Validation of DNA barcoding as an efficient tool for taxon identification and detection of species diversity in Italian conifers     

Laura Armenise  Marco C. Simeone  Roberta Piredda  Bartolomeo Schirone 《European Journal of Forest Research》2012,131(5):1337-1353

DNA barcoding may be particularly important in impacting the current trends of world’s biodiversity crisis, public economic issues and science. Forests play a crucial role in self-sustaining natural ecosystems and human environment at both local and regional scales. Over 39% of the world’s forests are formed by conifers; most species are highly exposed to threats and exploited at high frequency. Conifers have an urgent need to be identified through DNA barcodes, but received little attention up to date. The application of standard barcoding protocols appears to be hampered by a lack of consensus on the selection of markers and low rates of successful species identification. We examined whether four marker regions (trnh-psba, rbcL, rpoc1 and matK) matched conifer species taxonomy in a practical biodiversity survey of Italian forested land. Our objective was to provide a test of future in situ applications of DNA barcodes by evaluating the efficacy of species discrimination under the criteria of uniformity of methods and natural co-occurrence of the species. Twenty-five conifer species were included in a floristic study based on regional samplings. Genetic distance, similarity and phylogeny approaches were used to assess identification of taxa and species monophyly. We obtained 100% total discrimination success, with rbcL?+?trnH-psbA as the suggested two-locus barcode in terms of universality and efficacy. Consistent barcoding gaps, supported monophyly and regional patterns of diversity, were evidenced. Species requiring further investigation to be fully assessed at a broader context are indicated. We conclude that the time seems now ripe for coherent barcoding campaigns of entire forest tree regional floras.  相似文献   

Detection and phylogenetic analysis of an atypical pestivirus, strain IZSPLV_To     

Peletto S  Zuccon F  Pitti M  Gobbi E  Marco LD  Caramelli M  Masoero L  Acutis PL 《Research in veterinary science》2012,92(1):147-150

Recently, atypical bovine pestiviruses (BVDV-3) have been identified in batches of contaminated foetal calf serum (FCS) and in naturally infected cattle. During routine screening of FCS by conventional panpestivirus PCR assay, one batch showed traces of pestivirus nucleic acids, and the contaminating virus was typed as BVDV-3-like. Phylogenetic analysis based on three genome regions (5'UTR, N(pro) and E2) showed that this strain, named IZSPLV_To, clusters in a separate clade with CH_KaHo/cont, a cell culture contaminant detected in Switzerland. This study is the first report of the detection in Italy of a FCS batch contaminated with BVDV-3 and adds more evidence that atypical pestiviruses represent a serious cause for concern in cell culture laboratories, with potential repercussions on BVD control and vaccine biosafety. Our findings suggest that the BE/B2 primers may be able to detect BVDV-3 in a panpestivirus assay, but testing of a larger number of strains is required.  相似文献   

Impacts of climate change on plant diseases—opinions and trends     

Marco Pautasso  Thomas F. D?ring  Matteo Garbelotto  Lorenzo Pellis  Mike J. Jeger 《European journal of plant pathology / European Foundation for Plant Pathology》2012,133(1):295-313

There has been a remarkable scientific output on the topic of how climate change is likely to affect plant diseases. This overview addresses the need for review of this burgeoning literature by summarizing opinions of previous reviews and trends in recent studies on the impacts of climate change on plant health. Sudden Oak Death is used as an introductory case study: Californian forests could become even more susceptible to this emerging plant disease, if spring precipitations will be accompanied by warmer temperatures, although climate shifts may also affect the current synchronicity between host cambium activity and pathogen colonization rate. A summary of observed and predicted climate changes, as well as of direct effects of climate change on pathosystems, is provided. Prediction and management of climate change effects on plant health are complicated by indirect effects and the interactions with global change drivers. Uncertainty in models of plant disease development under climate change calls for a diversity of management strategies, from more participatory approaches to interdisciplinary science. Involvement of stakeholders and scientists from outside plant pathology shows the importance of trade-offs, for example in the land-sharing vs. sparing debate. Further research is needed on climate change and plant health in mountain, boreal, Mediterranean and tropical regions, with multiple climate change factors and scenarios (including our responses to it, e.g. the assisted migration of plants), in relation to endophytes, viruses and mycorrhiza, using long-term and large-scale datasets and considering various plant disease control methods.  相似文献   

Ultrafast laser-driven microlens to focus and energy-select mega-electron volt protons     

Toncian T  Borghesi M  Fuchs J  d'Humières E  Antici P  Audebert P  Brambrink E  Cecchetti CA  Pipahl A  Romagnani L  Willi O 《Science (New York, N.Y.)》2006,312(5772):410-413

We present a technique for simultaneous focusing and energy selection of high-current, mega-electron volt proton beams with the use of radial, transient electric fields (10(7) to 10(10) volts per meter) triggered on the inner walls of a hollow microcylinder by an intense subpicosecond laser pulse. Because of the transient nature of the focusing fields, the proposed method allows selection of a desired range out of the spectrum of the polyenergetic proton beam. This technique addresses current drawbacks of laser-accelerated proton beams, such as their broad spectrum and divergence at the source.  相似文献   

Decreased levels of metalloproteinase-9 and angiogenic factors in skin lesions of patients with psoriatic arthritis after therapy with anti-TNF-α     

Paola Cordiali-Fei  Elisabetta Trento  Giovanna D'Agosto  Valentina Bordignon  Anna Mussi  Marco Ardigò  Antonio Mastroianni  Antonella Vento  Francesco Solivetti  Enzo Berardesca  Fabrizio Ensoli 《Journal of Autoimmune Diseases》2006,3(1):5

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Stability of stored canine plasma for hemostasis testing     

