Acclimation to different depths by the marine angiosperm Posidonia oceanica: transcriptomic and proteomic profiles

For seagrasses, seasonal and daily variations in light and temperature represent the mains factors driving their distribution along the bathymetric cline. Changes in these environmental factors, due to climatic and anthropogenic effects, can compromise their survival. In a framework of conservation and restoration, it becomes crucial to improve our knowledge about the physiological plasticity of seagrass species along environmental gradients. Here, we aimed to identify differences in transcriptomic and proteomic profiles, involved in the acclimation along the depth gradient in the seagrass Posidonia oceanica, and to improve the available molecular resources in this species, which is an important requisite for the application of eco-genomic approaches. To do that, from plant growing in shallow (−5 m) and deep (−25 m) portions of a single meadow, (i) we generated two reciprocal Expressed Sequences Tags (EST) libraries using a Suppressive Subtractive Hybridization (SSH) approach, to obtain depth/specific transcriptional profiles, and (ii) we identified proteins differentially expressed, using the highly innovative USIS mass spectrometry methodology, coupled with 1D-SDS electrophoresis and labeling free approach. Mass spectra were searched in the open source Global Proteome Machine (GPM) engine against plant databases and with the X!Tandem algorithm against a local database. Transcriptional analysis showed both quantitative and qualitative differences between depths. EST libraries had only the 3% of transcripts in common. A total of 315 peptides belonging to 64 proteins were identified by mass spectrometry. ATP synthase subunits were among the most abundant proteins in both conditions. Both approaches identified genes and proteins in pathways related to energy metabolism, transport and genetic information processing, that appear to be the most involved in depth acclimation in P. oceanica. Their putative rules in acclimation to depth were discussed

Physiological, metabolite and volatile analysis of cut size in melon during postharvest storage

Melons are an important component of fresh fruit salads, however, they suffer from limited shelf life. Processing of melon fruit for use in fruit salads induces a number of changes including alterations in colour and texture. In addition, respiration rate and ethylene production are affected. Processing also elicits changes in flavour (sweetness) and aroma (production of volatile organic compounds – VOCs), of critical importance to the consumer. Several parameters govern shelf life; temperature is a critical factor. In this study we tested whether cut size is another parameter that can affect quality indicators. Melon (Cucumis melo ‘Arapaho’) cubes of three sizes were stored at 4°C and assessed for quality at five time-points over a 15-day period. We assessed a number of parameters including firmness, loss of fresh weight, respiration rate, antioxidant capacity, phenolic compounds and carotenoid content. In addition we measured VOC profiles to assess whether there were any qualitative changes associated with storage period and/or cut size. Fresh weight (FW) loss and respiration rate increased significantly with storage time and FW loss was affected by cut size. Total carotenoid levels remained stable during the storage time as did antioxidant capacity in all cut sizes. However, cinnamic acid levels tended to decrease in the last stage of the storage period and changes in β-carotene content correlated with cut size (though not significantly). We were also able to separate the VOC profiles from the different cut sizes indicating that VOCs may be useful markers as indicators of the effects of cut size and storage time on quality

Spectra of High-Redshift Type Ia Supernovae and a Comparison with their Low-Redshift Counterparts

We present spectra for 14 high-redshift (0.17 < z < 0.83) supernovae, which were discovered by the Supernova Cosmology Project as part of a campaign to measure cosmological parameters. The spectra are used to determine the redshift and classify the supernova type, essential information if the supernovae are to be used for cosmological studies. Redshifts were derived either from the spectrum of the host galaxy or from the spectrum of the supernova itself. We present evidence that these supernovae are of Type Ia by matching to spectra of nearby supernovae. We find that the dates of the spectra relative to maximum light determined from this fitting process are consistent with the dates determined from the photometric light curves, and moreover the spectral time-sequence for SNe Type Ia at low and high redshift is indistinguishable. We also show that the expansion velocities measured from blueshifted CaHK are consistent with those measured for low-redshift Type Ia supernovae. From these first-level quantitative comparisons we find no evidence for evolution in SNIa properties between these low- and high-redshift samples. Thus even though our samples may not be complete, we conclude that there is a population of SNe Ia at high redshift whose spectral properties match those at low redshift.Comment: Accepted for publication in AJ. Also available at http://supernova.lbl.gov

Establishing research strategies, methodologies and technologies to link genomics and proteomics to seagrass productivity, community metabolism, and ecosystem carbon fluxes

A complete understanding of the mechanistic basis of marine ecosystem functioning is only possible through integrative and interdisciplinary research. This enables the prediction of change and possibly the mitigation of the consequences of anthropogenic impacts. One major aim of the European Cooperation in Science and Technology (COST) Action ES0609 “Seagrasses productivity. From genes to ecosystem management,” is the calibration and synthesis of various methods and the development of innovative techniques and protocols for studying seagrass ecosystems. During 10 days, 20 researchers representing a range of disciplines (molecular biology, physiology, botany, ecology, oceanography, and underwater acoustics) gathered at The Station de Recherches Sous-marines et Océanographiques (STARESO, Corsica) to study together the nearby Posidonia oceanica meadow. STARESO is located in an oligotrophic area classified as “pristine site” where environmental disturbances caused by anthropogenic pressure are exceptionally low. The healthy P. oceanica meadow, which grows in front of the research station, colonizes the sea bottom from the surface to 37 m depth. During the study, genomic and proteomic approaches were integrated with ecophysiological and physical approaches with the aim of understanding changes in seagrass productivity and metabolism at different depths and along daily cycles. In this paper we report details on the approaches utilized and we forecast the potential of the data that will come from this synergistic approach not only for P. oceanica but for seagrasses in general

