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Plant-Pathogen Interactions - Science topic

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I am planning to study adaptation strategies of farmers to climate
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Dear Brother, could you tell us the crop and the pest being assessed? Thank you.
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What could be the probable techniques applied from transcriptomics to study metabolomics of plant pathogen interaction ?
Need suggestion.
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You can conduct RNA-Seq analysis (only in host or dual in both pathogen and host) to get the DEGs between infected and non-infected conditions and get a bit of idea regarding the genes and metabolic pathways which might be involved in inciting the disease response
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Hello everybody,
I work on plant science, more specificlly in plant pathogen interaction. In my project I need to analyse an interaction of some proteins related to host and virus interaction, but before I'd like to do this analyses in silico.
Do you have any idea of a good software/program, online or not?
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Dear Athithan,
you can use PDBsum. I think it is very useful and intuitive.
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Reactive oxygen species are produced during early plant-pathogen interactions as a plant defence response. Sometimes, necrotrophic pathogens also produce ROS to cause necrosis or plant cell death. Now the question arises, how can we distinguish between both the ROS, specially during infection? Is there any approach available to do so?
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Typically, superoxide (O2*-) is the first ROS being produced in most cells under aerobic conditions.
For bacterial cells, while it is true that a fraction of molecular oxygen consumed during respiration and ATP production is converted to superoxide, this amount of superoxide cannot be compared to the level of the host cells (which contains multiple mitochondria as a source of superoxide at resting state and during inflammation).
In modeling infection, typically host cell densities used are 1x10^4 to 1x10^5 cells /mL. In realistic terms, clinical infections involve infecting pathogens at densities at or below 10^7 microbes / mL at most (because the nutrient requirements including aeration in vivo won't allow them to grow to supraphysiological levels like 10^8 / mL) .
Also, typically, infection experiments use MOI (multiplicity of infection) ranging from 1 to 10. MOI like 100 (equivalent to 10^7/mL or more) again seems unrealistic for the reasons stated above.
Most bacteria possess multiple enzymatic and non-enzymatic antioxidant defenses to deal with superxide -- first by dismutation by SOD, then catalase or peroxiredoxins to terminate the ROS reactions. So, effectively, what you can expect to detect or see in resting bacteria for endogenous superoxide / ROS is very very low (we have some unpublished imaging data). Certainly not to be compared with a resting host cell.
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Having said that, it means endogenous bacterial superoxide (or ROS) in host-pathogen interactions may not be a key concern in measuring the overall ROS turnover. It is expected to be a small contribution.
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If you have an appropriately selective chemical probe for ROS (say superoxide), then what you do is to use enzyme inhibitors (e.g. NOX inhbitors) or antioxidants (say mito-TEMOL for mitochondrial superoxide) to measure the effects of the intervention, compared to un-intervened controls.
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Also, if you are absolutely interested in finding about ROS in the bacteria/microbe, fluorescent protein based H2O2 reporting has been established (the HyPer series). Those can be integrated into your model strains by transgenesis. Then, you can image or quantify H2O2 changes during infection.
Currently with the known tools, precise investigation on ROS kinetics and dynamics remain quite challenging.
Good luck on your experiments!
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How can we determine which pathogen (bacteria, fungi, virus) is responsible for a given plant disease from a phenotypic observation (for example: spots, smudges on leaves) ??
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All instrumental methods can be applied for the pathogen identification (microscopic analysis, wet chamber, pure culture isolation, artificial inoculation tests, biochemical tests like LOPAT for Pseudomonas, ELISA, FAME, PCR, LAMP, DNA sequencing, MALDI), but they are quite far from the simple phenotypic observation.
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What are the potential effects of on interactions between nonvectors and vectors on the spread of plant pathogens in managed and natural ecosystems?
Previous studies have shown that different herbivore and plant pathogen species elicit different hormone responses in plants.
Mediated by plant defenses, could herbivores and plant pathogens interact to affect the spread of the disease across landscapes?
Any thoughts?
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Hi Juan, Alex and Bertrand,
First of all, thank you all so much for your valued feedback and suggestions on the proposed subject. I agree that this is indeed a very complex and interesting question to be asked.
And these fairly complex answers (studies) address just one aspect of by far more complex interactions in managed systems. timing of hormones produced (i.e., salicylic acid [SA] stimulates compounds targeting pathogens and jasmonic acid [JA] tends to produce compounds targeting insects) and further, in some plants, the production of one (SA or JA) inhibits production of the other as shown by Thaler et al. (2010). Also a more recent preliminary work by Chisholm et al. (2014) showed that Pea enation Mosaic Virus indirectly promotes aphid (Acyrthosiphon pisum; vectors) fitness by suppressing plant defenses and that Pea leaf weevil (Sitona lineatus; non vector generlists) indirectly benefits aphid (Acyrthosiphon pisum; vectors) behavior by increasing plant palatability.
