Ultrasound attenuation and a P-B-T phase diagram of superfluid 3He in 98% aerogel

Longitudinal sound attenuation measurements in superfluid 3He in 98% aerogel were conducted at pressures between 14 and 33 bar and in magnetic fields up to 4.44 kG. The temperature dependence of the ultrasound attenuation in the A-like phase was determined for the entire superfluid region exploiting the field induced meta-stable A-like phase at the highest field. In the lower field, the A-B transition in aerogel was identified by a smooth jump in attenuation on both cooling and warming. Based on the transitions observed on warming, a phase diagram as a function of pressure (P), temperature (T) and magnetic field (B) is constructed. We find that the A-B phase boundary in aerogel recedes in a drastically different manner than in bulk in response to an increasing magnetic field. The implications of the observed phase diagram are discussed.Comment: 9 pages, 13 figures, accepted to PR

Isolation and functional characterization of cold-regulated promoters, by digitally identifying peach fruit cold-induced genes from a large EST dataset

<p>Abstract</p> <p>Background</p> <p>Cold acclimation is the process by which plants adapt to the low, non freezing temperatures that naturally occur during late autumn or early winter. This process enables the plants to resist the freezing temperatures of winter. Temperatures similar to those associated with cold acclimation are also used by the fruit industry to delay fruit ripening in peaches. However, peaches that are subjected to long periods of cold storage may develop chilling injury symptoms (woolliness and internal breakdown). In order to better understand the relationship between cold acclimation and chilling injury in peaches, we isolated and functionally characterized cold-regulated promoters from cold-inducible genes identified by digitally analyzing a large EST dataset.</p> <p>Results</p> <p>Digital expression analyses of EST datasets, revealed 164 cold-induced peach genes, several of which show similarities to genes associated with cold acclimation and cold stress responses. The promoters of three of these cold-inducible genes (<it>Ppbec1</it>, <it>Ppxero2 </it>and <it>Pptha1</it>) were fused to the GUS reporter gene and characterized for cold-inducibility using both transient transformation assays in peach fruits (<it>in fruta</it>) and stable transformation in <it>Arabidopsis thaliana</it>. These assays demonstrate that the promoter <it>Pptha1 </it>is not cold-inducible, whereas the <it>Ppbec1 and Ppxero2 </it>promoter constructs are cold-inducible.</p> <p>Conclusion</p> <p>This work demonstrates that during cold storage, peach fruits differentially express genes that are associated with cold acclimation. Functional characterization of these promoters in transient transformation assays <it>in fruta </it>as well as stable transformation in Arabidopsis, demonstrate that the isolated <it>Ppbec1 </it>and <it>Ppxero2 </it>promoters are cold-inducible promoters, whereas the isolated <it>Pptha1 </it>promoter is not cold-inducible. Additionally, the cold-inducible activity of the <it>Ppbec1 </it>and <it>Ppxero2 </it>promoters suggest that there is a conserved heterologous cold-inducible regulation of these promoters in peach and Arabidopsis. These results reveal that digital expression analyses may be used in non-model species to identify candidate genes whose promoters are differentially expressed in response to exogenous stimuli.</p

RNAseq reveals different transcriptomic responses to GA3 in early and midseason varieties before ripening initiation in sweet cherry fruits

