Expression patterns of novel wound-inducible plant genes in Medicago truncatula

Terpenoids are an important class of defensive compounds that can accumulate in plants after pathogen infection or injury by chewing insects. Clones encoding putative terpene synthases and an oxidosqualene synthase, isolated from insect-damaged Medicagotruncatula leaves, were selected from an expressed sequence tag (EST) database. The cDNA clones were used as radiolabeled probes to analyze gene expression in leaves treated by known factors that can trigger a defense response in plants. Transcript levels for all of the genes examined increased in response to artificial wounding, insect herbivory, and methyl jasmonate (meJA) treatments, whereas salicylic acid (SA) and glucose oxidase (GOX) had no measurable effects on transcript levels. Furthermore, the genome of M. truncatula was analyzed via DNA blots for an estimation of the number of copies of enzyme isoforms; these data indicate that each of the enzymes examined is encoded by a single-copy gene or a small gene family

Effects of virus infection on release of volatile organic compounds from insect-damaged bean, Phaseolus vulgaris

Insects can serve as important vectors of plant pathogens, especially viruses. Insect feeding on plants causes the systemic release of a wide range of plant volatile compounds that can serve as an indirect plant defense by attracting natural enemies of the herbivorous insect. Previous work suggests that the Mexican bean beetle (Epilachna varivestis) prefers to feed on plants infected by either of two viruses that it is known to transmit: Southern bean mosaic virus (SBMV) or Bean pod mottle virus (BPMV). A possible explanation for the preferred feeding on virus-infected tissues is that the beetles are attracted by volatile signals released from leaves. The purpose of this work was to determine whether volatile compounds from virus-infected plants are released differentially from those emitted by uninfected plants. To test the hypothesis, common bean plants (Phaseolus vulgaris cv. Black Valentine) were inoculated with either BPMV, SBMV, or a mixture of both viruses, and infected plants were compared to uninfected plants. An Ouchterlony assay was used with SBMVand BPMV-specific antisera to confirm the presence of virus in inoculated plants. RNA blot analysis was performed on tissue from each plant and indicated that a well-characterized defense gene, encoding phenylalanine ammonia-lyase (PAL), was not induced in systemic tissue following virus infection. Plant volatiles were collected—and analyzed via gas chromatography (GC)—from plants that were either undamaged or beetle-damaged. In undamaged plants, there were no measurable differences in profiles or quantities of compounds released by uninfected and virus-infected plants. After Mexican bean beetles were allowed to feed on plants for 48 h, injured plants released several compounds that were not released from undamaged plants. Lower quantities of volatile compounds were released from virus-infected plants suggesting that enhanced release of plant-derived volatile organic compounds is not the cause for attraction of Mexican bean beetles to virus-infected plants

Deep and Comparative Transcriptome Analysis of Rice Plants Infested by the Beet Armyworm (\u3ci\u3eSpodoptera exigua\u3c/i\u3e) and Water Weevil (\u3ci\u3eLissorhoptrus oryzophilus\u3c/i\u3e)

The beet armyworm (Spodoptera exigua) and the rice water weevil (Lissorhoptrus oryzophilus) are two important insect pests in rice production. To identify insect-responsive genes in rice, we performed a deep transcriptome analysis of Nipponbare rice leaves infested with both beet armyworm and water weevil using massively parallel signature sequencing (MPSS). Many antisense, alternative, and novel transcripts were commonly and specifically induced and suppressed in the infested tissue. Key genes involved in the defense metabolic pathways such as salicylic acid and jasmonic acid biosynthesis pathways were up-regulated in the infested leaves. To validate theMPSS results, we analyzed the transcriptome of the rice leaves infested with water weevils using Solexa’s sequencing-bysynthesis (SBS) method. The MPSS and SBS data were highly correlated (Pearson’s correlation coefficient=0.85), and 83% of genes had similar gene expression in both libraries. Our comprehensive and in-depth survey of the insect-infested libraries provides a rich genomic resource for further analyzing the function of key regulatory genes involved in insect resistance in rice. Supplementary files are attached below

Allantoate amidohydrolase transcript expression is independent of drought tolerance in soybean

