Search

The widespread Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) occurs along a steep gradient of diverse climates throughout its natural range, which is expected to result in spatially varying selection to local climate conditions. However, phenotypic signals of climatic adaptation can often be confounded, because unraveled clines covary with signals caused by neutral evolutionary processes such as gene flow and genetic drift. Here, we present phenotypic and genotypic data from a common garden experiment showing a putative signal of adaptation to climate after trees have been growing for 40 years in a common environment. Sixteen Douglas-fir provenances originating from a North-to-South gradient of approx. 1,000 km were analyzed and genomic information was obtained from exome capture, which resulted in an initial genomic dataset of >90,000 single nucleotide polymorphisms. We used a restrictive and conservative filtering approach which permitted us to include only SNPs and individuals in environmental association analysis (EAA) that were free of potentially confounding effects (LD, relatedness among trees, heterozygosity deficiency and deviations from Hardy-Weinberg proportions). We used four conceptually different genome scan methods based on FST outlier detection and gene-environment association in order to disentangle truly adaptive SNPs from neutral SNPs and found that a relatively small proportion of the exome showed a truely adaptive signal (0.01-0.17%) when population substructuring and multiple testing was accounted for. Nevertheless, the unraveled SNP candidates showed significant relationship with climate at provenance origins which strongly suggests that they have most likely featured adaption in Douglas-fir across a steep climatic gradient. Two SNPs were independently found by three of the employed algorithms and one could be assigned with high probability to a Picea abies homolog gene involved in circadian clock control as was also found in Populus balsamifera.

Cancer-type organic anion transporting polypeptide 1B3 (Ct-OATP1B3) has been identified as a cancer-specific transcript in various solid cancers, including colorectal cancer. Given its excellent cancer-specific expression profile, we hypothesized that Ct-OATP1B3 could represent a promising target for cancer-specific expression of the suicide gene, herpes simplex virus 1 thymidine kinase (HSV-tk), via a spliceosome-mediated RNA trans-splicing (SMaRT) approach. SMaRT technology is used to recombine two RNA molecules to generate a chimeric transcript. In this study, we engineered an RNA trans-splicing molecule carrying a translation-defective HSV-tk sequence (RTM44), which was capable of inducing its own trans-splicing to the desired Ct-OATP1B3 pre-mRNA target. RTM44 expression in LS180 cells resulted in generation of Ct-OATP1B3/HSV-tk fusion mRNA. A functional translation start site contributed by the target pre-mRNA restored HSV-tk protein expression, rendering LS180 cells sensitive to ganciclovir treatment in vitro and in xenografted mice. The observed effects are ascribed to accurate and efficient trans-splicing, as they were absent in cells carrying a splicing-deficient mutant of RTM44. Collectively, our data highlights Ct-OATP1B3 as an ideal target for the HSV-tk SMaRT suicide system, which opens up new translational avenues for Ct-OATP1B3-targeted cancer therapy.

Despite of a number of studies on the genetic nature of plant adaptation to drought stress there is still no conclusion on the core mechanism of defense. Extraction of knowledge gained from experiments on different plant species under different conditions and subsequent interpolation thus appears to be a challenge. Here we applied a sequence similarity-based approach to identify computationally the components of defense against water deprivation. The prediction in silico was based on the available scientific data. We identified a subset of defense gene candidates, of which 2 % were experimentally proven to be drought-responsive. The transcriptomic analysis of drought-stressed poplar roots generated data that confirm and/or complement previous reports on plant responses to drought. On the other hand, we observed suppression of genes involved in antioxidative defense that seems to contradict many foregoing observations. The results, advantages and possible drawbacks of our prediction approach are discussed in light of experimental data.

a b s t r a c t Long-term drought during one and two growing seasons, respectively strongly affected the timing and number of flushes of oak plants (Quercus robur L.), and negatively influenced subsequent growth. In con- trast, strong compensation growth was observed upon rewatering. The defence response of experimental plants was assessed by analyzing stress metabolites and transcriptome changes. Our data revealed that while during mild and/or short drought stress only readily metabolizable carbohydrates e.g. glucose, fructose, and galactose are accumulated, prolonged drought stress results in accumulation of more sta- ble and protective osmolytes such as quercitol and mannitol. At transcriptome level more than 3% of the expressed sequences tags (ESTs) represented on the microarray were differentially expressed reflecting the activation of defence responses in oak which appear to be stronger in the second year of persist- ing stress. The transcriptome changes are in good agreement with both the metabolic data as well as morphological observations. We conclude that mild long-term drought stress over two years triggers adaptation processes in oak plants that ensure survival, while irreversible damage is kept low facilitating full recovery upon rewatering. © 2011 Elsevier B.V. All rights reserved.