11openInternationalInternational coauthor/editorGibberellin (GA) negatively affects color evolution and other ripening-related processes in non-climacteric fruits. The bioactive GA, gibberellic acid (GA3), is commonly applied at the light green-to-straw yellow transition to increase firmness and delay ripening in sweet cherry (Prunus avium L.), though causing different effects depending on the variety. Recently, we reported that GA3 delayed the IAD parameter (a ripening index) in a mid-season variety, whereas GA3 did not delay IAD but reduced it at ripeness in an early-season variety. To further explore this contrasting behavior between varieties, we analyzed the transcriptomic responses to GA3 applied on two sweet cherry varieties with different maturity time phenotypes. At harvest, GA3 produced fruits with less color in both varieties. Similar to our previous report, GA3 delayed fruit color initiation and IAD only in the mid-season variety and reduced IAD at harvest only in the early-season variety. RNA-seq analysis of control- and GA3-treated fruits revealed that ripening-related categories were overrepresented in the early-season variety, including ‘photosynthesis’ and ‘auxin response’. GA3 also changed the expression of carotenoid and abscisic acid (ABA) biosynthetic genes in this variety. In contrast, overrepresented categories in the mid-season variety were mainly related to metabolic processes. In this variety, some PP2Cs putative genes were positively regulated by GA3, which are negative regulators of ABA responses, and MYB44-like genes (putative repressors of PP2Cs expression) were downregulated. These results show that GA3 differentially modulates the transcriptome at the onset of ripening in a variety-dependent manner and suggest that GA3 impairs ripening through the modification of ripening associated gene expression only in the early-season variety; whereas in the mid-season variety, control of the ripening timing may occur through the PP2C gene expression regulation. This work contributes to the understanding of the role of GA in non-climacteric fruit ripeningopenKuhn, N.; Maldonado, J.; Ponce, C.; Arellano, M.; Time, A.; Multari, S.; Martens, S.; Carrera, E.; Donoso, J.M.; Sagredo, B.; Meisel, L.A.Kuhn, N.; Maldonado, J.; Ponce, C.; Arellano, M.; Time, A.; Multari, S.; Martens, S.; Carrera, E.; Donoso, J.M.; Sagredo, B.; Meisel, L.A

Proteomic analysis of peach fruit mesocarp softening and chilling injury using difference gel electrophoresis (DIGE)

<p>Abstract</p> <p>Background</p> <p>Peach fruit undergoes a rapid softening process that involves a number of metabolic changes. Storing fruit at low temperatures has been widely used to extend its postharvest life. However, this leads to undesired changes, such as mealiness and browning, which affect the quality of the fruit. In this study, a 2-D DIGE approach was designed to screen for differentially accumulated proteins in peach fruit during normal softening as well as under conditions that led to fruit chilling injury.</p> <p>Results</p> <p>The analysis allowed us to identify 43 spots -representing about 18% of the total number analyzed- that show statistically significant changes. Thirty-nine of the proteins could be identified by mass spectrometry. Some of the proteins that changed during postharvest had been related to peach fruit ripening and cold stress in the past. However, we identified other proteins that had not been linked to these processes. A graphical display of the relationship between the differentially accumulated proteins was obtained using pairwise average-linkage cluster analysis and principal component analysis. Proteins such as endopolygalacturonase, catalase, NADP-dependent isocitrate dehydrogenase, pectin methylesterase and dehydrins were found to be very important for distinguishing between healthy and chill injured fruit. A categorization of the differentially accumulated proteins was performed using Gene Ontology annotation. The results showed that the 'response to stress', 'cellular homeostasis', 'metabolism of carbohydrates' and 'amino acid metabolism' biological processes were affected the most during the postharvest.</p> <p>Conclusions</p> <p>Using a comparative proteomic approach with 2-D DIGE allowed us to identify proteins that showed stage-specific changes in their accumulation pattern. Several proteins that are related to response to stress, cellular homeostasis, cellular component organization and carbohydrate metabolism were detected as being differentially accumulated. Finally, a significant proportion of the proteins identified had not been associated with softening, cold storage or chilling injury-altered fruit before; thus, comparative proteomics has proven to be a valuable tool for understanding fruit softening and postharvest.</p

Comparative EST transcript profiling of peach fruits under different post-harvest conditions reveals candidate genes associated with peach fruit quality

