Use of RAPD patterns for clone verification and in studying provenance relationships in Norway spruce (Picea abies)

 We have used the RAPD technique to analyse samples of Picea abies obtained from an improvement forestry station. Two types of plant material were harvested, the first being clones and the second provenances from various regions. We first checked the clonal identity of elite tree cuttings and clones; some differences in the RAPD patterns resulting from mis-planting or mis-labelling of cuttings were found. We also established a reference library of RAPD fingerprints for 96 clones, which will serve as a reference source in cases of litigation concerning clone identity. The RAPD technique was also used to study the genetic relationship between nine European provenances of Norway spruce. A dendogram was obtained by individual pairwise comparison of 42 RAPD bands, which separated the nine provenances into two major groups, one containing the Nordic provenances (Sweden and Bielorussia) and another the Alpine provenances (France, Austria, Germany and Belgium). The Belgian provenance, which is not indigenous, is most closely related to the German provenance. We conclude that the RAPD technique is a useful tool for forestry stations in managing propagation operations. Received: 15 June 1996 / Accepted: 11 October 1996     

Evidence for the Presence of a Free C-Terminal Fragment of Cx43 in Cultured Cells

Migration of the gap junction protein connexin 43 (Cx43) in SDS-PAGE yields 2 to 4 distinct bands, detectable in the 40-47 kDa range. Here, we show that antibodies against the carboxy-terminal domain of Cx43 recognized an additional 20-kDa product. This protein was detected in some culture cell lysates. The presence of the 20-kDa band was not prevented by the use of protease inhibitors (Complete® and phenylmethylsulfonyl fluoride (PMSF), 1-5 mM). The band was absent from cells treated with Cx43-specific RNAi, and from those derived from Cx43-deficient mice, indicating that this Cx43-immunoreactive protein is a product of the Cx43 gene. Treatment of CHO cells with cyclosporin A caused a reduction in the amount of full-length Cx43 and a concomitant increase in the amount of the 20-kDa band. Overall, our data show that a fraction of the Cx43-immunoreactive protein pool within a given cell may correspond to a C-terminal fragment of the protein.     

Ultrastructural immunolocalization of elastic fibers in rat blood vessels using the protein A-gold technique

Identification of elastic fibers at the ultrastructural level is accomplished by a post-embedding immunohistochemical technique using the protein A-colloidal gold method. Antisera against elastins from human dermis and rat aorta have been characterized by radioimmunoassay and then applied to thin sections of rat blood vessels. Two fixative solutions and two embedding media have been tested. Both antibodies bind to elastic fibers of normal arteries and veins, indicating crossreactions among organs and species. The high sensitivity of this method is demonstrated by its application to the detection of neo-elastogenesis in the intimal thickening of aortic grafts.     

A Long-Term Experimental Study Demonstrates the Costs of Begging That Were Not Found over the Short Term

Parent–offspring conflict theory predicts that begging behaviour could escalate continuously over evolutionary time if it is not prevented by costliness of begging displays. Three main potential physiological costs have been proposed: growth, immunological and metabolic costs. However, empirical evidence on this subject remains elusive because published results are often contradictory. In this study, we test for the existence of these three potential physiological costs of begging in house sparrow (Passer domesticus) nestlings by stimulating a group of nestlings to beg for longer and another group for shorter periods than in natural conditions. All nestlings were fed with the same quantity of food. Our study involves a long-term experimental treatment for begging studies (five consecutive days). Long-term studies frequently provide clearer results than short-term studies and, sometimes, relevant information not reported by the latter ones. Our long-term experiment shows (i) a clear effect on the immune response even since the first measurement (6 hours), but it was higher during the second (long-term) than during the first (short-term) test; (ii) evidence of a growth cost of begging in house sparrow nestlings not previously found by other studies; (iii) body condition was affected by our experimental manipulation only after 48 hour; (iv) a metabolic cost of begging never previously shown in any species, and (v) for the first time, it has shown a simultaneous effect of the three potential physiological costs of begging: immunocompetence, growth, and metabolism. This implies first, that a multilevel trade-off can occur between begging and all physiological costs and, second, that a lack of support in a short-term experiment for the existence of a tested cost of begging does not mean absence of that cost, because it can be found in a long-term experiment.     

Contribution to the diatom flora of Cambodia: Five new recent freshwater taxa

Cambodian aquatic ecosystems are extremely diversified and constitute major preservation targets.However,the species composition,diversity,and distribution of the inhabiting algal communities are large...     

