Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm

Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OC_B), one of Occidental landraces (POP2OC_T) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs.     

Prediction of Nociceptive Responses during Sedation by Linear and Non-Linear Measures of EEG Signals in High Frequencies

The level of sedation in patients undergoing medical procedures evolves continuously, affected by the interaction between the effect of the anesthetic and analgesic agents and the pain stimuli. The monitors of depth of anesthesia, based on the analysis of the electroencephalogram (EEG), have been progressively introduced into the daily practice to provide additional information about the state of the patient. However, the quantification of analgesia still remains an open problem. The purpose of this work is to improve the prediction of nociceptive responses with linear and non-linear measures calculated from EEG signal filtered in frequency bands higher than the traditional bands. Power spectral density and auto-mutual information function was applied in order to predict the presence or absence of the nociceptive responses to different stimuli during sedation in endoscopy procedure. The proposed measures exhibit better performances than the bispectral index (BIS). Values of prediction probability of P_k above 0.75 and percentages of sensitivity and specificity above 70% were achieved combining EEG measures from the traditional frequency bands and higher frequency bands.     

Cytotoxicity and enzymatic activity inhibition in cell lines treated with novel iminosugar derivatives

Iminosugars are monosaccharide analogues that have been demonstrated to be specific inhibitors for glycosidases and are currently used therapeutically in several human disorders. N-alkylated derivatives of d-fagomine and (2R,3S,4R,5S)-2-(hydroxymethyl)-5-methylpyrrolidine-3,4-diol with aliphatic chains were tested in eight human cancer cell lines to analyze their cytotoxicity and the inhibitory effect in the activities of specific glycosidases. Results indicate that these compounds were more cytotoxic as the length of the alkyl chain increases. N-dodecyl-d-fagomine inhibited specifically the α-d-glucosidase activity in cell lysates, whereas no effect was detected in other glycosidases. The N-dodecyl derivative of (2R,3S,4R,5S)-2-(Hydroxymethyl)-5-methylpyrrolidine-3,4-diol induced specific inhibition against α-l-fucosidase in cell lysates. Our results indicated that the length of the alkyl chain linked to the iminosugars determine their cytotoxicity as well as the inhibitory effect on the enzymatic activities of specific glycosidases, in human cancer cell lines.     

ZmMYB31 directly represses maize lignin genes and redirects the phenylpropanoid metabolic flux

Few regulators of phenylpropanoids have been identified in monocots having potential as biofuel crops. Here we demonstrate the role of the maize (Zea mays) R2R3-MYB factor ZmMYB31 in the control of the phenylpropanoid pathway. We determined its in vitro consensus DNA-binding sequence as ACC(T)/(A) ACC, and chromatin immunoprecipitation (ChIP) established that it interacts with two lignin gene promoters in vivo. To explore the potential of ZmMYB31 as a regulator of phenylpropanoids in other plants, its role in the regulation of the phenylpropanoid pathway was further investigated in Arabidopsis thaliana. ZmMYB31 downregulates several genes involved in the synthesis of monolignols and transgenic plants are dwarf and show a significantly reduced lignin content with unaltered polymer composition. We demonstrate that these changes increase cell wall degradability of the transgenic plants. In addition, ZmMYB31 represses the synthesis of sinapoylmalate, resulting in plants that are more sensitive to UV irradiation, and induces several stress-related proteins. Our results suggest that, as an indirect effect of repression of lignin biosynthesis, transgenic plants redirect carbon flux towards the biosynthesis of anthocyanins. Thus, ZmMYB31 can be considered a good candidate for the manipulation of lignin biosynthesis in biotechnological applications.     

Analysis of a continuous culture of Fibrobacter succinogenes S85 on a standardized glucose medium

Continuous cultures of Fibrobacter succinogenes S85 were performed on a standardized fully synthetic culture medium with glucose as carbon source at a dilution rate (D = 0.02 h⁻¹) in a 5-L bioreactor. The culture was stabilized during 20 days and demonstrated the ability of Fibrobacter succinogenes to grow in this synthetic medium. CO₂ partial pressure and redox potential probes were used to check the anaerobic state of the culture. The biomass yield was calculated 0.206 g (g glucose)⁻¹ and the production yield of succinate, the major end-product, was 0.63 mol (mol glucose)⁻¹. The consistency of the experimental data was checked by proton and mass (C, N) balances. The results were satisfactory (90–110% recovery) leading to derive a stoichiometric equation representative of the growth on glucose. The stoichiometric coefficients were calculated using data reconciliation and linear algebra methods enabling to obtain a complete modeling of all conversion yields possible.     

Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy

Background  

Cucumis melo (melon) belongs to the Cucurbitaceae family, whose economic importance among horticulture crops is second only to Solanaceae. Melon has a high intra-specific genetic variation, morphologic diversity and a small genome size (454 Mb), which make it suitable for a great variety of molecular and genetic studies. A number of genetic and genomic resources have already been developed, such as several genetic maps, BAC genomic libraries, a BAC-based physical map and EST collections. Sequence information would be invaluable to complete the picture of the melon genomic landscape, furthering our understanding of this species' evolution from its relatives and providing an important genetic tool. However, to this day there is little sequence data available, only a few melon genes and genomic regions are deposited in public databases. The development of massively parallel sequencing methods allows envisaging new strategies to obtain long fragments of genomic sequence at higher speed and lower cost than previous Sanger-based methods.     

