MonarchBase: the monarch butterfly genome database

The monarch butterfly (Danaus plexippus) is emerging as a model organism to study the mechanisms of circadian clocks and animal navigation, and the genetic underpinnings of long-distance migration. The initial assembly of the monarch genome was released in 2011, and the biological interpretation of the genome focused on the butterfly\u27s migration biology. To make the extensive data associated with the genome accessible to the general biological and lepidopteran communities, we established MonarchBase (available at http://monarchbase.umassmed.edu). The database is an open-access, web-available portal that integrates all available data associated with the monarch butterfly genome. Moreover, MonarchBase provides access to an updated version of genome assembly (v3) upon which all data integration is based. These include genes with systematic annotation, as well as other molecular resources, such as brain expressed sequence tags, migration expression profiles and microRNAs. MonarchBase utilizes a variety of retrieving methods to access data conveniently and for integrating biological interpretations

Laboratory Study Of Frequency Dependent Streaming Potentials

Frequency dependent streaming potentials were measured on a glass capillary, porous filter, and a sample of Boise sandstone. The pore diameters for these three samples range from 1 millimeter to 34 micrometers. The frequencies used in these experiments range from 0-600 Hz with the critical frequencies being 6.8 Hz, 90 Hz, and 400 Hz for the three specimens. The fluid was moved relative to the sample with the pressure measured by hydrophones and the streaming potential measured using silver silverchloride electrodes. Both Packard's (1953) and Pride's (1994) models satisfactorily predict the streaming potential behavior for these frequencies, and the measured critical frequencies are directly related to the sample pore diameters.United States. Air Force Office of Scientific Research (Grant F49620-95-1-0224)Massachusetts Institute of Technology. Borehole Acoustics and Logging ConsortiumMassachusetts Institute of Technology. Earth Resources Laboratory. Reservoir Delineation Consortiu

Dimorphic cocoons of the cecropia moth (Hyalophora cecropia): Morphological, behavioral, and biophysical differences

The larvae of the giant silk moth (Hyalophora cecropia) spin strikingly dimorphic, multilayered cocoons that are either large and fluffy (baggy) or significantly smaller and tightly woven (compact). Although these cocoon-morphs share the same function (i.e., housing for pupal to adult development during overwintering), previous work has been unable to determine why cocoon dimorphism exists. We addressed this issue in cecropia moth cocoons collected along power line right-of-way habitats in Massachusetts. We first characterized the architectural differences between cocoon-morphs for all three cocoon sections (outer and inner envelopes, and the intermediate layer separating the two). We show that outer envelope structural and ultrastructural differences are what underlie dimorphism. Using a common spinning arena, we next show that the behavioral suites used to construct the outer envelopes of the two morphs are significantly different in behavioral time investment and patterning, as well as in the location of silk placement in the common spinning arena. Finally, we compared the cocoon-morphs in response to various environmental stressors to ask whether dimorphism is an adaptive response to such pressures. In contrast to compact cocoons, we find that baggy cocoons act as heat sinks and allow greater moisture permeability; differences in outer envelope architecture underlie these characteristics. These two biophysical properties could be advantageous for pupae in baggy cocoons, during unseasonably cold or dry conditions encountered during development prior to adult emergence. Our results suggest that cocoon dimorphism in the cecropia moth may provide a bet-hedging strategy for dealing with varying environmental conditions in Massachusetts and perhaps over its entire habitat range, during pupal to adult development

Direct association between mouse PERIOD and CKIepsilon is critical for a functioning circadian clock

The mPER1 and mPER2 proteins have important roles in the circadian clock mechanism, whereas mPER3 is expendable. Here we examine the posttranslational regulation of mPER3 in vivo in mouse liver and compare it to the other mPER proteins to define the salient features required for clock function. Like mPER1 and mPER2, mPER3 is phosphorylated, changes cellular location, and interacts with other clock proteins in a time-dependent manner. Consistent with behavioral data from mPer2/3 and mPer1/3 double-mutant mice, either mPER1 or mPER2 alone can sustain rhythmic posttranslational events. However, mPER3 is unable to sustain molecular rhythmicity in mPer1/2 double-mutant mice. Indeed, mPER3 is always cytoplasmic and is not phosphorylated in the livers of mPer1-deficient mice, suggesting that mPER3 is regulated by mPER1 at a posttranslational level. In vitro studies with chimeric proteins suggest that the inability of mPER3 to support circadian clock function results in part from lack of direct and stable interaction with casein kinase Iepsilon (CKIepsilon). We thus propose that the CKIepsilon-binding domain is critical not only for mPER phosphorylation but also for a functioning circadian clock

Comments on the optical lineshape function: Application to transient hole-burned spectra of bacterial reaction centers

