Molecular adaptation within the coat protein-encoding gene of Tunisian almond isolates of Prunus necrotic ringspot virus

The sequence alignments of five Tunisian isolates of Prunus necrotic ringspot virus (PNRSV) were searched for evidence of recombination and diversifying selection. Since failing to account for recombination can elevate the false positive error rate in positive selection inference, a genetic algorithm (GARD) was used first and led to the detection of potential recombination events in the coat protein-encoding gene of that virus. The Recco algorithm confirmed these results by identifying, additionally, the potential recombinants. For neutrality testing and evaluation of nucleotide polymorphism in PNRSV CP gene, Tajima’s D, and Fu and Li’s D and F statistical tests were used. About selection inference, eight algorithms (SLAC, FEL, IFEL, REL, FUBAR, MEME, PARRIS, and GA branch) incorporated in HyPhy package were utilized to assess the selection pressure exerted on the expression of PNRSV capsid. Inferred phylogenies pointed out, in addition to the three classical groups (PE-5, PV-32, and PV-96), the delineation of a fourth cluster having the new proposed designation SW6, and a fifth clade comprising four Tunisian PNRSV isolates which underwent recombination and selective pressure and to which the name Tunisian outgroup was allocated.     

Tracking island colonization history and phenotypic shifts in Indian Ocean bulbuls (Hypsipetes: Pycnonotidae)

Molecular phylogenies of island organisms provide useful systems for testing hypotheses of convergent or parallel evolution, since selectively neutral molecular characters are likely to be independent of phenotype, and the existence of similar environments on multiple isolated islands provides numerous opportunities for populations to evolve independently under the same constraints. Here we construct a phylogenetic hypothesis for Hypsipetes bulbuls of the western Indian Ocean, and use this to test hypotheses of colonization pattern and phenotypic change among islands of the region. Mitochondrial sequence data were collected from all extant taxa of the region, combined with sequence data from relevant lineages in Asia. Data are consistent with a single Hypsipetes colonization of the western Indian Ocean from Asia within the last 2.6 Myr. The expansion of Hypsipetes appears to have occurred rapidly, with descendants found across the breadth of its western Indian Ocean range. The data suggest that a more recent expansion of Hypsipetes madagascariensis from Madagascar led to the colonization of Aldabra and a secondary colonization of the Comoros. Groupings of western Indian Ocean Hypsipetes according to phenotypic similarities do not correspond to mtDNA lineages, suggesting that these similarities have evolved by convergence or parallelism. The direction of phenotypic change cannot be inferred with confidence, since the primary expansion occurred rapidly relative to the rate of mtDNA substitution, and the colonization sequence remains uncertain. However, evidence from biogeography and comparison of independent colonization events are consistent with the persistence of a small grey continental bulbul in India and Madagascar, and multiple independent origins of large size and green plumage in insular island populations of the Comoros, Mascarenes and Seychelles. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 85 , 271–287.     

The mixed xylem sap proteome of Fusarium oxysporum-infected tomato plants

Secreted proteins are known to play decisive roles in plant–fungus interactions. To study the molecular details of the interaction between the xylem-colonizing, plant-pathogenic fungus Fusarium oxysporum and tomato, the composition of the xylem sap proteome of infected tomato plants was investigated and compared with that of healthy plants. Two-dimensional gel separation and mass spectrometry yielded peptide masses and peptide sequences of 33 different proteins. Despite the absence of complete genome sequences of either tomato or F. oxysporum , 21 proteins were identified as tomato proteins and seven as fungal proteins. Thirteen of the tomato proteins were specific for infected plants. Sixteen tomato proteins were found in xylem sap for the first time, four of which were identified based on matches to expressed sequences only. Coding sequences for new proteins from F. oxysporum were identified through either direct matching to a database sequence, matching of peptide sequences to genome or expressed sequence tag databases of other Fusarium species, or PCR with degenerate primers on cDNA derived from infected plants followed by screening of a F. oxysporum BAC library. Together, these findings provide an excellent basis for further exploration of the interaction between xylem-colonizing pathogens and their hosts.     

