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Plant Gene Seeker -PGS
Absolutely Fascinated for plant & genomes
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PLOS ONE: Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes

PLOS ONE: Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes | Plant Gene Seeker -PGS | Scoop.it

Next-generation sequencing plays a central role in the characterization and quantification of transcriptomes. Although numerous metrics are purported to quantify the quality of RNA, there have been no large-scale empirical evaluations of the major determinants of sequencing success. We used a combination of existing and newly developed methods to isolate total RNA from 1115 samples from 695 plant species in 324 families, which represents >900 million years of phylogenetic diversity from green algae through flowering plants, including many plants of economic importance. We then sequenced 629 of these samples on Illumina GAIIx and HiSeq platforms and performed a large comparative analysis to identify predictors of RNA quality and the diversity of putative genes (scaffolds) expressed within samples. Tissue types (e.g., leaf vs. flower) varied in RNA quality, sequencing depth and the number of scaffolds. Tissue age also influenced RNA quality but not the number of scaffolds ≥1000 bp. Overall, 36% of the variation in the number of scaffolds was explained by metrics of RNA integrity (RIN score), RNA purity (OD 260/230), sequencing platform (GAIIx vs HiSeq) and the amount of total RNA used for sequencing. However, our results show that the most commonly used measures of RNA quality (e.g., RIN) are weak predictors of the number of scaffolds because Illumina sequencing is robust to variation in RNA quality. These results provide novel insight into the methods that are most important in isolating high quality RNA for sequencing and assembling plant transcriptomes. The methods and recommendations provided here could increase the efficiency and decrease the cost of RNA sequencing for individual labs and genome centers.

 

PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.

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Policy Coherence for Food Security in Developing Countries- OECD

Policy Coherence for Food Security in Developing Countries- OECD | Plant Gene Seeker -PGS | Scoop.it

Policy Coherence for Food Security in Developing Countries

Introductory remarks by Angel Gurría, OECD Secretary-General at the OECD Global Forum on Agriculture 2012

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Misexpression of a PISTILLATA-like MADS-box gene prevents fruit development in grapevine - Fernandez - The Plant Journal - Wiley Online Library

Misexpression of a PISTILLATA-like MADS-box gene prevents fruit development in grapevine - Fernandez - The Plant Journal - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it

Summary
The FLESHLESS BERRY (FLB) somatic variant identified in the grapevine cultivar Ugni Blanc develops grape berries without flesh suggesting a role for the altered gene in the differentiation of flesh cells. Here we report the identification of the molecular defect responsible for this phenotype. Using a combination of genetic and transcriptomic approaches we detected the presence of a miniature inverted-repeat transposable element insertion in the promoter region of the PISTILLATA-like (VvPI) gene the grapevine homolog of Arabidopsis PISTILLATA. The transposon insertion causes specific ectopic expression of the corresponding VvPI allele during early fruit development causing the expression of genes specific for petal and stamen development within the fruit. Causal relationship between the insertion and the phenotype was demonstrated by the phenotypic and molecular analyses of somatic revertants showing that ectopic expression and mutant phenotype were always linked to the presence of the transposon insertion. The different phenotypic effects of the flb mutation on ovary morphology, fruit set and fruit development, depending on the cell lineage affected, are presented with each phenotype offering unique insights into floral and fleshly fruit development. The results highlight the importance of VvPI repression after fertilization to achieve normal fleshy fruit development and the complex genetic, genomic and cellular interactions for the flower to fruit transition in grapevine.

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Find A PhD Project: Temperature- regulation of plant root development at University of Bristol

Find A PhD Project: Temperature- regulation of plant root development at University of Bristol | Plant Gene Seeker -PGS | Scoop.it
Apply for a PhD in: Temperature- regulation of plant root development at School of Biological Sciences; University of Bristol...
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Clocks are ticking and climate is changing: Increasing plant productivity in a changing climate

Clocks are ticking and climate is changing: Increasing plant productivity in a changing climate | Plant Gene Seeker -PGS | Scoop.it
Scientists are looking to cellular biological clocks as a target for genetic modification for increasing plant productivity.
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Fundamental dilemma facing world agriculture over the next decade

Fundamental dilemma facing world agriculture over the next decade | Plant Gene Seeker -PGS | Scoop.it
AN increasing number of plant species are under threat from the demands being put on agriculture to produce more food to support the growing world population which is increasing by 160,000 every day.

