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Rescooped by wangzuoqian from Publications!

bioRxiv: The MoT3 assay does not distinguish between Magnaporthe oryzae wheat and rice blast isolates from Bangladesh (2018)

bioRxiv: The MoT3 assay does not distinguish between Magnaporthe oryzae wheat and rice blast isolates from Bangladesh (2018) | wangzuoqian |

The blast fungus Magnaporthe oryzae is comprised of lineages that exhibit varying degrees of specificity on about 50 grass hosts, including rice, wheat and barley. Reliable diagnostic tools are essential given that the pathogen has a propensity to jump to new hosts and spread to new geographic regions. Of particular concern is wheat blast, which has suddenly appeared in Bangladesh in 2016 before spreading to neighboring India. In these Asian countries, wheat blast strains are now co-occurring with the destructive rice blast pathogen raising the possibility of genetic exchange between these destructive pathogens. We assessed the recently described MoT3 diagnostic assay and found that it did not distinguish between wheat and rice blast isolates from Bangladesh. The assay is based on primers matching the WB12 sequence corresponding to a fragment of the M. oryzae MGG_02337 gene annotated as a short chain dehydrogenase. These primers could not reliably distinguish between wheat and rice blast isolates from Bangladesh based on DNA amplification experiments performed in separate laboratories in Bangladesh and in the UK. In addition, comparative genomics of the WB12 sequence revealed a complex underlying genetic structure with related sequences across M. oryzae strains and in both rice and wheat blast isolates. We, therefore, caution against the indiscriminate use of this assay to identify wheat blast.

Via Kamoun Lab @ TSL
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Plant-derived antifungal agent poacic acid targets β-1,3-glucan

Plant-derived antifungal agent poacic acid targets β-1,3-glucan | wangzuoqian |

The search for new antifungal compounds is struggling to keep pace with emerging fungicide resistance. Through chemoprospecting of an untapped reservoir of inhibitory compounds, lignocellulosic hydrolysates, we have identified a previously undescribed antifungal agent, poacic acid. Using both chemical genomics and morphological analysis together for the first time, to our knowledge, we identified the cellular target of poacic acid as β-1,3-glucan. Through its action on the glucan layer of fungal cell walls, poacic acid is a natural antifungal agent against economically significant fungi and oomycete plant pathogens. This work highlights the chemical diversity within lignocellulosic hydrolysates as a source of potentially valuable chemicals.

A rise in resistance to current antifungals necessitates strategies to identify alternative sources of effective fungicides. We report the discovery of poacic acid, a potent antifungal compound found in lignocellulosic hydrolysates of grasses. Chemical genomics using Saccharomyces cerevisiae showed that loss of cell wall synthesis and maintenance genes conferred increased sensitivity to poacic acid. Morphological analysis revealed that cells treated with poacic acid behaved similarly to cells treated with other cell wall-targeting drugs and mutants with deletions in genes involved in processes related to cell wall biogenesis. Poacic acid causes rapid cell lysis and is synergistic with caspofungin and fluconazole. The cellular target was identified; poacic acid localized to the cell wall and inhibited β-1,3-glucan synthesis in vivo and in vitro, apparently by directly binding β-1,3-glucan. Through its activity on the glucan layer, poacic acid inhibits growth of the fungi Sclerotinia sclerotiorum and Alternaria solani as well as the oomycete Phytophthora sojae. A single application of poacic acid to leaves infected with the broad-range fungal pathogen S. sclerotiorum substantially reduced lesion development. The discovery of poacic acid as a natural antifungal agent targeting β-1,3-glucan highlights the potential side use of products generated in the processing of renewable biomass toward biofuels as a source of valuable bioactive compounds and further clarifies the nature and mechanism of fermentation inhibitors found in lignocellulosic hydrolysates.
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Rescooped by wangzuoqian from Plant Biology Teaching Resources (Higher Education)!

Resources for academic writing and publishing


I led a workshop on academic writing and publishing last week, and this is a list of resources I gave to the participants. It's not an exhaustive list, so if you have any favorites let me know and I'll add them!

Links and resources


General writing resources


Strunk, W. Jr. (1999).The Elements of Style.




Guidelines and lessons for good scientific writing


Cargill, M., and O’Connor, P. (2011). Writing Scientific Research Articles: Strategy and Steps. Wiley.


Doumont, J., ed. (2010). English Communication for Scientists. Cambridge, MA: NPG Education. (Free ebook - very useful)


Duke University Graduate School. Scientific Writing Resource. Short, online course for graduate students with examples and worksheets


Editorial (2010). Scientific writing 101. Nat Struct Mol Biol. 17: 139-139.


European Association of Science Editors. EASE Toolkit for Authors.


Nature Scitable Effective Writing.


Nature Scitable Scientific Papers.


Lichtfouse, E. (2013). Scientific Writing for Impact Factor Journals. Nova Scientific Publishers, Inc. (New York).


