Vortex dynamics

Vortex flows of interest to aerodynamicists cover a wide range of scales from a fraction of an inch in boundary layer flows to many feet in wake flows. In many applications these flows are poorly understood and, due to their complexity, present a challenge both analytically and experimentally. Four topics representing the spectrum of experimental and analytical vortex research are presented

Multilevel Governance: Framing the Integration of Top-Down and Bottom-Up Policymaking

Scholars embrace multilevel governance as an analytical framework for complex problems, such as climate change or water pollution. However, the elements needed to comprehensively operationalize multilevel governance remain undefined in the literature. This paper describes the five necessary ingredients to a multilevel framework: sanctioning and coordinating authority, provision of capacity, knowledge co-production, framing of co-benefits, and inclusion of civil society. The framework’s analytical utility is illustrated through two contrasting case examples – watershed management in the U.S. and air quality management in China. The framework balances local and central actors, which can promote a more effective governance regime

Two-temperature coronal flow above a thin disk

We extended the disk corona model (Meyer & Meyer-Hofmeister 1994; Meyer, Liu, & Meyer-Hofmeister 2000a) to the inner region of galactic nuclei by including different temperatures in ions and electrons as well as Compton cooling. We found that the mass evaporation rate and hence the fraction of accretion energy released in the corona depend strongly on the rate of incoming mass flow from outer edge of the disk, a larger rate leading to more Compton cooling, less efficient evaporation and a weaker corona. We also found a strong dependence on the viscosity, higher viscosity leading to an enhanced mass flow in the corona and therefore more evaporation of gas from the disk below. If we take accretion rates in units of the Eddington rate our results become independent on the mass of the central black hole. The model predicts weaker contributions to the hard X-rays for objects with higher accretion rate like narrow-line Seyfert 1 galaxies (NLS1s), in agreement with observations. For luminous active galactic nuclei (AGN) strong Compton cooling in the innermost corona is so efficient that a large amount of additional heating is required to maintain the corona above the thin disk.Comment: 17 pages, 6 figures. ApJ accepte

Graphene Oxidation: Thickness Dependent Etching and Strong Chemical Doping

Patterned graphene shows substantial potential for applications in future molecular-scale integrated electronics. Environmental effects are a critical issue in a single layer material where every atom is on the surface. Especially intriguing is the variety of rich chemical interactions shown by molecular oxygen with aromatic molecules. We find that O2 etching kinetics vary strongly with the number of graphene layers in the sample. Three-layer-thick samples show etching similar to bulk natural graphite. Single-layer graphene reacts faster and shows random etch pits in contrast to natural graphite where nucleation occurs at point defects. In addition, basal plane oxygen species strongly hole dope graphene, with a Fermi level shift of ~0.5 eV. These oxygen species partially desorb in an Ar gas flow, or under irradiation by far UV light, and readsorb again in an O2 atmosphere at room temperature. This strongly doped graphene is very different than graphene oxide made by mineral acid attack.Comment: 15 pages, 5 figure

Stress-Driven Selection of Novel Phenotypes

A process has been developed that can confer novel properties, such as metal resistance, to a host bacterium. This same process can also be used to produce RNAs and peptides that have novel properties, such as the ability to bind particular compounds. It is inherent in the method that the peptide or RNA will behave as expected in the target organism. Plasmid-born mini-gene libraries coding for either a population of combinatorial peptides or stable, artificial RNAs carrying random inserts are produced. These libraries, which have no bias towards any biological function, are used to transform the organism of interest and to serve as an initial source of genetic variation for stress-driven evolution. The transformed bacteria are propagated under selective pressure in order to obtain variants with the desired properties. The process is highly distinct from in vitro methods because the variants are selected in the context of the cell while it is experiencing stress. Hence, the selected peptide or RNA will, by definition, work as expected in the target cell as the cell adapts to its presence during the selection process. Once the novel gene, which produces the sought phenotype, is obtained, it can be transferred to the main genome to increase the genetic stability in the organism. Alternatively, the cell line can be used to produce novel RNAs or peptides with selectable properties in large quantity for separate purposes. The system allows for easy, large-scale purification of the RNAs or peptide products. The process has been reduced to practice by imposing sub-inhibitory concentrations of NiCl2 on cells of the bacterium Escherichia coli that were transformed separately with the peptide library and RNA library. The evolved resistant clones were isolated, and sequences of the selected mini-gene variants were established. Clones resistant to NiCl2 were found to carry identical plasmid variants with a functional mini-gene that specifically conferred significant nickel tolerance on the host cells. Sequencing of the selected mini-gene revealed a propensity of the encoded peptide to bind transient metal ions. Expression of the mini-gene markedly improved growth parameters of the evolved clones at sub-inhibitory concentrations of NiCl2 while being slightly detrimental in the absence of stress. Similar results have been obtained with the RNA libraries. Overall, the results demonstrate a very natural outcome of the selection experiments in which the mini-genes were expected to be either successfully integrated into bacterial genetic networks, or rejected depending upon their effect on host fitness. This described approach can be useful as a laboratory model to study the dynamics of bacterial adaptive evolution on the molecular level. It can also provide a strategy for screening expressed DNA libraries in search of novel genes with desirable properties

DNAzyme-mediated recovery of small recombinant RNAs from a 5S rRNA-derived chimera expressed in Escherichia coli

