Rita vignani pdf

Characterization of the different enzymes and their differential expression in normal and tumor cells will help to clarify their cellular functions and their significance to human cancer. Clear differences in the occurrence of the various enzyme forms in normal and tumor cells have been demonstrated and variations between different tumors appear to be linked to their degree of resistance to alkylating cytostatic drugs.

Modulation of catalytic activities in vitro by administration of enzyme inhibitors may help to overcome this resistance. The effect of methyl mercury on cytoskeleton and glutathion-dependent enzymes of CHO cultured cells more. Antinuclear human autoantibodies as markers in Nicotiana tabacum pollen tubes.

Plant Biology. A strain grows on endogenous carbon of deteriorated fresco fragments Santissima Annunziata, Siena producing a biofilm on the surface more. A TEM micrograph A TEM micrograph showing adhesion of strain S. Conclusions A major difficulty of this study was the small weight of samples.

In situ techniques were therefore useful, because they only require small amounts of material. Areas A and B showed the highest total sulphur concentrations. Site A was the most damaged and had the highest total carbon content. Transparency as regards the origin of foodstuffs is now considered an important component of quality and safety, as perceived by consumers. DNA analysis represents one of the most advantageous methods for monitoring products throughout DNA analysis represents one of the most advantageous methods for monitoring products throughout the entire production chain.

It is precisely for this reason that a method of molecular traceability for the Cinta Senese meat and by-products has been developed that enables the creation of a specific genetic profile for each animal.

The possibility of combining a kind of analytical traceability with a documentary one for Cinta Senese meat and its by-products, either butchered or processed, would guarantee an added value to the product to the advantage of not only consumers but also of producers and meat processors if they should decide to adopt this as a form of voluntary certification. Publication Name: Advances in Horticultural Science.

Vitis Vinifera and Horticultural Science. Study of polymorphism some native varietes of sistan grape using molecular marker RAPD more. RAPD Marker was used in order to study the genetic variations and assessment of the characters of the grape fruit on the molecular level. For this research 6 genotypes related to the different areas of season were assessed by 50 primers For this research 6 genotypes related to the different areas of season were assessed by 50 primers.

Out of these 50 primers which were tested on the genetic DNA, 21 primers were selected for the genetic analysis. Selected primers produced evident bands. Resulted proliferations lead to the formation of bands ranging in size from base pairs. To draw the dendogram of the genetic distances of the characters with the help of analysis of clusters were classified in 4 principle groups in which Red Yaghooti and White Yaghooti had the maximum similarity and Red Yaghooti and Lal had the minimum.

Considerations multishape bands , efficiency of RAPD marker for the class Genotyping and Food sciences and nutrition. Preliminary communication about the identification of DNA in leaves and in olive oil of Olea europaea more. Horticultural Science. Genetic characterization of Durella found in Lunigiana area assisted by molecular markers [Vitis vinifera L. Male-sterile mutation alters Z: ea m 1l accumulation in more. The limitations of this approach, combined with the known phenotypic variability within a cultivar, allow the possibility that some variants may erroneously be included in a cultivar, as has been recently suggested by Silvestroni et al.

The efficacy of DNA polymorphism analysis for the resolution of identification questions in grapes has been demonstrated Bowers et al. By RFLP analysis, the DNA profiles of several wine grapes grown in California under local names were shown to be identical to those of European grapes thought to be synonymous.

As robust as the RFLP method is, it is slow and laborious and DNA probes must be physically exchanged if laboratories are to compare results or coordinate investigations.

Furthermore, results are difficult to quantify and must typically be communicated as images of band patterns. The analysis of length polymorphisms at microsatellite simple sequence repeat, SSR loci offers significant advantages.

This PCR-based approach is not only faster and easier, but collaborating laboratories need only communicate primer sequences and allele lengths in order to share both methodology and results.

Dinucleotide repeats are abundant in the grape genome Thomas et al. Intrieri and Prof. The clone names are registered Italian designations as described in Moretti Total DNA was extracted from young leaves and shoot tips by a modification of the method reported in Mulcahy et al. DNA was quantified either by visual comparison with lambda DNA on ethidium bromide stained agarose gels or by fluorometry. Per amplification of microsatellite loci DNA from each sample was diluted to a final concentration of 2.

