Variation in peach fruit susceptibility to Monilinia laxa and gene expression

Brown rot caused by Monilinia laxa and Monilinia fructigena is considered one of the most important diseases affecting Prunus species. Although some losses can result from the rotten fruits in the orchard, most of the damage is caused to fruits during the post-harvest phase. Several studies reported that brown rot incidence during fruit development highly varies; it was found that at a period corresponding to the the pit hardening stage, fruit susceptibility drastically decreases, to be quickly restored afterwards. However the molecular basis of this phenomenon is still not well understood. Furthermore, no difference in the rot incidence was found between wound and un-wound fruits, suggesting that resistance associated more to a specifc biochemical response of the fruit, rather than to a higher mechanical resistance. So far, the interaction Monilinia-peach was analyzed through chemical approaches. In this study, a bio-molecular approach was undertaken in order to reveal alteration in gene expression associated to the variation of susceptibility. In this thesis three different methods for gene expression analysis were used to analyze the alterations in gene expression occurring in peach fruits during the pit hardening stage, in a period encompassing the temporary change in Monilinia susceptibility: real time PCR, microarray and cDNA AFLP techniques. In 2005, peach fruits (cv.K2) were weekly harvested during a 19-week long-period, starting from the fourth week after full bloom, until full maturity. At each sampling time, three replicates of 5 fruits each were dipped in the M.laxa conidial suspension or in distilled water, as negative control. The fruits were maintained at room temperature for 3 hours; afterwards, they were peeled with a scalpel; the peel was immediately frozen in liquid nitrogen and transferred to -80 °C until use. The degree of susceptibility of peach fruit to the pathogen was determined on 3 replicates of 20 fruits each, as percentage of infected fruits, after one week at 20 °C. Real time PCR analysis was performed to study the variation in expression of those genes encoding for the enzymes of the phenylpropanoid pathway (phenylalanine ammonia lyase (PAL), chalcone synthase (CHS), cinnamate 4-hydroxylase (C4H), leucoanthocyanidine reductase (LAR), hydroxycinnamoyl CoA quinate hydroxycinnamoyl transferase (HQT) and of the jasmonate pathway, such as lipoxygenase (LOX), both involved in the production of important defense compounds. Alteration in gene expression was monitored on fruit samples of a period encompassing the pit hardening stage and the corresponding temporary resistance to M.laxa infections, weekly, from the 6thto the 12th week after full bloom (AFB) inoculated with M. laxa or mock-inoculated. The data suggest a critical change in the expression level of the phenylpropanoid pathway from the 7th to the 8th week AFB; such change could be directly physiologically associated to the peach growth and it could indirectly determine the decrease of susceptibility of peach fruit to Monilinia rot during the subsequent weeks. To investigate on the transcriptome variation underneath the temporary loss of susceptibility of peach fruits to Monilinia rot, the microarray and the cDNA AFLP techniques were used. The samples harvested on the 8th week AFB (named S, for susceptible ones) and on the 12th week AFB (named R, for resistant ones) were compared, both inoculated or mock-inoculated. The microarray experiments were carried out at the University of Padua (Dept. of Environmental Agronomy and Crop Science), using the μPEACH1.0 microarray together with the suited protocols. The analysis showed that 30 genes (corresponding to the 0.6% of the total sequences (4806) contained in the μPeach1.0 microarray) were found up-regulated and 31 ( 0.6%) down regulated in RH vs. SH fruits. On the other hand, 20 genes (0.4%) were shown to be up-regulated and 13 (0.3%) down-regulated in the RI vs. SI fruit. No genes were found differentially expressed in the mock-inoculated resistant fruits (RH) vs. the inoculated resistant ones (RI). Among the up-regulated genes an ATP sulfurylase, an heat shock protein 70, the major allergen Pru P1, an harpin inducing protein and S-adenosylmethionine decarboxylase were found, conversely among the down-regulated ones, cinnamyl alcohol dehydrogenase, an histidine- containing phosphotransfer protein and the ferritin were found. The microarray experimental results and the data indirectly derived, were tested by Real Time PCR analysis. cDNA AFLP analysis was also performed on the same samples. 339 transcript derived fragments considered significant for Monilinia resistance, were selected, sequenced and classified. Genes potentially involved in cell rescue and defence were well represented (8%); several genes (12.1%) involved in the protein folding, post-transductional modification and genes (9.2%) involved in cellular transport were also found. A further 10.3% of genes were classified as involved in the metabolism of aminoacid, carbohydrate and fatty acid. On the other hand, genes involved in the protein synthesis (5.7%) and in signal transduction and communication (5.7%) were found. Among the most interesting genes found differentially expressed between susceptible and resistant fruits, genes encoding for pathogenesis related (PR) proteins were found. To investigate on the association of Monilinia resistance and PR biological function, the major allergen Pru P1 (GenBank accession AM493970) and its isoform (here named Pru P2), were expressed in heterologous system and in vitro assayed for their anti-microbial activity. The ribonuclease activity of the recombinant Pru P1 and Pru P2 proteins was assayed against peach total RNA. As the other PR10 proteins, they showed a ribonucleolytic activity, that could be important to contrast pathogen penetration. Moreover Pru P1 and Pru P2 recombinant proteins were checked for direct antimicrobial activity. No inhibitory effect of Pru P1 or Pru P2 was detected against the selected fungi.

