Mixed Model Analysis of Within-plant Variation of Fruit Weight with Implications for Sampling of Kiwifruit Vines

In relation to horticultural crops, for purposes of predictingmean plant attributes, there has recently been an interest inusing model based approaches such as kriging that account forspatial dependencies within a plant. These models assume stationarity,i.e. observed values for two fruit on a plant depend only ontheir physical separation and not on their location. However,in most situations systematic trends exist within a plant, andthese need to be included in formulating the spatial modelsfor studying within-plant variation patterns. We propose theuse of mixed models which can simultaneously model fixed andrandom effects as well as the underlying covariance structureon the residual variation. The method is illustrated by analysisof two data sets of kiwifruit fruit sizes. The results indicatesystematic trends in fruit size within a vine, due to the positionof cane along the cordon and the shoot position along the cane.There is also evidence of a positive correlated response (     

Expansion of gallery forests into central Brazilian savannas

Upland tropical forests have expanded and contracted in response to past climates, but it is not clear whether similar dynamics were exhibited by gallery (riparian) forests within savanna biomes. Because such forests generally have access to ample water, their extent may be buffered against changing climates. We tested the long‐term stability of gallery forest boundaries by characterizing the border between gallery forests and savannas and tracing the presence of gallery forest through isotopic analysis of organic carbon in the soil profile. We measured leaf area index, grass vs. shrub or tree coverage, the organic carbon, phosphorus, nitrogen and calcium concentrations in soils and the carbon isotope ratios of soil organic matter in two transitions spanning gallery forests and savanna in a Cerrado ecosystem. Gallery forests without grasses typically show a greater leaf area index in contrast to savannas, which show dense grass coverage. Soils of gallery forests have significantly greater concentrations of organic carbon, phosphorus, nitrogen and calcium than those of savannas. Soil organic carbon of savannas is significantly more enriched in ¹³C compared with that of gallery forests. This difference in enrichment is in part caused by the presence of C₄ grasses in savanna ecosystem and its absence in gallery forests. Using the ¹³C abundance as a signature for savanna and gallery forest ecosystems in 1 m soil cores, we show that the borders of gallery forests have expanded into the savanna and that this process initiated at least 3000–4000 bp based on ¹⁴C analysis. Gallery forests, however, may be still expanding as we found more recent transitions according to ¹⁴C activity measurements. We discuss the possible mechanisms of gallery forest expansion and the means by which nutrients required for the expansion of gallery forest might accumulate.     

Past century changes in Araucaria angustifolia (Bertol.) Kuntze water use efficiency and growth in forest and grassland ecosystems of southern Brazil: implications for forest expansion

Araucaria angustifolia (Bertol.) Kuntze is an indigenous conifer tree restricted to the southern region of South America that plays a key role in the dynamics of regional ecosystems where forest expansion over grasslands has been observed. Here, we evaluate the changes in intrinsic water use efficiency (iWUE) and basal area increment (BAI) of this species in response to atmospheric CO₂, temperature and precipitation over the last century. Our investigation is based on tree-rings taken from trees located in forest and grassland sites in southern Brazil. Differences in carbon isotopic composition ( δ ¹³C), ¹³CO₂ discrimination (Δ¹³C) and intracellular carbon concentration ( C _i ) are also reported. Our results indicate an age effect on Δ¹³C in forest trees during the first decades of growth. This age effect is not linked to an initial BAI suppression, suggesting the previous existence of nonforested vegetation in the forest sites. After maturity all trees show similar temporal trends in carbon isotope-derived variables and increasing iWUE, however, absolute values are significantly different between forest and grassland sites. The iWUE is higher in forest trees, indicating greater water competition or nutritional availability, relative to grassland, or both. BAI is also higher in forest trees, but it is not linked with iWUE or atmospheric CO₂. Nevertheless, in both forest and grassland sites A. angustifolia has had growth limitations corresponding to low precipitation and high temperatures observed in the 1940s.     