Moreira, A., and Haahtela, T. (2011). How to write a scientific paper--and win the game scientists play! Rev. Port. Pneumol. 17:146-149. doi: 10.1016/j.rppneu.2011.03.007.


Plaxco, K.W. (2010). The art of writing science. Protein Science 19: 2261 – 2266.


Rogers, Silvia M. (2014). Mastering Scientific and Medical Writing: A Self-Help Guide. Springer.


Writing Center University of Wisconsin. (2014) The Writers Handbook: Reverse Outlines.




Guidance from journals


J Exp Bot:




Plant Cell:




Figures preparation and ethical issues


Blatt, M. and Martin, C. (2013). Manipulation and Misconduct in the Handling of Image Data. Plant Physiology. 163: 3-4.


Cromey, D.W. (2010). Avoiding twisted pixels: ethical guidelines for the appropriate use and manipulation of scientific digital images. Sci. Eng. Ethics 16: 639–667


Rossner, M., and Yamada, K.M. (2004). What’s in a picture? The temptation of image manipulation. J. Cell Biol 166: 11–15.




Peer Review Guidelines and Policies, Post-publication peer review


Bastian, H. (2014) A Stronger Post-Publication Culture Is Needed for Better Science. PLoS Med 11(12): e1001772. doi:10.1371/journal.pmed.1001772






Mole. (2007). Rebuffs and rebuttals I: how rejected is rejected? J Cell Sci. 120: 1143-1144.




Office of Research Integrity. (US Dept of Health and Human Services) The Lab.


Office of Research Integrity. Research Clinic Case Book.






Provenzale, J.M. and Stanley, R.J. (2006). A Systematic Guide to Reviewing a Manuscript. J. Nuclear Med.Techn.. 34: 92-99.


Times Higher Education:






RavenBlog (2010). Ultimate list of online content readability tests.




Communicating more broadly


Kuehne, L.M., et al. (2014). Practical science communication strategies for graduate students. Conservation Biology. 28: 1225–1235. .DOI: 10.1111/cobi.12305


Osterrieder, A. (2013). The value and use of social media as communication tool in the plant sciences. Plant Methods. 9: 26.



Via Mary Williams
Bibhya Sharma's curator insight, February 3, 2015 8:58 PM

Very helpful for teachers and researchers. 

Andres Zurita's curator insight, February 4, 2015 12:53 PM
Outstanding source of fine material! Thanks Mary!
Rescooped by wangzuoqian from Molecular basis of fungicide resistance!

The Y137H mutation in the FgCYP51B protein confers reduced sensitivity to tebuconazole in Fusarium graminearum

The Y137H mutation in the FgCYP51B protein confers reduced sensitivity to tebuconazole in Fusarium graminearum | wangzuoqian |
Fusarium graminearum is the main pathogen of Fusarium Head Blight (FHB), a worldwide plant disease and one of the most significant wheat diseases in China. Demethylation inhibitor (DMI) fungicides, such as tebuconazole (TEC), are widely used to control FHB, but long-term use leads to low efficacy against FHB. Earlier studies showed that DMI resistance is associated with the fungal sterol 14α-demethylase (CYP51) gene, and that point mutations in the CYP51 gene are the primary mechanism of resistance to DMI fungicides. The aims of this study were to clarify the molecular mechanisms of resistance to TEC and identify the binding sites on the FgCYP51B protein.

Site-directed mutagenesis was used to change the FgCYP51B gene of wide-type strain PH-1 from tyrosine to histidine at residue 137 (Y137H) to generate mutant transformant, which was confirmed to be resistant to TEC compared to the parental strains. A three-dimensional FgCYP51B model was constructed, and molecular docking simulation studies were conducted to identify the optimum binding mode with TEC. The wild-type FgCYP51B protein displayed stronger affinity to TEC than that of the mutational FgCYP51B in the molecular docking analysis.

These results indicate that a Tyr137 amino acid mutation in the FgCYP51B gene could lead to resistance to TEC and that Y137 forms part of the tebuconazole binding pocket.

Via Melvin Bolton
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Rescooped by wangzuoqian from Plant-Microbe Interaction!

Systematic humanization of yeast genes reveals conserved functions and genetic modularity

Systematic humanization of yeast genes reveals conserved functions and genetic modularity | wangzuoqian |

To determine whether genes retain ancestral functions over a billion years of evolution and to identify principles of deep evolutionary divergence, we replaced 414 essential yeast genes with their human orthologs, assaying for complementation of lethal growth defects upon loss of the yeast genes. Nearly half (47%) of the yeast genes could be successfully humanized. Sequence similarity and expression only partly predicted replaceability. Instead, replaceability depended strongly on gene modules: Genes in the same process tended to be similarly replaceable (e.g., sterol biosynthesis) or not (e.g., DNA replication initiation). Simulations confirmed that selection for specific function can maintain replaceability despite extensive sequence divergence. Critical ancestral functions of many essential genes are thus retained in a pathway-specific manner, resilient to drift in sequences, splicing, and protein interfaces.

Via Niklaus Grunwald, Guogen Yang
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