Le produzioni agroalimentari di qualità nelle aziende agricole dell’Emilia-Romagna: un’analisi comparativa con le aziende agricole convenzionali

Il tema dei prodotti agroalimentari di qualità ha ormai assunto un ruolo rilevante all’interno del dibattito riguardante l’agricoltura e l’economia agroalimentare, ponendosi al centro dell’interesse delle politiche europee (PAC post 2013, Pacchetto Qualità). La crescente attenzione verso le produzioni con marchio Dop\Igp mette però in luce la sostanziale carenza di informazioni dettagliate relativamente alle aziende che operano in questo comparto. Da questo punto di vista il VI° Censimento generale dell’agricoltura costituisce una preziosa fonte di informazioni statistiche. L’obiettivo di questo lavoro è quello di utilizzare i dati, ancora provvisori, del censimento per analizzare la struttura delle aziende con produzioni di qualità, ponendola in confronto con quella delle aziende convenzionali. Inoltre è stata fatta una classificazione delle aziende con prodotti Dop\Igp, in base alla rilevanza di queste produzioni sul reddito lordo aziendale. Le aziende sono quindi state classificate come “Specializzate” e “Miste”, con un’ulteriore distinzione di queste ultime tra quelle “Prevalentemente Dop\Igp” e quelle “Prevalentemente non Dop\Igp”. Tale ripartizione ha consentito una definizione dettagliata degli orientamenti produttivi delle aziende analizzate.

A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER ESTIMATION USING SNP ARRAYS

Submicroscopic changes in chromosomal DNA copy number dosage are common and have been implicated in many heritable diseases and cancers. Recent high-throughput technologies have a resolution that permits the detection of segmental changes in DNA copy number that span thousands of basepairs across the genome. Genome-wide association studies (GWAS) may simultaneously screen for copy number-phenotype and SNP-phenotype associations as part of the analytic strategy. However, genome-wide array analyses are particularly susceptible to batch effects as the logistics of preparing DNA and processing thousands of arrays often involves multiple laboratories and technicians, or changes over calendar time to the reagents and laboratory equipment. Failure to adjust for batch effects can lead to incorrect inference and requires inefficient post-hoc quality control procedures that exclude regions that are associated with batch. Our work extends previous model-based approaches for copy number estimation by explicitly modeling batch effects and using shrinkage to improve locus-specific estimates of copy number uncertainty. Key features of this approach include the use of diallelic genotype calls from experimental data to estimate batch- and locus-specific parameters of background and signal without the requirement of training data. We illustrate these ideas using a study of bipolar disease and a study of chromosome 21 trisomy. The former has batch effects that dominate much of the observed variation in quantile-normalized intensities, while the latter illustrates the robustness of our approach to datasets where as many as 25% of the samples have altered copy number. Locus-specific estimates of copy number can be plotted on the copy-number scale to investigate mosaicism and guide the choice of appropriate downstream approaches for smoothing the copy number as a function of physical position. The software is open source and implemented in the R package CRLMM available at Bioconductor (http:www.bioconductor.org).