Conservation and ecological implications of the use of space by chilla foxes and free‐ranging dogs in a human‐dominated landscape in southern Chile

We investigated whether domestic dogs (Canis lupus familiaris) influenced the use of space by chilla foxes (Lycalopex griseus) in southern Chile and tested the hypothesis that dogs interfere with chillas. We used scent stations and occurrence of scats within systematically placed plots to assess habitat use by both species and to test whether dogs were associated to the use of space by chillas. Activity data were obtained from captures for both species, and telemetry for foxes. Diet of both species was analysed in order to tease out the potential existence of exploitation competition. We found that, when active, chillas used prairies more and native forest less than expected according to availability, whereas inactive chillas (during the day) preferred native forest, the only habitat type that dogs did not use. The odds of dog occurrence increased at shorter distance to human houses, whereas the inverse pattern was observed for chillas. Poisson models showed that the number of chilla visits to scent stations was negatively correlated with the number of dog visits. We observed dogs persecuting and/or killing chillas which was also corroborated by local people that used dogs to prevent chilla‐related poultry losses, supporting the idea that dogs harass foxes actively. The analysis of scats showed that dogs fed mainly on house food and domestic ruminant carcasses whereas foxes fed on hare, hens, mice and wild birds, thus suggesting that exploitation competition is not a strong alternative hypothesis as a proximate cause for the patterns observed. We conclude that dogs seem to constrain the use of space by wild carnivores via interference.     

Tobacco blue mould disease caused by Peronospora hyoscyami f. sp. tabacina

Blue mould [ Peronospora hyoscyami f. sp. tabacina (Adam) Skalicky 1964] is one of the most important foliar diseases of tobacco that causes significant losses in the Americas, south-eastern Europe and the Middle East. This review summarizes the current knowledge of the mechanisms employed by this oomycete pathogen to colonize its host, with emphasis on molecular aspects of pathogenicity. In addition, key biochemical and molecular mechanisms involved in tobacco resistance to blue mould are discussed.
Taxonomy: Kingdom: Chromista (Straminipila); Phylum: Heterokontophyta; Class: Oomycete; Order: Peronosporales; Family: Peronosporaceae; Genus: Peronospora ; Species: Peronospora hyoscyami f. sp. tabacina .
Disease symptoms: The pathogen typically causes localized lesions on tobacco leaves that appear as single, or groups of, yellow spots that often coalesce to form light-brown necrotic areas. Some of the leaves exhibit grey to bluish downy mould on their lower surfaces. Diseased leaves can become twisted, such that the lower surfaces turn upwards. In such cases, the bluish colour of the diseased plants becomes quite conspicuous, especially under moist conditions when sporulation is abundant. Hence the name of the disease: tobacco blue mould.
Infection process: The pathogen develops haustoria within plant cells that are thought to establish the transfer of nutrients from the host cell, and may also act in the delivery of effector proteins during infection.
Resistance: Several defence responses have been reported to occur in the Nicotiana tabacum – P. hyoscyami f. sp. tabacina interaction. These include the induction of pathogenesis-related genes, and a correlated increase in the activities of typical pathogenesis-related proteins, such as peroxidases, chitinases, β-1,3-glucanases and lipoxygenases. Systemic acquired resistance is one of the best characterized tobacco defence responses activated on pathogen infection.     

Chromosome numbers in Brazilian species of Crotalaria (Leguminosae, Papilionoideae) and their taxonomic significance

Chromosome numbers were counted for 23 species of Crotalaria native to Brazil. Among these data there were new counts for 15 taxa, and some confirmed previous reports or represented numbers that were different from those cited previously. The chromosome numbers most frequently found were 2 n  = 16 and 2 n  = 32. Only C. incana L. had 2 n  = 14 and C. tweediana Benth. had 2 n  = 54. The counts 2 n  = 32 and 54 were found in species of section Calycinae and 2 n  = 16 and 14 in species of section Chrysocalycinae . The data revealed the importance of chromosomal parameters in the characterization of sections Calycinae and Chrysocalycinae in Brazil. We discuss the systematic significance and evolutionary aspects for the genus, comparing the results with the two sections that are native in Brazil.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 271–277.     