Each reaction was overlaid with one drop of mineral oil. The amplifications were carried out with a Perkin-Elmer Cents Model thermal cycler. Vignani et ai. The size of each allele was estimated by visual comparison to a standard sequencing reaction Ml3 forward primer on pGEM. Results and discussion The results are summarized in Table 2. Eleven of the clones were identical at all seven loci. At these four loci, the 11 identical clones were heterozygous and, at each locus, SG 8T shared one of the two alleles.

The sizes of the distinctive alleles of SG 8T were not determined. Our findings are also consistent with those of Silvestroni et al. As a consequence of somatic mutation, some genetic variation is to be expected within ancient grape cultivars that originate from a single seedling.

Thus an occasional Table 2 Analysis of 12 Sangiovese clones at seven microsatellite loci. VVS4, B. VVMD6, C.

VVMD7, D. Montalcino 42, AP SG 1. DNA difference might normally be detected between clones, but differences between SG 8T and the other 11 clones at four of the seven microsatellite loci analyzed in this study, and in our RFLP study, argue strongly that SG 8T did not originate from the same seedling as the others.

If one imposes a strict definition of cultivar i. However, our finding that SG 8T shares with the other 11 clones one allele at each of the four polymorphic loci and both alleles at the other three loci i. Rives, and which is commonly held in the grape research community. Microsatellite analysis clearly offers the potential for resolving this interesting question. The fact that the 11 homogeneous clones in our study were identical at all seven microsatellite loci studied as well as the RFLP loci from our earlier study argues strongly for a monoclonal origin for these clones.

An quantitative estimate of the probability that two different genotypes, whether of independent origin or genetically related, would share the same alleles at all seven loci cannot be made until a sufficiently large and genetically broad database of microsatellite alleles has been established. This may be due to an instrument failure, lack of amplification reaction or low DNA concentration in the mixture.

Low DNA concentration or the presence of contaminants such as proteins or DNA residues, may still give a very noisy signal making it difficult for the software to catch up. Instead, a large amount of DNA and primers in the reactions, such as in the plant varietal references, generates numerous fragments, which in turn gives rise to a very high signal but still interpretable by the software for the presence of an internal standard. However, an excessive amount of DNA would hinder electrophoresis in the capillaries, resulting in a shift of the peaks.

This phenomenon may render the direct comparison of WDF and possible candidate varietal references difficult, especially in blended wines where more than a single variety contributes to the DNA admixture. The alleles composing the wine and grapevine respective genetic profiles derive from validation of observed alleles in both technical replicas from 3 to 6, depending on the wine complexity and multiple experiments.

The SSR allele size is obtained using plant references as internal calibrators in each experiment and the interpretation of WDF and plant profiles takes into account the most recurrent values of allele size. Therefore, it is highly recommended to strictly follow an established protocol which includes the systematic use of technical replicas of wines and of plant references, and an accurate phase of data interpretation and genotyping assignment, when possible supervised by an external party skilled at genotyping.

Concerning the choice of the marker type to be used in WDF, there are several options that can be undertaken. Currently, there are technical limitations for using SNPs for wine varietal diagnosis, especially related to the relatively high quantity of template DNA required for carrying out the analysis, which is not compatible with the average quantity of grapevine DNA extractable from wines. An interesting approach that permits by-passing PCR and labeling of probes consists in the use of bio-sensors [ 29 ].

This method is very sensitive and is promising for fast varietal determination, but the diagnostic capability is focused on specific sets of cultivars where the target genes have been re-sequenced in a restricted panel of varieties. The use of SSR-based genotyping guarantees a universality trait, in the sense that any variety can be detected in a wine once the profile is known. General issues on wine varietal identification pose a question regarding the integration of multiple analytical approaches chemical profiling, molecular profiling.

It is feasible that molecular-based techniques for food and wine authenticity assessment will be extended and implemented in the light of new bioinformatics and genomics knowledge, applicable in the near future to the grapevine. In a market characterized by growing competitiveness and ever-expanding borders it is necessary to inspire a positive interest in wine. Consumers are increasingly attracted and influenced by a number of attributes that affect product value, such as guarantees declared on labels like DOC and DOCG, product name, genuineness, and transparency.