Via Rob Dawson, Mary Williams
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World Changing Ideas 2012

World Changing Ideas 2012 | Plant Gene Seeker -PGS | Scoop.it
10 innovations that are radical enough to alter our lives...

Via S. Diez de Medina
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New allelic variants found in key rice salt-tolerance genes: an association study - Negrão - 2012 - Plant Biotechnology Journal - Wiley Online Library

New allelic variants found in key rice salt-tolerance genes: an association study - Negrão - 2012 - Plant Biotechnology Journal - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it

"Salt stress is a complex physiological trait affecting plants by limiting growth and productivity. Rice, one of the most important food crops, is rated as salt-sensitive. High-throughput screening methods are required to exploit novel sources of genetic variation in rice and further improve salinity tolerance in breeding programmes. To search for genotypic differences related to salt stress, we genotyped 392 rice accessions by EcoTILLING. We targeted five key salt-related genes involved in mechanisms such as Na+/K+ ratio equilibrium, signalling cascade and stress protection, and we found 40 new allelic variants in coding sequences. By performing association analyses using both general and mixed linear models, we identified 11 significant SNPs related to salinity. We further evaluated the putative consequences of these SNPs at the protein level using bioinformatic tools. Amongst the five nonsynonymous SNPs significantly associated with salt-stress traits, we found a T67K mutation that may cause the destabilization of one transmembrane domain in OsHKT1;5, and a P140A alteration that significantly increases the probability of OsHKT1;5 phosphorylation. The K24E mutation can putatively affect SalT interaction with other proteins thus impacting its function. Our results have uncovered allelic variants affecting salinity tolerance that may be important in breeding."


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Vf scab resistance of Malus - Online First - Springer

Vf scab resistance of Malus - Online First - Springer | Plant Gene Seeker -PGS | Scoop.it

The apple production in temperate regions with spring rains, the Scab caused by the fungus Venturia inaequalis is the most important constraint. To produce spotless apples and avoid damage that develops during storage, growers apply fungicide on a regular or weather-determined basis. All major apple cultivars are highly susceptible to this disease. To limit the need for fungicide applications, apple breeders are currently introgressing disease resistance from wild Malus accessions into commercial lines. The first attempts to do this were made 100 years ago. As apples are self-incompatible, pseudo-backcrossing is used to eliminate unwanted traits from wild Malus and select new cultivars that are attractive to both producers and consumers. This process, from the first cross of a commercial cultivar with a wild, disease-resistant Malus, is extremely long due to apple’s long juvenile phase, the need for more than seven backcross steps and the high heterozygosity of this genus. Therefore, most of today’s scab-resistant cultivars rely on a single introduction of scab resistance from Malus floribunda 821, referred to as Vf. In this paper, we trace the history of Vf from its initial identification through its use in breeding and commercial production. We sum up the literature describing how and where Vf resistance has been overcome by new pathotypes of V. inaequalis. Finally, we describe the current knowledge of the genes behind Vf resistance, its mode of action and the use of Vf genes in gene technology.


Via Jean-Pierre Zryd
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PLOS Genetics: Plant Vascular Cell Division Is Maintained by an Interaction between PXY and Ethylene Signalling

PLOS Genetics: Plant Vascular Cell Division Is Maintained by an Interaction between PXY and Ethylene Signalling | Plant Gene Seeker -PGS | Scoop.it

The procambium and cambium are meristematic tissues from which vascular tissue is derived. Vascular initials differentiate into phloem towards the outside of the stem and xylem towards the inside. A small peptide derived from CLV-3/ESR1-LIKE 41 (CLE41) is thought to promote cell divisions in vascular meristems by signalling through the PHLOEM INTERCALLATED WITH XYLEM (PXY) receptor kinase. pxy mutants, however, display only small reductions in vascular cell number, suggesting a mechanism exists that allows plants to compensate for the absence of PXY. Consistent with this idea, we identify a large number of genes specifically upregulated in pxy mutants, including several AP2/ERF transcription factors. These transcription factors are required for normal cell division in the cambium and procambium. These same transcription factors are also upregulated by ethylene and in ethylene-overproducing eto1 mutants. eto1 mutants also exhibit an increase in vascular cell division that is dependent upon the function of at least 2 of these ERF genes. Furthermore, blocking ethylene signalling using a variety of ethylene insensitive mutants such as ein2 enhances the cell division defect of pxy. Our results suggest that these factors define a novel pathway that acts in parallel to PXY/CLE41 to regulate cell division in developing vascular tissue. We propose a model whereby vascular cell division is regulated both by PXY signalling and ethylene/ERF signalling. Under normal circumstances, however, PXY signalling acts to repress the ethylene/ERF pathway.

