SPPADBASE: the first on-line searchable database of PCR primers for phytopathogenic fungi

The fast and unambiguous identification of microbial pathogens affecting plants or plant products is an essential prerequisite for obtaining high-quality and safe production. Ecologically friendly practice of the modern agriculture requires the adoption of diagnostic techniques able to detect minimum inoculum levels of pathogens in soil, seeds, transplants or crops, to limit the raise of epidemics and to address the adoption of rational and efficient control means. Moreover, there is an increasing public and official awareness of the potential threat of bio-terrorism directed against food and agriculture (Monke, 2004). Rapid detection techniques for bioweapon agents are a critical need for the first-responder community. Among the nucleic acid-based diagnostic techniques, those involving the Polymerase Chain Reaction (PCR; Mullis and Faloona, 1987) are the most suited for early detection of phytopathogenic agents, due to their high sensitivity and the potential for automation. Many sequence source types could be selected and used as target for specific primer design. These may include, for instance, Random Amplified Polymorphic DNAs (Williams et al., 1990; Welsh and McClelland, 1990), internal transcribed spacer (ITS) regions of the ribosomal RNA genes (White et al., 1990) or other specific gene sequences. Primer sets can be designed to target specificity at the genus, species, or physiological race level, to distinguish a particular pathogen from closely related organisms. A common and tedious task for researchers and technicians is to search for and retrieve bibliographic references of published and validated specific primer sets for a given pathogen querying the Internet, abstract collections and monthly journals’ tables of contents. Very few examples of specific primer set collections for phytopathogenic agents have been released: a summary of primers for the diagnostic characterization of phytopathogenic bacteria seems to be the only one printed so far (Louws et al., 1999). Moreover, among 719 molecular biology databases publicly available recorded by Galperin (2006) or among the 2470 BMC biomedical databases catalog available at http://databases.biomedcentral.com/, no online repository of primer sets of this kind is accessible. To overcome this lack of information, we released the first online searchable database of primer sets useful for the detection and identification of plant pathogenic fungi

Pyrosequencing analysis of fungal assemblages from geographically distant, disparate soils reveals spatial patterning and a core mycobiome

Identifying a soil core microbiome is crucial to appreciate the established microbial consortium, which is not usually subjected to change and, hence, possibly resistant/resilient to disturbances and a varying soil context. Fungi are a major part of soil biodiversity, yet the mechanisms driving their large-scale ecological ranges and distribution are poorly understood. The degree of fungal community overlap among 16 soil samples from distinct ecosystems and distant geographic localities (truffle grounds, a Mediterranean agro-silvo-pastoral system, serpentine substrates and a contaminated industrial area) was assessed by examining the distribution of fungal ITS1 and ITS2 sequences in a dataset of 454 libraries. ITS1 and ITS2 sequences were assigned to 1,660 and 1,393 Operational Taxonomic Units (OTUs; as defined by 97% sequence similarity), respectively. Fungal beta-diversity was found to be spatially autocorrelated. At the level of individual OTUs, eight ITS1 and seven ITS2 OTUs were found in all soil sample groups. These ubiquitous taxa comprised generalist fungi with oligotrophic and chitinolytic abilities, suggesting that a stable core of fungi across the complex soil fungal assemblages is either endowed with the capacity of sustained development in the nutrient-poor soil conditions or with the ability to exploit organic resources (such as chitin) universally distributed in soils

At the nexus of three kingdoms: the genome of the mycorrhizal fungus Gigaspora margarita provides insights into plant, endobacterial and fungal interactions.

As members of the plant microbiota, arbuscular mycorrhizal fungi (AMF, Glomeromycotina) symbiotically colonize plant roots. AMF also possess their own microbiota, hosting some uncultivable endobacteria. Ongoing research has revealed the genetics underlying plant responses to colonization by AMF, but the fungal side of the relationship remains in the dark. Here, we sequenced the genome of Gigaspora margarita, a member of the Gigasporaceae in an early diverging group of the Glomeromycotina. In contrast to other AMF, G. margarita may host distinct endobacterial populations and possesses the largest fungal genome so far annotated (773.104 Mbp), with more than 64% transposable elements. Other unique traits of the G. margarita genome include the expansion of genes for inorganic phosphate metabolism, the presence of genes for production of secondary metabolites and a considerable number of potential horizontal gene transfer events. The sequencing of G. margarita genome reveals the importance of its immune system, shedding light on the evolutionary pathways that allowed early diverging fungi to interact with both plants and bacteria

Identification of Fusarium oxysporum f. sp. basilici isolated from soil, basil seed, and plants by RAPD analysis

