Barley development as affected by rate of change of photoperiod

The rate of leaf appearance of barley varies substantially with time of sowing. This variation has been related to both the length and the rate of change of photoperiod at the time of plant emergence. An outdoor pot experiment was conducted to test if rate of change of photoperiod directly affects phasic development and rate of leaf emergence of spring barley. Two photoperiod-sensitive cultivars (Bandulla and Galleon) were subjected to five photoperiod regimes: two constant photoperiods, of 14 and 15·5 h, and three different rates of change of photoperiod of c. 2, 9 and 13 min/day from seedling emergence to awn initiation. Photoperiod treatments significantly affected the duration from seedling emergence to awn initiation in both cultivars. Rate of change of photoperiod did not affect the rate of development towards awn initiation independently of the absolute daylength it produced. Although Bandulla had a longer duration than Galleon at any photoperiod regime, the cultivars did not vary in their sensitivity to photoperiod. When this phase was divided into the leaf initiation (LI) and spikelet initiation (SI) phases, it was evident that the sensitivity to photoperiod was not constant, being in general higher during the SI than during the LI phase. However, the magnitude of the change in sensitivity was cultivar-dependent, indicating that sensitivity to photoperiod during the different phases could be under independent genetic control. Final numbers of primordia (leaves together with maximum spikelet number) were negatively affected by increasing photoperiods, but once again, there was no evidence of any effect of the rate of change of photoperiod which was independent of the average photoperiod. Both cultivars showed similar sensitivities for final leaf number but maximum spikelet number was more sensitive to photoperiod in Galleon than in Bandulla. Highly significant linear relationships between leaf number and thermal time were found for all combinations of cultivars and photoperiod regimes (r2 > 0·98). The rate of leaf appearance (RLA) was similar for both cultivars (c. 0·0185 leaves/°Cd) and did not alter during plant development or in response to the change in photoperiod at awn initiation. The range in RLA was greater for Galleon (0·0170–0·0205 leaves/°Cd) than for Bandulla (0·0173–0·0186 leaves/°Cd). Neither of these cultivars exhibited a significant relationship between rate of leaf emergence and photoperiod or rate of change of photoperiod. The lack of significant relationships between RLA and length or rate of change of photoperiod is in contrast with previous reports using time of sowing as a main treatment.

Stable carbon isotopes in archaeobotanical remains and palaeoclimate

Es descriu una metodologia recent per a inferir la precipitació en el passat basada en l’anàlisi de la composició isotòpica del carboni (δ13C) en restes arqueobotàniques. Un cop descrita la base fisiològica de la tècnica, s’il·lustra l’aplicabilitat de δ13C mitjançant un exemple referent al NE peninsular. Hom pretén proporcionar una estimació quantitativa de l’evolució de la precipitació estacional (primavera) i anual al llarg dels darrers quatre mil anys basada en δ13C. Les mostres analitzades comprenen carbons (pi blanc) i llavors carbonitzades (blat i ordi), i s’obtenen estimes pluviomètriques superiors en el passat que actualment, amb una tendència gradual cap a condicions progressivament més àrides. No obstant això, aquesta tendència no esdevé uniforme, i es detecten dues fases de major precipitació (1800-900 aC; 300 aC - 300 dC) alternadament amb períodes relativament secs (900-300 aC; 900 dC - present). Dels resultats presentats també es desprèn que la importància relativa de la pluja primaveral en el passat fou variable. Des d’aproximadament el 300 aC en endavant, el període primaveral subministrà una major proporció de pluja anual que actualment. Contràriament, durant el període 1800-800 dC la seva contribució va esdevenir inferior, i va aparèixer una fase transitòria (800-300 aC) que mostra una recuperació sobtada en aportació primaveral. Posteriorment a aquesta fase la sincronia de canvis en δ13C en granes i carbons suggereix l’arribada del clima mediterrani a la regió.

