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Concept: Botany


Hexachlorocyclohexane (HCH) has been used for plant protection and sanitation world-widely, and its isomers have been detected in water, soil, and air as well as in vegetation. As a sink for lipophilic pollutants, vegetation is very important for the degradation and fate of organic contamination; however, little was known about their phytotoxicity and mechanisms of toxic effect. In this study, the stereoselective phototoxicity of four isomers (α, β, γ, and δ) of HCHs mediated by independent as well as interconnecting systems of photosynthesis and enzymatic antioxidant defense system in Arabidopsis thaliana were assessed.

Concepts: Plant, Botany


The Italian herbal products market is the most prosperous in Europe. The proof is represented by the use of these products in several marketing categories, ranging from medicine to nutrition and cosmetics. Market and legislation in Italy are at the same time cause and consequence of this peculiar situation. In fact, the legislation on botanical food supplements in Italy is very permissive and at the same time the market shows an overall satisfaction of users and strong feedback in terms of consumption, which brings a widening use of medicinal plants, formerly the prerogative of pharmaceuticals, to other fields such as nutrition. This review summarizes the market and normative panorama of herbal products in Italy, highlighting the blurred boundaries of health indications, marketing authorizations and quality controls between herbal medicines and non pharmaceutical products, such as food supplements, cosmetics and other herbal-based “parapharmaceuticals”.

Concepts: Pharmacology, Medicine, Botany, Pharmaceutical drug, Herbalism, Herb, Pharmacy, Food and Drug Administration


Many studies have reported the phytotoxicity of allelopathic compounds under controlled conditions. However, more field studies are required to provide realistic evidences for the significance of allelopathic interference in natural communities. We conducted a 2-years field experiment in a semiarid plant community (NE Spain). Specifically, we planted juvenile individuals and sowed seeds of Salsola vermiculata L., Lygeum spartum L. and Artemisia herba-alba Asso. (three co-dominant species in the community) beneath adult individuals of the allelopathic shrub A. herba-alba, and assessed the growth, vitality, seed germination and seedling survival of those target species with and without the presence of chemical interference by the incorporation of activated carbon (AC) to the soil. In addition, juveniles and seeds of the same three target species were planted and sown beneath the canopy of adults of S. vermiculata (a shrub similar to A. herba-alba, but non-allelopathic) and in open bare soil to evaluate whether the allelopathic activity of A. herba-alba modulates the net outcome of its interactions with neighboring plants under contrasting abiotic stress conditions. We found that vitality of A. herba-alba juveniles was enhanced beneath A. herba-alba individuals when AC was present. Furthermore, we found that the interaction outcome in A. herba-alba microsite was neutral, whereas a positive outcome was found for S. vermiculata microsite, suggesting that allelopathy may limit the potential facilitative effects of the enhanced microclimatic conditions in A. herba-alba microsite. Yet, L. spartum juveniles were facilitated in A. herba-alba microsite. The interaction outcome in A. herba-alba microsite was positive under conditions of very high abiotic stress, indicating that facilitative interactions predominated over the interference of allelopathic plants under those conditions. These results highlight that laboratory studies can overestimate the significance of allelopathy in nature, and consequently, results obtained under controlled conditions should be interpreted carefully.

Concepts: Plant, Botany, Seed, Plant morphology, Germination, Seedling, Weed, Allelopathy


The use of chemical genomics approaches allows the identification of small molecules that integrate into biological systems, thereby changing discrete processes that influence growth, development or metabolism. Libraries of chemicals are applied to living systems, and changes in phenotype are observed, potentially leading to the identification of new growth regulators. This work describes an approach that is the nexus of chemical-genomics and synthetic biology. Here each plant in an extensive population synthesizes a unique small peptide arising from a transgene composed of a randomized nucleic acid sequence core, flanked by translational start, stop, and cysteine-encoding (for disulfide cyclization) sequences. Ten and sixteen amino acid sequences, bearing a core of six and twelve random amino acids, have been synthesized in Arabidopsis thaliana plants. Populations were screened for phenotypes from seedling stage through senescence. Dozens of phenotypes were observed in over 2000 plants analyzed. Ten conspicuous phenotypes were verified through separate transformation and analysis of multiple independent lines. The results indicate that these populations contain sequences that often influence discrete aspects of plant biology. Novel peptides that affect photosynthesis, flowering, and red light response are described. The challenge now is to identify the mechanistic integrations of these peptides into biochemical processes. These populations serve as a new tool to identify small molecules that modulate discrete plant functions that could be later produced in transgenic plants or potentially applied exogenously to impart their effects. These findings could usher in a new generation of agricultural growth regulators, herbicides, or defense compounds.

Concepts: Protein, Gene, Evolution, Amino acid, Metabolism, Botany, Arabidopsis thaliana, Biochemistry


We present EU-Forest, a dataset that integrates and extends by almost one order of magnitude the publicly available information on European tree species distribution. The core of our dataset (~96% of the occurrence records) came from an unpublished, large database harmonising forest plot surveys from National Forest Inventories on an INSPIRE-compliant 1 km×1 km grid. These new data can potentially benefit several disciplines, including forestry, biodiversity conservation, palaeoecology, plant ecology, the bioeconomy, and pest management.

Concepts: Biodiversity, Conservation biology, Evolution, Species, Plant, Ecology, Botany, Tree


LEGO bricks are commercially available interlocking pieces of plastic that are conventionally used as toys. We describe their use to build engineered environments for cm-scale biological systems, in particular plant roots. Specifically, we take advantage of the unique modularity of these building blocks to create inexpensive, transparent, reconfigurable, and highly scalable environments for plant growth in which structural obstacles and chemical gradients can be precisely engineered to mimic soil.

