Universidade Federal de Viçosa

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

GENES is a software package used for data analysis and processing with different biometric models and is essential in genetic studies applied to plant and animal breeding. It allows parameter estimation to analyze biological phenomena and is fundamental for the decision-making process and predictions of success and viability of selection strategies. The program can be downloaded from the Internet (http://www.ufv.br/dbg/genes/genes.htm or http://www.ufv.br/dbg/biodata.htm) and is available in Portuguese, English and Spanish. Specific literature (http://www.livraria.ufv.br/) and a set of sample files are also provided, making GENES easy to use. The software is integrated into the programs MS Word, MS Excel and Paint, ensuring simplicity and effectiveness in data import and export of results, figures and data. It is also compatible with the free software R and Matlab, through the supply of useful scripts available for complementary analyses in different areas, including genome wide selection, prediction of breeding values and use of neural networks in genetic improvement.

Francis Martin and colleagues report genome sequences for 18 species of mycorrhizal fungi and a phylogenomic analysis including 32 other fungal genomes. The study identifies cell wall-degradation genes lost in all true ectomycorrhizal species and, using gene expression data, finds candidate genes for the establishment of symbiosis. To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall–degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7–38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.

Eucalypts are the world’s most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology. The Eucalyptus grandis genome has been sequenced, revealing the greatest number of tandem duplications of any plant genome sequenced so far, and the highest diversity of genes for specialized metabolites that act as chemical defence and provide unique pharmaceutical oils; genome sequencing of the sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. Fast-growing Eucalyptus trees form the basis of an international pulp, paper and chemical cellulose industry and they are also seen as potential biomass feedstocks for bioenergy and biomaterials. The genome of Eucalyptus grandis has now been sequenced. It contains the greatest number of tandem duplications so far found in a plant genome, as well as the highest diversity of genes for specialized metabolites that act as chemical defence and provide unique pharmaceutical oils. Comparison with the sister species E. globulus and with other E. grandis lines reveals dynamic genome evolution and hotspots of inbreeding depression. The availability of comprehensive genomic data will be of use in work on accelerating breeding cycles for productivity and wood quality and developing eucalypt strains suited to a variety of habitats.

The geminiviruses are a family of small, non-enveloped viruses with single-stranded, circular DNA genomes of 2500-5200 bases. Geminiviruses are transmitted by various types of insect (whiteflies, leafhoppers, treehoppers and aphids). Members of the genus Begomovirus are transmitted by whiteflies, those in the genera Becurtovirus, Curtovirus, Grablovirus, Mastrevirus and Turncurtovirus are transmitted by specific leafhoppers, the single member of the genus Topocuvirus is transmitted by a treehopper and one member of the genus Capulavirus is transmitted by an aphid. Geminiviruses are plant pathogens causing economically important diseases in most tropical and subtropical regions of the world. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Geminiviridae which is available at www.ictv.global/report/geminiviridae.

The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV.

Various data indicate that nitric oxide (NO) is an endogenous signal in plants that mediates responses to several stimuli. Experimental evidence in support of such signalling roles for NO has been obtained via the application of NO, usually in the form of NO donors, via the measurement of endogenous NO, and through the manipulation of endogenous NO content by chemical and genetic means. Stomatal closure, initiated by abscisic acid (ABA), is effected through a complex symphony of intracellular signalling in which NO appears to be one component. Exogenous NO induces stomatal closure, ABA triggers NO generation, removal of NO by scavengers inhibits stomatal closure in response to ABA, and ABA-induced stomatal closure is reduced in mutants that are impaired in NO generation. The data indicate that ABA-induced guard cell NO generation requires both nitric oxide synthase-like activity and, in Arabidopsis, the NIA1 isoform of nitrate reductase (NR). NO stimulates mitogen-activated protein kinase (MAPK) activity and cGMP production. Both these NO-stimulated events are required for ABA-induced stomatal closure. ABA also stimulates the generation of H2O2 in guard cells, and pharmacological and genetic data demonstrate that NO accumulation in these cells is dependent on such production. Recent data have extended this model to maize mesophyll cells where the induction of antioxidant defences by water stress and ABA required the generation of H2O2 and NO and the activation of a MAPK. Published data suggest that drought and salinity induce NO generation which activates cellular processes that afford some protection against the oxidative stress associated with these conditions. Exogenous NO can also protect cells against oxidative stress. Thus, the data suggest an emerging model of stress responses in which ABA has several ameliorative functions. These include the rapid induction of stomatal closure to reduce transpirational water loss and the activation of antioxidant defences to combat oxidative stress. These are two processes that both involve NO as a key signalling intermediate.

