Commencement Address

Commencement address given by David L. Denlinger, Distinguished University Professor of Entomology, to the Summer 2008 graduating class of The Ohio State University, Jerome Schottenstein Center, Columbus, Ohio, August 24, 2008

Non-Fermi liquid angle resolved photoemission lineshapes of Li0.9Mo6O17

A recent letter by Xue et al. (PRL v.83, 1235 ('99)) reports a Fermi-Liquid (FL) angle resolved photoemission (ARPES) lineshape for quasi one-dimensional Li0.9Mo6O17, contradicting our report (PRL v.82, 2540 ('99)) of a non-FL lineshape in this material. Xue et al. attributed the difference to the improved angle resolution. In this comment, we point out that this reasoning is flawed. Rather, we find that their data have fundamental differences from other ARPES results and also band theory.Comment: To be published as a PRL Commen

ARPES and NMTO Wannier Orbital Theory of LiMo6_{6}O17_{17} - Implications for Unusually Robust Quasi-One Dimensional Behavior

We present the results of a combined study by band theory and angle resolved photoemission spectroscopy (ARPES) of the purple bronze, Li$_{1-x}$Mo$_{6}$O$_{17}$. Structural and electronic origins of its unusually robust quasi-one dimensional (quasi-1D) behavior are investigated in detail. The band structure, in a large energy window around the Fermi energy, is basically 2D and formed by three Mo $t_{2g}$-like extended Wannier orbitals, each one giving rise to a 1D band running at a 120$^\circ$ angle to the two others. A structural "dimerization" from $\mathbf{c}/2$ to $\mathbf{c}$ gaps the $xz$ and $yz$ bands while leaving the $xy$ bands metallic in the gap, but resonantly coupled to the gap edges and, hence, to the other directions. The resulting complex shape of the quasi-1D Fermi surface (FS), verified by our ARPES, thus depends strongly on the Fermi energy position in the gap, implying a great sensitivity to Li stoichiometry of properties dependent on the FS, such as FS nesting or superconductivity. The strong resonances prevent either a two-band tight-binding model or a related real-space ladder picture from giving a valid description of the low-energy electronic structure. We use our extended knowledge of the electronic structure to newly advocate for framing LiMo$_{6}$O$_{17}$ as a weak-coupling material and in that framework can rationalize both the robustness of its quasi-1D behavior and the rather large value of its Luttinger liquid (LL) exponent $\alpha$. Down to a temperature of 6$\,$K we find no evidence for a theoretically expected downward renormalization of perpendicular single particle hopping due to LL fluctuations in the quasi-1D chains.Comment: 53 pages, 17 Figures, 6 year

The GeoClaw software for depth-averaged flows with adaptive refinement

Many geophysical flow or wave propagation problems can be modeled with two-dimensional depth-averaged equations, of which the shallow water equations are the simplest example. We describe the GeoClaw software that has been designed to solve problems of this nature, consisting of open source Fortran programs together with Python tools for the user interface and flow visualization. This software uses high-resolution shock-capturing finite volume methods on logically rectangular grids, including latitude--longitude grids on the sphere. Dry states are handled automatically to model inundation. The code incorporates adaptive mesh refinement to allow the efficient solution of large-scale geophysical problems. Examples are given illustrating its use for modeling tsunamis, dam break problems, and storm surge. Documentation and download information is available at www.clawpack.org/geoclawComment: 18 pages, 11 figures, Animations and source code for some examples at http://www.clawpack.org/links/awr10 Significantly modified from original posting to incorporate suggestions of referee

Cold-shock injury and rapid cold-hardening in the flesh fly, Sarcophaga crassipalpis.