Concepts: Species, Plant, Botany, Tree, Root, Toy, Civil engineering, Lego


A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data, and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (, a visual analytic tool for exploring multiple levels of Arabidopsis data through a zoomable user interface. ePlant connects to several publicly available web services to download genome, proteome, interactome, transcriptome, and 3D molecular structure data for one or more genes or gene products of interest. Data are displayed with a set of visualization tools that are presented using a conceptual hierarchy from big to small, and many of the tools combine information from more than one data type. We describe the development of ePlant in this paper and present several examples illustrating its integrative features for hypothesis generation. We also describe the process of deploying ePlant as an “app” on Araport. Building on readily available web services, the code for ePlant is freely available for any other biological species research.

Concepts: DNA, Gene, Biology, Organism, Genome, Species, Botany, User interface


Arsenic is a toxic metalloid and recognized carcinogen. Arsenate and arsenite are the most common arsenic species available for uptake by plants. As an inorganic phosphate (Pi) analog, arsenate is acquired by plant roots through endogenous Pi transport systems. Inside the cell, arsenate is reduced to the thiol-reactive form arsenite. Glutathione (GSH)-conjugates of arsenite may be extruded from the cell or sequestered in vacuoles by members of the ATP-binding cassette (ABC) family of transporters. In the present study we sought to enhance both plant arsenic uptake through Pi transporter overexpression, and plant arsenic tolerance through ABC transporter overexpression. We demonstrate that Arabidopsis thaliana plants overexpressing the high-affinity Pi transporter family members, AtPht1;1 or AtPht1;7, are hypersensitive to arsenate due to increased arsenate uptake. These plants do not exhibit increased sensitivity to arsenite. Co-overexpression of the yeast ABC transporter YCF1 in combination with AtPht1;1 or AtPht1;7 suppresses the arsenate-sensitive phenotype while further enhancing arsenic uptake. Taken together, our results support an arsenic transport mechanism in which arsenate uptake is increased through Pi transporter overexpression, and arsenic tolerance is enhanced through YCF1-mediated vacuolar sequestration. This work substantiates the viability of coupling enhanced uptake and vacuolar sequestration as a means for developing a prototypical engineered arsenic hyperaccumulator.

Concepts: Photosynthesis, Plant, Botany, Arabidopsis thaliana, Arabidopsis, Transport, Root, Arsenic


A potential DNA barcode, ITS2, was studied to discriminate herbal materials to confirm their identities and ensure their safe application in pharmaceuticals. Here, a total of 4385 samples of 2431 species were collected, and these samples are from 61 commonly used herbs and their closely related species or adulterants. Based on assessments of the extent of genetic divergence, the DNA barcoding gap and the ability for species discrimination, our results suggest that ITS2 is a powerful tool for distinguishing herbs. For the first dataset including 61 herbs, ITS2 correctly identified 100 % of them. For the second dataset containing 51 herbs and their 2382 closely related species, ITS2 could discriminate correctly 48 herbs from their closely related species. For the third dataset comprising 34 herbs and their 111 adulterants, ITS2 could distinguish successfully all the herbs from their adulterants. In conclusion, the ITS2 region is an efficient marker for the authentication of herbal materials, and our study will accelerate the process of the application of the DNA barcoding technique in differentiating herbs.

Concepts: DNA, Genetics, Bioinformatics, Species, Botany, DNA barcoding, Cryptic species complex, Identification


BACKGROUND: Landscape ethnoecology focuses on the ecological features of the landscape, how the landscape is perceived, and used by people who live in it. Though studying folk classifications of species has a long history, the comparative study of habitat classifications is just beginning. I studied the habitat classification of herders in a Hungarian steppe, and compared it to classifications of botanists and laymen. METHODS: For a quantitative analysis the picture sort method was used. Twenty-three pictures of 7-11 habitat types were sorted by 25 herders. ‘Density’ of pictures along the habitat gradient of the Hortobagy salt steppe was set as equal as possible, but pictures differed in their dominant species, wetness, season, etc. Before sorts, herders were asked to describe pictures to assure proper recognition of habitats. RESULTS: Herders classified the images into three main (and 6 smaller) groups: (1) fertile habitats at the higher parts of the habitat gradient (partos, lit. on the shore); (2) saline habitats (szik, lit. salt or saline place), and (3) meadows and marshes (lapos, lit. flooded) at the lower end of the habitat gradient. Sharpness of delimitation changed along the gradient. Saline habitats were the most isolated from the rest. Botanists identified 6 groups. Laymen grouped habitats in a less coherent way. As opposed to my expectations, botanical classification was not more structured than that done by herders. I expected and found high correspondence between the classifications by herders, botanists and laymen. All tended to recognize similar main groups: wetlands, “good grass” and dry/saline habitats. Two main factors could have been responsible for similar classifications: salient features correlated (e.g. salinity recognizable by herders and botanists but not by laymen correlated with the density of grasslands or height of vegetation recognizable also for laymen), or the same salient features were used as a basis for sorting (wetness, and abiotic stress). CONCLUSIONS: Despite all the difficulties of studying habitat classifications (more implicit, more variable knowledge than knowledge on species), conducting landscape ethnoecological research will inevitably reveal a deeper human understanding of biological organization at a supraspecific level, where natural discontinuities are less sharp than at the species or population level.

Concepts: Biology, Species, Botany, Vegetation, Grassland, Biological classification, Hungary, Habitat fragmentation