 

PLOS Genetics is an open-access journal

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PLOS ONE: Genome-Wide Survey and Expression Analysis of Amino Acid Transporter Gene Family in Rice (Oryza sativa L.)

PLOS ONE: Genome-Wide Survey and Expression Analysis of Amino Acid Transporter Gene Family in Rice (Oryza sativa L.) | Plant Gene Seeker -PGS | Scoop.it

"Comprehensive analyses were performed to investigate the expression profiles of OsAAT genes in various stages of vegetative and reproductive development by using data from EST, Microarrays, MPSS and Real-time PCR. Many OsAAT genes exhibited abundant and tissue-specific expression patterns. Moreover, 21 OsAAT genes were found to be differentially expressed under the treatments of abiotic stresses. Comparative analysis indicates that 26 AAT genes with close evolutionary relationships between rice and Arabidopsis exhibited similar expression patterns."


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The potential of beneficial microorganisms in agricultural systems - Andrews - 2011 - Annals of Applied Biology - Wiley Online Library

The potential of beneficial microorganisms in agricultural systems - Andrews - 2011 - Annals of Applied Biology - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it

Problems and concerns in relation to the use of inorganic fertilisers, irrigation, herbicides and pesticides have led to the search for alternative strategies to combat limiting soil nutrient and water levels and the effects of weeds and pests on crops. Microorganisms can improve crop nutrition and the ability of crops to resist biotic and abiotic stress. Thus, greater utilisation of microorganisms in agricultural systems has the potential to allow reductions in the use of inorganic fertilisers, water, herbicides and pesticides. Here, we introduce a Virtual Special Issue of Annals of Applied Biology featuring seven recently published papers in this journal, which focused on the utilisation of positive plant microbial interactions in agricultural systems (Andrews et al., 2010, 2011; Dodd et al., 2010; Newton et al., 2010; Novak, 2010; Raven, 2010; Tikhonovich & Provorov, 2011). We also highlight cases within and outside these papers where microorganisms have been utilised as a viable alternative to chemical inputs into agricultural systems or have had a substantial impact on chemical losses from them.

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CSH Press: Genome Science: A Practical and Conceptual Introduction to Molecular Genetic Analysis in Eukaryotes

CSH Press: Genome Science: A Practical and Conceptual Introduction to Molecular Genetic Analysis in Eukaryotes | Plant Gene Seeker -PGS | Scoop.it

I haven't looked at this book beyond the ToC and preview availabe on this page, but it looks like it might be of interest to plant biologists It's a "textbook and lab manual" - here's what the publisher says:

 

"Genome Science is a textbook and laboratory manual for advanced secondary and post-secondary education. It combines approachable narrative with extensively tested lab exercises that illustrate key concepts of genome biology in humans, invertebrates, and plants.

 Eighteen labs, organized into four chapters, engage students with both bioinformatics exercises and in vitro experiments. Each chapter also includes an extensive introduction that provides an historical and conceptual framework. This modular structure offers many options for enhancing existing courses, starting new courses, or supporting student research projects. The book is complete with advice for instructors, laboratory planning guidelines, recipes for solutions, and answers to student questions."

 

All that for only $55!


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Molecular elements of low-oxygen signaling in plants

Molecular elements of low-oxygen signaling in plants | Plant Gene Seeker -PGS | Scoop.it

Oxygen and its limitation are emerging as a crucial factor in plant fitness, growth and development. Recent studies revealed the mechanisms by which oxygen is perceived by plant cells. This sensory system partly relies on an oxygen mediated branch of the N-end rule pathway for protein degradation acting on a specific clade of Ethylene Responsive Transcription Factors (ERF-VII). A complementary regulative step is provided by aerobic sequestration of an ERF-VII protein at the plasma membrane and its timely release when hypoxia occurs. Complete absence of oxygen triggers the transient accumulation of reactive hydrogen peroxide and induces an additional set of ROS-related genes involved in both signaling and attenuation of oxidative-stress. Moreover, temporary hypoxic environments that are built up as consequence of dense cell-packing have been demonstrated to trigger cell-fate determination in maize anthers. Similarly, limited oxygen delivery in bulky fruit or tuber tissues growing in aerobic conditions were shown to stimulate anaerobic-like responses. These advances in low oxygen signaling and its effect on cell-development highlight the importance of taking hypoxia into account in agronomical practices as well as in breeding programs.