Fifty-two isolates of Fusarium oxysporum, obtained from infected basil plants, seed, flower residues, and soil from different growing areas in Italy and Israel, were analyzed by random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR), coupled to a DNA extraction protocol from colonies grown on Fusarium-selective medium. In a pathogenicity assay, 35 isolates caused 32 to 92% disease on seedlings of the highly susceptible basil cultivar Fine verde, while 17 isolates were nonpathogenic on basil. Thirty of the F. oxysporum f. sp. basilici isolates obtained from soil or wilted plants gave identical amplification patterns using 31 different random primers. All tested primers allowed clear differentiation of F. oxysporum f. sp. basilici from representatives of other formae speciales and from nonpathogenic strains of F. oxysporum. RAPD profiles obtained from DNA of isolates extracted directly from cultures grown on Fusarium selective medium were identical to those obtained from DNA extracted from lyophilized myceli

SPPADBASE: the first on-line searchable database of PCR primers for phytopathogenic fungi

The fast and unambiguous identification of microbial pathogens affecting plants or plant products is an essential prerequisite for obtaining high-quality and safe production. Ecologically friendly practice of the modern agriculture requires the adoption of diagnostic techniques able to detect minimum inoculum levels of pathogens in soil, seeds, transplants or crops, to limit the raise of epidemics and to address the adoption of rational and efficient control means. Moreover, there is an increasing public and official awareness of the potential threat of bio-terrorism directed against food and agriculture (Monke, 2004). Rapid detection techniques for bioweapon agents are a critical need for the first-responder community. Among the nucleic acid-based diagnostic techniques, those involving the Polymerase Chain Reaction (PCR; Mullis and Faloona, 1987) are the most suited for early detection of phytopathogenic agents, due to their high sensitivity and the potential for automation. Many sequence source types could be selected and used as target for specific primer design. These may include, for instance, Random Amplified Polymorphic DNAs (Williams et al., 1990; Welsh and McClelland, 1990), internal transcribed spacer (ITS) regions of the ribosomal RNA genes (White et al., 1990) or other specific gene sequences. Primer sets can be designed to target specificity at the genus, species, or physiological race level, to distinguish a particular pathogen from closely related organisms. A common and tedious task for researchers and technicians is to search for and retrieve bibliographic references of published and validated specific primer sets for a given pathogen querying the Internet, abstract collections and monthly journals’ tables of contents. Very few examples of specific primer set collections for phytopathogenic agents have been released: a summary of primers for the diagnostic characterization of phytopathogenic bacteria seems to be the only one printed so far (Louws et al., 1999). Moreover, among 719 molecular biology databases publicly available recorded by Galperin (2006) or among the 2470 BMC biomedical databases catalog available at http://databases.biomedcentral.com/, no online repository of primer sets of this kind is accessible. To overcome this lack of information, we released the first online searchable database of primer sets useful for the detection and identification of plant pathogenic fungi

A dehydration-inducible gene in the truffle Tuber borchii identifies a novel group of dehydrins

BACKGROUND: The expressed sequence tag M6G10 was originally isolated from a screening for differentially expressed transcripts during the reproductive stage of the white truffle Tuber borchii. mRNA levels for M6G10 increased dramatically during fruiting body maturation compared to the vegetative mycelial stage. RESULTS: Bioinformatics tools, phylogenetic analysis and expression studies were used to support the hypothesis that this sequence, named TbDHN1, is the first dehydrin (DHN)-like coding gene isolated in fungi. Homologs of this gene, all defined as "coding for hypothetical proteins" in public databases, were exclusively found in ascomycetous fungi and in plants. Although complete (or almost complete) fungal genomes and EST collections of some Basidiomycota and Glomeromycota are already available, DHN-like proteins appear to be represented only in Ascomycota. A new and previously uncharacterized conserved signature pattern was identified and proposed to Uniprot database as the main distinguishing feature of this new group of DHNs. Expression studies provide experimental evidence of a transcript induction of TbDHN1 during cellular dehydration. CONCLUSION: Expression pattern and sequence similarities to known plant DHNs indicate that TbDHN1 is the first characterized DHN-like protein in fungi. The high similarity of TbDHN1 with homolog coding sequences implies the existence of a novel fungal/plant group of LEA Class II proteins characterized by a previously undescribed signature pattern