<p>Abstract</p> <p>Background</p> <p>Cold storage is used to inhibit peach fruit ripening during shipment to distant markets. However, this cold storage can negatively affect the quality of the fruit when it is ripened, resulting in disorders such as wooliness, browning or leathering. In order to understand the individual and combined biological effects that factors such as cold storage and ripening have on the fruit and fruit quality, we have taken a comparative EST transcript profiling approach to identify genes that are differentially expressed in response to these factors.</p> <p>Results</p> <p>We sequenced 50,625 Expressed Sequence Tags (ESTs) from peach mesocarp <it>(Prunus persica </it>O'Henry variety) stored at four different postharvest conditions. A total of 10,830 Unigenes (4,169 contigs and 6,661 singletons) were formed by assembling these ESTs. Additionally, a collection of 614 full-length and 1,109 putative full-length cDNA clones within flanking loxP recombination sites was created.</p> <p>Statistically analyzing the EST population, we have identified genes that are differentially expressed during ripening, in response to cold storage or the combined effects of cold storage and ripening. Pair-wise comparisons revealed 197 contigs with at least one significant difference in transcript abundance between at least two conditions. Gene expression profile analyses revealed that the contigs may be classified into 13 different clusters of gene expression patterns. These clusters include groups of contigs that increase or decrease transcript abundance during ripening, in response to cold or ripening plus cold.</p> <p>Conclusion</p> <p>These analyses have enabled us to statistically identify novel genes and gene clusters that are differentially expressed in response to post-harvest factors such as long-term cold storage, ripening or a combination of these two factors. These differentially expressed genes reveal the complex biological processes that are associated with these factors, as well as a large number of putative gene families that may participate differentially in these processes. In particular, these analyzes suggest that woolly fruits lack the increased boost of metabolic processes necessary for ripening. Additionally, these results suggest that the mitochondria and plastids play a major role in these processes. The EST sequences and full-length cDNA clones developed in this work, combined with the large population of differentially expressed genes may serve as useful tools and markers that will enable the scientific community to better define the molecular processes that affect fruit quality in response to post-harvest conditions and the organelles that participate in these processes.</p

Low-lying level structure of 56^{56}Cu and its implications on the rp process

The low-lying energy levels of proton-rich $^{56}$Cu have been extracted using in-beam $\gamma$-ray spectroscopy with the state-of-the-art $\gamma$-ray tracking array GRETINA in conjunction with the S800 spectrograph at the National Superconducting Cyclotron Laboratory at Michigan State University. Excited states in $^{56}$Cu serve as resonances in the $^{55}$Ni(p,$\gamma$)$^{56}$Cu reaction, which is a part of the rp-process in type I x-ray bursts. To resolve existing ambiguities in the reaction Q-value, a more localized IMME mass fit is used resulting in $Q=639\pm82$~keV. We derive the first experimentally-constrained thermonuclear reaction rate for $^{55}$Ni(p,$\gamma$)$^{56}$Cu. We find that, with this new rate, the rp-process may bypass the $^{56}$Ni waiting point via the $^{55}$Ni(p,$\gamma$) reaction for typical x-ray burst conditions with a branching of up to $\sim$40$\%$. We also identify additional nuclear physics uncertainties that need to be addressed before drawing final conclusions about the rp-process reaction flow in the $^{56}$Ni region.Comment: 8 pages, accepted for Phys. Rev.

The three-dimensional Anderson model of localization with binary random potential

We study the three-dimensional two-band Anderson model of localization and compare our results to experimental results for amorphous metallic alloys (AMA). Using the transfer-matrix method, we identify and characterize the metal-insulator transitions as functions of Fermi level position, band broadening due to disorder and concentration of alloy composition. The appropriate phase diagrams of regions of extended and localized electronic states are studied and qualitative agreement with AMA such as Ti-Ni and Ti-Cu metallic glasses is found. We estimate the critical exponents nu_W, nu_E and nu_x when either disorder W, energy E or concentration x is varied, respectively. All our results are compatible with the universal value nu ~ 1.6 obtained in the single-band Anderson model.Comment: 9 RevTeX4 pages with 11 .eps figures included, submitted to PR

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow

BACKGROUND: Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task. RESULTS: In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project. The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses. Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access. CONCLUSION: JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in fruit exportation". However, due to its ability to organize and visualize data from external pipelines, JUICE is a flexible data management system that should be useful for other EST/Genome projects. The JUICE data management system is released under the Open Source GNU Lesser General Public License (LGPL). JUICE may be downloaded from or