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Engineering nitrogen use efficient crop plants: the current status - McAllister - 2012 - Plant Biotechnology Journal - Wiley Online Library

Engineering nitrogen use efficient crop plants: the current status - McAllister - 2012 - Plant Biotechnology Journal - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it

Summary
In the last 40 years the amount of synthetic nitrogen (N) applied to crops has risen drastically, resulting in significant increases in yield but with considerable impacts on the environment. A requirement for crops that require decreased N fertilizer levels has been recognized in the call for a ‘Second Green Revolution’ and research in the field of nitrogen use efficiency (NUE) has continued to grow. This has prompted a search to identify genes that improve the NUE of crop plants, with candidate NUE genes existing in pathways relating to N uptake, assimilation, amino acid biosynthesis, C/N storage and metabolism, signalling and regulation of N metabolism and translocation, remobilization and senescence. Herein is a review of the approaches taken to determine possible NUE candidate genes, an overview of experimental study of these genes as effectors of NUE in both cereal and non-cereal plants and the processes of commercialization of enhanced NUE crop plants. Patents issued regarding increased NUE in plants as well as gene pyramiding studies are also discussed as well as future directions of NUE research.

 

OpenAccess

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Special Issue: Nutrient Sensing in Plants

Special Issue: Nutrient Sensing in Plants | Plant Gene Seeker -PGS | Scoop.it

"Higher plants require a number of essential nutrient elements for completing their life cycles. Mineral nutrients are mainly acquired by roots from the rhizosphere and are subsequently distributed to shoots. To cope with nutrient limitations, plants have evolved a set of elaborate responses consisting of sensing mechanisms and signaling processes to perceive and adapt to external nutrient availability."


Via Plant Breeding and Genomics News
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Current Opinion in Creativity, Innovation and Entrepreneurship (CUOCIENT) Vol 1, No 2 (2012)

Current Opinion in Creativity, Innovation and Entrepreneurship (CUOCIENT) Vol 1, No 2 (2012) | Plant Gene Seeker -PGS | Scoop.it

Current Opinion in Creativity, Innovation and Entrepreneurship (CUOCIENT) is a monthly online, international journal. The objectives of CUOCIENT are to stimulate interdisciplinary, multi-scale debate and exchange of ideas related to creativity, innovation and entrepreneurship (CIE) issues. 


Via S. Diez de Medina
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Climate change: It's even worse than we thought - New Scientist

Climate change: It's even worse than we thought - New Scientist | Plant Gene Seeker -PGS | Scoop.it

Five years ago, the last report of the Intergovernmental Panel on Climate Change painted a gloomy picture of our planet’s future. As climate scientists gather evidence for the next report, due in 2014, Michael Le Page gives seven reasons why things are looking even grimmer

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Trends in Ecology and Evolution - Ecological intensification: harnessing ecosystem services for food security

RT @plantbiology: Trends in Ecology and Evolution 'Ecological intensification: harnessing ecosystem services for food security' http://t.co/q60UgZzg...

Via Luigi Guarino
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Volatile isoprenoid emissions from plastid to planet - Harrison - 2012 - New Phytologist - Wiley Online Library

Volatile isoprenoid emissions from plastid to planet - Harrison - 2012 - New Phytologist - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it

Approximately 1–2% of net primary production by land plants is re-emitted to the atmosphere as isoprene and monoterpenes. These emissions play major roles in atmospheric chemistry and air pollution–climate interactions. Phenomenological models have been developed to predict their emission rates, but limited understanding of the function and regulation of these emissions has led to large uncertainties in model projections of air quality and greenhouse gas concentrations. We synthesize recent advances in diverse fields, from cell physiology to atmospheric remote sensing, and use this information to propose a simple conceptual model of volatile isoprenoid emission based on regulation of metabolism in the chloroplast. This may provide a robust foundation for scaling up emissions from the cellular to the global scale.


Via Jean-Pierre Zryd
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Receptor properties and features of cytokinin s... [Acta Naturae. 2012] - PubMed - NCBI

Cytokinins belong to one of the most important and well-known classes of plant hormones. Discovered over half a century ago, cytokinins have retained the attention of researchers due to the variety of the effects they have on the growth and development of vegetable organisms, their participation in a plant adaptation to external conditions, and the potential to be used in biotechnology, agriculture, medicine and even cosmetics. The molecular mechanism by which cytokinins function remained unknown for a long time. Things started to change only in the 21(st)century, after the discovery of the receptors for these phytohormones. It appeared that plants found ways to adapt a two-component signal transduction system borrowed from prokaryotic organisms for cytokinin signalling. This review covers the recent advances in research of the molecular basis for the perception and transduction of the cytokinin signal. Emphasis is placed on cytokinin receptors, their domain and three-dimensional structures, subcellular localization, signalling activity, effect of mutations, ligand-binding properties, and phylogeny.