The origin of the putatively autotriploid plant with 2n=3X=24 chromosomes growing in Mediterranean and Near East countries is unclear. As saffron is male sterile and thus vegetatively propagated, it is assumed that there is just one saffron cultivar grown worldwide. Still there are differences in quality and phenotype reported, this being attributed to clonal differences. So far molecular analyses only concentrated on the identification of the putative ancestors of C. sativus L. using RAPD, AFLP, IRAP or ISSR markers, but no extensive study has been conducted to prove the genetic identity and the putative clonality of cultured saffron. In the limited phylogenetic studies conducted so far, C. sativus L. exhibited little to no genetic variation. In our study we concentrated on C. sativus L. exclusively, using maternally inherited choloropalst (cp) markers as well as microsatellite regions contained in expressed genes (EST-SSRs) to investigate genetic diversity. Out of the 6803 available saffron ESTs (D'Agostino et al., http://www.saffrongenes.org) 200 sequences proved to contain SSR regions. Out of these, for 38 sequences primers could be developed and tested on 29 different saffron accessions. In addition to the nuclear SSRs, 8 cp regions were investigated. Due to the fact that none of the regions revealed any genetic difference among the investigated probes, sequencing of 5 genes was conducted in order to identify single base pair mutations in the respective genomic areas.

Helicobacter pylori is the most prevalent human pathogen and although, it remains silent in most individuals for lifetime, colonization may develop into severe gastric and duodenal conditions. Rapidly developing resistance to antibiotic treatment urgently calls for the development of effective vaccines. We determined the ANTIGENome of two clinical isolates of H. pylori, KTH-Ca1 and KTH-Du, derived from patients with gastric cancer and duodenal ulcer, respectively. Using disease-relevant human sera from well-characterized donors we identified 124 annotated ORFs and 54 non-annotated peptides as antigens. Through in vitro validation assays we selected the 20 most promising vaccine candidates. Importantly, two candidates represent proteins that were previously shown to provide protection in models of H. pylori infection. One of the most frequently selected and conserved protein, the siderophore-dependent transporter HP1341, was confirmed to show high reactivity with human serum IgGs. These analyses provide the means to identify novel antigens for the selection of vaccine candidates, as well as disease associated biomarkers.

Head blight of wheat (FHB, scab) caused by Fusarium spp. has been associated with yield and quality losses in many wheat-growing regions. In tetraploid wheat sources of resistance are scarce. In the search for novel sources of resistance, 151 Triticum dicoccoides genotypes, originating from 16 habitats in Israel and one habitat in Turkey together with several control genotypes, were evaluated for reaction to fungal spread (Type II resistance) in replicated greenhouse experiments. Significant genetic diversity was found among the tested genotypes, the broad sense heritability for Type II FHB resistance was 0.71. Most of the tetraploid accessions were highly susceptible, only a few showed moderate resistance. Among the eight T. dicoccoides lines with the lowest relative infection rates, five originated from the Mt. Gerizim population, and three from the Mt. Hermon population. None of the T. dicoccoides lines reached the level of resistance present in the common wheat cultivar Sumai3.

Background Many northern-hemisphere forests are dominated by oaks. These species extend over diverse environmental conditions and are thus interesting models for studies of plant adaptation and speciation. The genomic toolbox is an important asset for exploring the functional variation associated with natural selection. Results The assembly of previously available and newly developed long and short sequence reads for two sympatric oak species, Quercus robur and Quercus petraea, generated a comprehensive catalog of transcripts for oak. The functional annotation of 91 k contigs demonstrated the presence of a large proportion of plant genes in this unigene set. Comparisons with SwissProt accessions and five plant gene models revealed orthologous relationships, making it possible to decipher the evolution of the oak genome. In particular, it was possible to align 9.5 thousand oak coding sequences with the equivalent sequences on peach chromosomes. Finally, RNA-seq data shed new light on the gene networks underlying vegetative bud dormancy release, a key stage in development allowing plants to adapt their phenology to the environment. Conclusion In addition to providing a vast array of expressed genes, this study generated essential information about oak genome evolution and the regulation of genes associated with vegetative bud phenology, an important adaptive traits in trees. This resource contributes to the annotation of the oak genome sequence and will provide support for forward genetics approaches aiming to link genotypes with adaptive phenotypes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1331-9) contains supplementary material, which is available to authorized users.