Evaluating northern hardwood management using retrospective analysis and diameter distributions

Northern hardwood management was assessed throughout the state of Michigan using data collected on recently harvested stands in 2010 and 2011. Methods of forensic estimation of diameter at breast height were compared and an ideal, localized equation form was selected for use in reconstructing pre-harvest stand structures. Comparisons showed differences in predictive ability among available equation forms which led to substantial financial differences when used to estimate the value of removed timber. Management on all stands was then compared among state, private, and corporate landowners. Comparisons of harvest intensities against a liberal interpretation of a well-established management guideline showed that approximately one third of harvests were conducted in a manner which may imply that the guideline was followed. One third showed higher levels of removals than recommended, and one third of harvests were less intensive than recommended. Multiple management guidelines and postulated objectives were then synthesized into a novel system of harvest taxonomy, against which all harvests were compared. This further comparison showed approximately the same proportions of harvests, while distinguishing sanitation cuts and the future productive potential of harvests cut more intensely than suggested by guidelines. Stand structures are commonly represented using diameter distributions. Parametric and nonparametric techniques for describing diameter distributions were employed on pre-harvest and post-harvest data. A common polynomial regression procedure was found to be highly sensitive to the method of histogram construction which provides the data points for the regression. The discriminative ability of kernel density estimation was substantially different from that of the polynomial regression technique.

Effects of forest management and time on herbaceous species dynamics in the western Upper Peninsula of Michigan

The herbaceous layer is a dynamic layer in a forest ecosystem which often contains the highest species richness in northern temperate forests. Few long-term studies exist in northern hardwood forests with consistent management practices to observe herbaceous species dynamics. The Ford Forest (Michigan Technological University) reached its 50th year of management during the winter of 2008-2009. Herbaceous species were sampled during the summers pre- and post-harvest. Distinct herbaceous communities developed in the 13-cm diameter-limit treatment and the uncut control. After the harvest, the diameter-limit treatments had herbaceous communities more similar to the 13-cm diameter-limit treatment than the uncut control; the herbaceous layer contained more exotic and early successional species. Fifty years of continuous management changed the herbaceous community especially in the diameter-limit treatments. Sites used in the development of habitat classification systems based on the presence and absence of certain herbaceous species can also be used to monitor vegetation change over time. The Guide to Forest Communities and Habitat Types of Michigan was developed to aid forest managers in understanding the potential productivity of a stand, and often aid in the development of ecologically-based forest management practices. Subsets of plots used to create the Western Upper Peninsula Guide were resampled after 10 years. During the resampling, both spring and summer vegetation were sampled and earthworm populations were estimated through liquid extraction. Spring sampling observed important spring ephemerals missed during summer sampling. More exotic species were present during the summer 2010 sampling than the summer 2000 sampling. Invasive European earthworms were also observed at all sample locations in all habitat types; earthworm densities increased with increasing habitat richness. To ensure the accuracy of the guide book, plots should be monitored to see how herbaceous communities are changing. These plots also offer unique opportunities to monitor for invasive species and the effects of a changing climate.

