayed 32 phenotypic traits, many of which were altered during maize domestication or improvement. We observed several significant associations between SNPs in the selection-candidate genes and trait variation in teosinte. These included two associations that surpassed the Bonferroni correction and five instances where a gene significantly associated with the same trait in both of our association mapping panels. Despite these significant associations, when compared as a group the selection-candidate genes performed no better than randomly chosen genes. CONCLUSIONS:Our results suggest association analyses can be helpful for identifying traits under the control of selection-candidate genes. Indeed, we present evidence for new functions for several selection-candidate genes. However, with the current set of selection-candidate genes and our association mapping strategy, we found very few significant associations overall and no more than we would have found with randomly chosen genes. We discuss possible reasons that a large number of significant genotype-phenotype associations were not discovered

Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers

A newly developed maize Illumina GoldenGate Assay with 1536 SNPs from 582 loci was used to genotype a highly diverse global maize collection of 632 inbred lines from temperate, tropical, and subtropical public breeding programs. A total of 1229 informative SNPs and 1749 haplotypes within 327 loci was used to estimate the genetic diversity, population structure, and familial relatedness. Population structure identified tropical and temperate subgroups, and complex familial relationships were identified within the global collection. Linkage disequilibrium (LD) was measured overall and within chromosomes, allelic frequency groups, subgroups related by geographic origin, and subgroups of different sample sizes. The LD decay distance differed among chromosomes and ranged between 1 to 10 kb. The LD distance increased with the increase of minor allelic frequency (MAF), and with smaller sample sizes, encouraging caution when using too few lines in a study. The LD decay distance was much higher in temperate than in tropical and subtropical lines, because tropical and subtropical lines are more diverse and contain more rare alleles than temperate lines. A core set of inbreds was defined based on haplotypes, and 60 lines capture 90% of the haplotype diversity of the entire panel. The defined core sets and the entire collection can be used widely for different research targets

Critical-Layer Structures and Mechanisms in Elastoinertial Turbulence

Simulations of elastoinertial turbulence (EIT) of a polymer solution at low Reynolds number are shown to display localized polymer stretch fluctuations. These are very similar to structures arising from linear stability (Tollmien-Schlichting modes) and resolvent analyses, i.e., critical-layer structures localized where the mean fluid velocity equals the wave speed. Computations of self-sustained nonlinear Tollmien-Schlichting waves reveal that the critical layer exhibits stagnation points that generate sheets of large polymer stretch. These kinematics may be the genesis of similar structures in EIT

A protocol for rapid and parallel isolation of myocytes and non-myocytes from multiple mouse hearts.

This protocol features parallel isolation of myocytes and non-myocytes from murine hearts. It was designed with considerations for (1) time required to extract cardiac cells, (2) cell viability, and (3) protocol scalability. Here, a peristaltic pump and 3D-printed elements are combined to perfuse the heart with enzymes to dissociate cells. Myocytes and non-myocytes extracted using this protocol are separated by centrifugation and/or fluorescence-activated cell sorting for use in downstream applications including single-cell omics or other bio-molecular analyses. For complete details on the use and execution of this protocol, please refer to McLellan et al. (2020)