Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) is a powerful technique to quantify gene expression. To facilitate gene expression study and obtain accurate results, ...normalization relative to stably expressed reference genes is crucial. The monarch butterfly, Danaus plexippus (L.), is one of the most recognized insect species for its spectacular annual migration across North America. Besides its great voyages, D. plexippus has drawn attention to its role as a bio-indicator, ranging from genetically modified organisms (GMOs) to natural ecosystems. In this study, nine reference genes from D. plexippus genome were selected as the candidate reference genes. The expression profiles of these candidates under various biotic and abiotic conditions were evaluated using the four readily available computational programs, BestKeeper, Normfinder, geNorm, and ΔCt method, respectively. Moreover, RefFinder, a web-based computational platform integrating the four above mentioned algorisms, provided a comprehensive ranking of the stability of these reference genes. As a result, a suite of reference genes were recommended for each experimental condition. Specifically, elongation factor 1α (EF1A) and ribosomal protein 49 (RP49) were the most stable reference genes, respectively, under biotic (development, tissue, and sex) and abiotic (photoperiod, temperature, and dietary RNAi) conditions. With the recent release of a 273-million base pair draft genome, results from this study allow us to establish a standardized RT-qPCR analysis and lay a foundation for the subsequent genomic and functional genomic research in D. plexippus, a major bio-indicator and an emerging model for migratory animals.
Giant lobes of plasma extend approximate55degrees above and below the Galactic center, glowing in emission from gamma rays (the Fermi Bubbles) to microwaves and polarized radio waves. We use ...ultraviolet absorption-line spectra from the Hubble Space Telescope to constrain the velocity of the outflowing gas within these regions, targeting the quasar PDS 456 (scriptl b = 10degrees.4, +11degrees.2). This sightline passes through a clear biconical structure seen in hard X-ray and gamma-ray emission near the base of the northern Fermi Bubble. We report two high-velocity metal absorption components, at upsilon sub(LSR) = -235 and +250 km s super(-1), which cannot be explained by co-rotating gas in the Galactic disk or halo. Their velocities are suggestive of an origin on the front and back side of an expanding biconical outflow emanating from the Galactic center. We develop simple kinematic biconical outflow models that can explain the observed profiles with an outflow velocity of > ~900 km s super(-1) and a full opening angle of approximate110degrees (matching the X-ray bicone). This indicates Galactic center activity over the last approximate2.5-4.0 Myr, in line with age estimates of the Fermi Bubbles. The observations illustrate the use of UV spectroscopy to probe the properties of swept-up gas venting into the Fermi Bubbles.
Many viral pathogens cycle between humans and insects. These viruses must have evolved strategies for rapid adaptation to different host environments. However, the mechanistic basis for the ...adaptation process remains poorly understood. To study the mosquito-human adaptation cycle, we examined changes in RNA structures of the dengue virus genome during host adaptation. Deep sequencing and RNA structure analysis, together with fitness evaluation, revealed a process of host specialization of RNA elements of the viral 3'UTR. Adaptation to mosquito or mammalian cells involved selection of different viral populations harvesting mutations in a single stem-loop structure. The host specialization of the identified RNA structure resulted in a significant viral fitness cost in the non-specialized host, posing a constraint during host switching. Sequence conservation analysis indicated that the identified host adaptable stem loop structure is duplicated in dengue and other mosquito-borne viruses. Interestingly, functional studies using recombinant viruses with single or double stem loops revealed that duplication of the RNA structure allows the virus to accommodate mutations beneficial in one host and deleterious in the other. Our findings reveal new concepts in adaptation of RNA viruses, in which host specialization of RNA structures results in high fitness in the adapted host, while RNA duplication confers robustness during host switching.