Differential proteomics of dehydration and rehydration in bryophytes: evidence towards a common desiccation tolerance mechanism

All bryophytes evolved desiccation tolerance (DT) mechanisms during the invasion of terrestrial habitats by early land plants. Are these DT mechanisms still present in bryophytes that colonize aquatic habitats? The aquatic bryophyte Fontinalis antipyretica Hedw. was subjected to two drying regimes and alterations in protein profiles and sucrose accumulation during dehydration and rehydration were investigated. Results show that during fast dehydration, there is very little variation in protein profiles, and upon rehydration proteins are leaked. On the other hand, slow dehydration induces changes in both dehydration and rehydration protein profiles, being similar to the protein profiles displayed by the terrestrial bryophytes Physcomitrella patens (Hedw.) Bruch and Schimp. and, to what is comparable with Syntrichia ruralis (Hedw.) F. Weber and D. Mohr. During dehydration there was a reduction in proteins associated with photosynthesis and the cytoskeleton, and an associated accumulation of proteins involved in sugar metabolism and plant defence mechanisms. Upon rehydration, protein accumulation patterns return to control values for both photosynthesis and cytoskeleton whereas proteins associated with sugar metabolism and defence proteins remain high. The current results suggest that bryophytes from different ecological adaptations may share common DT mechanisms.     

On the terms in the International Code of Botanical Nomenclature

The most recent edition of the International Code of Botanical Nomenclature (Vienna Code) has superseded all previous editions. One of the notable changes in the Vienna Code is that it contains a glossary of nomenclatural terms defined and used in the Code. It has been made clear that the glossary of these terms is an integral part of the Code. This paper presents a Chinese translation of the definitions of the nomenclatural terms in the Code.     

Population genomics of wild and laboratory zebrafish (Danio rerio)

Understanding a wider range of genotype–phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large‐scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh, and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1832 polymorphic EST‐based single nucleotide polymorphisms (SNPs) and the cytb mitochondrial gene in 13 wild populations and three lab strains. Natural populations were subdivided into three major mitochondrial DNA clades with an average among‐clade sequence divergence of 5.8%. SNPs revealed five major evolutionarily and genetically distinct groups with an overall F_ST of 0.170 (95% CI 0.105–0.254). These genetic groups corresponded to discrete geographic regions and appear to reflect isolation in refugia during past climate cycles. We detected 71 significantly divergent outlier loci (3.4%) and nine loci (0.5%) with significantly low F_ST values. Valleys of reduced heterozygosity, consistent with selective sweeps, surrounded six of the 71 outliers (8.5%). The lab strains formed two additional groups that were genetically distinct from all wild populations. An additional subset of outlier loci was consistent with domestication selection within lab strains. Substantial genetic variation that exists in zebrafish as a whole is missing from lab strains that we analysed. A combination of laboratory and field studies that incorporates genetic variation from divergent wild populations along with the wealth of molecular information available for this model organism provides an opportunity to advance our understanding of genetic influences on phenotypic variation for a vertebrate species.     

Enzymatic deconstruction of xylan for biofuel production

The combustion of fossil-derived fuels has a significant impact on atmospheric carbon dioxide (CO₂) levels and correspondingly is an important contributor to anthropogenic global climate change. Plants have evolved photosynthetic mechanisms in which solar energy is used to fix CO₂ into carbohydrates. Thus, combustion of biofuels, derived from plant biomass, can be considered a potentially carbon neutral process. One of the major limitations for efficient conversion of plant biomass to biofuels is the recalcitrant nature of the plant cell wall, which is composed mostly of lignocellulosic materials (lignin, cellulose, and hemicellulose). The heteropolymer xylan represents the most abundant hemicellulosic polysaccharide and is composed primarily of xylose, arabinose, and glucuronic acid. Microbes have evolved a plethora of enzymatic strategies for hydrolyzing xylan into its constituent sugars for subsequent fermentation to biofuels. Therefore, microorganisms are considered an important source of biocatalysts in the emerging biofuel industry. To produce an optimized enzymatic cocktail for xylan deconstruction, it will be valuable to gain insight at the molecular level of the chemical linkages and the mechanisms by which these enzymes recognize their substrates and catalyze their reactions. Recent advances in genomics, proteomics, and structural biology have revolutionized our understanding of the microbial xylanolytic enzymes. This review focuses on current understanding of the molecular basis for substrate specificity and catalysis by enzymes involved in xylan deconstruction.