Drought is a limiting factor for N2 fixation in soybean [Glycine max (L.) Merr.] thereby resulting in reduced biomass accumulation and yield. Drought-sensitive genotypes accumulate ureides, a product of N2 fixation, during drought stress; however, drought-tolerant genotypes have lower shoot ureide concentrations, which appear to alleviate drought stress on N2 fixation. A key enzyme involved in ureide breakdown in shoots is allantoate amidohydrolase (AAH). It is hypothesized that AAH gene expression in soybean determines shoot ureide concentrations during water-deficit stress and is responsible for the differential sensitivities of the N2-fixation response to drought among soybean genotypes. The objectives were to examine the relationship between AAH transcript levels and shoot ureide concentration and drought tolerance. Drought-tolerant (Jackson) and drought-sensitive (Williams) genotypes were subjected to three water-availability treatments: well-watered control, moderate water-deficit stress, and severe water-deficit stress. Shoot ureide concentrations were examined, in addition to gene expression of AAH and DREB2, a gene expressed during water-deficit stress. As expected, DREB2 expression was detected only during severe water-deficit stress, and shoot ureide concentrations were greatest in the drought-sensitive genotype relative to the drought-tolerant genotype during water-deficit stress. However, expression of AAH transcripts was similar among water treatments and genotypes, indicating that AAH mRNA was not closely associated with drought tolerance. Ureide concentrations in shoots were weakly associated with AAH mRNA levels. These results indicate that AAH expression is probably not associated with the increased ureide catabolism observed in drought-tolerant genotypes, such as Jackson. Further study of AAH at the post-translational and enzymatic levels is warranted in order to dissect the potential role of this gene in drought tolerance

The Energy Computation Paradox and ab initio Protein Folding

The routine prediction of three-dimensional protein structure from sequence remains a challenge in computational biochemistry. It has been intuited that calculated energies from physics-based scoring functions are able to distinguish native from nonnative folds based on previous performance with small proteins and that conformational sampling is the fundamental bottleneck to successful folding. We demonstrate that as protein size increases, errors in the computed energies become a significant problem. We show, by using error probability density functions, that physics-based scores contain significant systematic and random errors relative to accurate reference energies. These errors propagate throughout an entire protein and distort its energy landscape to such an extent that modern scoring functions should have little chance of success in finding the free energy minima of large proteins. Nonetheless, by understanding errors in physics-based score functions, they can be reduced in a post-hoc manner, improving accuracy in energy computation and fold discrimination

Identification and mitigation of narrow spectral artifacts that degrade searches for persistent gravitational waves in the first two observing runs of Advanced LIGO

Searches are under way in Advanced LIGO and Virgo data for persistent gravitational waves from continuous sources, e.g. rapidly rotating galactic neutron stars, and stochastic sources, e.g. relic gravitational waves from the Big Bang or superposition of distant astrophysical events such as mergers of black holes or neutron stars. These searches can be degraded by the presence of narrow spectral artifacts (lines) due to instrumental or environmental disturbances. We describe a variety of methods used for finding, identifying and mitigating these artifacts, illustrated with particular examples. Results are provided in the form of lists of line artifacts that can safely be treated as non-astrophysical. Such lists are used to improve the efficiencies and sensitivities of continuous and stochastic gravitational wave searches by allowing vetoes of false outliers and permitting data cleaning

Search of the Orion spur for continuous gravitational waves using a loosely coherent algorithm on data from LIGO interferometers

We report results of a wideband search for periodic gravitational waves from isolated neutron stars within the Orion spur towards both the inner and outer regions of our Galaxy. As gravitational waves interact very weakly with matter, the search is unimpeded by dust and concentrations of stars. One search disk (A) is 6.87° in diameter and centered on 20h10m54.71s+33°33′25.29′′, and the other (B) is 7.45° in diameter and centered on 8h35m20.61s-46°49′25.151′′. We explored the frequency range of 50-1500 Hz and frequency derivative from 0 to -5×10-9 Hz/s. A multistage, loosely coherent search program allowed probing more deeply than before in these two regions, while increasing coherence length with every stage. Rigorous follow-up parameters have winnowed the initial coincidence set to only 70 candidates, to be examined manually. None of those 70 candidates proved to be consistent with an isolated gravitational-wave emitter, and 95% confidence level upper limits were placed on continuous-wave strain amplitudes. Near 169 Hz we achieve our lowest 95% C.L. upper limit on the worst-case linearly polarized strain amplitude h0 of 6.3×10-25, while at the high end of our frequency range we achieve a worst-case upper limit of 3.4×10-24 for all polarizations and sky locations. © 2016 American Physical Society

First low-frequency Einstein@Home all-sky search for continuous gravitational waves in Advanced LIGO data

We report results of a deep all-sky search for periodic gravitational waves from isolated neutron stars in data from the first Advanced LIGO observing run. This search investigates the low frequency range of Advanced LIGO data, between 20 and 100 Hz, much of which was not explored in initial LIGO. The search was made possible by the computing power provided by the volunteers of the Einstein@Home project. We find no significant signal candidate and set the most stringent upper limits to date on the amplitude of gravitational wave signals from the target population, corresponding to a sensitivity depth of 48.7 [1/root Hz]. At the frequency of best strain sensitivity, near 100 Hz, we set 90% confidence upper limits of 1.8 x 10(-25). At the low end of our frequency range, 20 Hz, we achieve upper limits of 3.9 x 10(-24). At 55 Hz we can exclude sources with ellipticities greater than 10(-5) within 100 pc of Earth with fiducial value of the principal moment of inertia of 10(38) kg m(2)