Simulations of the formation of large-scale structures predict that dark matter, low density highly ionized gas, and galaxies form 10 to 40 Mpc scale filaments. These structures are easily recognized ...in the distribution of galaxies. Here we use Ly alpha absorption lines to study the gas in 30 x 6 Mpc filament at cz ~ 3500km s super(-1), defined using a new catalog of nearby (cz < 10,000 km s super(-1)) galaxies, which is complete down to a luminosity of about 0.05 Llow * for the region of space analyzed here. Using Hubble Space Telescope spectra of 24 active galactic nuclei, we sample the gas in this filament. All of our sightlines pass outside the virial radius of any known filament galaxy. Within 500 kpc of the filament axis the detection rate is ~80%, but no detections are seen more than 2.1 Mpc from the filament axis. The width of the Ly alpha lines correlates with filament impact parameter and the four BLAs in our sample occur within 400 kpc of the filament axis, indicating increased temperature and/or turbulence. Comparing to simulations, we find that the recent Haardt & Madau extragalactic ionizing background predicts a factor of 3-5 too few ionizing photons. Using a more intense radiation field matches the hydrogen density profile within 2.1 Mpc of the filament axis, but the simulations still overpredict the detection rate between 2.1 and 5 Mpc from the axis. The baryonic mass inside filament galaxies is 1.4 x 10 super(13) M sub(middot in circle), while the mass of filament gas outside galaxy halos is found to be 5.2 x 10 super(13) M sub(middot in circle).
Nearly a century after Einstein first predicted the existence of gravitational waves, a global network of Earth-based gravitational wave observatories is seeking to directly detect this faint ...radiation using precision laser interferometry. Photon shot noise, due to the quantum nature of light, imposes a fundamental limit on the attometre-level sensitivity of the kilometre-scale Michelson interferometers deployed for this task. Here, we inject squeezed states to improve the performance of one of the detectors of the Laser Interferometer Gravitational-Wave Observatory (LIGO) beyond the quantum noise limit, most notably in the frequency region down to 150 Hz, critically important for several astrophysical sources, with no deterioration of performance observed at any frequency. With the injection of squeezed states, this LIGO detector demonstrated the best broadband sensitivity to gravitational waves ever achieved, with important implications for observing the gravitational-wave Universe with unprecedented sensitivity.
Towards the elements of successful insect RNAi Scott, Jeffrey G.; Michel, Kristin; Bartholomay, Lyric C. ...
Journal of insect physiology,
12/2013, Volume:
59, Issue:
12
Journal Article
Peer reviewed
Open access
•RNAi is a highly valuable tool for understanding gene function.•RNAi holds great potential for pest management.•RNAi efficiency varies among insect species and genes.•Development of RNAi protocols ...is a highly empirical process.•Systematic analysis of RNAi mechanisms in insects will facilitate future research.
RNA interference (RNAi), the sequence-specific suppression of gene expression, offers great opportunities for insect science, especially to analyze gene function, manage pest populations, and reduce disease pathogens. The accumulating body of literature on insect RNAi has revealed that the efficiency of RNAi varies between different species, the mode of RNAi delivery, and the genes being targeted. There is also variation in the duration of transcript suppression. At present, we have a limited capacity to predict the ideal experimental strategy for RNAi of a particular gene/insect because of our incomplete understanding of whether and how the RNAi signal is amplified and spread among insect cells. Consequently, development of the optimal RNAi protocols is a highly empirical process. This limitation can be relieved by systematic analysis of the molecular physiological basis of RNAi mechanisms in insects. An enhanced conceptual understanding of RNAi function in insects will facilitate the application of RNAi for dissection of gene function, and to fast-track the application of RNAi to both control pests and develop effective methods to protect beneficial insects and non-insect arthropods, particularly the honey bee (Apis mellifera) and cultured Pacific white shrimp (Litopenaeus vannamei) from viral and parasitic diseases.
Adiabatic quantum computing has evolved in recent years from a theoretical field into an immensely practical area, a change partially sparked by D-Wave System’s quantum annealing hardware. These ...multimillion-dollar quantum annealers offer the potential to solve optimization problems millions of times faster than classical heuristics, prompting researchers at Google, NASA and Lockheed Martin to study how these computers can be applied to complex real-world problems such as NASA rover missions. Unfortunately, compiling (embedding) an optimization problem into the annealing hardware is itself a difficult optimization problem and a major bottleneck currently preventing widespread adoption. Additionally, while finding a single embedding is difficult, no generalized method is known for tuning embeddings to use minimal hardware resources. To address these barriers, we introduce a graph-theoretic framework for developing structured embedding algorithms. Using this framework, we introduce a biclique virtual hardware layer to provide a simplified interface to the physical hardware. Additionally, we exploit bipartite structure in quantum programs using odd cycle transversal (OCT) decompositions. By coupling an OCT-based embedding algorithm with new, generalized reduction methods, we develop a new baseline for embedding a wide range of optimization problems into fault-free D-Wave annealing hardware. To encourage the reuse and extension of these techniques, we provide an implementation of the framework and embedding algorithms.
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