Lensed Type Ia supernovae as probes of cluster mass models

Using three magnified Type Ia supernovae (SNe Ia) detected behind CLASH (Cluster Lensing and Supernovae with Hubble) clusters, we perform a first pilot study to see whether standardizable candles can be used to calibrate cluster mass maps created from strong lensing observations. Such calibrations will be crucial when next-generation Hubble Space Telescope cluster surveys (e.g. Frontier) provide magnification maps that will, in turn, form the basis for the exploration of the high-redshift Universe. We classify SNe using combined photometric and spectroscopic observations, finding two of the three to be clearly of Type Ia and the third probable. The SNe exhibit significant amplification, up to a factor of 1.7 at ∼5σ significance (SN-L2). We conducted this as a blind study to avoid fine-tuning of parameters, finding a mean amplification difference between SNe and the cluster lensing models of 0.09 ± 0.09stat ± 0.05sys舁mag. This impressive agreement suggests no tension between cluster mass models and high-redshift-standardized SNe Ia. However, the measured statistical dispersion of σμ = 0.21舁mag appeared large compared to the dispersion expected based on statistical uncertainties (0.14). Further work with the SN and cluster lensing models, post-unblinding, reduced the measured dispersion to σμ = 0.12. An explicit choice should thus be made as to whether SNe are used unblinded to improve the model, or blinded to test the model. As the lensed SN samples grow larger, this technique will allow improved constraints on assumptions regarding e.g. the structure of the dark matter halo

Spectroscopic Observations and Analysis of the Unusual Type Ia SN 1999ac

We present optical spectra of the peculiar Type Ia supernova (SN Ia) 1999ac. The data extend from -15 to +42 days with respect to B-band maximum and reveal an event that is unusual in several respects. Prior to B-band maximum, the spectra resemble those of SN 1999aa, a slowly declining event, but possess stronger SiII and CaII signatures (more characteristic of a spectroscopically normal SN). Spectra after B-band maximum appear more normal. The expansion velocities inferred from the Iron lines appear to be lower than average; whereas, the expansion velocity inferred from Calcium H and K are higher than average. The expansion velocities inferred from SiII are among the slowest ever observed, though SN 1999ac is not particularly dim. The analysis of the parameters v_10, R(SiII), dv(SiII)/dt, and d_m15 further underlines the unique characteristics of SN 1999ac. We find convincing evidence of CII 6580 in the day -15 spectrum with ejection velocity v > 16,000 km/s, but this signature disappears by day -9. This rapid evolution at early times highlights the importance of extremely early-time spectroscopy.Comment: 40 pages, 24 figures, accepted for publication in The Astronomical Journa

Restframe I-band Hubble diagram for type Ia supernovae up to redshift z ~0.5

We present a novel technique for fitting restframe I-band light curves on a data set of 42 Type Ia supernovae (SNe Ia). Using the result of the fit, we construct a Hubble diagram with 26 SNe from the subset at 0.01< z<0.1. Adding two SNe at z~0.5 yields results consistent with a flat Lambda-dominated``concordance universe'' ($\Omega_M,\Omega_\Lambda$)=(0.25,0.75). For one of these, SN 2000fr, new near infrared data are presented. The high redshift supernova NIR data are also used to test for systematic effects in the use of SNe Ia as distance estimators. A flat, Lambda=0, universe where the faintness of supernovae at z~0.5 is due to grey dust homogeneously distributed in the intergalactic medium is disfavoured based on the high-z Hubble diagram using this small data-set. However, the uncertainties are large and no firm conclusion may be drawn. We explore the possibility of setting limits on intergalactic dust based on B-I and B-V colour measurements, and conclude that about 20 well measured SNe are needed to give statistically significant results. We also show that the high redshift restframe I-band data points are better fit by light curve templates that show a prominent second peak, suggesting that they are not intrinsically underluminous.Comment: Accepted for publication in A&A (01/04/2005

DNA replication timing is deterministic at the level of chromosomal domains but stochastic at the level of replicons in Xenopus egg extracts

Replication origins in Xenopus egg extracts are located at apparently random sequences but are activated in clusters that fire at different times during S phase under the control of ATR/ATM kinases. We investigated whether chromosomal domains and single sequences replicate at distinct times during S phase in egg extracts. Replication foci were found to progressively appear during early S phase and foci labelled early in one S phase colocalized with those labelled early in the next S phase. However, the distribution of these two early labels did not coincide between single origins or origin clusters on single DNA fibres. The 4 Mb Xenopus rDNA repeat domain was found to replicate later than the rest of the genome and to have a more nuclease-resistant chromatin structure. Replication initiated more frequently in the transcription unit than in the intergenic spacer. These results suggest for the first time that in this embryonic system, where transcription does not occur, replication timing is deterministic at the scale of large chromatin domains (1–5 Mb) but stochastic at the scale of replicons (10 kb) and replicon clusters (50–100 kb)

Looking Beyond Lambda with the Union Supernova Compilation

The recent robust and homogeneous analysis of the world's supernova distance-redshift data, together with cosmic microwave background and baryon acoustic oscillation data, provides a powerful tool for constraining cosmological models. Here we examine particular classes of scalar field, modified gravity, and phenomenological models to assess whether they are consistent with observations even when their behavior deviates from the cosmological constant Lambda. Some models have tension with the data, while others survive only by approaching the cosmological constant, and a couple are statistically favored over LCDM. Dark energy described by two equation of state parameters has considerable phase space to avoid Lambda and next generation data will be required to constrain such physics.Comment: 32 pages, 19 figure