Citation: Reppert, M., Kell, A., Pruitt, T., & Jankowiak, R. (2015). Comments on the optical lineshape function: Application to transient hole-burned spectra of bacterial reaction centers. Journal of Chemical Physics, 142(9), 7. doi:10.1063/1.4913685The vibrational spectral density is an important physical parameter needed to describe both linear and non-linear spectra of multi-chromophore systems such as photosynthetic complexes. Low-temperature techniques such as hole burning (HB) and fluorescence line narrowing are commonly used to extract the spectral density for a given electronic transition from experimental data. We report here that the lineshape function formula reported by Hayes et al. [J. Phys. Chem. 98, 7337 (1994)] in the mean-phonon approximation and frequently applied to analyzing HB data contains inconsistencies in notation, leading to essentially incorrect expressions in cases of moderate and strong electron-phonon (el-ph) coupling strengths. A corrected lineshape function L(omega) is given that retains the computational and intuitive advantages of the expression of Hayes et al. [J. Phys. Chem. 98, 7337 (1994)]. Although the corrected lineshape function could be used in modeling studies of various optical spectra, we suggest that it is better to calculate the lineshape function numerically, without introducing the mean-phonon approximation. New theoretical fits of the P870 and P960 absorption bands and frequency-dependent resonant HB spectra of Rb. sphaeroides and Rps. viridis reaction centers are provided as examples to demonstrate the importance of correct lineshape expressions. Comparison with the previously determined el-ph coupling parameters [Johnson et al., J. Phys. Chem. 94, 5849 (1990); Lyle et al., ibid. 97, 6924 (1993); Reddy et al., ibid. 97, 6934 (1993)] is also provided. The new fits lead to modified el-ph coupling strengths and different frequencies of the special pair marker mode, omega(sp), for Rb. sphaeroides that could be used in the future for more advanced calculations of absorption and HB spectra obtained for various bacterial reaction centers. (c) 2015 AIP Publishing LLC

A magnetic compass aids monarch butterfly migration

Convincing evidence that migrant monarch butterflies (Danaus plexippus) use a magnetic compass to aid their fall migration has been lacking from the spectacular navigational capabilities of this species. Here we use flight simulator studies to show that migrants indeed possess an inclination magnetic compass to help direct their flight equatorward in the fall. The use of this inclination compass is light-dependent utilizing ultraviolet-A/blue light between 380 and 420 nm. Notably, the significance of light monarchs, the inclination compass may serve as an important orientation mechanism when directional daylight cues are unavailable and may also augment time-compensated sun compass orientation for appropriate directionality throughout the migration

Insect cryptochromes: gene duplication and loss define diverse ways to construct insect circadian clocks

Cryptochrome (CRY) proteins are components of the central circadian clockwork of metazoans. Phylogenetic analyses show at least 2 rounds of gene duplication at the base of the metazoan radiation, as well as several losses, gave rise to 2 cryptochrome (cry) gene families in insects, a Drosophila-like cry1 gene family and a vertebrate-like cry2 family. Previous studies have shown that insect CRY1 is photosensitive, whereas photo-insensitive CRY2 functions to potently inhibit clock-relevant CLOCK:CYCLE-mediated transcription. Here, we extended the transcriptional repressive function of insect CRY2 to 2 orders--Hymenoptera (the honeybee Apis mellifera and the bumblebee Bombus impatiens) and Coleoptera (the red flour beetle Tribolium castaneum). Importantly, the bee and beetle CRY2 proteins are not light sensitive in culture, in either degradation of protein levels or inhibitory transcriptional response, suggesting novel light input pathways into their circadian clocks as Apis and Tribolium do not have CRY1. By mapping the functional data onto a cryptochrome/6-4 photolyase gene tree, we find that the transcriptional repressive function of insect CRY2 descended from a light-sensitive photolyase-like ancestral gene, probably lacking the ability to repress CLOCK:CYCLE-mediated transcription. These data provide an evolutionary context for proposing novel circadian clock mechanisms in insects

A re-evaluation of silk measurement by the cecropia caterpillar (Hyalophora cecropia) during cocoon construction reveals use of a silk odometer that is temporally regulated

The late 5th instar caterpillar of the cecropia silk moth (Hyalophora cecropia) spins a silken cocoon with a distinct, multilayered architecture. The cocoon construction program, first described by the seminal work of Van der Kloot and Williams, consists of a highly ordered sequence of events. We perform behavioral experiments to re-evaluate the original cecropia work, which hypothesized that the length of silk that passes through the spinneret controls the orderly execution of each of the discrete events of cocoon spinning. We confirm and extend by three-dimensional scanning and quantitative measurements of silk weights that if cocoon construction is interrupted, upon re-spinning, the caterpillar continues the cocoon program from where it left off. We also confirm and extend by quantitative measurements of silk weights that cecropia caterpillars will not bypass any of the sections of the cocoon during the construction process, even if presented with a pre-spun section of a cocoon spun by another caterpillar. Blocking silk output inhibits caterpillars from performing normal spinning behaviors used for cocoon construction. Surprisingly, unblocking silk output 24-hr later did not restart the cocoon construction program, suggesting the involvement of a temporally-defined interval timer. We confirm with surgical reductions of the silk glands that it is the length of silk itself that matters, rather than the total amount of silk extracted by individuals. We used scanning electron microscopy to directly show that either mono- or dual-filament silk (i.e., equal silk lengths but which vary in their total amount of silk extracted) can be used to construct equivalent cocoons of normal size and that contain the relevant layers. We propose that our findings, taken together with the results of prior studies, strongly support the hypothesis that the caterpillar uses a silk odometer to measure the length of silk extracted during cocoon construction but does so in a temporally regulated manner. We further postulate that our examination of the anatomy of the silk spinning apparatus and ablating spinneret sensory output provides evidence that silk length measurement occurs upstream of output from the spinneret