Le auto-osservazioni nell'ambito della behavior based safety

LAUREA SPECIALISTICAIl raggiungimento dell’obiettivo “zero infortuni” è ormai un traguardo che molte aziende si sono poste e che cercano di raggiungere attraverso l’implementazione di diversi metodi per migliorare la sicurezza aziendale (intesa come sicurezza di macchine, impianti, ambienti, ecc.). Oggi, anche in Italia, si sta sviluppando sempre di più la consapevolezza che molti infortuni sono la conseguenza di comportamenti a rischio adottati dai lavoratori e quindi oltre ad agire su macchine/impianti e attrezzature di lavoro, è sempre maggiore la consapevolezza del ruolo cardine che il comportamento del singolo assume nella dinamica degli eventi incidentali. Agire a seguito di un infortunio, che, di fatto, non è altro che il risultato ottenuto a valle di un comportamento non sicuro, poco influisce in termini di prevenzione. È quindi evidente l’importanza di trovare un modo per agire direttamente sui comportamenti non sicuri prima che questi vengano esibiti. In campo internazionale sono disponibili moltissime prove di efficacia del protocollo di sicurezza comportamentale denominato Behavior-Based Safety, studi scientifici che dimostrano che questo è l’unico metodo effettivamente capace di agire sui comportamenti non sicuri, in modo da modificarli in comportamenti sicuri. Questo è il motivo del grande successo internazionale del protocollo e la ragione per cui numerose aziende all’estero e in Italia l’hanno adottato e continuano ad adottarlo. In questo lavoro di tesi verranno analizzati e discussi i risultati ottenuti nel corso dell’implementazione di un processo di Behavior-Based Safety nello stabilimento di Comun Nuovo (BG) della Heineken durante il quale, nell’ambito dell’observation process previsto dal protocollo B-BS, si è voluto verificare quanto presente in letteratura.1 con riferimento alla veridicità ed efficacia del processo di osservazione basato su auto-osservazione (il lavoratore osserva solo se stesso prima di compilare la checklist) rispetto alla etero - osservazione (un osservatore osserva se stesso e gli altri prima di compilare la checklist) solitamente prevista nei processi di B-BS. Questa modalità di effettuazione delle osservazioni, è stata scelta tenendo conto che la realtà aziendale in esame è caratterizzata da molte lavorazioni che vengono eseguite in solitario dagli operatori, oppure sono tali per cui, essendo condotte in ambienti molto estesi, spesso i lavoratori riescono ad osservare solo il proprio comportamento. Questo lavoro di tesi è strutturato in nove capitoli nell’ambito dei quali, dopo aver illustrato il quadro generale dell’andamento del fenomeno infortunistico europeo e la normativa nazionale in materia di salute e sicurezza nei luoghi di lavoro, verrà esaminata l’origine comportamentale degli infortuni e quali sono le modalità per poter modificare i comportamenti non sicuri mediante l’applicazione del protocollo di B-BS. Successivamente verranno descritte le fasi operative dell’implementazione del processo di sicurezza comportamentale, così come applicato in una realtà aziendale, e verranno analizzati i risultati ottenuti paragonandoli a quelli riportati in letteratura per applicazioni analoghe.I dati raccolti dagli osservatori (auto-osservazioni) e quelli delle osservazioni effettuate dalla scrivente (etero - osservazioni), sono stati confrontati utilizzando il test statistico z basato su due frequenze al fine di valutare la concordanza dei risultati nei due casi. I risultati dell’analisi statistica hanno dimostrato la sostanziale concordanza dei dati e quindi la veridicità delle auto-osservazioni.Come più volte affermato in letteratura, si è dimostrato che le auto-osservazioni effettuate dagli operatori sono idonee a rappresentare l’effettiva percentuale dei comportamenti di sicurezza e quindi, implicitamente, anche il più generale livello di sicurezza delle attività operativeThe reaching aim “zero accident” is by now a goal that many firms have followed and that they try to reach with the implementation of different methods to improve the firm safety (safety of machines, installation, surrounding, etc.). Nowadays also in Italy the awareness that many accidents are the consequence of risk behaviours adopted by workers are developing. So, besides operating on machines/installation and working equipment, it’s more and more important the consciousness that the behaviour of the single has in the dynamics of the incidental events. Acting after an accident, that is the result obtained after a no safe behaviour, influences a bit in prevention terms. For this reason it’s important to find a way to act directly on no safe behaviours before they are made. In the international field many proofs are available about the efficacy of the behaviour safety protocol named Behavior-Based Safety, scientific studies show that is the only method which is really able to act on no safe behaviours in order to transform them into safe behaviours. This is the reason of the international great success of the protocol and the reason of the why several firms abroad and in Italy have adopted it and keep on adopting. In this work of thesis the results obtained during the implantation process of B-BS in the firm of ComunNuovo (BG) “Heineken” will be analysed and discussed. During the observation process estimated by the protocol B-BS what is present in literature referring in the veracity and the efficacy of the observation process based an auto-observation (the worker observes only himself before filling the checklist) are usually expected in the B-BS processing. This method of observation execution has been chosen considering that the firm reality in exam in characterized by many processing that are made in solitary by operators, or as they are made in very large surroundings, the workers can only observe their behaviour. This work of thesis is structured in nine chapters. After illustrating the general frame of the European industrial accident research phenomenon and the national regulations about health and safety in working places, the behavioural origin of the accidents will be examined. Also the modalities to be able to modify the no-safe behaviours with the application of the B-BS protocol will be studied. Then the operative stages of the behavioural safety processing implementation will be described as applied in a firm realty. The obtained results will be analysed comparing them with the ones written in literature for similar applications. The data taken by the observers (auto-observations) and the ones of the observations made by the writer (ethero-observations) have been compared using the statistic test z based on two frequencies in order to estimate the accordance of the results in the two cases. The results of the statistic analysis have demonstrated the substantial accordance of the data and so the veracity of the auto-observations. As confirmed many times in literature, the auto-observation made by the operators are suitable to represent the effective percentage of safety behaviours and, implicitly, also the most general safety level of the operative activities