Fenología, dinámica poblacional y daños de Eucallipterus tiliae Linnaeus (Horn., Aphididae) en tilos ornamentales de la ciudad de Lleida

La fenología y la dinámica poblacional del pulgón del tilo Eucallipterus tiliae Linnaeus han sido estudiadas en parques y jardines de la ciudad de Lleida durante el periodo 2002-2003 en árboles no tratados y en árboles sometidos a tratamiento químico convencional. Los primeros individuos aparecen a comienzos de primavera (abril) y las densidades de población crecen exponencialmente hasta alcanzarse un máximo a finales de mayo. Inmediatamente después del máximo poblacional se produce un descenso brusco de la población hasta la práctica desaparición de los pulgones del árbol. En otoño se detectan machos y hembras ovíparas que hacen la puesta. Esta especie pasa el invierno en forma de huevo. Durante el periodo de mayor abundancia, los pulgones produjeron gran cantidad de melaza causando daños estéticos a los árboles y molestias a los ciudadanos. Estos efectos negativos del pulgón se produjeron a pesar de la estrategia de control utilizada: la aplicación sistemática de insecticidas. El análisis de esta estrategia mostró un número excesivo de tratamientos y una falta de sincronización con la dinámica del pulgón, lo que pone de manifiesto que la estrategia de control de E. tiliae en Lleida puede ser mejorada. Se registró la presencia de diversos enemigos naturales asociados a E. tiliae, principalmente coccinélidos y parasitoides (Hym., Braconidae, Aphidiinae). Sin embargo, no parece que la abundancia de éstos fuera la suficiente para mantener las poblaciones de pulgones por debajo de los niveles considerados molestos.

De vegetatione notulae, III

Synusie and association. Application to the therophytic Mediterranean communities. The Agropyro-Lygeetum (=Eremopyro-Lygeetum) of the Ebro Basin is a two-layered community. The aerian organs of the chamaephytic and therophytic synusies appears mosaic-like distributed, but the roots of chamaephytes forms a continuous layer under the roots of spring therophytes. The structure of other Mediterranean therophytic associations is similar.

The cave (La caverna -1952-1969) by Josep Palau i Fabre: theatre versus philosophical allegory in order both to perform and stop the tragic and dark end of the bright art of thinking

What is the use of representing in performance the image of the cave from book VII of Plato’s Republic? Josep Palau i Fabre considers that in Plato’s dialogues the speakers are mere instruments at the service of his dialectical purpose. The aim of this article is to show how, by turning the myth into a tragedy and relying on Heraclitus’s conflict or war of opposites, the playwright succeeds in favouring a sort of thought which is not one-sided or univocal. On the contrary, in Palau i Fabre’s La Caverna, the tragic hero, the released prisoner transformed by the light of Reality and finally killed by his “cavemates” –after having been imprisoned again and having tried to rescue them from their ignorance or shadows– still leaves them his powerful experience of the agonistikós thought, which might bear fruit in their life to come.

Toxic phytoplankton response to warming in two Mediterranean bays of the Ebro Delta

The analysis of the phytoplankton and environmental parameters of the time series in Alfacs and Fangar bays (north western Mediterranean) from 1990 to 2009 shows some trends. There is an increase in the average water column temperature, 0.11, 0.01, 0.80 and 0.23 ºC for spring, summer, fall and winter respectively in Alfacs Bay and 1.76, 0.71, 1.33, 0.89 ºC for spring, summer, fall and winter in Fangar Bay. The trends in phytoplankton populations show a shift in the timing of occurrence of Karlodinium spp. blooms and an increase of the Pseudo-nitzschia spp. abundances. There is a lack of correlation between the average seasonal temperatures and the toxic phytoplankton abundances.

Evaluation of detection methods for Virus, Viroids and Phytoplasmas affecting pear and apple

The RT-PCR technique for the detection of apple stem grooving virus (ASGV), apple stem pitting virus (ASPV), apple chlorotic leaf spot virus (ACLSV), apple mosaic virus (ApMV) and pear blister canker viroid (PBCV) was evaluated for health control of fruit plants from nurseries. The technique was evaluated in purified RNA and crude extracts and also in phloem collected in autumn and from young spring shoots. The results obtained for phytoplasma detection with ribosomal and non-ribosomal primers are also presented.

Análisis, diseño e implementación de un mini gestor de contenidos en un Framework Spring

Memoria del trabajo de fin de carrera donde se detalla la implementación de un mini gestor de contenidos utilizando el framework Spring.

Perspectives on the green construction of the new European Energy Policy

The EU has been one of the main actors involved in the construction process of an international climate change regime, adopting it as an identity sign in the international arena. This activism has reverted in the European political agenda and in the one of its Members States. Therefore, climate change has become a driver for the EU growing participation in energy policy and for its governance evolution. In this context, much attention has been paid to the climate and energy policies integration agreed after the 2007 spring European Council. Apparently, this decision meant a decisive step towards the incorporation of the environmental variable in the energy policy-making. Moreover, the Action Plan [2007-2009] “Energy Policy for Europe” outlined priority actions in a variety of energy-related areas, implying the new European Energy Policy commencement. Against this background, there is still much left to understand about its formulation and its further development. Rooted on the Environmental Policy Integration approach, this paper traces the increasing proximity between environment and energy policies in order to understand the green contribution to the European Energy Policy construction.