Furlanello T  Caldin M  Stocco A  Tudone E  Tranquillo V  Lubas G  Solano-Gallego L 《Veterinary clinical pathology / American Society for Veterinary Clinical Pathology》2006,35(2):204-207

BACKGROUND: A review of the literature revealed limited information about the stability of samples for coagulation testing in dogs. OBJECTIVE: The aim of this study was to evaluate the stability of individual coagulation factors, clotting times, and other parameters of hemostasis in stored canine plasma. METHODS: Citrated plasma samples were obtained from 21 dogs. Prothrombin time (PT), activated partial thromboplastin time (aPTT), fibrinogen concentration, and factor I, II, V, VII, VIII, IX, X, XI, and XII activities were measured on an automated coagulation analyzer with commercially available reagents. Antithrombin (AT) activity and D-dimer concentration were measured on an automated chemistry analyzer using validated kits. Samples were analyzed within 1 hour after collection (initial analysis) and once daily for 2 or 4 consecutive days following storage at room temperature (RT) or 4 degrees C, respectively. RESULTS: Storage time at either temperature did not have any effect on PT, factor II, V, VII, X, or XII activities, D-dimer concentration, or AT activity. In contrast, aPTT was significantly prolonged after 72 and 96 hours at 4 degrees C; fibrinogen concentration was decreased after 48 hours at RT; the activities of factors VIII and IX were decreased after 48, 72, and 96 hours at 4 degrees C; and factor XI activity was decreased after 72 hours at 4 degrees C. CONCLUSIONS: Results suggest that storage of canine plasma for 2 days at RT does not have a significant effect on hemostasis test results with the exception of a slight decrease in fibrinogen concentration. In contrast, aPTT and factors VIII, IX, and XI were unstable in refrigerated plasma after 48 or 72 hours of storage.  相似文献   

Polymorphism of the PE domain of PE/PE_PGRS sequences in clinical isolates of Mycobacterium bovis in Mexico     

Santillan-Flores MA  Flores J  Arriaga-Diaz C  Romero-Torres C  Suárez-Güemes F  Espitia C 《Veterinary microbiology》2006,115(4):364-369

Polymorphism of the PE domain of PE/PE_PGRS sequences was studied in Mycobacterium bovis isolates from different Mexican states. Samples were analyzed by spolygotyping and RFLP using IS6110 and a 235-bp fragment of the PE domain of PE/PE_PGRS as probes. With the PE probe, three different genotypes were observed, one being predominant in all states. These results confirm the high conservation of the PE domain and suggests a potential role for PE sequence as a stable genetic marker for bovine tuberculosis.  相似文献   

Wnt gradient formation requires retromer function in Wnt-producing cells     

Coudreuse DY  Roël G  Betist MC  Destrée O  Korswagen HC 《Science (New York, N.Y.)》2006,312(5775):921-924

Wnt proteins function as morphogens that can form long-range concentration gradients to pattern developing tissues. Here, we show that the retromer, a multiprotein complex involved in intracellular protein trafficking, is required for long-range signaling of the Caenorhabditis elegans Wnt ortholog EGL-20. The retromer functions in EGL-20-producing cells to allow the formation of an EGL-20 gradient along the anteroposterior axis. This function is evolutionarily conserved, because Wnt target gene expression is also impaired in the absence of the retromer complex in vertebrates. These results demonstrate that the ability of Wnt to regulate long-range patterning events is dependent on a critical and conserved function of the retromer complex within Wnt-producing cells.  相似文献   

Antioxidant composition in cherry and high-pigment tomato cultivars     

Lenucci MS  Cadinu D  Taurino M  Piro G  Dalessandro G 《Journal of agricultural and food chemistry》2006,54(7):2606-2613

Fourteen cultivars of cherry tomatoes and four cultivars of high-pigment tomato hybrids were cultivated in southern Italy, and the red-ripe fruits were analyzed for their content in different classes of antioxidants and for their antioxidant activity. Among the different cultivars, significant differences were found between lycopene, beta-carotene, alpha-tocopherol, vitamin C (ascorbic acid and dehydroascorbic acid), and total phenolic and flavonoid contents. LS203 and Corbus appear to be the cultivars with the highest content of lipophilic and hydrophilic antioxidants among cherry tomatoes, respectively. All cultivars of high-pigment tomato hybrids showed an expected exceptionally high lycopene content. Among them, the highest content of lipophilic and hydrophilic antioxidants was found in cv. HLY 13. Hydrophilic and lipophilic antioxidant activities were both significantly influenced by genotype. Such results highlight an existing unexploited variability in tomato germplasm and stress the need to evaluate the biodiversity and to support conventional breeding programs to improve tomato nutritional value.  相似文献   

Chemometrical characterization of four italian rice varieties based on genetic and chemical analyses     

Brandolini V  Coïsson JD  Tedeschi P  Barile D  Cereti E  Maietti A  Vecchiati G  Martelli A  Arlorio M 《Journal of agricultural and food chemistry》2006,54(26):9985-9991

This paper describes a method for achieving qualitative identification of four rice varieties from two different Italian regions. To estimate the presence of genetic diversity among the four rice varieties, we used polymerase chain reaction-randomly amplified polymorphic DNA (PCR-RAPD) markers, and to elucidate whether a relationship exists between the ground and the specific characteristics of the product, we studied proximate composition, fatty acid composition, mineral content, and total antioxidant capacity. Using principal component analysis on genomic and compositional data, we were able to classify rice samples according to their variety and their district of production. This work also examined the discrimination ability of different parameters. It was found that genomic data give the best discrimination based on varieties, indicating that RAPD assays could be useful in discriminating among closely related species, while compositional analyses do not depend on the genetic characters only but are related to the production area.  相似文献