DNA barcoding identifies cryptic animal tool materials.

Some animals fashion tools or constructions out of plant materials to aid foraging, reproduction, self-maintenance, or protection. Their choice of raw materials can affect the structure and properties of the resulting artifacts, with considerable fitness consequences. Documenting animals' material preferences is challenging, however, as manufacture behavior is often difficult to observe directly, and materials may be processed so heavily that they lack identifying features. Here, we use DNA barcoding to identify, from just a few recovered tool specimens, the plant species New Caledonian crows (Corvus moneduloides) use for crafting elaborate hooked stick tools in one of our long-term study populations. The method succeeded where extensive fieldwork using an array of conventional approaches-including targeted observations, camera traps, radio-tracking, bird-mounted video cameras, and behavioral experiments with wild and temporarily captive subjects-had failed. We believe that DNA barcoding will prove useful for investigating many other tool and construction behaviors, helping to unlock significant research potential across a wide range of study systems.

Carbon fractions in the world's dead wood.

A key uncertainty in quantifying dead wood carbon (C) stocks-which comprise ~8% of total forest C pools globally-is a lack of accurate dead wood C fractions (CFs) that are employed to convert dead woody biomass into C. Most C estimation protocols utilize a default dead wood CF of 50%, but live tree studies suggest this value is an over-estimate. Here, we compile and analyze a global database of dead wood CFs in trees, showing that dead wood CFs average 48.5% across forests, deviating significantly from 50%, and varying systematically among biomes, taxonomic divisions, tissue types, and decay classes. Utilizing data-driven dead wood CFs in tropical forests alone may correct systematic overestimates in dead wood C stocks of ~3.0 Pg C: an estimate approaching nearly the entire dead wood C pool in the temperate forest biome. We provide for the first time, robust empirical dead wood CFs to inform global forest C estimation.

Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus.

BACKGROUND: Allopolyploidy is widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modifications to exhibit stronger vigor and adaptability. To explore the changes in homologous gene expression patterns in the natural allotetraploid Brassica napus (AnAnCnCn) relative to its two diploid progenitors, B. rapa (ArAr) and B. oleracea (CoCo), after approximately 7500 years of domestication, the global gene pair expression patterns in four major tissues (stems, leaves, flowers and siliques) of these three species were analyzed using an RNA sequencing approach. RESULTS: The results showed that the 'transcriptomic shock' phenomenon was alleviated in natural B. napus after approximately 7500 years of natural domestication, and most differentially expressed genes (DEGs) in B. napus were downregulated relative to those in its two diploid progenitors. The KEGG analysis indicated that three pathways related to photosynthesis were enriched in both comparison groups (AnAnCnCn vs ArAr and AnAnCnCn vs CoCo), and these pathways were all downregulated in four tissues of B. napus. In addition, homoeolog expression bias and expression level dominance (ELD) in B. napus were thoroughly studied through analysis of expression levels of 27,609 B. rapa-B. oleracea orthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napus maintained their expression pattern in two diploid progenitors, and approximately 78.1% of the gene pairs showed expression bias with a preference toward the A subgenome. Overall, an average of 48, 29.7 and 22.3% homologous gene pairs exhibited additive expression, ELD and transgressive expression in B. napus, respectively. The ELD bias varies from tissue to tissue; specifically, more gene pairs in stems and siliques showed ELD-A, whereas the opposite was observed in leaves and flowers. More transgressive upregulation, rather than downregulation, was observed in gene pairs of B. napus. CONCLUSIONS: In general, these results may provide a comprehensive understanding of the changes in homologous gene expression patterns in natural B. napus after approximately 7500 years of evolution and domestication and may enhance our understanding of allopolyploidy.

Automated interpretation of 3D laserscanned point clouds for plant organ segmentation.

BACKGROUND: Plant organ segmentation from 3D point clouds is a relevant task for plant phenotyping and plant growth observation. Automated solutions are required to increase the efficiency of recent high-throughput plant phenotyping pipelines. However, plant geometrical properties vary with time, among observation scales and different plant types. The main objective of the present research is to develop a fully automated, fast and reliable data driven approach for plant organ segmentation. RESULTS: The automated segmentation of plant organs using unsupervised, clustering methods is crucial in cases where the goal is to get fast insights into the data or no labeled data is available or costly to achieve. For this we propose and compare data driven approaches that are easy-to-realize and make the use of standard algorithms possible. Since normalized histograms, acquired from 3D point clouds, can be seen as samples from a probability simplex, we propose to map the data from the simplex space into Euclidean space using Aitchisons log ratio transformation, or into the positive quadrant of the unit sphere using square root transformation. This, in turn, paves the way to a wide range of commonly used analysis techniques that are based on measuring the similarities between data points using Euclidean distance. We investigate the performance of the resulting approaches in the practical context of grouping 3D point clouds and demonstrate empirically that they lead to clustering results with high accuracy for monocotyledonous and dicotyledonous plant species with diverse shoot architecture. CONCLUSION: An automated segmentation of 3D point clouds is demonstrated in the present work. Within seconds first insights into plant data can be deviated - even from non-labelled data. This approach is applicable to different plant species with high accuracy. The analysis cascade can be implemented in future high-throughput phenotyping scenarios and will support the evaluation of the performance of different plant genotypes exposed to stress or in different environmental scenarios.

