Molecular-Kinetic Simulations of Escape from the Ex-planet and Exoplanets: Criterion for Transonic Flow

The equations of gas dynamics are extensively used to describe atmospheric loss from solar system bodies and exoplanets even though the boundary conditions at infinity are not uniquely defined. Using molecular-kinetic simulations that correctly treat the transition from the continuum to the rarefied region, we confirm that the energy-limited escape approximation is valid when adiabatic expansion is the dominant cooling process. However, this does not imply that the outflow goes sonic. In fact in the sonic regime, the energy limited approximation can significantly under estimate the escape rate. Rather large escape rates and concomitant adiabatic cooling can produce atmospheres with subsonic flow that are highly extended. Since this affects the heating rate of the upper atmosphere and the interaction with external fields and plasmas, we give a criterion for estimating when the outflow goes transonic in the continuum region. This is applied to early terrestrial atmospheres, exoplanet atmospheres, and the atmosphere of the ex-planet, Pluto, all of which have large escape rates. The paper and its erratum, combined here, are published: ApJL 768, L4 (2013); ApJ, 779, L30 (2013).Comment: 11 pages, 3 figure

Aging in the Drosophila ovary: contrasting changes in the expression of the piRNA machinery and mitochondria but no global release of transposable elements

A grant from the One-University Open Access Fund at the University of Kansas was used to defray the author's publication fees in this Open Access journal. The Open Access Fund, administered by librarians from the KU, KU Law, and KUMC libraries, is made possible by contributions from the offices of KU Provost, KU Vice Chancellor for Research & Graduate Studies, and KUMC Vice Chancellor for Research. For more information about the Open Access Fund, please see http://library.kumc.edu/authors-fund.xml.Background Evolutionary theory indicates that the dynamics of aging in the soma and reproductive tissues may be distinct. This difference arises from the fact that only the germline lineage establishes future generations. In the soma, changes in the landscape of heterochromatin have been proposed to have an important role in aging. This is because redistribution of heterochromatin during aging has been linked to the derepression of transposable elements and an overall loss of somatic gene regulation. A role for changes in the chromatin landscape in the aging of reproductive tissues is less well established. Whether or not epigenetic factors, such as heterochromatin marks, are perturbed in aging reproductive tissues is of interest because, in special cases, epigenetic variation may be heritable. Using mRNA sequencing data from late-stage egg chambers in Drosophila melanogaster, we characterized the landscape of altered gene and transposable element expression in aged reproductive tissues. This allowed us to test the hypothesis that reproductive tissues may differ from somatic tissues in their response to aging. Results We show that age-related expression changes in late-stage egg chambers tend to occur in genes residing in heterochromatin, particularly on the largely heterochromatic 4th chromosome. However, these expression differences are seen as both decreases and increases during aging, inconsistent with a general loss of heterochromatic silencing. We also identify an increase in expression of the piRNA machinery, suggesting an age-related increased investment in the maintenance of genome stability. We further identify a strong age-related reduction in the expression of mitochondrial transcripts. However, we find no evidence for global TE derepression in reproductive tissues. Rather, the observed effects of aging on TEs are primarily strain and family specific. Conclusions These results identify unique responses in somatic versus reproductive tissue with regards to aging. As in somatic tissues, female reproductive tissues show reduced expression of mitochondrial genes. In contrast, the piRNA machinery shows increased expression during aging. Overall, these results also indicate that global loss of TE control observed in other studies may be unique to the soma and sensitive to genetic background and TE family.NSF Graduate Research Fellowship ProgramGlenn/AFAR Scholarship for Research in the Biology of AgingNSF Award 1413532COBRE CMADP program (P20GM103638)University of Kansa

piRNAs Are Associated with Diverse Transgenerational Effects on Gene and Transposon Expression in a Hybrid Dysgenic Syndrome of D. virilis