Nutrient resorption in plants influences nutrient availability and cycling and is a key process in biogeochemical models. Improved estimates of resorption parameters are needed for predicting long‐term primary productivity and for improving such models. Currently, most models assume a value of 50% resorption for nitrogen (N) and phosphorus (P) and lack resorption data for other nutrients and for specific vegetation types. We provide global estimates of resorption efficiencies and nutrient concentrations for carbon (C), N, and P and the first global‐scale estimates for essential nutrients such as potassium (K), calcium (Ca), and magnesium (Mg). We also examine leaf mass loss during senescence (LML) globally and for different plant types, thus defining a mass loss correction factor (MLCF) needed to quantify unbiased resorption values. We used a global meta‐analysis of 86 studies and ∼1000 data points across climates for green and senesced leaves in six plant types: ferns, forbs, graminoids, conifers, and evergreen and deciduous woody angiosperms. In general, N and P resorption differed significantly from the commonly used global value of 50% (62.1%, 64.9%, respectively; P < 0.05). Ca, C, and Mg showed lower average resorptions of 10.9%, 23.2%, and 28.6%, respectively, while K had the highest resorption, at 70.1%. We also found that resorption of all nutrients except Ca depended on leaf nutrient‐status; globally, C, N, P, K, and Mg showed a decrease in resorption with increased nutrient status. On average, global leaf mass loss was 24.2%. Overall, our resorption data differ substantially from commonly assumed values and should help improve ecological theory and biogeochemical and land‐surface models.

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More than six decades after the onset of wide-scale commercial use of synthetic pesticides and more than fifty years after Rachel Carson's Silent Spring, pesticides, particularly insecticides, arguably remain the most influential pest management tool around the globe. Nevertheless, pesticide use is still a controversial issue and is at the regulatory forefront in most countries. The older generation of insecticide groups has been largely replaced by a plethora of novel molecules that exhibit improved human and environmental safety profiles. However, the use of such compounds is guided by their short-term efficacy; the indirect and subtler effects on their target species, namely arthropod pest species, have been neglected. Curiously, comprehensive risk assessments have increasingly explored effects on nontarget species, contrasting with the majority of efforts focused on the target arthropod pest species. The present review mitigates this shortcoming by hierarchically exploring within an ecotoxicology framework applied to integrated pest management the myriad effects of insecticide use on arthropod pest species.