A containment experiment was carried out in order to evaluate possible shifts in eubacterial and Pseudomonas rhizosphere community structures due to the release of genetically modified Basta-tolerant oilseed rape and the associated herbicide application. Treatments included cultivation of the transgenic plant as well as of the wild-type cultivar in combination with mechanical removal of weeds and the application of the herbicides Basta (active ingredient: glufosinate) and Butisan S (active ingredient: metazachlor). Rhizosphere soil was sampled from early and late flowering plants as well as from senescent plants. A culture-independent approach was chosen to characterize microbial communities based on denaturing gradient gel electrophoresis of 16S rRNA gene fragments amplified from rhizosphere DNA using eubacterial and Pseudomonas-specific PCR primers. Dominant pseudomonads in the rhizosphere were analyzed by sequence analysis. Whole community and Pseudomonas electrophoresis fingerprints revealed slightly altered microbial communities in the rhizosphere of transgenic plants; however, effects were minor as compared to the plant developmental stage-dependent shifts. Both herbicides caused transient changes in the eubacterial and Pseudomonas population structure, whereas differences due to the genetic modification were still detected at the senescent growth stage. The observed differences between transgenic and wild-type lines were most likely due to unintentionally modified plant characteristics such as altered root exudation.

Responses of plant tissue to environmental challenges can vary among different plant parts and among plants of different ages. Investment into defense has been proposed to be influenced by fitness value and/or allocation of available resources. Here we show at first time at transcriptome level that plant defense is non-linear. On very young, expanding, adult and old leaves of Populus nigra plants exposed to air perturbation, we studied the ontogenic trajectory of gene expression changes to such a low-dose factor similar to wind. Although plant responses to mechanical sensation (wind, touch) are described and summarized as thigmomorphogenesis, the knowledge on the molecular background of plant responses to wind is largely incomplete. Our data describe which genes are activated during a ubiquitous and continuous environmental factor such as wind, and based on existing knowledge complement the picture on ongoing processes.

The aim of this study was to describe the technique of rhinolaryngotracheobronchoscopy and oesophagoscopy in small ruminants and to report the normal endoscopic appearance of the structures of the upper respiratory tract and oesophagus. Thirty sheep and 30 goats, all clinically normal, underwent rhinolaryngotracheobronchoscopy and oesophagoscopy using a flexible endoscope (length 100 cm; diameter 4 mm). The anatomical features of the structures and the appearance of the mucosa were investigated. The degree of mucosal pigmentation varied between breeds. The appearance of the pharyngeal tonsil and the shape of the trachea in cross-section showed most individual variation. The technique was easily performed and sedation was necessary in only a few cases. No major complications were encountered. It was concluded that the procedure facilitated more accurate diagnosis and prognosis of conditions of the upper respiratory tract and oesophagus.

Fusarium head blight (FHB, scab) is a fungal disease of wheat and other small cereals that is found in both temperate and semi-tropical regions. FHB causes severe yield and quality losses, but the most-serious concern is the possible mycotoxin contamination of cereal food and feed. Breeding for FHB resistance by conventional selection is feasible, but tedious and expensive. This study was conducted to identify and map DNA markers associated with FHB resistance genes in wheat. A population of 364 F(1)-derived doubled-haploid (DH) lines from the cross 'CM-82036' (resistant)/'Remus' (susceptible) was evaluated for Type II resistance (spread within the spike) during 2 years under field conditions. Marker analysis was performed on 239 randomly chosen DH lines. Different marker types were applied, with an emphasis on AFLP and SSR markers. Analysis of variance, as well as simple and composite interval mapping, were applied. Three genomic regions were found significantly associated with FHB resistance. The most-prominent effect was detected on the short arm of chromosome 3B, explaining up to 60% of the phenotypic variance for Type II FHB resistance. A further QTL was located on chromosome 5A and a third one on 1B. The QTL regions on 3B and 5A were tagged with flanking SSR markers, the 1B QTL was found associated with the high-molecular-weight glutenin locus. These results indicate that FHB resistance is under control of a few major QTLs operating together with unknown numbers of minor genes. Marker-assisted selection for these major QTLs involved in FHB resistance appears feasible and should accelerate the development of resistant and agronomically improved wheat cultivars.