Seasonal changes of whole root system conductance by a drought-tolerant grape root system

The role of root systems in drought tolerance is a subject of very limited information compared with above-ground responses. Adjustments to the ability of roots to supply water relative to shoot transpiration demand is proposed as a major means for woody perennial plants to tolerate drought, and is often expressed as changes in the ratios of leaf to root area (AL:AR). Seasonal root proliferation in a directed manner could increase the water supply function of roots independent of total root area (AR) and represents a mechanism whereby water supply to demand could be increased. To address this issue, seasonal root proliferation, stomatal conductance (gs) and whole root system hydraulic conductance (kr) were investigated for a drought-tolerant grape root system (Vitis berlandieri×V. rupestris cv. 1103P) and a non-drought-tolerant root system (Vitis riparia×V. rupestris cv. 101-14Mgt), upon which had been grafted the same drought-sensitive clone of Vitis vinifera cv. Merlot. Leaf water potentials (ψL) for Merlot grafted onto the 1103P root system (–0.91±0.02 MPa) were +0.15 MPa higher than Merlot on 101-14Mgt (–1.06±0.03 MPa) during spring, but dropped by approximately –0.4 MPa from spring to autumn, and were significantly lower by –0.15 MPa (–1.43±0.02 MPa) than for Merlot on 101-14Mgt (at –1.28±0.02 MPa). Surprisingly, gs of Merlot on the drought-tolerant root system (1103P) was less down-regulated and canopies maintained evaporative fluxes ranging from 35–20 mmol vine−1 s−1 during the diurnal peak from spring to autumn, respectively, three times greater than those measured for Merlot on the drought-sensitive rootstock 101-14Mgt. The drought-tolerant root system grew more roots at depth during the warm summer dry period, and the whole root system conductance (kr) increased from 0.004 to 0.009 kg MPa−1 s−1 during that same time period. The changes in kr could not be explained by xylem anatomy or conductivity changes of individual root segments. Thus, the manner in which drought tolerance was conveyed to the drought-sensitive clone appeared to arise from deep root proliferation during the hottest and driest part of the season, rather than through changes in xylem structure, xylem density or stomatal regulation. This information can be useful to growers on a site-specific basis in selecting rootstocks for grape clonal material (scions) grafted to them.

Comparison of splice sites in mammals and chicken

We have carried out an initial analysis of the dynamics of the recent evolution of the splice-sites sequences on a large collection of human, rodent (mouse and rat), and chicken introns. Our results indicate that the sequences of splice sites are largely homogeneous within tetrapoda. We have also found that orthologous splice signals between human and rodents and within rodents are more conserved than unrelated splice sites, but the additional conservation can be explained mostly by background intron conservation. In contrast, additional conservation over background is detectable in orthologous mammalian and chicken splice sites. Our results also indicate that the U2 and U12 intron classes seem to have evolved independently since the split of mammals and birds; we have not been able to find a convincing case of interconversion between these two classes in our collections of orthologous introns. Similarly, we have not found a single case of switching between AT-AC and GT-AG subtypes within U12 introns, suggesting that this event has been a rare occurrence in recent evolutionary times. Switching between GT-AG and the noncanonical GC-AG U2 subtypes, on the contrary, does not appear to be unusual; in particular, T to C mutations appear to be relatively well tolerated in GT-AG introns with very strong donor sites.

SGP-1: prediction and validation of homologous genes based on sequence alignments

Conventional methods of gene prediction rely on the recognition of DNA-sequence signals, the coding potential or the comparison of a genomic sequence with a cDNA, EST, or protein database. Reasons for limited accuracy in many circumstances are species-specific training and the incompleteness of reference databases. Lately, comparative genome analysis has attracted increasing attention. Several analysis tools that are based on human/mouse comparisons are already available. Here, we present a program for the prediction of protein-coding genes, termed SGP-1 (Syntenic Gene Prediction), which is based on the similarity of homologous genomic sequences. In contrast to most existing tools, the accuracy of SGP-1 depends little on species-specific properties such as codon usage or the nucleotide distribution. SGP-1 may therefore be applied to nonstandard model organisms in vertebrates as well as in plants, without the need for extensive parameter training. In addition to predicting genes in large-scale genomic sequences, the program may be useful to validate gene structure annotations from databases. To this end, SGP-1 output also contains comparisons between predicted and annotated gene structures in HTML format. The program can be accessed via a Web server at http://soft.ice.mpg.de/sgp-1. The source code, written in ANSI C, is available on request from the authors.

