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An important area of modern biology consists of understanding the relationship between genotype and phenotype. However, to understand this relationship it is essential to investigate one of the principal links between them: the proteome. With the development of recent mass-spectrometry approaches, it is now possible to quantify entire proteomes and thus relate them to different phenotypes. Here, we present a comparison of the proteome of two extreme developmental states in the well-established model organism Drosophila melanogaster: adult and embryo. Protein modules such as ribosome, proteasome, tricarboxylic acid cycle, glycolysis, or oxidative phosphorylation were found differentially expressed between the two developmental stages. Analysis of post-translation modifications of the proteins identified in this study indicates that they generally follow the same trend as their corresponding protein. Comparison between changes in the proteome and the transcriptome highlighted patterns of post-transcriptional regulation for the subunits of protein complexes such as the ribosome and the proteasome, whereas protein from modules such as TCA cycle, glycolysis, and oxidative phosphorylation seem to be coregulated at the transcriptional level. Finally, the impact of the endosymbiont Wolbachia pipientison the proteome of both developmental states was also investigated.

Acoustic waves with a wide range of frequencies are generated by lightning strokes during thunderstorms, including infrasonic waves (0.1 to 20 Hz). The source mechanism for these low‐frequency acoustic waves is still debated, and studies have so far been limited to ground‐based instruments. Here we report the first confirmed detection of lightning‐generated infrasound with acoustic instruments suspended at stratospheric altitudes using a free‐flying balloon. We observe high‐amplitude signals generated by lightning strokes located within 100 km of the balloon as it flew over the Tasman Sea on 17 May 2016. The signals share many characteristics with waveforms recorded previously by ground‐based instruments near thunderstorms. The ability to measure lightning activity with high‐altitude infrasound instruments has demonstrated the potential for using these platforms to image the full acoustic wavefield in the atmosphere. Furthermore, it validates the use of these platforms for recording and characterizing infrasonic sources located beyond the detection range of ground‐based instruments. Lightning generates sound waves across a wide range of frequencies, including below the threshold for human hearing at 20 Hz. How these waves at less than 20 Hz, also known as infrasound waves, are generated during a lightning stroke is currently an area for debate. So far, measurements of lightning infrasound waves have been limited to microphones fixed to the ground, and models have shown that only a small section of sound waves actually reach the ground. Here we show lightning infrasound that has been detected using microphones suspended over a thunderstorm using a balloon flying at 32 km height. This opens up the possibility of using balloons in future studies to make better measurements of infrasound waves generated by lightning activity and, in turn, give a better idea of how they are generated. It also shows how balloons can be used to record infrasound waves far away from land and therefore beyond the detection limit of ground‐based microphones. First lightning infrasound was detected using free‐flying balloon at stratospheric altitudes over Tasman Sea in May 2016Infrasonic signals matched with a few lightning strokes within 100 km range of balloon as it flew over at least two thundercloudsOnly a fraction of the expected infrasound signals were detected, and the cause of this remains unclear

Mechanisms that produce seismic and acoustic wavefields near rivers are poorly understood because of a lack of observations relating temporally dependent river conditions to the near‐river seismoacoustic fields. This controlled study at the Harry W. Morrison Dam (HWMD) on the Boise River, Idaho, explores how temporal variation in fluvial systems affects surrounding acoustic and seismic fields. Adjusting the configuration of the HWMD changed the river bathymetry and therefore the form of the standing wave below the dam. The HWMD was adjusted to generate four distinct wave regimes that were parameterized through their dimensionless Froude numbers (Fr) and observations of the ambient seismic and acoustic wavefields at the study site. To generate detectable and coherent signals, a standing wave must exceed a threshold Frvalue of 1.7, where a nonbreaking undular jump turns into a breaking weak hydraulic jump. Hydrodynamic processes may partially control the spectral content of the seismic and acoustic energies. Furthermore, spectra related to reproducible wave conditions can be used to calibrate and verify fluvial seismic and acoustic models. For detectable and coherent seismoacoustic energies to be generated, a standing wave must exceed a threshold Frvalue of approximately 1.7Hydrodynamic processes may partially control the spectral content of the seismic and acoustic energiesVariations in the width and amplitude of seismoacoustic spectral peaks may be explained by horizontal variations across a hydraulic jump

The shallow magma system beneath Sierra Negra was imaged using attenuation tomographic methods. The t∗spectral decay method for Pwave phases was used to highlight regions of high Qp−1which suggest the presence of magma melt. High‐ Qp−1anomalies ranging from 0.005 to 0.04 are concentrated below the caldera from 0.5 to 10.5 km depths. Attenuation is sensitive to temperature and fluid presence; thus, this high attenuation is interpreted as possible zones of magma accumulation. An imaged shallow body is consistent with geodetic studies on caldera deformation that modeled a magma sill or flattopped diapir of unknown thickness at ∼1 km depth below sea level. t* spectral decay method was used to obtain attenuation structure beneath Sierra NegraHigh‐attenuation anomaly from 0.5 to 10.5 km depth interpreted as possible magma accumulation zonesResults support a shallow magma body described and modeled in caldera deformation studies

We present an acoustic waveform inversion technique for infrasound data to estimate volume fluxes from volcanic eruptions. Previous inversion techniques have been limited by the use of a 1‐D Green's function in a free space or half space, which depends only on the source‐receiver distance and neglects volcanic topography. Our method exploits full 3‐D Green's functions computed by a numerical method that takes into account realistic topographic scattering. We apply this method to vulcanian eruptions at Sakurajima Volcano, Japan. Our inversion results produce excellent waveform fits to field observations and demonstrate that full 3‐D Green's functions are necessary for accurate volume flux inversion. Conventional inversions without consideration of topographic propagation effects may lead to large errors in the source parameter estimate. The presented inversion technique will substantially improve the accuracy of eruption source parameter estimation (cf. mass eruption rate) during volcanic eruptions and provide critical constraints for volcanic eruption dynamics and ash dispersal forecasting for aviation safety. Application of this approach to chemical and nuclear explosions will also provide valuable source information (e.g., the amount of energy released) previously unavailable. First waveform inversion of volcano infrasound using a 3‐D Green's functionStrong topographic scattering must be considered for source inversionThe method substantially improves the accuracy of eruption source parameter estimation

ABSTRACTWe previously reported the development of a prototype antibiotic sensitivity assay to detect drug-resistant Mycobacterium tuberculosisusing infection by mycobacteriophage to create a novel nucleic acid transcript, a surrogate marker of mycobacterial viability, detected by reverse transcriptase PCR (M. C. Mulvey et al., mBio 3:e00312-11, 2012). This assay detects antibiotic resistance to all drugs, even drugs for which the resistance mechanism is unknown or complex: it is a phenotypic readout using nucleic acid detection. In this report, we describe development and characteristics of an optimized reporter system that directed expression of the RNA cyclase ribozyme, which generated circular RNA through an intramolecular splicing reaction and led to accumulation of a new nucleic acid sequence in phage-infected bacteria. These modifications simplified the assay, increased the limit of detection from 104to <102M. tuberculosiscells, and correctly identified the susceptibility profile of M. tuberculosisstrains exposed for 16 h to either first-line or second-line antitubercular drugs. In addition to phenotypic drug resistance or susceptibility, the assay reported streptomycin MICs and clearly detected 10% drug-resistant cells in an otherwise drug-susceptible population.

Chronic pain represents a major health burden; this maladaptive pain state occurs as a consequence of hypersensitivity within the peripheral and central components of the somatosensory system. High throughput technologies (genomics, transciptomics, lipidomics, and proteomics) are now being applied to tissue derived from pain patients as well as experimental pain models to discover novel pain mediators. The use of clustering, meta‐analysis and other techniques can help refine potential candidates. Of particular importance are systems biology methods, such as co‐expression network generating algorithms, which infer potential associations/interactions between molecules and build networks based on these interactions. Protein–protein interaction networks allow the lists of potential targets generated by these different platforms to be analyzed in their biological context. Outputs from these different methods must also be related to the clinical pain phenotype. The improved and standardized phenotyping of pain symptoms and sensory signs enables much better subject stratification. Our hope is that, in the future, the use of computational approaches to integrate datasets including sensory phenotype as well as the outputs of high throughput technologies will help define novel pain mediators and provide insights into the pathogenesis of chronic pain. WIREs Syst Biol Med2013, 5:11–35. doi: 10.1002/wsbm.1192

Abstract: Fifteen earthquakes (Mw 4.1–6.4) occurring at ten major segments of the Sumatran Fault Zone (SFZ) were analyzed to identify their respective fault planes. The events were relocated in order to assess hypocenter uncertainty. Earthquake source parameters were determined from three-component local waveforms recorded by IRIS-DMC and GEOFON broadband lA networks. Epicentral distances of all stations were less than 10°. Moment tensor solutions of the events were calculated, along with simultaneous determination of centroid position. Joint analysis of hypocenter position, centroid position, and nodal planes produced clear outlines of the Sumatran fault planes. The preferable seismotectonic interpretation is that the events activated the SFZ at a depth of approximately 14–210 km, corresponding to the interplate Sumatran fault boundary. The identification of this seismic fault zone is significant to the investigation of seismic hazards in the region.