Sexual reproduction allows transposable elements (TEs) to proliferate, leading to rapid divergence between populations and species. A significant outcome of divergence in the TE landscape is evident in hybrid dysgenic syndromes, a strong form of genomic incompatibility that can arise when (TE) family abundance differs between two parents. When TEs inherited from the father are absent in the mother's genome, TEs can become activated in the progeny, causing germline damage and sterility. Studies in Drosophila indicate that dysgenesis can occur when TEs inherited paternally are not matched with a pool of corresponding TE silencing PIWI-interacting RNAs (piRNAs) provisioned by the female germline. Using the D. virilis syndrome of hybrid dysgenesis as a model, we characterize the effects that divergence in TE profile between parents has on offspring. Overall, we show that divergence in the TE landscape is associated with persisting differences in germline TE expression when comparing genetically identical females of reciprocal crosses and these differences are transmitted to the next generation. Moreover, chronic and persisting TE expression coincides with increased levels of genic piRNAs associated with reduced gene expression. Combined with these effects, we further demonstrate that gene expression is idiosyncratically influenced by differences in the genic piRNA profile of the parents that arise though polymorphic TE insertions. Overall, these results support a model in which early germline events in dysgenesis establish a chronic, stable state of both TE and gene expression in the germline that is maintained through adulthood and transmitted to the next generation. This work demonstrates that divergence in the TE profile is associated with diverse piRNA-mediated transgenerational effects on gene expression within populations

Heme ligation and redox chemistry in two bacterial thiosulfate dehydrogenase (TsdA) enzyme

Thiosulfate dehydrogenases (TsdA) are bidirectional bacterial di-heme enzymes that catalyze the interconversion of tetrathionate and thiosulfate at measurable rates in both directions. In contrast to our knowledge of TsdA activities, information on the redox properties in the absence of substrates is rather scant. To address this deficit, we combined magnetic circular dichroism (MCD) spectroscopy and protein film electrochemistry (PFE) in a study to resolve heme ligation and redox chemistry in two representative TsdAs. We examined the TsdAs from Campylobacter jejuni, a micro-aerobe human pathogen, and from the purple sulfur bacterium Allochromatium vinosum. In these organisms, the enzyme functions as a tetrathionate reductase and a thiosulfate oxidase respectively. The active site Heme 1 in both enzymes has His/Cys− ligation in the ferric and ferrous states and the midpoint potentials (Em) of the corresponding redox transformations are similar, −185 mV versus standard hydrogen electrode (SHE). However, fundamental differences are observed in the properties of the second, electron transferring, Heme 2. In C. jejuni TsdA Heme 2 has His/Met ligation and an Em of +172 mV. In A. vinosum TsdA, Heme 2 reduction triggers a switch from His/Lys ligation (Em, −129 mV) to His/Met (Em,+266 mV) but the rates of interconversion are such that His/Lys ligation would be retained during turnover. In summary, our findings have unambiguously assigned Em values to defined axial ligand sets in TsdAs, specified the rates of Heme 2 ligand exchange in the A. vinosum enzyme, and provided information relevant to describing their catalytic mechanism(s)

Scaling and universality in coupled driven diffusive models

Inspired by the physics of magnetohydrodynamics (MHD) a simplified coupled Burgers-like model in one dimension (1d), a generalization of the Burgers model to coupled degrees of freedom, is proposed to describe 1dMHD. In addition to MHD, this model serves as a 1d reduced model for driven binary fluid mixtures. Here we have performed a comprehensive study of the universal properties of the generalized d-dimensional version of the reduced model. We employ both analytical and numerical approaches. In particular, we determine the scaling exponents and the amplitude-ratios of the relevant two-point time-dependent correlation functions in the model. We demonstrate that these quantities vary continuously with the amplitude of the noise cross-correlation. Further our numerical studies corroborate the continuous dependence of long wavelength and long time-scale physics of the model on the amplitude of the noise cross-correlations, as found in our analytical studies. We construct and simulate lattice-gas models of coupled degrees of freedom in 1d, belonging to the universality class of our coupled Burgers-like model, which display similar behavior. We use a variety of numerical (Monte-Carlo and Pseudospectral methods) and analytical (Dynamic Renormalization Group, Self-Consistent Mode-Coupling Theory and Functional Renormalization Group) approaches for our work. The results from our different approaches complement one another. Possible realizations of our results in various nonequilibrium models are discussed.Comment: To appear in JSTAT (2009); 52 pages in JSTAT format. Some figure files have been replace

In vitro and in vivo Assessment of Keratose as a Novel Excipient of Paclitaxel Coated Balloons