The abundance,distribution and structural characteristics of tree‐holes in Nothofagus forest,New Zealand

Tree‐holes provide an important microhabitat that is used for feeding, roosting and breeding by numerous species around the world. Yet despite their ecological importance for many of New Zealand's endangered species, few studies have investigated the abundance or distribution of tree‐holes in native forests. We used complementary ground and climbed tree surveys to determine the abundance, distribution and characteristics of tree‐holes in undisturbed Nothofagus forest in the Lewis Pass, New Zealand. We found that hole‐bearing trees were surprisingly abundant compared with many other studies, including Australian Eucalyptus species and American beech. In fact, we estimated as many as 3906 tree‐holes per hectare, of which 963 holes per hectare were potentially large enough to provide roost sites for hole‐nesting bats in New Zealand, while only eight holes per hectare were potentially suitable for specialist hole‐nesting birds. This was of great interest as primary cavity‐excavating animals are absent from New Zealand forests, compared with North America and Australia. Moreover, tree‐hole formation in New Zealand is likely to be dominated by abiotic processes, such as branch breakage from windstorms and snow damage. As has been found in many other studies, tree‐holes were not uniformly distributed throughout the forest. Tree‐holes were significantly more abundant on the least abundant tree species, Nothofagus fusca, than on either N. menziesii or N. solandri. In addition to tree species, tree size was also an important factor influencing the structural characteristics of tree‐holes and their abundance in this forest. Moreover, these trends were not fully evident without climbed tree surveys. Our results revealed that ground‐based surveys consistently underestimated the number of tree‐holes present on Nothofagus trees, and illustrate the importance of using climbed inspections where possible in tree‐hole surveys. We compare our results with other studies overseas and discuss how these are linked to the biotic and abiotic processes involved in tree‐hole formation. We consider the potential implications of our findings for New Zealand's hole‐dwelling fauna and how stand dynamics and past and future forest management practices will influence the structural characteristics of tree‐holes and their abundance in remnant forest throughout New Zealand.     

Is biofuel policy harming biodiversity in Europe?

We assessed the potential impacts of land-use changes resulting from a change in the current biofuel policy on biodiversity in Europe. We evaluated the possible impact of both arable and woody biofuel crops on changes in distribution of 313 species pertaining to different taxonomic groups. Using species-specific information on habitat suitability as well as land use simulations for three different biofuel policy options, we downscaled available species distribution data from the original resolution of 50 to 1 km. The downscaled maps were then applied to analyse potential changes in habitat size and species composition at different spatial levels. Our results indicate that more species might suffer from habitat losses rather than benefit from a doubled biofuel target, while abolishing the biofuel target would mainly have positive effects. However, the possible impacts vary spatially and depend on the biofuel crop choice, with woody crops being less detrimental than arable crops. Our results give an indication for policy and decision makers of what might happen to biodiversity under a changed biofuel policy in the European Union. The presented approach is considered to be innovative as to date no comparable policy impact assessment has been applied to such a large set of key species at the European scale.     

The influence of leaf litter on zooplankton in floodplain wetlands: changes resulting from river regulation

1. The loss of input of leaf litter through clearing of riparian vegetation may result in significant changes to aquatic ecosystems. River red gums (Eucalyptus camaldulensis) surrounding floodplain wetlands in the Murray–Darling Basin, Australia, contribute large quantities of leaf litter, but the quality of this resource may change depending on the timing of inundation. 2. We used experimental mesocosms to test the hypotheses that zooplankton would have a greater abundance with an input of leaf litter and that fewer zooplankton would emerge from egg banks in cleared than forested wetlands. The experiment was carried out in summer/autumn and in spring to test a third hypothesis that zooplankton would respond to changes in the timing of wetland inundation as a result of river regulation. 3. In summer/autumn, leaf litter reduced zooplankton abundance by 89% at the beginning of the experiment through its influence on water quality. Only a few taxa (Polyarthra spp., Colurella spp. and the cladoceran Family Moinidae) responded positively to leaf litter when water quality improved later in the experiment, indicating a switch in the role of leaf litter from a non‐trophic to a trophic pathway. 4. In spring, microcrustaceans emerged in smaller numbers from sediment sourced from cleared compared to forested wetlands, reflecting different communities in these two wetland types and/or disturbances to the sediment that interfere with emergence. 5. Although leaf litter appears not to be an important resource for zooplankton in floodplain wetlands, riparian clearing may have lasting effects on future emerging zooplankton communities. Additionally, river regulation may have considerable impacts on the influence of leaf litter on zooplankton, which has implications for the management of floodplain river systems.     