Tomographic inversion is applied to delay times from aftershocks of the 1986 ML5.9 North Palm Springs (NPS) earthquake to image 3‐D velocity variations within the northern Coachella Valley. P‐wave arrival times from 1074 earthquakes, with depths ranging from 3 to 20 km, were used as sources recorded by 12 portable and 4 permanent stations. Preliminary results show well‐defined high‐ and low‐velocity anomalies (2–7%) that correlate with the rupture distribution of the 1986 mainshock. At depths less than 8 km, a low‐velocity anomaly predominates between the two NE‐dipping Banning and Mission Creek faults. From 8 to 12 km in depth, where the NPS mainshock and most of the aftershocks occur, a high‐velocity anomaly is observed. This high‐velocity feature is interpreted as imaging the asperity responsible for the 1986 rupture; and suggests that velocity information may help to define important elements, such as asperities, that control fault rupture, and thus, may help to predict the location and size of future events.

Detailed tomographic images of the collision zone between the northern edge of the Philippine Sea and the Eurasian plates reveal a high correlation between tectonic features inferred from seismicity and P- and S-wave velocity structures. The linear tomographic inversion covered a 150 × 150 × 60 km region in the South Fossa Magna centered on the northern Izu Peninsula. Thirty-three three-component stations were located in the target region and 3823 high-quality earthquakes were selected from the catalogues of the NRIESDP, giving rise to 53,593 P- and 50,059 S-wave phase arrivals used in the inversion. The model was parameterized by 60 × 60 × 10 rectilinear blocks, measuring 2.5 km per side horizontally and 5–10 km varying thicknesses in depth. Three-dimensional perturbations from the one-dimensional, NRIESDP, layered model were derived by minimizing the squared misfit of the travel-time residuals. Regularization was employed to reduce the effects of noisy data by constraining the two-dimensional Laplacian of the model, within horizontal layers, to be small. The large sparse matrix was solved using the conjugate gradient algorithm LSQR. Reduction of misfit was 50% for the P-wave inversion and 57% for the S-wave inversion.

Motivation: Circular Dichroism (CD) spectroscopy is a long-established technique for studying protein secondary structures in solution. Empirical analyses of CD data rely on the availability of reference datasets comprised of far-UV CD spectra of proteins whose crystal structures have been determined. This article reports on the creation of a new reference dataset which effectively covers both secondary structure and fold space, and uses the higher information content available in synchrotron radiation circular dichroism (SRCD) spectra to more accurately predict secondary structure than has been possible with existing reference datasets. It also examines the effects of wavelength range, structural redundancy and different means of categorizing secondary structures on the accuracy of the analyses. In addition, it describes a novel use of hierarchical cluster analyses to identify protein relatedness based on spectral properties alone. The databases are shown to be applicable in both conventional CD and SRCD spectroscopic analyses of proteins. Hence, by combining new bioinformatics and biophysical methods, a database has been produced that should have wide applicability as a tool for structural molecular biology. Contact: b.wallace@mail.cryst.bbk.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Circular dichroism (CD) spectroscopy is an important tool in structural biology, especially for protein secondary structure analyses. Synchrotron radiation circular dichroism (SRCD) spectroscopy is a modified version of the technique that uses the intense light from a synchrotron source to enable the collection of data to much lower wavelengths than possible on conventional circular dichroism (cCD) instruments. There is a need for standardization of calibration methods amongst and between cCD and SRCD instruments to ensure consistency and the ability to use common reference databases for empirical secondary structural analyses. In a previous study (Spectroscopy17 (2003), 653–661), we compared optical rotation measurements on several cCD and SRCD instruments, whilst holding constant other experimental factors. In this study, other experimental parameters which contribute to the spectral magnitude, such as cell pathlength and protein concentration determinations, are examined. In addition, the extent of wavelength calibration variations between instruments and their effects on secondary structure calculations have been examined. Hence, this paper provides additional practical guidance for “good practice” in the measurement of CD data.

Synchrotron radiation circular dichroism (SRCD) is an emerging technique in structural biology with particular value in protein secondary structure analyses since it permits the collection of data down to much lower wavelengths than conventional circular dichroism (cCD) instruments. Reference database spectra collected on different SRCD instruments in the future as well as current reference datasets derived from cCD spectra must be compatible. Therefore there is a need for standardization of calibration methods to ensure quality control. In this study, magnitude and optical rotation measurements on four cCD and three SRCD instruments were compared at 192.5, 219, 290 and 490 nm. At high wavelengths, all gave comparable results, however, at the lower wavelengths, some variations were observable. The consequences of these differences on the spectrum, and the calculated secondary structure, of a representative protein (myoglobin) are demonstrated. A method is proposed for standardising spectra obtained on any CD instrument, conventional or synchrotron‒based, with respect to existing and future databases.