Relações fisiológicas em mudas de pata-de-vaca (Bauhinia forficata Link) / Physiologic relationships in Brazilian Orchid Tree (Bauhinia forficata Link) seedlings

Os fatores ambientais, tais como: temperatura do ar, umidade relativa do ar e radiação solar, influenciam no comportamento fisiológico dos vegetais refletindo no seu crescimento e desenvolvimento. O objetivo do trabalho foi avaliar o comportamento fisiológico em mudas de pata-de-vaca ao longo do dia e constatar qual o melhor horário para a realização de determinações de trocas gasosas. Para tanto, foram realizadas avaliações de temperatura da folha, radiação fotossinteticamente ativa, resistência estomática e transpiração, utilizando-se um porômetro, das 8:00 às 17:00 horas, em intervalos de uma hora entre as medidas. A espécie apresenta oscilações no seu mecanismo fisiológico em função do horário de avaliação e das condições climáticas, sendo o intervalo mais indicado para a realização de determinações das trocas gasosas das 10:00 às 13:00 horas.

Environmental elements, such as air temperature, relative humidity and solar radiation, affect the physiological behavior of plants, which is reflected in their growth and development. The objective of this study was to evaluate the physiological changes of Brazilian Orchid Tree seedlings over a typical day and find the best time to carry out determinations of gas exchanges. For this end, we evaluated temperature of the leaf, photosynthetically active radiation, stomatal resistance and perspiration, using a porometer, from 8:00 a.m. to 05:00 p.m., in intervals of one hour between measurements. The species presents oscillations in its physiologic mechanism in function of the time of evaluation and climatic conditions, being the most suitable interval to determine gas exchanges from 10:00 a.m. to 01:00 p.m.

Surface feature based classification of plant organs from 3D laserscanned point clouds for plant phenotyping.

BACKGROUND: Laserscanning recently has become a powerful and common method for plant parameterization and plant growth observation on nearly every scale range. However, 3D measurements with high accuracy, spatial resolution and speed result in a multitude of points that require processing and analysis. The primary objective of this research has been to establish a reliable and fast technique for high throughput phenotyping using differentiation, segmentation and classification of single plants by a fully automated system. In this report, we introduce a technique for automated classification of point clouds of plants and present the applicability for plant parameterization. RESULTS: A surface feature histogram based approach from the field of robotics was adapted to close-up laserscans of plants. Local geometric point features describe class characteristics, which were used to distinguish among different plant organs. This approach has been proven and tested on several plant species. Grapevine stems and leaves were classified with an accuracy of up to 98%. The proposed method was successfully transferred to 3D-laserscans of wheat plants for yield estimation. Wheat ears were separated with an accuracy of 96% from other plant organs. Subsequently, the ear volume was calculated and correlated to the ear weight, the kernel weights and the number of kernels. Furthermore the impact of the data resolution was evaluated considering point to point distances between 0.3 and 4.0 mm with respect to the classification accuracy. CONCLUSION: We introduced an approach using surface feature histograms for automated plant organ parameterization. Highly reliable classification results of about 96% for the separation of grapevine and wheat organs have been obtained. This approach was found to be independent of the point to point distance and applicable to multiple plant species. Its reliability, flexibility and its high order of automation make this method well suited for the demands of high throughput phenotyping. HIGHLIGHTS: • Automatic classification of plant organs using geometrical surface information• Transfer of analysis methods for low resolution point clouds to close-up laser measurements of plants• Analysis of 3D-data requirements for automated plant organ classification.

Molecular characterization and expression analysis of the Rab GTPase family in Vitis vinifera reveal the specific expression of a VvRabA protein.