The Effect of Heat Treatment of Forages on Degradation Kinetics and Escape Protein Concentration

An in situ study was conducted to evaluate the effects of heat treatments on the degradation kinetics and escape protein concentrations of forages (alfalfa and berseem clover). Alfalfa collected at 4 and 7 weeks post-harvest and berseem clover collected at 5 and 7 weeks postharvest were freeze-dried and then heated to 100, 125, and 150o C for 2 hours. Heat treatment effects were determined by placing two bags of sample (for each treatment, maturity, and forage species for a given incubation times) into the rumen of one fistulated steer fed alfalfa hay. Bags were incubated for periods of 0 to 48 hours. Increasing levels of heat treatments of forages increased concentrations of neutral detergent fiber (NDF), acid detergent fiber (ADF), and acid detergent insoluble nitrogen (ADIN) and non-degradable protein (NDP), potentially degradable protein proportion (PDP), and protein escaping rumen degradation (PEP) while decreasing water soluble protein (WSP) and the rates of crude protein (CP), except immature berseem clover and cell wall (CW) degradation. PEP was greater and rate of CP degradation was lower at 100 and 150o C compared to 125o C in immature berseem clover.

Entre puertos, campos y acopios : Trabajo y transporte de granos en torno al Sudeste bonaerense

En este artículo, se analiza el proceso de trabajo en el transporte automotor de granos en torno al sudeste bonaerense. Desde un abordaje cualitativo, se describen y analizan las prácticas durante la cosecha y pos-cosecha, y los trayectos campo-acopio, acopio-puerto. También se analizan las relaciones laborales a partir de una perspectiva ampliada de las relaciones laborales clásicas (asalariadas, estables, protegidas).Los rasgos que asume el trabajo en el transporte de granos están asociados a los cambios técnicos y tecnológicos de la producción de granos, así como a procesos de flexibilización laboral, vinculados a la disponibilidad permanente para fletar, la extensión de la jornada laboral y la intensidad del trabajo camionero

Entre puertos, campos y acopios : Trabajo y transporte de granos en torno al Sudeste bonaerense

En este artículo, se analiza el proceso de trabajo en el transporte automotor de granos en torno al sudeste bonaerense. Desde un abordaje cualitativo, se describen y analizan las prácticas durante la cosecha y pos-cosecha, y los trayectos campo-acopio, acopio-puerto. También se analizan las relaciones laborales a partir de una perspectiva ampliada de las relaciones laborales clásicas (asalariadas, estables, protegidas).Los rasgos que asume el trabajo en el transporte de granos están asociados a los cambios técnicos y tecnológicos de la producción de granos, así como a procesos de flexibilización laboral, vinculados a la disponibilidad permanente para fletar, la extensión de la jornada laboral y la intensidad del trabajo camionero

Entre puertos, campos y acopios : Trabajo y transporte de granos en torno al Sudeste bonaerense

En este artículo, se analiza el proceso de trabajo en el transporte automotor de granos en torno al sudeste bonaerense. Desde un abordaje cualitativo, se describen y analizan las prácticas durante la cosecha y pos-cosecha, y los trayectos campo-acopio, acopio-puerto. También se analizan las relaciones laborales a partir de una perspectiva ampliada de las relaciones laborales clásicas (asalariadas, estables, protegidas).Los rasgos que asume el trabajo en el transporte de granos están asociados a los cambios técnicos y tecnológicos de la producción de granos, así como a procesos de flexibilización laboral, vinculados a la disponibilidad permanente para fletar, la extensión de la jornada laboral y la intensidad del trabajo camionero

Entre puertos, campos y acopios : Trabajo y transporte de granos en torno al Sudeste bonaerense

En este artículo, se analiza el proceso de trabajo en el transporte automotor de granos en torno al sudeste bonaerense. Desde un abordaje cualitativo, se describen y analizan las prácticas durante la cosecha y pos-cosecha, y los trayectos campo-acopio, acopio-puerto. También se analizan las relaciones laborales a partir de una perspectiva ampliada de las relaciones laborales clásicas (asalariadas, estables, protegidas).Los rasgos que asume el trabajo en el transporte de granos están asociados a los cambios técnicos y tecnológicos de la producción de granos, así como a procesos de flexibilización laboral, vinculados a la disponibilidad permanente para fletar, la extensión de la jornada laboral y la intensidad del trabajo camionero

Physical parameters in relation to physiological changes of avocado during ripening (20ºc) and cold storage (6ºc) in different conditions.