The phenomenon of counterfeiting and adulteration are dangerous to both producer reputation and human health. Technological analysis is a tool that allows producers to protect their wine and strengthens their relationship with consumers. For this reason, anti-counterfeiting technologies are increasing as effective and incontrovertible strategic tools for protecting wine lovers.

However, in a globalized market analytical traceability is still only voluntarily adopted. Controls are not regularly undertaken on imported wines or on national products. Therefore, the systemic introduction of analytical methods for assessing wine genuineness before market delivery seems essential. Identifying the predominant variety in a blend helps to understand if the wine was produced according to local and national regulations.

Here we would like to contextualise our work within a general framework for assessing a wine. In other words, our bioinformatics approach needs to be seen as part of a roadmap towards integrative nucleic acids, metabolites, chemicals, cultural, etc.

How to draw this roadmap? The statistical methodologies inspired by bioinformatics used in this paper demonstrate how there are common tools shared between WDF elaborations and methods based on algorithms known for phylogenies reconstruction and statistical clustering.

There are multiple bioinformatics and statistical analysis of data that may apply to the wine case. The Neighbor-Joining associated to statistical hierarchical clustering estimating the confidence intervals were the most suitable tools in our hands for depicting the varietal nature of the wines by WDF. It should also be noticed that the power of the analysis will be improved at the increasing of wine ontology and genetic databases. Productive data utilization in wine quality assessment brings evidence-based inference into play.

Consequently, systems-integrated data put the focus on methodological instruments to be considered in this work as Evidence Synthesis. Signals may be referred to patterns based on Multiparameter Evidence Synthesis. Models for potentially biased evidence in meta-analysis use empirically-based priors to build a coherent and flexible analytical framework that accommodates a disparate body of chemical and bioinformatics evidence available regarding admixture and prevalence estimation.

Data integration and evidence synthesis could be generated by using methods such as Decision trees and Random Forests. Decision trees are commonly used in disease classification and prediction of knowledge discovery in medical field [ 64 ]; it graphically illustrates its final output in a tree based model which does not require detailed explanation for data scientist or clinicians. It is widely used in modelling and prediction as it encompasses many advantages [ 65 ].

Moreover, RF classifier can be modelled for both continuous and categorical variables and also handle missing values. Another meaningful way to combine chemical composition and bioinformatics is to use a multilayer network [ 66 ] which provides a meaningful description of both social, nutritional and metabolic networks [ 67 ].

Following [ 68 , 69 , 70 , 71 ], a multilayer network M is a family of graphs that can be directed, undirected, weighted or unweighted and defines the layers of M for example one layer could represent the nucleic acids information, another layer the chemicals ; there is a set of interlayer connections between nodes of different layers.

Taking into account the previous assumptions and descriptions, the matrix M could be written as:. In a single-layered-network with unweighted edges a useful property is that the number of walks of length k between the nodes p and q is given by the p,q-entry of the kth power of the adjacency matrix of the network.

In a multiplex network formed of unweighted graphs it follows that the walks of length k in the multiplex are given by entries of M k. The strength of interaction between each data type can be modeled by a weight, connecting each layer in the multiplex. In each layer, each node has a weighted, undirected edge connecting it to every other node in the same layer.

In addition, each wine is connected to itself in every other layer by the strength of interaction between the data types. In this case, we consider that the strength of interaction is undirected and symmetric, i.

Since the weight between nodes is a measure of similarity or information shared between the nodes, it follows that the weight of the path provides a measure of information flowing through the path. There are a number of ways we can provide a new measure of similarity between two nodes given the properties of the multiplex network.

One way would be to take a mean of the direct paths connecting each wine to and from another wine in each and every layer. In many situations, a pair of nodes in a network does not communicate only through the shortest-path routes connecting both nodes, but also through all possible routes connecting both nodes. The number of these possible routes can be enormous. Moreover, the information can also go back and forth before connecting the pair of nodes.

In multiplex networks, a communicability metric between two nodes p and q, is a weighted sum of all walks from p to q This leads to derive the relationships of the communicability between each pair of nodes.

