Evaluation of a PCR kit for the detection ofErwinia carotovora subsp.atroseptica on potato tubers

Summary A PCR-based kit, Probelia^TM, for the detection ofErwinia carotovora subsp.atroseptica (Eca) on potatoes was evaluated at five laboratories in four countries. The kit is based on DNA-specific PCR amplification followed by detection of amplicons by hybridization to a peroxidase-labelled DNA probe in a microplate. Specificity of the PCR primers for Eca, regardless of serogroups, was confirmed by testing against 246 bacterial, fungal and plant species. Detection limits of the assay varied little between six Eca strains in pure cultures (1.3×10² to 1.5×10³ cells ml⁻¹). When Eca-free tuber peel extract from four cultivars was inoculated with known numbers of 15 Eca strains, detection limits were more variable (1.0×10¹ to 6.2×10³ cells ml⁻¹ peel extract), attributed probably to inconsistency in the recovery of DNA during extraction. When the PCR assay was compared with three current commercial Eca detection methods, using naturally contaminated tubers, results matched most closely those from viable counts on a selective medium, the most sensitive method (88%), followed by enrichment ELISA (72%) and last ELISA (30%), the least sensitive method.     

Identifying and mapping biodiversity processes for conservation planning in islands: A case study in Réunion Island (Western Indian Ocean)

Over the last century, island biodiversity has become one of the most threatened in the world. Although many island conservation plans address biodiversity requirements at the species level, few plans address the spatial requirements of the biodiversity processes that underpin the persistence of these species. Using systematic conservation planning principles, we map the spatial components of biodiversity processes (SCBPs) and use these to design broad-scale conservation corridors for Réunion Island. Our method is based upon a literature review, expert knowledge, spatially explicit base data, conservation planning software, and spatial modelling. We combine a target-driven algorithm with least-cost path analyses to delineate optimal corridors for capturing key biodiversity processes while simultaneously considering biodiversity pattern targets, conservation opportunities, and future threats. We identify five SCBPs: the oceanic-terrestrial interface; riverine corridors; macrohabitat interfaces; the boundaries of isolated topographic units; and lowland-upland gradients. A large proportion of the SCBPs (81.3%) is currently untransformed, whereas 3% is irreversibly transformed by urbanisation and 15.7% is transformed but restorable. However, SCBPs are almost fully disrupted by urbanisation in the lowlands, thereby compromising functional corridors along full altitudinal gradients. This study is a contribution toward the reconciliation of conservation versus development objectives on Réunion Island but we believe that the delineation method is sufficiently general to be applied to other islands. Our results highlight the need for integrating marine, coastal and terrestrial conservation planning as a matter of urgency, given the rapid transformation of coastal areas on islands.     

Morphological and molecular characterization of Colletotrichum nymphaeae and C. fructicola associated with anthracnose symptoms of grape in Santa Catarina State,southern Brazil

Journal of Plant Diseases and Protection - Recent review described that grape anthracnose in Brazil is caused by Elsinoe ampelina. However, in many countries, anthracnose can be associated with...     

Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase

Recent findings suggest important roles for nuclear organization in gene expression. In contrast, little is known about how nuclear organization contributes to genome stability. Epistasis analysis (E-MAP) using DNA repair factors in yeast indicated a functional relationship between a nuclear pore subcomplex and Slx5/Slx8, a small ubiquitin-like modifier (SUMO)-dependent ubiquitin ligase, which we show physically interact. Real-time imaging and chromatin immunoprecipitation confirmed stable recruitment of damaged DNA to nuclear pores. Relocation required the Nup84 complex and Mec1/Tel1 kinases. Spontaneous gene conversion can be enhanced in a Slx8- and Nup84-dependent manner by tethering donor sites at the nuclear periphery. This suggests that strand breaks are shunted to nuclear pores for a repair pathway controlled by a conserved SUMO-dependent E3 ligase.     

Discovery of gene function by expression profiling of the malaria parasite life cycle

The completion of the genome sequence for Plasmodium falciparum, the species responsible for most malaria human deaths, has the potential to reveal hundreds of new drug targets and proteins involved in pathogenesis. However, only approximately 35% of the genes code for proteins with an identifiable function. The absence of routine genetic tools for studying Plasmodium parasites suggests that this number is unlikely to change quickly if conventional serial methods are used to characterize encoded proteins. Here, we use a high-density oligonucleotide array to generate expression profiles of human and mosquito stages of the malaria parasite's life cycle. Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes.     

Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum

The detection of single-nucleotide polymorphisms in pathogenic microorganisms has normally been carried out by trial and error. Here we show that DNA hybridization with high-density oligonucleotide arrays provides rapid and convenient detection of single-nucleotide polymorphisms in Plasmodium falciparum, despite its exceptionally high adenine-thymine (AT) content (82%). A disproportionate number of polymorphisms are found in genes encoding proteins associated with the cell membrane. These genes are targets for only 22% of the oligonucleotide probes but account for 69% of the polymorphisms. Genetic variation is also enriched in subtelomeric regions, which account for 22% of the chromosome but 76% of the polymorphisms.     

Genetic isolation and morphological divergence of Black Sea bottlenose dolphins

The Black Sea is a semi-enclosed body of water that differs from the adjacent Mediterranean Sea in terms of its biodiversity, oceanographical and ecological characteristics. There is growing international concern about pollution in the Black Sea and other anthropogenic threats to its fauna. The bottlenose dolphin (Tursiops truncatus) is one of three species of cetaceans living in the Azov-Black Sea basin. Despite considerable research on bottlenose dolphins elsewhere, the extent of human impacts on the Black Sea populations is unknown. Previous attempts to award special conservation status to Black Sea cetaceans have failed specifically because policy makers have viewed their ecological and evolutionary uniqueness as equivocal. This study assessed divergence between Black Sea, Mediterranean Sea and Atlantic Ocean bottlenose dolphins for 26 cranial measurements (n = 75 adult bottlenose dolphin skulls) and mitochondrial DNA (n = 99 individuals). Black Sea bottlenose dolphins are smaller than those in the Mediterranean, and possess a uniquely shaped skull. As in a previous study, we found the Black Sea population to be genetically distinct, with relatively low levels of mtDNA diversity. Population genetic models suggest that Black Sea bottlenose dolphins have so little gene flow with the Mediterranean due to historical isolation that they should be managed separately.     

Forest pasturing of livestock in Norway: effects on spruce regeneration

Forest pasturing of free-roaming livestock is a common practice in many parts of the world, but knowledge on how it affects tree regeneration in boreal forests is lacking. We mapped tree density, livestock site use and accumulated damage to young trees of commercial interest(Norway spruce, Picea abies L. Karst.) on 56 clearcuts inside and outside a fenced forest area used for livestock pasturing in Ringsaker, Norway. Inside the fence 56±1.8% of spruce trees were damaged compared to 37±3.4% outside. Proportion of damaged spruce trees was positively related to cattle use of the clearcut, but not so for sheep. On the most intensively used clearcuts, four out of five trees were damaged. The density of deciduous trees was five times lower inside compared to outside of the fence(varying with plant species). While livestock grazing may reduce resource competition in favour of spruce, the current animal density clearly is impeding forest regeneration in the study area.