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

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

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

Life history traits of adults and embryos of the Antarctic midge Belgica antarctica

Abstract Although larvae of the Antarctic midge, Belgica antarctica, live for more than 2 years, the adult and embryonic stages are brief and are less well known than the larvae. In this report, we provide additional details of these understudied life stages with laboratory observation on adult emergence, longevity, preoviposition period and embryonic development. Male adults emerged slightly earlier than females, and they also lived longer. More than a half (57 %) of the adults that emerged in the laboratory were males. Females produced only a single egg mass and died within a day after oviposition. Embryonic development required 16 days at 4°C, and prior to hatching, the pharate larvae perform a distinct sequence of behaviors that include drinking and peristaltic movement. We also discuss points that need to be resolved for laboratory propagation of this species

Soft x-ray spectroscopy experiments on the near K-edge of B in MB2 (M=Mg, Al, Ta, and Nb)

Soft X-ray absorption and emission measurements are performed for the K- edge of B in MB$_2$ (M=Mg, Al, Ta and Nb). Unique feature of MgB$_2$ with a high density of B 2$p_{xy}(\sigma)$-state below and above the Fermi edge, which extends to 1 eV above the edge, is confirmed. In contrast, the B 2$p$ density of states in AlB$_2$ and TaB$_2$, both of occupied and unoccupied states, decreased linearly towards the Fermi energy and showed a dip at the Fermi energy. Furthermore, there is a broadening of the peaks with $p\sigma$-character in XES and XAS of AlB$_2$, which is due to the increase of three dimensionality in the $p\sigma$-band in AlB$_2$. The DOS of NbB$_2$ has a dip just below the Fermi energy. The present results indicate that the large DOS of B-2$p\sigma$ states near the Fermi energy are crucial for the superconductivity of MgB$_2$.Comment: 3 pages text and 4 pages figures. accepted for publication to Phys. Rev.

Compact genome of the Antarctic midge is likely an adaptation to an extreme environment

The midge, Belgica antarctica, is the only insect endemic to Antarctica, and thus it offers a powerful model for probing responses to extreme temperatures, freeze tolerance, dehydration, osmotic stress, ultraviolet radiation and other forms of environmental stress. Here we present the first genome assembly of an extremophile, the first dipteran in the family Chironomidae, and the first Antarctic eukaryote to be sequenced. At 99 megabases, B. antarctica has the smallest insect genome sequenced thus far. Although it has a similar number of genes as other Diptera, the midge genome has very low repeat density and a reduction in intron length. Environmental extremes appear to constrain genome architecture, not gene content. The few transposable elements present are mainly ancient, inactive retroelements. An abundance of genes associated with development, regulation of metabolism and responses to external stimuli may reflect adaptations for surviving in this harsh environment

A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation

<p>Abstract</p> <p>Background</p> <p>Many temperate insects survive the harsh conditions of winter by undergoing photoperiodic diapause, a pre-programmed developmental arrest initiated by short day lengths. Despite the well-established ecological significance of photoperiodic diapause, the molecular basis of this crucial adaptation remains largely unresolved. The Asian tiger mosquito, <it>Aedes albopictus </it>(Skuse), represents an outstanding emerging model to investigate the molecular basis of photoperiodic diapause in a well-defined ecological and evolutionary context. <it>Ae. albopictus </it>is a medically significant vector and is currently considered the most invasive mosquito in the world. Traits related to diapause appear to be important factors contributing to the rapid spread of this mosquito. To generate novel sequence information for this species, as well as to discover transcripts involved in diapause preparation, we sequenced the transcriptome of <it>Ae. albopictus </it>oocytes destined to become diapausing or non-diapausing pharate larvae.</p> <p>Results</p> <p>454 GS-FLX transcriptome sequencing yielded >1.1 million quality-filtered reads, which we assembled into 69,474 contigs (N50 = 1,009 bp). Our contig filtering approach, where we took advantage of strong sequence similarity to the fully sequenced genome of <it>Aedes aegypti</it>, as well as other reference organisms, resulted in 11,561 high-quality, conservative ESTs. Differential expression estimates based on normalized read counts revealed 57 genes with higher expression, and 257 with lower expression under diapause-inducing conditions. Analysis of expression by qPCR for 47 of these genes indicated a high correlation of expression levels between 454 sequence data and qPCR, but congruence of statistically significant differential expression was low. Seven genes identified as differentially expressed based on qPCR have putative functions that are consistent with the insect diapause syndrome; three genes have unknown function and represent novel candidates for the transcriptional basis of diapause.</p> <p>Conclusions</p> <p>Our transcriptome database provides a rich resource for the comparative genomics and functional genetics of <it>Ae. albopictus</it>, an invasive and medically important mosquito. Additionally, the identification of differentially expressed transcripts related to diapause enriches the limited knowledge base for the molecular basis of insect diapause, in particular for the preparatory stage. Finally, our analysis illustrates a useful approach that draws from a closely related reference genome to generate high-confidence ESTs in a non-model organism.</p