And these fairly complex answers (studies) address just one aspect of these by far more complex interactions in managed systems.
Looking at the effects of soil environment in managed systems adds another dimension to it. Thanks for sharing your research Juan!
As Alex mentioned, what about natural ecosystems which are by far more robust and more complex?
For sure, I agree that the question of pathology of a specific type of pathogen spreading across the biotope is complex, and needs a multidisciplinary approach. Thanks Bertrand!
Thanks!
Ivan
Credits:
Thaler, J.S., Agrawal, A.A. and Halitschke, R., 2010. Salicylate‐mediated interactions between pathogens and herbivores. Ecology, 91(4), pp.1075-1082.
Chisholm, P., Eigenbrode, S.D., Crowder, D. 2014. Can non-vector herbivores suppress the spread of a plant virus? Annual Meeting Entomological Society of America, Nov. 20

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Dear all,
We are going to use the Maxi-Pam (Imaging) to measure chlorophyll fluorescence and measure classic parameters in Arabidopsis leave or in potted plants (plant-pathogens interaction), and I'm looking for a reliable method to use this system in routine or some help to start. There are so many possibilities...And also, does anyone use green light in work room when you need to transfer your dark adapted plants? Do you wear some protection from blue light like glasses, when you don't use the red perspex hood? Many thanks, Alina
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Attention, plants absorb also green light!
Regards,
Michele
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I want to perform genome wide association mapping for plant disease resistance gene. Since, I am completely a beginner in this field, it would be really helpful if someone can give me some advice on how to approach, how to design the GWAS pipeline, valuable publications etc. The genotyping and phenotyping of my genotypes have been done. I have all the data.
Looking forward to your help.
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Thanks a lot Christopher. Those links are really great.
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does anyone know how to give biotic stress to rice, if i have a specific bacterial culyure and want to see the effect of rice under biotic stress so what procedure should i use?
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I was analyzing several examples of plant pathogen interaction (pathosystems) and I was wondering if cell expansion comes first or second to cell division. Of course, I must considered that everything happens after a PAMP sequence of events and also to possible recognition of pathogen by plant cells.
Does anybody have some clues?
Thanks and Regards,
Dr. Joao Paulo R. Marques
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Actually, the question is very general. As far as, i have understood, the phenomenon of cell division or expansion is highly specific to individual plant-pathogen interactions. Some pathogens suppress cell division (for example, using CLE effectors) to colonize the host, whereas some pathogens modulate hosts' hormonal pathways and induce cell division (for example using AvrPtoB, TAL class effectors, etc.). Therefore, the process of cell division or cell expansion is highly controlled by the presence of certain types of effectors, metabolites and receptors of both pathogen and its host and also depends on the spatial (tissue) conformations, where the interaction is happening.
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Can any one guide me about what are all the insilico analysis I can do with defense genes I have isolated or obtained through Transcriptome sequencing of a resistant variety of black pepper after challenge inoculation with Phytophthora capsici
I have done expression analysis of these defense genes through qPCR. There are about 40 number of defense genes or defense related genes. I have very little knowledge about insilico tools and bioinformatics techniques.Kindly help
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Thank You Mr. Laith
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I want to know wich are the better tissues that i can use, if depend of the local that  the pathogen attack or the tissue content. Etc.
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Agree with the above; you should minimise subculturing outside of the plant. But what is the pathogen you're having trouble with? Is it fungal? Biotrophic or nectrotrophic? Are you sure that the variety of the host the you are trying to infect is susceptible to your pathogen strain? Have you checked that the temperature and humidity are right for infection?
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Can any one guide me about what are all the insilico analysis I can do with defense genes I have isolated or obtained through Transcriptome sequencing of a resistant variety of black pepper after challenge inoculation with Phytophthora capsici I have done expression analysis of these defense genes through qPCR. There are about 40 number of defense genes or defense related genes. I have very little knowledge about insilico tools and bioinformatics techniques.Kindly help
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this article might be quite helpful as contains a detailed in silico strategy with strong tools
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Hello.
Nowadays, I am studying on seed storage protein in wheat and their relatives.
HMW glutenin is well-known and it has been studied a lot, but LMW glutenin has studied less than HMW glutenin although LMW has a relatively shorter sequence than HMW because it is harder to distinguish LMW bands than HMW bands.
Glu-1 encodes HMW glutenins, and a lot of Glu-1 such as Glu-A1, Glu-B1, Glu-D1 in wheat, Glu-H1 in barley, and Glu-R1 in rye have been characterized.