Nitrogen allocation in response to partial shading of a plant: Possible mechanisms

The significance of photosynthetic and transpiration rates for the perception by plants of light gradients in leaf canopies has been investigated with regard to nitrogen allocation and re-allocation. A gradient of photon flux density (PFD) over a plant's foliage was simulated by shading one leaf of a pair of primary leaves of bean ( Phaseolus vulgaris L. cv. Rentegever). Photosynthetic rate was manipulated independently of PFD and, to some extent, also of transpiration, by subjecting the leaf to different CO₂ concentrations. Transpiration rate was changed independently of PFD and photosynthetic rate by subjecting the leaf to different vapour pressure differences (VPD). A reduced partial pressure of CO₂ reduced specific leaf mass (SLM) as did a decreased PFD, but did not change leaf N per unit area (N_LA) and light saturated rate of photosynthesis (A_max). A reduced VPD caused several effects consistent with the effect of PFD. It decreased N_LA and A_max and increased the chlorophyll to N ratio in old and young leaves. Furthermore, it decreased the chlorophyll a to b ratio and inhibited leaf growth in young leaves. The transpiration stream is partitioned among the leaves of a plant according to their transpiration rates. The results suggest that relative rates of import of xylem sap into leaves of a plant play an important role in the perception of partial shading of a plant, a situation normally found in dense vegetations. The possible role of cytokinin influx into leaves as controlled by transpiration rate, is discussed.     

Acorn dispersal estimated by radio-tracking

Bird-dispersed seeds are difficult to track, especially in the case of long-distance dispersal events. To estimate the oak dispersal distance and the seed shadow generated by the European jay (Garrulus glandarius), we inserted radio-transmitters in 239 acorns, placed them in bird-feeders and then located them by radio-tracking. Using this methodology we located the exact caching site of 94 Quercus ilex and 54 Q. suber acorns and determined the caching habitat characteristics (vegetation type, distance, spatial distribution). The results show that: (1) there is no differences in the dispersal distance distribution between the different acorn species or sizes, (2) dispersal distances range from approximately 3 m up to approximately 550 m (mean = 68.6 m; median = 49.2 m), (3) recently abandoned fields and forest tracks were the sites preferred by jays to cache acorns, whereas fields and shrublands were avoided and (4) seed shadows showed acorn aggregation zones (i.e. clusters of caches) close to the feeder as well as isolated caches at longer distances. The results also suggest that radio-transmitters are a cheap and reliable way to determine seed shadows and quantify both seed dispersal and post-dispersal seed predation for medium to large seeds.     

Ethylene insensitivity results in down-regulation of rubisco expression and photosynthetic capacity in tobacco

Little is known about the effect of hormones on the photosynthetic process. Therefore, we studied Rubisco content and expression along with gas exchange parameters in transgenic tobacco (Nicotiana tabacum) plants that are not able to sense ethylene. We also tested for a possible interaction between ethylene insensitivity, abscisic acid (ABA), and sugar feedback on photosynthesis. We measured Rubisco content in seedlings grown in agar with or without added sugar and fluridone, and Rubisco expression in hydroponically grown vegetative plants grown at low and high CO(2). Furthermore, we analyzed gas exchange and the photosynthetic machinery of transformants and wild-type plants grown under standard conditions. In the presence of exogenous glucose (Glc), agar-grown seedlings of the ethylene-insensitive genotype had lower amounts of Rubisco per unit leaf area than the wild type. No differences in Rubisco content were found between ethylene-insensitive and wild-type seedlings treated with fluridone, suggesting that inhibition of ABA production nullified the effect of Glc application. When larger, vegetative plants were grown at different atmospheric CO(2) concentrations, a negative correlation was found between Glc concentration in the leaves and Rubisco gene expression, with stronger repression by high Glc concentrations in ethylene-insensitive plants. Ethylene insensitivity resulted in plants with comparable fractions of nitrogen invested in light harvesting, but lower amounts in electron transport and Rubisco. Consequently, photosynthetic capacity of the insensitive genotype was clearly lower compared with the wild type. We conclude that the inability to perceive ethylene results in increased sensitivity to Glc, which may be mediated by a higher ABA concentration. This increased sensitivity to endogenous Glc has negative consequences for Rubisco content and photosynthetic capacity of these plants.     

SIRT1 deacetylase protects against neurodegeneration in models for Alzheimer's disease and amyotrophic lateral sclerosis

A progressive loss of neurons with age underlies a variety of debilitating neurological disorders, including Alzheimer's disease (AD) and amyotrophic lateral sclerosis (ALS), yet few effective treatments are currently available. The SIR2 gene promotes longevity in a variety of organisms and may underlie the health benefits of caloric restriction, a diet that delays aging and neurodegeneration in mammals. Here, we report that a human homologue of SIR2, SIRT1, is upregulated in mouse models for AD, ALS and in primary neurons challenged with neurotoxic insults. In cell-based models for AD/tauopathies and ALS, SIRT1 and resveratrol, a SIRT1-activating molecule, both promote neuronal survival. In the inducible p25 transgenic mouse, a model of AD and tauopathies, resveratrol reduced neurodegeneration in the hippocampus, prevented learning impairment, and decreased the acetylation of the known SIRT1 substrates PGC-1alpha and p53. Furthermore, injection of SIRT1 lentivirus in the hippocampus of p25 transgenic mice conferred significant protection against neurodegeneration. Thus, SIRT1 constitutes a unique molecular link between aging and human neurodegenerative disorders and provides a promising avenue for therapeutic intervention.