Overexpression of the <Emphasis Type="Italic">Arabidopsis</Emphasis> anaphase promoting complex subunit <Emphasis Type="Italic">CDC27a</Emphasis> increases growth rate and organ size

The Anaphase Promoting Complex (APC) controls CDK activity by targeting the ubiquitin-dependent proteolysis of S-phase and mitosis-promoting cyclins. Here, we report that the ectopic expression of the Arabidopsis CDC27a, an APC subunit, accelerates plant growth and results in plants with increased biomass production. CDC27a overexpression was associated to apical meristem restructuration, protoplasts with higher ³H-thimidine incorporation and altered cell-cycle marker expression. Total protein extracts immunoprecipitated with a CDC27a antibody showed ubiquitin ligase activity, indicating that the Arabidopsis CDC27a gets incorporated into APC complexes. These results indicate a role of AtCDC27a in regulation of plant growth and raise the possibility that the activity of the APC and the rates of plant cell division could be regulated by the concentration of the CDC27a subunit. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Cristian Antonio Rojas and Nubia Barbosa Eloy contributed equally to this work.     

A Dual Pressure Linear Ion Trap Orbitrap Instrument with Very High Sequencing Speed

Since its introduction a few years ago, the linear ion trap Orbitrap (LTQ Orbitrap) instrument has become a powerful tool in proteomics research. For high resolution mass spectrometry measurements ions are accumulated in the linear ion trap and passed on to the Orbitrap analyzer. Simultaneously with acquisition of this signal, the major peaks are isolated in turn, fragmented and recorded at high sensitivity in the linear ion trap, combining the strengths of both mass analyzer technologies. Here we describe a next generation LTQ Orbitrap system termed Velos, with significantly increased sensitivity and scan speed. This is achieved by a vacuum interface using a stacked ring radio frequency ion guide with 10-fold higher transfer efficiency in MS/MS mode and 3–5-fold in full scan spectra, by a dual pressure ion trap configuration, and by reduction of overhead times between scans. The first ion trap efficiently captures and fragments ions at relatively high pressure whereas the second ion trap realizes extremely fast scan speeds at reduced pressure. Ion injection times for MS/MS are predicted from full scans instead of performing automatic gain control scans. Together these improvements routinely enable acquisition of up to ten fragmentation spectra per second. Furthermore, an improved higher-energy collisional dissociation cell with increased ion extraction capabilities was implemented. Higher-collision energy dissociation with high mass accuracy Orbitrap readout is as sensitive as ion trap MS/MS scans in the previous generation of the instrument.Proteomics experiments typically involve the analysis of peptide mixtures obtained by the enzymatic digestion of proteomes that can be as complex as complete cell lysates (1, 2). Dynamic range of peptide abundances and the sheer number of peptides encountered in these mixtures require extremely sensitive and fast peptide detection and fragmentation (3). Although a first comprehensively identified and quantified proteome has recently been reported (4), further gains in instrumental performance are clearly needed to reduce overall measurement time, improve sequence coverage of identified proteins, and for the in-depth analysis of mammalian proteomes.Among many different instrumental formats (5), the combination of a linear ion trap (6) with a Fourier transform (FT)1 mass spectrometer has rapidly become a popular technological platform in proteomics because it combines the sensitivity, speed, and robustness of ion traps with the high resolution capabilities of FT instruments. The first implementation of this principle used an ion cyclotron resonance instrument with a 7T magnet as the high resolution device (7). Later, the Orbitrap^TM analyzer developed by Makarov was coupled to the LTQ, combining the linear ion trap with a very small and powerful analyzer (8–11).Here we describe a next generation linear ion trap-Orbitrap instrument with significant improvements in ion source transmission and with a new ion trap configuration. We show that this instrument, termed the LTQ Orbitrap Velos, is capable of much higher scan speeds compared with the current LTQ Orbitrap. Furthermore, we implemented more efficient ion extraction for the higher-energy collisional dissociation (HCD) cell (12). Due to this improvement and the 10-fold higher transmission of ions from atmosphere, high resolution and high mass accuracy MS/MS can now routinely be obtained at very high sensitivity and at scan speeds of up to 5 Hz acquisition rates. A related instrument, the LTQ-Velos, which does not contain the Orbitrap analyzer for high resolution measurements, has been described very recently (13).     

A high-density consensus map of barley linking DArT markers to SSR,RFLP and STS loci and agricultural traits

Background

Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a large scale EST sequencing approach was undertaken by the Functional Genomics of Abiotic Stress (FGAS) project.

Results

We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets). Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology.

Conclusion

We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in wheat and other cereals.