Twenty-four multiparous dairy cows (eight with ruminal cannulae) were blocked by days in milk and assigned to six balanced 4 x 4 Latin squares with 21-d periods. The four diets, formulated from alfalfa silage plus a concentrate mix based on ground high moisture ear corn, contained (dry matter basis): 1) 20% concentrate, 80% alfalfa silage (24% nonfiber carbohydrate; NFC), 2) 35% concentrate, 65% alfalfa silage (30% NFC), 3) 50% concentrate, 50% alfalfa silage (37% NFC), or 4) 65% concentrate, 35% alfalfa silage (43% NFC). Soybean meal and urea were added to make diets isonitrogenous with equal nonprotein nitrogen (NPN) (43% of total N). Total urine was collected with indwelling Folley catheters for 24 h during each period. There was no effect of diet on urinary creatinine excretion (average 29 mg/kg of BW/d). There were quadratic effects of diet on total urinary ecretion of allantoin, uric acid, and purine derivatives (allantoin plus uric acid), and on ruminal synthesis of microbial N estimated from purine derivatives; maxima occurred at about 35% dietary NFC. Urinary excretion also was estimated with spot urine samples from creatinine concentration and the mean daily creatinine excretion. Daily excretion of allantoin, uric acid, and purine derivatives estimated from spot urine sampling followed the same pattern as that observed with total collection; differences between measured and estimated urine volume were significant only for 35% dietary concentrate. Spot urine sampling appeared to yield satisfactory estimates of purine derivative excretion. Maximal urea N excretion was estimated to occur at about 31% dietary NFC. Milk allantoin secretion increased linearly with concentrate and accounted for 4 to 6% of the total purine derivative excretion. Microbial yield was maximal at 35% dietary NFC, suggesting that this was the optimal level for utilization of dietary NPN from alfalfa silage and other sources.

Overall, drought and unfavourable temperatures are the major climatic limitations for coffee production. These limitations are expected to become increasingly important in several coffee growing regions due to the recognized changes in global climate, and also because coffee cultivation has spread towards marginal lands, where water shortage and unfavourable temperatures constitute major constraints to coffee yield. In this review, we examine the impacts of such limitations on the physiology, and consequently on the production of mainly Coffea arabica and C. canephora, which account for about 99 % of the world coffee bean production. The first section deals with climatic factors and the coffee plant’s requirements. The importance of controlling oxidative stress for the expression of drought and cold tolerance abilities is emphasized in the second section. In the third section, we examine the impacts of drought on cell-water relations, stomatal behaviour and water use, photosynthesis and crop yield, carbon and nitrogen metabolism, root growth and characteristics, and on drought tolerance. In the fourth section, the impacts of low positive and high temperatures on coffee physiology are discussed; some insights about effects of negative temperatures are also presented. Finally, the last section deals with shading in harsh environments as a mean of buffering climatic fluctuations, as well as of increasing environmental sustainability in coffee exploitation.

Lipopolysaccharide (LPS) may play an important role in chronic diseases through the activation of inflammatory responses. The type of diet consumed is of major concern for the prevention and treatment of these diseases. Evidence from animal and human studies has shown that LPS can diffuse from the gut to the circulatory system in response to the intake of high amounts of fat. The method by which LPS move into the circulatory system is either through direct diffusion due to intestinal paracellular permeability or through absorption by enterocytes during chylomicron secretion. Considering the impact of metabolic diseases on public health and the association between these diseases and the levels of LPS in the circulatory system, this review will mainly discuss the current knowledge about high-fat diets and subclinical inflammation. It will also describe the new evidence that correlates gut microbiota, intestinal permeability and alkaline phosphatase activity with increased blood LPS levels and the biological effects of this increase, such as insulin resistance. Although the majority of the studies published so far have assessed the effects of dietary fat, additional studies are necessary to deepen the understanding of how the amount, the quality and the structure of the fat may affect endotoxaemia. The potential of food combinations to reduce the negative effects of fat intake should also be considered in future studies. In these studies, the effects of flavonoids, prebiotics and probiotics on endotoxaemia should be investigated. Thus, it is essential to identify dietetic strategies capable of minimising endotoxaemia and its postprandial inflammatory effects.

Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve with nearly all forms of cellular life. The route of virus replication and protein expression is determined by the viral genome type. Comparison of these routes led to the classification of viruses into seven “Baltimore classes” (BCs) that define the major features of virus reproduction. However, recent phylogenomic studies identified multiple evolutionary connections among viruses within each of the BCs as well as between different classes.