Finally, our model could be visualized in the following way as in Fig 9. The edge weights between nodes represent a measure of similarity between nodes in the same layer, normalized between zero and one. We wish to use the multiplex model to predict the response of a new wine given knowledge of other wines. Therefore, given the data of a set of wines with known response we want our aggregate network to match the response network as closely as possible, i. Aggregate clustering from all the layers could be considered.

See [ 66 ] for further mathematical details. Given that the bioinformatics elaboration of WDFs complies with the need of verifying the varietal nature of a wine, it can be assumed that the DNA analysis carried out in the wine is somehow related to its chronological age; and together with multiple integrated input data, expresses information on the biological age of wine.

Even if the chemical and physical status of DNA in wine is not well studied, one can suppose, based on what is described in other fields of study, that the average age of wines is not at risk of genetic information loss. In fact, it is reported by palaeogeneticist that DNA has a year half-life and that it would cease to be readable after roughly 1. In spite of the developments made in wine DNA profiling some may believe that grapevine DNA recovered in an aqueous phase, such as wine, will have no forensic value; and therefore argue against the reliability of DNA analysis for wine varietal ascertainment.

Recent forensic work demonstrates how the latent DNA fingerprint can be recovered even from saline seawater, and that the reliability of the test depends very much on specific environmental conditions [ 72 ]. It is reasonable to suppose that in the alcoholic wine environment total DNA, including the minority deriving from the grapevine, may be able to survive at least several years. It is therefore not to be excluded that DNA analysis will comply with legal issues of wine composition in the future, and in special cases e.

In agreement with increasing sensitiveness toward the natural equilibrium of planet and ecosystem preservation, and in light of embracing a cruelty-free philosophy, lab-grown food is progressively expanding in research centers and a near, future market [ 73 ].

In the future the development of integrated and advanced bioinformatics and molecular analytical tools may render immediate detection of natural wines against "synthetic" ones based on DNA detection of DNA residue in the bottle. In addition, thanks to the wide genomic knowledge of the Vitis genus family members, the wine molecular recognition databanks will progressively expand, allowing for the classification of large sets of wine types.

The bioinformatics applied to DNA analysis in wine reveals to be an effective tool, confirming the reliability of DNA analysis for wine varietal assessment that must comply to legal requisites concerning wine production and commercialization.

Data presented here can be implemented by multidisciplinary inputs Fig 10 deriving from progresses in the molecular, genomics, metabolomics, historical and cultural fields concerning the wine world, leading to future integration of portals existing on the web dedicated the wine ontology [ 74 ]. Bioinformatics is a common, essential tool for the validation of multiple, analytical approaches to wine authentication. Molecular, chemical, and metabolomic profiling merge into a comprehensive wine ontology databank fed by bioinformatics tools [ 75 ] Fig We believe that the discussion of the results should be coupled with well grounded considerations of how dry-lab methodologies could transform the field towards elucidation of actionable target markers.

Our vision is that the biomolecular analysis applied to wine varietal diagnosis can be seen as the first proof of a wider wine quality concept; indexing the biological age of wine which is the result of multiple complex biotic and abiotic molecular interactions, more than mere physical timing measured in years.

Multidimensional networking among the main features influencing a wine. Wine traits DNA profile, metabolomic and chemical profiling are in turn interconnected to personal tastes and general environmental factors e.

Bioinformatics elaborates multilayer input data contributing to wine ontology fed by semantic web languages. According to a new wine ontology model based on a bioinformatics elaboration of multidimensional wine traits, a scientific unambiguous labeling of wine can be obtained. Bioinformatics is a common, essential tool for the validation of multiple, analytical approaches to wine authentication: molecular, chemical, metabolomic profiling, which merge into a comprehensive wine ontology databank fed by bioinformatic tools.

Electropherograms of commercial and experimental wines show alleles correspondence between wine and respective reference grapevines. The present work was co-funded by multiple public and private Entities and wine producers, depending on the wine type. We are grateful to the Amministrazione Provinciale di Siena, Italy and to the Consorzio della Denominazione San Gimignano for their support and participation in the study.

The Serge-genomics company contributed to the present work by supplying research materials, only. Serge-genomics did not have any additional role in the study design, data collection and analysis, decision to publish or preparation of the manuscript. National Center for Biotechnology Information , U. PLoS One. Published online Feb Walter Chitarra, Editor.