Background: Manufacturing large quantities of recombinant RNAs by overexpression in a bacterial host is hampered by their instability in intracellular environment. To overcome this problem, an RNA of interest can be fused into a stable bacterial RNA for the resulting chimeric construct to accumulate in the cytoplasm to a sufficiently high level. Being supplemented with cost-effective procedures for isolation of the chimera from cells and recovery of the recombinant RNA from stabilizing scaffold, this strategy might become a viable alternative to the existing methods of chemical or enzymatic RNA synthesis. Results: Sequence encoding a 71-nucleotide recombinant RNA was inserted into a plasmid-borne deletion mutant of the Vibrio proteolyticus 5S rRNA gene in place of helix III - loop C segment of the original 5S rRNA. After transformation into Escherichia coli, the chimeric RNA (3譸en aRNA) was expressed constitutively from E. coli rrnB P1 and P2 promoters. The RNA chimera accumulated to levels that exceeded those of the host's 5S rRNA. A novel method relying on liquid solid partitioning of cellular constituents was developed for isolation of total RNA from bacterial cells. This protocol avoids toxic chemicals, and is therefore more suitable for large scale RNA purification than traditional methods. A pair of biotinylated 8-17 DNAzymes was used to bring about the quantitative excision of the 71-nt recombinant RNA from the chimera. The recombinant RNA was isolated by sequence-specific capture on beads with immobilized complementary deoxyoligonucleotide, while DNAzymes were recovered by biotin affinity chromatography for reuse. Conclusions:The feasibility of a fermentation-based approach for manufacturing large quantities of small RNAs in vivo using a "5S rRNA scaffold" strategy is demonstrated. The approach provides a route towards an economical method for the large-scale production of small RNAs including shRNAs, siRNAs and aptamers for use in clinical and biomedical research

DNAzyme-mediated recovery of small recombinant RNAs from a 5S rRNA-derived chimera expressed in Escherichia coli

<p>Abstract</p> <p>Background</p> <p>Manufacturing large quantities of recombinant RNAs by overexpression in a bacterial host is hampered by their instability in intracellular environment. To overcome this problem, an RNA of interest can be fused into a stable bacterial RNA for the resulting chimeric construct to accumulate in the cytoplasm to a sufficiently high level. Being supplemented with cost-effective procedures for isolation of the chimera from cells and recovery of the recombinant RNA from stabilizing scaffold, this strategy might become a viable alternative to the existing methods of chemical or enzymatic RNA synthesis.</p> <p>Results</p> <p>Sequence encoding a 71-nucleotide recombinant RNA was inserted into a plasmid-borne deletion mutant of the <it>Vibrio proteolyticus </it>5S rRNA gene in place of helix III - loop C segment of the original 5S rRNA. After transformation into <it>Escherichia coli</it>, the chimeric RNA (3×<it>pen </it>aRNA) was expressed constitutively from <it>E. coli rrnB </it>P1 and P2 promoters. The RNA chimera accumulated to levels that exceeded those of the host's 5S rRNA. A novel method relying on liquid-solid partitioning of cellular constituents was developed for isolation of total RNA from bacterial cells. This protocol avoids toxic chemicals, and is therefore more suitable for large scale RNA purification than traditional methods. A pair of biotinylated 8-17 DNAzymes was used to bring about the quantitative excision of the 71-nt recombinant RNA from the chimera. The recombinant RNA was isolated by sequence-specific capture on beads with immobilized complementary deoxyoligonucleotide, while DNAzymes were recovered by biotin affinity chromatography for reuse.</p> <p>Conclusions</p> <p>The feasibility of a fermentation-based approach for manufacturing large quantities of small RNAs <it>in vivo </it>using a "5S rRNA scaffold" strategy is demonstrated. The approach provides a route towards an economical method for the large-scale production of small RNAs including shRNAs, siRNAs and aptamers for use in clinical and biomedical research.</p

Noise-resilient approach for deep tomographic imaging

We propose a noise-resilient deep reconstruction algorithm for X-ray tomography. Our approach shows strong noise resilience without obtaining noisy training examples. The advantages of our framework may further enable low-photon tomographic imaging.Comment: 2022 CLEO (the Conference on Lasers and Electro-Optics) conference submissio

Assessment of genome integrity with array CGH in cattle transgenic cell lines produced by homologous recombination and somatic cell cloning

<p>Abstract</p> <p>Background</p> <p>Transgenic cattle carrying multiple genomic modifications have been produced by serial rounds of somatic cell chromatin transfer (cloning) of sequentially genetically targeted somatic cells. However, cloning efficiency tends to decline with the increase of rounds of cloning. It is possible that multiple rounds of cloning compromise the genome integrity or/and introduce epigenetic errors in the resulting cell lines, rendering a decline in cloning. To test these possibilities, we performed 9 high density array Comparative Genomic Hybridization (CGH) experiments to test the genome integrity in 3 independent bovine transgenic cell lineages generated from genetic modification and cloning. Our plan included the control hybridizations (self to self) of the 3 founder cell lines and 6 comparative hybridizations between these founders and their derived cell lines with either high or low cloning efficiencies.</p> <p>Results</p> <p>We detected similar amounts of differences between the control hybridizations (8, 13 and 39 differences) and the comparative analyses of both "high" and "low" cell lines (ranging from 7 to 57 with a mean of ~20). Almost 75% of the large differences (>10 kb) and about 45% of all differences shared the same type (loss or gain) and were located in nearby genomic regions across hybridizations. Therefore, it is likely that they were not true differences but caused by systematic factors associated with local genomic features (e.g. GC contents).</p> <p>Conclusions</p> <p>Our findings reveal that large copy number variations are less likely to arise during genetic targeting and serial rounds of cloning, fortifying the notion that epigenetic errors introduced from serial cloning may be responsible for the cloning efficiency decline.</p