The Amazon Basin is one of the world's most important bioregions, harboring a rich array of plant and animal species and offering a wealth of goods and services to society. For years, ecological science has shown how large-scale forest clearings cause declines in biodiversity and the availability of forest products. Yet some important changes in the rainforests, and in the ecosystem services they provide, have been underappreciated until recently. Emerging research indicates that land use in the Amazon goes far beyond clearing large areas of forest; selective logging and other canopy damage is much more pervasive than once believed. Deforestation causes collateral damage to the surrounding forests – through enhanced drying of the forest floor, increased frequency of fires, and lowered productivity. The loss of healthy forests can degrade key ecosystem services, such as carbon storage in biomass and soils, the regulation of water balance and river flow, the modulation of regional climate patterns, and the amelioration of infectious diseases. We review these newly revealed changes in the Amazon rainforests and the ecosystem services that they provide.

The products formed by glycosylation of food proteins with carbohydrates via the Maillard reaction, also known as conjugates, are agents capable of changing and improving techno-functional characteristics of proteins. The Maillard reaction uses the covalent bond between a group of a reducing carbohydrates and an amino group of a protein. This reaction does not require additional chemicals as it occurs naturally under controlled conditions of temperature, time, pH, and moisture. Moreover, there is growing interest in modifying proteins for industrial food applications. This review analyses the current state of art of the Maillard reaction on food protein functionalities. It also discusses the influence of the Maillard reaction on the conditions and formulation of reagents that improve desirable techno-functional characteristics of food protein.

The South American tomato pinworm, Tuta absoluta (Meyrick), is native to the western Neotropics. After invading Spain in 2006, it spread rapidly throughout Afro-Eurasia and has become a major threat to world tomato production. Integrated pest management (IPM) strategies have been developed, but widespread insecticide use has caused selection for insecticide resistance as well as undesirable effects on key beneficial arthropods. Augmentation and conservation biological control relying on omnivorous mirid predators has proved successful for management of T. absoluta, where implementation is dependent on abiotic, biotic (e.g., alternative prey), and anthropogenic factors (e.g., pesticides). Research has been carried out on larval parasitoids, showing potential for further development of sustainable control. The development of resistant tomato varieties is ongoing, but they are not commercially available yet. Knowledge gaps remain to be filled to optimize IPM packages on tomato crops and to help prevent further spread worldwide.

Abstract Aim Tropical forests store 25% of global carbon and harbour 96% of the world's tree species, but it is not clear whether this high biodiversity matters for carbon storage. Few studies have teased apart the relative importance of forest attributes and environmental drivers for ecosystem functioning, and no such study exists for the tropics. Location Neotropics. Methods We relate aboveground biomass ( AGB ) to forest attributes (diversity and structure) and environmental drivers (annual rainfall and soil fertility) using data from 144,000 trees, 2050 forest plots and 59 forest sites. The sites span the complete latitudinal and climatic gradients in the lowland Neotropics, with rainfall ranging from 750 to 4350 mm year −1 . Relationships were analysed within forest sites at scales of 0.1 and 1 ha and across forest sites along large‐scale environmental gradients. We used a structural equation model to test the hypothesis that species richness, forest structural attributes and environmental drivers have independent, positive effects on AGB . Results Across sites, AGB was most strongly driven by rainfall, followed by average tree stem diameter and rarefied species richness, which all had positive effects on AGB . Our indicator of soil fertility (cation exchange capacity) had a negligible effect on AGB , perhaps because we used a global soil database. Taxonomic forest attributes (i.e. species richness, rarefied richness and Shannon diversity) had the strongest relationships with AGB at small spatial scales, where an additional species can still make a difference in terms of niche complementarity, while structural forest attributes (i.e. tree density and tree size) had strong relationships with AGB at all spatial scales. Main conclusions Biodiversity has an independent, positive effect on AGB and ecosystem functioning, not only in relatively simple temperate systems but also in structurally complex hyperdiverse tropical forests. Biodiversity conservation should therefore be a key component of the UN Reducing Emissions from Deforestation and Degradation strateg y.