Author information Article notes Copyright and License information Disclaimer. Received Sep 21; Accepted Jan This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

This article has been cited by other articles in PMC. Sangiovese SSR allelic profiles merged into a single data set. Varietal white wines SSR allelic profiles merged into a single data set.

Varietal red wines SSR allelic profiles merged into a single data set. Abstract The varietal authentication of wines is fundamental for assessing wine quality, and it is part of its compositional profiling.

Introduction In the last few years the quality and safety of food products has become an essential requirement guaranteed to consumers in all fields of agricultural production. Open in a separate window. Fig 1. Materials and methods Wines and grapevine references The eighteen samples, either experimental or commercial wines used for bioinformatics elaboration of the genetic profiles, are listed in Table 1.

Table 1 Wines list. Methods from bioinformatics, statistics and machine learning for wine admixture analysis, data interpretation and decision support system There are various bioinformatics, statistical and machine learning methods to analyze molecular, biochemical and sensory wine data. A broad list includes: Clustering methods This class of methods inputs vector data for calculating different distance matrices. Results DNA extraction from wines The quality of total DNA extracted from wines was evaluated on the basis of SSR amplification efficiency so as to have at least 7 nuclear markers to be correctly amplified.

Statistical analysis inspired by bioinformatics on wine DNA fingerprints The algorithm used to construct genetic distance trees, specific for the analysis of microsatellite loci, takes into account not only the distance between two individuals but also the distance between an individual and all the others, thus reconstructing a distance report.

Fig 2. Graphical representation of the Sangiovese-based WDFs. Fig 3. Fig 4. Fig 5. Fig 6. Consistency of WDF testing over time. Towards an integrated informative wine profiling databank system Multiple data was merged in single files in order to check the consistency and reliability of genetic data analysis in the optic of creating an integrated, informative system organized in on-line databanks for wine profiling that includes genetic, metabolomic and historical descriptions of the wines.

Fig 7. Clustering of Sangiovese-based wines. Fig 8. Clustering of US wines. Discussion WDF technique: Advantages and drawbacks Point-of-care technology demand along the wine making chain in the food industry in general focuses on rapid, low-cost and reliable analytical methodologies. DNA stability in wine From the molecular biology point of view wine is a difficult system to deal with due the complexity of the chemical environment and the great variability in terms of biological origin, technological processes and ageing which characterize the many kinds of wine worldwide.

Wine DNA quantification issue Since roughly there has been an increasing interest in developing molecular diagnostic tools for wine varietal characterization primarily based on the use of molecular markers. Capillary electrophoresis troubleshooting for allele sizing validation Allele sizing and subsequent validation of the observed genotypes can be complicated by electrophoretic technical issues.

DNA testing and analytical traceability in wines and diagnostic markers Concerning the choice of the marker type to be used in WDF, there are several options that can be undertaken. Perspective: Towards a decision support system for wine authentication Here we would like to contextualise our work within a general framework for assessing a wine. Fig 9. Method of aggregating different layers using regression or clustering approaches.

Wine forensics and wine age prediction Given that the bioinformatics elaboration of WDFs complies with the need of verifying the varietal nature of a wine, it can be assumed that the DNA analysis carried out in the wine is somehow related to its chronological age; and together with multiple integrated input data, expresses information on the biological age of wine.

Bioinformatics, WDF and synthetic wines In agreement with increasing sensitiveness toward the natural equilibrium of planet and ecosystem preservation, and in light of embracing a cruelty-free philosophy, lab-grown food is progressively expanding in research centers and a near, future market [ 73 ].

Conclusions The bioinformatics applied to DNA analysis in wine reveals to be an effective tool, confirming the reliability of DNA analysis for wine varietal assessment that must comply to legal requisites concerning wine production and commercialization. Fig Interdependent informative inputs and data networking for wine ontology implementation.

Towards a new wine ontology databank system. PDF Click here for additional data file. Funding Statement The present work was co-funded by multiple public and private Entities and wine producers, depending on the wine type.

Data Availability The data are all contained within the manuscript and Supporting Information files.