As a first step to investigate whether Rab GTPases are involved in grape berry development, the Vitis vinifera EST and gene databases were searched for members of the VvRab family. The grapevine genome was found to contain 26 VvRabs that could be distributed into all of the eight groups described in the literature for model plants. Genetic mapping was successfully performed; VvRabs were mostly located on independent chromosomes, apart from eight that were located on the as yet unassigned portions of the genome clustered in the ChrUn Random chromosome. Conserved and divergent regions between VvRab protein sequences were identified. Transcript expression of 11 VvRabs was analysed by real-time quantitative RT-PCR. Except for VvRabA5b, transcript expression was detected, in general, in all the organs investigated, but with different patterns. In grape berries, VvRab transcripts were expressed at all stages of fruit development, with different profiles, except in the case of members of the A family which displayed generally similar patterns. The response to growth regulators in cell cultures was generally specific to each VvRab, with a differential pattern of expression for ethylene, auxin, and abscisic acid according to the VvRab. Interestingly, and unexpectedly considering transcript expression, western blotting using a monoclonal antibody raised against AtRabA5c (ARA4) showed a specific expression in the exocarp of ripe grape berries, in all seven red and white berry varieties tested. By contrast, no expression was detected in any of the other organs or tissues investigated. This paper contains the first description of Rab GTPases in V. vinifera. The involvement of a specific VvRab in grape berry late development and the potential role of this Rab GTPase are discussed in relation to literature data.

The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant.

Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology. This facilitates cross species comparative studies and quantitative comparison of phenotypes and expression patterns. A major drawback is variable terminology that is used to describe plant anatomy and morphology in publications and genomic databases for different species. The same terms are sometimes applied to different plant structures in different taxonomic groups. Conversely, similar structures are named by their species-specific terms. To address this problem, we created the Plant Structure Ontology (PSO), the first generic ontological representation of anatomy and morphology of a flowering plant. The PSO is intended for a broad plant research community, including bench scientists, curators in genomic databases, and bioinformaticians. The initial releases of the PSO integrated existing ontologies for Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa); more recent versions of the ontology encompass terms relevant to Fabaceae, Solanaceae, additional cereal crops, and poplar (Populus spp.). Databases such as The Arabidopsis Information Resource, Nottingham Arabidopsis Stock Centre, Gramene, MaizeGDB, and SOL Genomics Network are using the PSO to describe expression patterns of genes and phenotypes of mutants and natural variants and are regularly contributing new annotations to the Plant Ontology database. The PSO is also used in specialized public databases, such as BRENDA, GENEVESTIGATOR, NASCArrays, and others. Over 10,000 gene annotations and phenotype descriptions from participating databases can be queried and retrieved using the Plant Ontology browser. The PSO, as well as contributed gene associations, can be obtained at www.plantontology.org.

Composição florística dos afloramentos rochosos do Morro do Forno, Altinópolis, São Paulo / Floristic composition of the rock outcrops of the Morro do Forno, Altinópolis-SP

Áreas de afloramentos rochosos em topos de morros abrigam uma vegetação bastante peculiar. Muitas das espécies que ocorrem nessas áreas apresentam uma série de características que permitem sua sobrevivência num ambiente com solo pobre e arenoso, com alta insolação e grande oscilação de temperatura entre o dia e a noite. Essas características particulares despertaram o interesse no estudo da flora das áreas de afloramentos rochosos do Morro do Forno (Altinópolis-SP). A flora apresenta um total de 157 espécies distribuídas em 48 famílias. Fabaceae (14 spp.), Asteraceae (12 spp.), Poaceae (12 spp.), Rubiaceae (11 spp.), Malpighiaceae (9 spp.) e Melastomataceae (8 spp.) são as famílias com o maior número de espécies. O estrato herbáceo-arbustivo caracteriza a área (61 por cento), seguido pelo arbóreo (19 por cento), sendo de menor representatividade as lianas (11 por cento) e os subarbustos (9 por cento). Muitas das espécies que ocorrem na área estão presentes em outros afloramentos rochosos brasileiros como, por exemplo, nos campos rupestres da Serra do Cipó e Serra da Canastra em Minas Gerais e nos cerrados rupestres da Chapada dos Guimarães no Mato Grosso.

Rock outcrops on the plateaus of hills have peculiar vegetation. The major part of the species occurring on these areas have various features that allow their survival under adverse environmental conditions as poor and sandy soil with intense solar radiation and great temperature ranging from day and night. These particular characteristics aroused the interest in the study of the flora on rock outcrops of Morro do Forno (Altinópolis-SP). A list of 157 species of 48 families was recorded. Fabaceae (14 spp.), Asteraceae (12 spp.), Poaceae (12 spp.), Rubiaceae (11 spp.), Malpighiaceae (9 spp.) and Melastomataceae (8 spp.) are the families with more number of species. The herbaceous-shruby stratum characterizes the area (61 percent), followed by arboreous (19 percent); lianas (11 percent) and subshruby (9 percent) are less representative. Many of the species occurring on the area are present another Brazilian rocky outcrops as, for example, the "campos rupestres" of the Minas Gerais state (Serra do Cipó and Serra da Canastra) and the "cerrados rupestres" of the Mato Grosso state (Chapada dos Guimarães).