The application of the response of fruits to low energy for mechanical impacts is described, for evaluation of post-harvest ripening of avocadoes of the variety "Hass". An impactor of 50g of weight, provided with an accelerometer, and free-falling from a height of 4 cm, is used; it is interfaced to a computer and uses a special software for retrieving and analyzing the deceleration data. Impact response parameters of individual fruits were compared to firmness of the pulp, measured by the most used method of double-plate puncture, as well as to other physical and physiological parameters: color, skin puncture ethylene production rate and others. Two groups of fruits were carefully selected, stored at 6º C (60 days) and ripened at 20ºC (11 days), and tested during the storage period. It is shown that, as in other types of fruits, impact response can be a good predictor of firmness in avocadoes, obtaining the same accuracy as with destructive firmness measurements. Mathematical and multiple regression models are calculated and compared to measured data, with which a prediction of storage period can be made for these fruits.

Sensing physical stage of fruits by their response to non destructive impacts.

Fruits of two varieties of both apples and pears were tested in the laboratory to measure their response to a small energy impact applied by an impact tester. Samples of fruits of increasing maturity were tested during several weeks. Non-destructive impacts and other destructive and non-destructive measurements of post-harvest ripeness were applied. A new software was created to control the impact test, calculate the eleven parameters, and sort out the fruit. This software needs a data base and may create new ones. The implementation of an on-line impact device for automatic detection of texture is being designed (patent pending).

Neural bruise prediction models for fruit handling and machinery evaluation.

Some neural bruise prediction models have been implemented in the laboratory, for the most traded fruit species and varieties, allowing the prediction of the acceptability or rejectability for damages, with respect to the EC Standards. Different models have been built for both quasi-static (compression) and dynamic (impact) loads covering the whole commercial ripening period of fruits. A simulation process has been developed gathering the information on laboratory bruise models and load sensor calibrations for different electronic devices (IS-100 and DEA-1, for impact and compression loads respectively). Some evaluation methodology has been designed gathering the information on the mechanical properties of fruits and the loading records of electronic devices. The evaluation system allows to determine the current stage of fruit handling process and machinery.

Controlling moisture loss as a tool to reduce bruise susceptibility.

A method to reduce the bruise susceptibility of apples by controlling the moisture loss of the fruit was evaluated. Previous research indicates that reduction of the relative humidity of the storage air leads to an immediate effect on the weight loss and on skin properties and to a lower bruise susceptibility of apples. The diffusion equation is used to determine the waterpotential profile inside the fruit during storage. Characteristics of the waterpotential distribution in the fruit are related to measured bruise volumes. The results indicate how /this model can be used to control bruise susceptibility.

Effects of chilling temperatures on ethylene binding by banana fruit

Banana fruit are highly susceptible to chilling injury during low temperature storage. Experiments were conducted to compare ethylene binding during storage at chilling (3 and 8 degreesC) versus optimum (13 degreesC) temperatures. The skins of fruit stored at 3 and 8 degreesC gradually darkened as storage duration increased. This chilling effect was reflected in increasing membrane permeability as shown by increased relative electrolyte leakage from skin tissue. In contrast, banana fruit stored for 8 days at 13 degreesC showed no chilling injury symptoms. Exposure of banana fruit to the ethylene binding inhibitor 1-methylcyclopropene (1 mul l(-1) 1-MCP) prevented ripening. However, this treatment also enhanced the chilling injury accelerated the occurrence of chilling injury-associated increased membrane permeability. C-14-ethylene release assay showed that ethylene binding by banana fruit stored at low temperature decreased with reduced storage temperature and/or prolonged storage time. Fruit exposed to 1-MCP for 12 h and then stored at 3 or 8 degreesC exhibited lower ethylene binding than those stored at 13 degreesC. Thus, chilling injury of banana fruit stored at low temperature is associated with a decrease in ethylene binding. The ability of tissue to respond to ethylene is evidently reduced, thereby resulting in failure to ripen.