Fusion of the human gene for the polyubiquitination co-effector UEV-1 with Kua, a newly identified gene

UEV proteins are enzymatically inactive variants of the E2 ubiquitin-conjugating enzymes that regulate noncanonical elongation of ubiquitin chains. In Saccharomyces cerevisiae, UEV is part of the RAD6-mediated error-free DNA repair pathway. In mammalian cells, UEV proteins can modulate c-FOS transcription and the G2-M transition of the cell cycle. Here we show that the UEV genes from phylogenetically distant organisms present a remarkable conservation in their exon–intron structure. We also show that the human UEV1 gene is fused with the previously unknown gene Kua. In Caenorhabditis elegans and Drosophila melanogaster, Kua and UEV are in separated loci, and are expressed as independent transcripts and proteins. In humans, Kua and UEV1 are adjacent genes, expressed either as separate transcripts encoding independent Kua and UEV1 proteins, or as a hybrid Kua–UEV transcript, encoding a two-domain protein. Kua proteins represent a novel class of conserved proteins with juxtamembrane histidine-rich motifs. Experiments with epitope-tagged proteins show that UEV1A is a nuclear protein, whereas both Kua and Kua–UEV localize to cytoplasmic structures, indicating that the Kua domain determines the cytoplasmic localization of Kua–UEV. Therefore, the addition of a Kua domain to UEV in the fused Kua–UEV protein confers new biological properties to this regulator of variant polyubiquitination.[Kua cDNAs isolated by RT-PCR and described in this paper have been deposited in the GenBank data library under accession nos. AF1155120 (H. sapiens) and AF152361 (D. melanogaster). Genomic clones containing UEV genes: S. cerevisiae, YGL087c (accession no. Z72609); S. pombe, c338 (accession no. AL023781); P. falciparum, MAL3P2 (accession no. AL034558); A. thaliana, F26F24 (accession no. AC005292); C. elegans, F39B2 (accession no. Z92834); D. melanogaster, AC014908; and H. sapiens, 1185N5 (accession no. AL034423). Accession numbers for Kua cDNAs in GenBank dbEST: M. musculus, AA7853; T. cruzi, AI612534. Other Kua-containing sequences: A. thaliana genomic clones F10M23 (accession no. AL035440), F19K23 (accession no. AC000375), and T20K9 (accession no. AC004786).

An assessment of gene prediction accuracy in large DNA sequences

One of the first useful products from the human genome will be a set of predicted genes. Besides its intrinsic scientific interest, the accuracy and completeness of this data set is of considerable importance for human health and medicine. Though progress has been made on computational gene identification in terms of both methods and accuracy evaluation measures, most of the sequence sets in which the programs are tested are short genomic sequences, and there is concern that these accuracy measures may not extrapolate well to larger, more challenging data sets. Given the absence of experimentally verified large genomic data sets, we constructed a semiartificial test set comprising a number of short single-gene genomic sequences with randomly generated intergenic regions. This test set, which should still present an easier problem than real human genomic sequence, mimics the approximately 200kb long BACs being sequenced. In our experiments with these longer genomic sequences, the accuracy of GENSCAN, one of the most accurate ab initio gene prediction programs, dropped significantly, although its sensitivity remained high. Conversely, the accuracy of similarity-based programs, such as GENEWISE, PROCRUSTES, and BLASTX was not affected significantly by the presence of random intergenic sequence, but depended on the strength of the similarity to the protein homolog. As expected, the accuracy dropped if the models were built using more distant homologs, and we were able to quantitatively estimate this decline. However, the specificities of these techniques are still rather good even when the similarity is weak, which is a desirable characteristic for driving expensive follow-up experiments. Our experiments suggest that though gene prediction will improve with every new protein that is discovered and through improvements in the current set of tools, we still have a long way to go before we can decipher the precise exonic structure of every gene in the human genome using purely computational methodology.

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution

Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are “genomic fossils” valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome’s structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct pseudogene annotation strategies and found that different approaches and parameters often resulted in rather distinct sets of pseudogenes. We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction (∼80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates. Analysis of sequence conservation and variation also demonstrated that most pseudogenes evolve neutrally, and processed pseudogenes appear to have lost their coding potential immediately or soon after their emergence. In order to explore the functional implication of pseudogene prevalence, we have extensively examined the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues.