GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified "baiting and iterative mapping" approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published plant datasets, we are able to reassemble the circular plastomes from 47 datasets using GetOrganelle. GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping. We also assemble complete mitochondrial genomes using GetOrganelle. GetOrganelle is freely released under a GPL-3 license ( https://github.com/Kinggerm/GetOrganelle ).

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Essential oils are complex mixtures isolated from aromatic plants which may possess antioxidant and anti-inflammatory activities of interest in thye food and cosmetic industries as well as in the human health field. In this work, a review was done on the most recent publications concerning their antioxidant and anti-inflammatory activities. At the same time a survey of the methods generally used for the evaluation of antioxidant activity and some of the mechanisms involved in the anti-inflammatory activities of essential oils are also reported.

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Polycyclic aromatic hydrocarbons (PAHs) are a large group of organic compounds with two or more fused aromatic rings. They have a relatively low solubility in water, but are highly lipophilic. Most of the PAHs with low vapour pressure in the air are adsorbed on particles. When dissolved in water or adsorbed on particulate matter, PAHs can undergo photodecomposition when exposed to ultraviolet light from solar radiation. In the atmosphere, PAHs can react with pollutants such as ozone, nitrogen oxides and sulfur dioxide, yielding diones, nitro- and dinitro-PAHs, and sulfonic acids, respectively. PAHs may also be degraded by some microorganisms in the soil. PAHs are widespread environmental contaminants resulting from incomplete combustion of organic materials. The occurrence is largely a result of anthropogenic emissions such as fossil fuel-burning, motor vehicle, waste incinerator, oil refining, coke and asphalt production, and aluminum production, etc. PAHs have received increased attention in recent years in air pollution studies because some of these compounds are highly carcinogenic or mutagenic. Eight PAHs (Car-PAHs) typically considered as possible carcinogens are: benzo(a)anthracene, chrysene, benzo(b)fluoranthene, benzo(k)fluoranthene, benzo(a)pyrene (B(a)P), dibenzo(a,h)anthracene, indeno(1,2,3-cd)pyrene and benzo(g,h,i)perylene. In particular, benzo(a)pyrene has been identified as being highly carcinogenic. The US Environmental Protection Agency (EPA) has promulgated 16 unsubstituted PAHs (EPA-PAH) as priority pollutants. Thus, exposure assessments of PAHs in the developing world are important. The scope of this review will be to give an overview of PAH concentrations in various environmental samples and to discuss the advantages and limitations of applying these parameters in the assessment of environmental risks in ecosystems and human health. As it well known, there is an increasing trend to use the behavior of pollutants (i.e. bioaccumulation) as well as pollution-induced biological and biochemical effects on human organisms to evaluate or predict the impact of chemicals on ecosystems. Emphasis in this review will, therefore, be placed on the use of bioaccumulation and biomarker responses in air, soil, water and food, as monitoring tools for the assessment of the risks and hazards of PAH concentrations for the ecosystem, as well as on its limitations.

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Background and aims After the initial boom in the application of flow cytometry in plant sciences in the late 1980s and early 1990s, which was accompanied by development of many nuclear isolation buffers, only a few efforts were made to develop new buffer formulas. In this work, recent data on the performance of nuclear isolation buffers are utilized in order to develop new buffers, general purpose buffer (GPB) and woody plant buffer (WPB), for plant DNA flow cytometry. Methods GPB and WPB were used to prepare samples for flow cytometric analysis of nuclear DNA content in a set of 37 plant species that included herbaceous and woody taxa with leaf tissues differing in structure and chemical composition. The following parameters of isolated nuclei were assessed: forward and side light scatter, propidium iodide fluorescence, coefficient of variation of DNA peaks, quantity of debris background, and the number of particles released from sample tissue. The nuclear genome size of 30 selected species was also estimated using the buffer that performed better for a given species. Key results In unproblematic species, the use of both buffers resulted in high quality samples. The analysis of samples obtained with GPB usually resulted in histograms of DNA content with higher or similar resolution than those prepared with the WPB. In more recalcitrant tissues, such as those from woody plants, WPB performed better and GPB failed to provide acceptable results in some cases. Improved resolution of DNA content histograms in comparison with previously published buffers was achieved in most of the species analysed. Conclusions WPB is a reliable buffer which is also suitable for the analysis of problematic tissues/species. Although GPB failed with some plant species, it provided high-quality DNA histograms in species from which nuclear suspensions are easy to prepare. The results indicate that even with a broad range of species, either GPB or WPB is suitable for preparation of high-quality suspensions of intact nuclei suitable for DNA flow cytometry.

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The use of and search for drugs and dietary supplements derived from plants have accelerated in recent years. Ethnopharmacologists, botanists, microbiologists, and natural-products chemists are combing the Earth for phytochemicals and "leads" which could be developed for treatment of infectious diseases. While 25 to 50% of current pharmaceuticals are derived from plants, none are used as antimicrobials. Traditional healers have long used plants to prevent or cure infectious conditions; Western medicine is trying to duplicate their successes. Plants are rich in a wide variety of secondary metabolites, such as tannins, terpenoids, alkaloids, and flavonoids, which have been found in vitro to have antimicrobial properties. This review attempts to summarize the current status of botanical screening efforts, as well as in vivo studies of their effectiveness and toxicity. The structure and antimicrobial properties of phytochemicals are also addressed. Since many of these compounds are currently available as unregulated botanical preparations and their use by the public is increasing rapidly, clinicians need to consider the consequences of patients self-medicating with these preparations.

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