Infrared spectroscopy as a tool for chemotaxonomic investigations within the Achillea millefolium group.

An FT-IR-based method for the rapid characterization and identification of Achillea species was developed. With the IR spectra of the CH2Cl2 extracts of A. aspleniifolia, A. collina, A. millefolium, A. millefolium ssp. sudetica, A. pannonica, A. pratensis, A. roseoalba, A. setacea, and A. styriaca, a spectrum library was created. This database allowed the identification of the respective taxa by comparison of IR spectra. Moreover, information concerning dominant structural elements of sesquiterpene constituents was obtained, providing hints about the composition of a plant sample of unknown origin.

A survey of potential huperzine A natural resources in China: the Huperziaceae.

The Huperziaceae is comprised of two genera, Huperzia and Phlegmariurus. Because of the content of Lycopodium alkaloids like huperzine A, which are used to treat a number of human ailments, plants of the Huperziaceae are experiencing a rapid decline in China, mostly due to over-harvesting. Because of this trend, we engaged from 1995 to 2001 in an investigation of the natural resources of the Huperziaceae in China. The main objectives of this study were: to catalog Huperziaceae plant resources including the occurrence, general distribution, and abundance of the various Huperziaceae species in China; and to determine traditional use and pharmaceutical values of each species. Twenty-nine species, 2 varieties, and 2 forma of Huperzia and 19 species of Phlegmariurus were identified through field investigation, collection, visits with local traditional doctors, and review of specimens in herbaria and of the literature. Ethnobotanical studies of these plants revealed that 33 of these species are used by the local communities for medicinal purposes. One species, Huperzia serrata, is one of the most popular. As a result, it is observing the greatest decline, mandating a change in collection practice and general attitude towards these plants. Introduction of conservation plans and training of the local communities regarding appropriate collection practices of these plants and their marketing in China are required to reverse the trend of decline among these species. In addition, development of cultivation or other propagation practices, such as in vitro propagation, would have the added benefits of socio-economic uplift of the local communities and sustainability of this important source of huperzine A.

Medicinal efficacy of plants utilized as temple food in traditional Korean Buddhism.

We investigated the medicinal efficacies of plants used as food in 27 Korean Buddhist temples from 1997 to 2002. We studied 161 species of plants belonging to 135 genera in 65 families. Twenty-one plant parts were utilized as food in 42 different preparations. Approximately 82% of the plants studied had medicinal effects, with a wide range of efficacies (126 types). Of the medicinal plants, 52% were used for digestive problems, circulatory illnesses, and respiratory diseases. These results demonstrate that a high proportion of the food consumed in Korean temples is medicinal, and is used for a wide variety of diseases.

Manual del botánico aficionado / Manual botanico amateur

El texto cuenta con siete partes que abarcan desde los conceptos básicos hasta cómo realizar estudios botánicos, incluyendo información sobre herbarios y jardines botánicos, además de explicar mapas de vegetación, sus utilidades y su importancia

Antimicrobial activity of essential oils isolated from Portuguese endemic species of Thymus.

AIMS: Thymus species are wild species mostly found in the arid lands of Portugal. Possible antimicrobial properties of Thymus essential oils have been investigated. The chemical composition of the essential oils and the antimicrobial activity of Thymus mastichina (L) L. subsp. mastichina, T. camphoratus and T. lotocephalus from different regions of Portugal were analysed. METHODS AND RESULTS: Hydrodistillation was used to isolate the essential oils and the chemical analyses were performed by gas chromatography (GC) and GC coupled to mass spectrometry. The antimicrobial activity was tested by the disc agar diffusion technique against Candida albicans, Escherichia coli, Listeria monocytogenes, Proteus mirabilis, Salmonella spp. and Staphylococcus aureus. Pure linalool, 1,8-cineole and a mixture (1 : 1) of these compounds were included. Linalool, 1,8-cineole or linalool/1,8-cineole and linalool/1,8-cineole/linalyl acetate were the major components of the essential oils, depending on the species or sampling place. The essential oils isolated from the Thymus species studied demonstrated antimicrobial activity but the micro-organisms tested had significantly different sensitivities. CONCLUSIONS: The antimicrobial activity of essential oils may be related to more than one component. SIGNIFICANCE AND IMPACT OF THE STUDY: Portuguese endemic species of Thymus can be used for essential oil production for food spoilage control, cosmetics and pharmaceutical use. Further studies will be required to elucidate the cell targets of the essential oil components.