Free PMC Article

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GRAST 1.0 - Genome Reduction Analysing Software Tool

GRAST 1.0 - Genome Reduction Analysing Software Tool | Plant Gene Seeker -PGS | Scoop.it
3D molecular model · Alignment / BLAST · Assembly Tools · Bio-chemical / Engineering · Bioinformatics Platform · Cluster Analysis · Cytometry / Cell · DNA / Genome Analysis · Education & Fun · File Conversion · Genetics & ...

Via Biswapriya Biswavas Misra
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PLOS ONE: Bioinformatic Analysis of Epigenetic and MicroRNA Mediated Regulation of Drought Responsive Genes in Rice

PLOS ONE: Bioinformatic Analysis of Epigenetic and MicroRNA Mediated Regulation of Drought Responsive Genes in Rice | Plant Gene Seeker -PGS | Scoop.it

Drought stress response is a complex trait regulated at multiple levels. Changes in the epigenetic and miRNA regulatory landscape can dramatically alter the outcome of a stress response. However, little is known about the scope and extent of these regulatory factors on drought related cellular processes and functions. To this end, we selected a list of 5468 drought responsive genes (DRGs) of rice identified in multiple microarray studies and mapped the DNA methylation regions found in a genome wide methylcytosine immunoprecipitation and sequencing (mCIP-Seq) study to their genic and promoter regions, identified the chromatin remodeling genes and the genes that are targets of miRNAs. We found statistically significant enrichment of DNA methylation reads and miRNA target sequences in DRGs compared to a random set of genes. About 75% of the DRGs annotated to be involved in chromatin remodeling were downregulated. We found one-third of the DRGs are targeted by two-thirds of all known/predicted miRNAs in rice which include many transcription factors targeted by more than five miRNAs. Clustering analysis of the DRGs with epigenetic and miRNA features revealed, upregulated cluster was enriched in drought tolerance mechanisms while the downregulated cluster was enriched in drought resistance mechanisms evident by their unique gene ontologies (GOs), protein-protein interactions (PPIs), specific transcription factors, protein domains and metabolic pathways. Further, we analyzed the proteome of two weeks old young rice plants treated with a global demethylating agent, 5-azacytidine (5-azaC), subjected to drought stress and identified 56 protein spots that are differentially expressed. Out of the 56 spots, 35 were differently expressed in the sample with both demethylation and drought stress treatments and 28 (50%) were part of DRGs considered in the bioinformatic analysis.

 

PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.

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Xylella fastidiosa Virtual Issue

Free access to key papers on the bacterial pathogen, Xylella fastidiosa, published in Phytopathology, Plant Disease, and Molecular Plant-Microbe Interactions for a limited time.


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PLOS ONE: Diuretics Prime Plant Immunity in Arabidopsis thaliana

PLOS ONE: Diuretics Prime Plant Immunity in Arabidopsis thaliana | Plant Gene Seeker -PGS | Scoop.it

Plant activators are agrochemicals that activate the plant immune system, thereby enhancing disease resistance. Due to their prophylactic and durable effects on a wide spectrum of diseases, plant activators can provide synergistic crop protection when used in combination with traditional pest controls. Although plant activators have achieved great success in wet-rice farming practices in Asia, their use is still limited. To isolate novel plant activators applicable to other crops, we screened a chemical library using a method that can selectively identify immune-priming compounds. Here, we report the isolation and characterization of three diuretics, bumetanide, bendroflumethiazide and clopamide, as immune-priming compounds. These drugs upregulate the immunity-related cell death of Arabidopsis suspension-cultured cells induced with an avirulent strain of Pseudomonas syringae pv. tomato in a concentration-dependent manner. The application of these compounds to Arabidopsis plants confers disease resistance to not only the avirulent but also a virulent strain of the pathogen. Unlike salicylic acid, an endogenous phytohormone that governs disease resistance in response to biotrophic pathogens, the three diuretic compounds analyzed here do not induce PR1 or inhibit plant growth, showing potential as lead compounds in a practical application.

 

PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.

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