Purpose: Drug coated balloons (DCB) are continually improving due to advances in coating techniques and more effective excipients. Paclitaxel, the current drug choice of DCB, is a microtubule-stabilizing chemotherapeutic agent that inhibits smooth muscle cell proliferation. Excipients work to promote coating stability and facilitate paclitaxel transfer and retention at the target lesion, although current excipients lack sustained, long-term paclitaxel retention. Keratose, a naturally derived protein, has exhibited unique properties allowing for tuned release of various therapeutic agents. However, little is known regarding its ability to support delivery of anti-proliferative agents such as paclitaxel. The goal of this project was to thus demonstrate the feasibility of keratose as a DCB-coating excipient to promote the release and delivery of paclitaxel.Methods: Keratose was combined with paclitaxel in vitro and the release kinetics of paclitaxel and keratose were evaluated through high performance liquid chromatograph-mass spectroscopy (HPLC-MS) and spectrophotometry, respectively. A custom coating method was developed to deposit keratose and paclitaxel on commercially available angioplasty balloons via an air spraying method. Coatings were then visualized under scanning electron microscopy and drug load quantified by HPLC-MS. Acute arterial transfer of paclitaxel at 1 h was assessed using a novel ex vivo model and further evaluated in vivo in a porcine ilio-femoral injury model.Results: Keratose demonstrated tunable release of paclitaxel as a function of keratose concentration in vitro. DCB coated via air spraying yielded consistent drug loading of 4.0 ± 0.70 μg/mm2. Under scanning electron microscopy, the keratose-paclitaxel DCB showed uniform coverage with a consistent, textured appearance. The acute drug transfer of the keratose-paclitaxel DCB was 43.60 ± 14.8 ng/mg at 1 h ex vivo. These measurements were further confirmed in vivo as the acute 1 h arterial paclitaxel levels were 56.60 ± 66.4 ng/mg.Conclusion: The keratose-paclitaxel coated DCB exhibited paclitaxel uptake and achieved acute therapeutic arterial tissue levels, confirming the feasibility of keratose as a novel excipient for DCB

Strong variability of Martian water ice clouds during dust storms revealed from ExoMars Trace Gas Orbiter/NOMAD

Observations of water ice clouds and aerosols on Mars can provide important insights into the complexity of the water cycle. Recent observations have indicated an important link between dust activity and the water cycle, as intense dust activity can significantly raise the hygropause, and subsequently increase the escape of water after dissociation in the upper atmosphere. Here present observations from NOMAD/TGO that investigate the variation of water ice clouds in the perihelion season of Mars Year 34 (April 2018‐19), their diurnal and seasonal behavior, and the vertical structure and microphysical properties of water ice and dust. These observations reveal the recurrent presence of a layer of mesospheric water ice clouds subsequent to the 2018 Global Dust Storm. We show that this layer rose from 45 to 80 km in altitude on a timescale of days from heating in the lower atmosphere due to the storm. In addition, we demonstrate that there is a strong dawn dusk asymmetry in water ice abundance, related to nighttime nucleation and subsequent daytime sublimation. Water ice particle sizes are retrieved consistently and exhibit sharp vertical gradients (from 0.1 to 4.0 μm), as well as mesospheric differences between the Global Dust Storm (<0.5 μm) and the 2019 regional dust storm (1.0 μm), which suggests differing water ice nucleation efficiencies. These results form the basis to advance our understanding of mesospheric water ice clouds on Mars, and further constrain the interactions between water ice and dust in the middle atmosphere

Coordinated optimization of visual cortical maps (I) Symmetry-based analysis

In the primary visual cortex of primates and carnivores, functional architecture can be characterized by maps of various stimulus features such as orientation preference (OP), ocular dominance (OD), and spatial frequency. It is a long-standing question in theoretical neuroscience whether the observed maps should be interpreted as optima of a specific energy functional that summarizes the design principles of cortical functional architecture. A rigorous evaluation of this optimization hypothesis is particularly demanded by recent evidence that the functional architecture of OP columns precisely follows species invariant quantitative laws. Because it would be desirable to infer the form of such an optimization principle from the biological data, the optimization approach to explain cortical functional architecture raises the following questions: i) What are the genuine ground states of candidate energy functionals and how can they be calculated with precision and rigor? ii) How do differences in candidate optimization principles impact on the predicted map structure and conversely what can be learned about an hypothetical underlying optimization principle from observations on map structure? iii) Is there a way to analyze the coordinated organization of cortical maps predicted by optimization principles in general? To answer these questions we developed a general dynamical systems approach to the combined optimization of visual cortical maps of OP and another scalar feature such as OD or spatial frequency preference.Comment: 90 pages, 16 figure