Direct exposure to -10 C, in the absence of tissue freezing, causes high mortality in Sarcophaga crassipalpis: this result suggests that injury is due to cold shock. However, brief acclimation at 0 C enables larvae, pupae, and pharate adults of Sarchophaga crassipalpis to survive -10 C. Chilling for as short a period as 10 minutes enabled 50% of the flies to survive a 2-hr exposure to -10 C. Enhancement of cold tolerance was linear over the first hour of chilling at 0 C. The optimal temperature range eliciting the rapid accumulation response was 6-0 C, but the effect could also be stimulated by high temperature (36 C). The rapid increase in cold tolerance correlates with concomitant increases in hemolymph osmolality and glycerol levels. This response suggests a novel role for glycerol in protecting insects against injury resulting from cold shock, although other unidentified mechanisms may be involved in this response. That both nondiapause- and diapause-programmed flies respond to short-term chilling indicates that this rapid response is not part of the diapause syndrome but probably functions in either type of fly as an adaptation to survive brief periods of low temperature

Mechanisms of animal diapause: Recent developments from nematodes, crustaceans, insects, and fish

© 2016 the American Physiological Society. Life cycle delays are beneficial for opportunistic species encountering suboptimal environments. Many animals display a programmed arrest of development (diapause) at some stage(s) of their development, and the diapause state may or may not be associated with some degree of metabolic depression. In this review, we will evaluate current advancements in our understanding of the mechanisms responsible for the remarkable phenotype, as well as environmental cues that signal entry and termination of the state. The developmental stage at which diapause occurs dictates and constrains the mechanisms governing diapause. Considerable progress has been made in clarifying proximal mechanisms of metabolic arrest and the signaling pathways like insulin/Foxo that control gene expression patterns. Overlapping themes are also seen in mechanisms that control cell cycle arrest. Evidence is emerging for epigenetic contributions to diapause regulation via small RNAs in nematodes, crustaceans, insects, and fish. Knockdown of circadian clock genes in selected insect species supports the importance of clock genes in the photoperiodic response that cues diapause. A large suite of chaperone-like proteins, expressed during diapause, protects biological structures during long periods of energy-limited stasis. More information is needed to paint a complete picture of how environmental cues are coupled to the signal transduction that initiates the complex diapause phenotype, as well as molecular explanations for how the state is terminated. Excellent examples of molecular memory in postdauer animals have been documented in Caenorhabditis elegans. It is clear that a single suite of mechanisms does not regulate diapause across all species and developmental stages

Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis

<p>Abstract</p> <p>Background</p> <p>Flesh flies in the genus <it>Sarcophaga </it>are important models for investigating endocrinology, diapause, cold hardiness, reproduction, and immunity. Despite the prominence of <it>Sarcophaga </it>flesh flies as models for insect physiology and biochemistry, and in forensic studies, little genomic or transcriptomic data are available for members of this genus. We used massively parallel pyrosequencing on the Roche 454-FLX platform to produce a substantial EST dataset for the flesh fly <it>Sarcophaga crassipalpis</it>. To maximize sequence diversity, we pooled RNA extracted from whole bodies of all life stages and normalized the cDNA pool after reverse transcription.</p> <p>Results</p> <p>We obtained 207,110 ESTs with an average read length of 241 bp. These reads assembled into 20,995 contigs and 31,056 singletons. Using BLAST searches of the NR and NT databases we were able to identify 11,757 unique gene elements (E<0.0001) representing approximately 9,000 independent transcripts. Comparison of the distribution of <it>S. crassipalpis </it>unigenes among GO Biological Process functional groups with that of the <it>Drosophila melanogaster </it>transcriptome suggests that our ESTs are broadly representative of the flesh fly transcriptome. Insertion and deletion errors in 454 sequencing present a serious hurdle to comparative transcriptome analysis. Aided by a new approach to correcting for these errors, we performed a comparative analysis of genetic divergence across GO categories among <it>S. crassipalpis</it>, <it>D. melanogaster</it>, and <it>Anopheles gambiae</it>. The results suggest that non-synonymous substitutions occur at similar rates across categories, although genes related to response to stimuli may evolve slightly faster. In addition, we identified over 500 potential microsatellite loci and more than 12,000 SNPs among our ESTs.</p> <p>Conclusion</p> <p>Our data provides the first large-scale EST-project for flesh flies, a much-needed resource for exploring this model species. In addition, we identified a large number of potential microsatellite and SNP markers that could be used in population and systematic studies of <it>S. crassipalpis </it>and other flesh flies.</p