四步法消除SYBR GreenⅠ实时定量RT-PCR中引物二聚体的影响

为建立一种新的SYBRgreenⅠ实时定量RT PCR方法 ,使之能够有效消除引物二聚体 (PDs)对实时定量结果的影响 .对RT PCR特异性扩增产物和PDs分别进行了凝胶电泳检测和熔解曲线分析 .依据PDs和扩增产物的熔解温度 (Tm)特点 ,在通用的三步法的延伸步骤之后 ,增加一个短暂的 (5s)恒温和荧光检测步骤 ,使这个步骤的温度高于PDs的Tm,但低于扩增产物的Tm,简称该法为四步法 .PDs的Tm 通常高于 72℃ ,但低于扩增产物的Tm .将四步法第四步的温度设置在高于PDs的Tm ,但低于扩增产物的Tm 时 ,四步法能够有效地消除PDs的影响 .对三步法和四步法SYBRgreenⅠ实时定量RT PCR进行了比较 ,发现三步法根本不能用于RNA的实时定量 ,而四步法能够实现包括低丰度RNA在内的RNA的定量 .选择Tm 值尽可能小的引物 ,使PDs与扩增产物Tm 值之间有足够的差距 ,将更有利于四步法的应用 ,并可成功地用于低丰度RNA的准确定量     

Error in the inference of fire history from grasstrees

Abstract A method for constructing fire histories has recently been proposed for fire‐prone southern Australia based on the pattern of coloured bands in the remnant leaf‐bases on stems of grasstrees (Xanthorrhoea species; Xanthorrhoeaceae). In the absence of alternative high‐resolution techniques extending into the premodern period, this method has been utilized to construct fire histories for forest, woodland and shrubland ecosystems, principally in south‐western Australia. However, the technique has not been validated against known fire histories spanning more than one fire interval. Here we compare fire records from 100 grasstrees with a 30‐year record (1973–2002) of fire data derived from satellite imagery in a region of sandplain shrubland vegetation near Eneabba in south‐western Australia. Fires occurred in eight of the 30 years of the satellite record, with sampled grasstrees burning between zero and four times. The grasstree and satellite records agreed in terms of the overall incidence of fires experienced over the 30‐year period, with the grasstree record matching the satellite record significantly better than chance. However, comparison of the grasstree and satellite records found substantial error in the rate of both false positives and false negatives. Grasstrees failed to identify fire in 83% of fire occurrences identified by the satellite record, down to 53% if an error of ±2 years in the attribution of year of fire was allowed. A similar proportion of grasstree fire incidents were not matched in the satellite record (false positives). The rate of false positives increased with time before present, suggesting a temporal bias in the grasstree record. It is clear that the grasstree record does reflect fire history to a degree, but that it contains at least as many false as true fire records and may tend towards over‐reporting the incidence of fire in the past.     

Dual Valorization of Olive Mill Wastewater by Bio‐Nanosynthesis of Magnesium Oxide and Yarrowia lipolytica Biomass Production

This research investigates an efficient dual valorization of olive mill wastewater in the biosynthesis of magnesium oxide nanoparticles and in the depollution of the effluent by Yarrowia lipolytica growth evaluation. After removal of polyphenols, the recovered biophenols were reacted with the magnesium precursor to provide magnesium oxide nanoparticles. In order to confirm the biosynthesized magnesium oxide nanoparticles, several analyses were undertaken. The Fourier transform infrared spectrum gives a broad absorption at 658 cm^?1 confirming the presence of the magnesium oxide nanoparticles, while the UV/VIS absorption spectroscopy reveals an intense transition with a maximum absorption at 300 nm. The X‐ray diffraction and transmission electron microscopy analyses show that nanoparticles are in pure cubic crystalline with spherical and hexagonal shapes (average size is 19.4 nm). The zeta potential analysis illustrates a negative potential proving a good stability of the biosynthesized nanoparticles. Nanoparticles were assigned for their in vitro antibacterial activity against Escherichia coli, Enterobacter aerogenes, Salmonella typhimurium, Staphylococcus cohnii, and Bacillus niacini. The evaluation of the growth of Yarrowia lipolytica on the recovered olive mill wastewater after removal of polyphenols yielded 3.2 g/L of the Yarrowia biomass in 72 h without nutriment additions, providing an important decrease of chemical oxygen demand (73 %).