The fate of Arabidopsis thaliana homeologous CNSs and their motifs in the Paleohexaploid Brassica rapa.

Following polyploidy, duplicate genes are often deleted, and if they are not, then duplicate regulatory regions are sometimes lost. By what mechanism is this loss and what is the chance that such a loss removes function? To explore these questions, we followed individual Arabidopsis thaliana-A. thaliana conserved noncoding sequences (CNSs) into the Brassica ancestor, through a paleohexaploidy and into Brassica rapa. Thus, a single Brassicaceae CNS has six potential orthologous positions in B. rapa; a single Arabidopsis CNS has three potential homeologous positions. We reasoned that a CNS, if present on a singlet Brassica gene, would be unlikely to lose function compared with a more redundant CNS, and this is the case. Redundant CNSs go nondetectable often. Using this logic, each mechanism of CNS loss was assigned a metric of functionality. By definition, proved deletions do not function as sequence. Our results indicated that CNSs that go nondetectable by base substitution or large insertion are almost certainly still functional (redundancy does not matter much to their detectability frequency), whereas those lost by inferred deletion or indels are approximately 75% likely to be nonfunctional. Overall, an average nondetectable, once-redundant CNS more than 30 bp in length has a 72% chance of being nonfunctional, and that makes sense because 97% of them sort to a molecular mechanism with deletion in its description, but base substitutions do cause loss. Similarly, proved-functional G-boxes go undetectable by deletion 82% of the time. Fractionation mutagenesis is a procedure that uses polyploidy as a mutagenic agent to genetically alter RNA expression profiles, and then to construct testable hypotheses as to the function of the lost regulatory site. We show fractionation mutagenesis to be a deletion machine in the Brassica lineage

Lack of an efficient endoplasmic reticulum-localized recycling system protects peroxiredoxin IV from hyperoxidation

Typical 2-cys peroxiredoxins are required to remove hydrogen peroxide from several different cellular compartments. Their activity can be regulated by hyperoxidation and consequent inactivation of the active site peroxidatic cysteine. Here we have developed a simple assay to quantify the hyperoxidation of peroxiredoxins. Hyperoxidation of peroxiredoxins can only occur efficiently in the presence of a recycling system usually based on thioredoxin and thioredoxin reductase. We demonstrate that there is a marked difference in the sensitivity of the endoplasmic reticulum-localized peroxiredoxin to hyperoxidation compared to either the cytosolic or mitochondrial enzymes. Each enzyme is equally sensitive to hyperoxidation in the presence of a robust recycling system. Our results demonstrate that the peroxiredoxin IV recycling in the ER is much less efficient than in the cytosol or mitochondria leading to the protection of peroxiredoxin IV from hyperoxidation

Comparison of CFD and DSMC Using Calibrated Transport Parameters

Hypersonic re-entry flows span a wide range of length scales where regions of both rarefied and continuum flow exist. Traditional computational fluid dynamics (CFD) techniques do not provide an accurate solution for the rarefied regions of such mixed flow fields. Although direct simulation Monte Carlo (DSMC) can be used to accurately capture both the continuum and rarefied features of mixed flow fields, they are computationally expensive when employed to simulate the low Knudsen number continuum regimes. Thus, a hybrid framework for seamlessly combining the two methodologies, CFD and DSMC, continues to be a topic of significant research effort. Ensuring consistency in the reaction kinetics and transport models employed within CFD and DSMC is a crucial requirement for obtaining a reliable solution from a hybrid framework for combined continuum/rarefied high speed flows. This paper represents one of the first studies to utilize the calibrated transport parameters developed to ensure consistency between CFD and DSMC solvers. The new variable soft sphere (VSS) parameters are compared to both previous standard variable hard sphere (VHS) parameters and also to solutions from the CFD transport properties that the new parameters were developed to reproduce

Genome sequence of a novel alloherpesvirus isolated from glass catfish (Kryptopterus bicirrhis)

The 149,343-bp genome of silurid herpesvirus 1, which was isolated in Thailand from glass catfish, was sequenced. The genome was most closely related to that of ictalurid herpesvirus 2, which infects black bullhead catfish. To our knowledge, this was the first silurid catfish alloherpesvirus genome to be sequenced

Diffractive wave guiding of hot electrons by the Au (111) herringbone reconstruction

The surface potential of the herringbone reconstruction on Au(111) is known to guide surface-state electrons along the potential channels. Surprisingly, we find by scanning tunneling spectroscopy that hot electrons with kinetic energies twenty times larger than the potential amplitude (38 meV) are still guided. The efficiency even increases with kinetic energy, which is reproduced by a tight binding calculation taking the known reconstruction potential and strain into account. The guiding is explained by diffraction at the inhomogeneous electrostatic potential and strain distribution provided by the reconstruction.Comment: 10 pages, 9 figure

Genome sequence of an alphaherpesvirus from a beluga whale (Delphinapterus leucas)

Beluga whale alphaherpesvirus 1 was isolated from a blowhole swab taken from a juvenile beluga whale. The genome is 144,144 bp in size and contains 86 putative genes. The virus groups phylogenetically with members of the genus Varicellovirus in subfamily Alphaherpesvirinae and is the first alphaherpesvirus sequenced from a marine mammal

Functional interpretation of single cell similarity maps.

We present Vision, a tool for annotating the sources of variation in single cell RNA-seq data in an automated and scalable manner. Vision operates directly on the manifold of cell-cell similarity and employs a flexible annotation approach that can operate either with or without preconceived stratification of the cells into groups or along a continuum. We demonstrate the utility of Vision in several case studies and show that it can derive important sources of cellular variation and link them to experimental meta-data even with relatively homogeneous sets of cells. Vision produces an interactive, low latency and feature rich web-based report that can be easily shared among researchers, thus facilitating data dissemination and collaboration

Lineage dynamics of murine pancreatic development at single-cell resolution.

Organogenesis requires the complex interactions of multiple cell lineages that coordinate their expansion, differentiation, and maturation over time. Here, we profile the cell types within the epithelial and mesenchymal compartments of the murine pancreas across developmental time using a combination of single-cell RNA sequencing, immunofluorescence, in situ hybridization, and genetic lineage tracing. We identify previously underappreciated cellular heterogeneity of the developing mesenchyme and reconstruct potential lineage relationships among the pancreatic mesothelium and mesenchymal cell types. Within the epithelium, we find a previously undescribed endocrine progenitor population, as well as an analogous population in both human fetal tissue and human embryonic stem cells differentiating toward a pancreatic beta cell fate. Further, we identify candidate transcriptional regulators along the differentiation trajectory of this population toward the alpha or beta cell lineages. This work establishes a roadmap of pancreatic development and demonstrates the broad utility of this approach for understanding lineage dynamics in developing organs