However, I couldn't find Glu-R3 in Secale cereale. I could find only one study about Glu-R3 in Secale sylvestre. But as far as I know, Secale sylvestre is not a cultivated rye but a kind of wild rye. Also, there is no Glu-R3 protein or nucleotide information of S. cereale in NCBI database. 
I want to know LMW glutenin in Secale cereale because it can affect to the quality of 1RS wheat-rye translocation varieties. I can't find any related reference. Please help me.
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Intuitively, this kind of infection would be detrimental to the host because there are more things exploiting it. But assuming that there is interference competition between the two species, isn’t it possible for them to lower each other’s pathogenicity because of the mutual reduction in fitness?
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HJ Bremermann, J Pickering - Journal of Theoretical Biology, 1983‏ - Elsevier‏
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Broadly, SA induces defense against biotrophic pathogens, whereas JA activates defense against necrotrophic pathogens. Are there any reports regarding the synergistic relation of salicylic and jasmonic acids in pathogen defense, especially against necrotrophs?
Many thanks in advance.
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Dear Ritesh Ghosh
Vidhyasekaran, P. Book. 2015 . will answers all your question, all about signals and pathways, good luck
Pls. find the attached files
Hoping this will be helpful
Regards
Prof. Houda Kawas
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Plant probiotic bacteria are known to enhance salinity tolerance in host plant. However, mechanism of their action on host plants are poorly understood. We wish to study the underlying molecular mechanisms plant probiotic bacteria in enhancing salinity tolerance in rice.
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there are different bacteria responsible for growth of plants, some are such as nitrogen fixing, phosphate solubilizing, hormone and other growth promoting factors  to the plants, all these are called growth promoting rizospheric bacteria, bioinoculants, biopesticdes or probiotic bacteria : Which name should be more appropriate? Should be on the basis of the mechanism of disease control !
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I am investigating the defense mechanism of an edible crop to Xanthomonas infection. I would like to know how to determine the sample collection and analysis time points e.g. 2, 4, 8, 24, 48, hours post inoculation (hpi) and what is the duration of the experiment e.g. 5 days post-inoculation? Can these same time points be used when analyzing for metabolomic studies?
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I agree to Jemal, it depends on the pathogen type. The time points suggested by you are good for leaf spot pathogens (X. vesicatoria, X. raphani, etc.), but, you will have problems for vascular pathogens like X. campestris. It is better to collect distant from inoculation point tissues, affected by bacteria through xylem in days after inoculation.  
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My work is on the assessment of the SAR ( Systemic acquired Resistance) and ISR (Induced Systemic Resistance) by the measurement of some molecular markers such as Phytohormones and proteines.
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I am interested to learn about other elicitors than chitosan which can be used to induce responses like upon pathogen infection in the moss Physcomitrella patens. Thanks a lot for your suggestions!
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Chitin oligomers, if you can find them (japanese chemical companies?), elicit different phenotypic response than chitosan. Beta 1->3 glucan (Laminarin, sigma L9634) might be worth trying.
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Plant apoplast contains various antimicrobial peptides e.g., defensins. As part of their antifungal mode of action, these defensins (not all defensins) are known to interact specifically with membrane-resident bioactive phospholipids, such as PA, PI(4,5)P2 with high affinity.  We know that these pathogens have different life style. Very importantly, when biotrophic pathogens thrive in the apoplst, they encounter various antifungal proteins and fungus needs to protect itself from these proteins which subsequently determine the outcome.  However, necrotrophic pathogens produce different cell wall-degrading enzymes (CWDEs) and toxins to kill the host plant cell.  When necrotrophic pathogens damage the cell wall and plasma membrane, the antimicrobial peptides (e.g., defensins) which are present in the apoplast, may encounter plant membrane-resident bioactive phospholipids. Do you think these defensins highly interact with plant phospholipids (instead of fungal membrane-resident bioactive phospholipids) and indirectly regulate its own plant lipid metabolism? If so, why does it prefer binding to its own phospholipids? Does this non-specific interaction leads to toxicity to the plant cells? What about binding to fungal membrane-resident bioactive phospholipids? Does defensin loses it ability to bind to fungal phospholipids, subsequently paving the way to infect the plant? How do transgenic (and also non-transgenic) plants over expressing phospholipid-binding proteins (e.g., defensins) control itself of these non-specific interactions?  Do you think the change in the environment (e.g., pH) can limit these non-specific interactions in both non-transgenic and overexpressing plants ?
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Dear Siva, You have a lot of very interesting questions there and I don't think they can be answered just yet without resorting to conjecture. what is known at present is that there are general reasons as to why fungal membranes are more sensitive to defensins and this will include the presence of differing sterols and the presentation of charged surfaces as well as the distribution of various lipids frim one leaflet to another. For those defensins that do have a specific interactions with e.g. PI lipids then the accessibility of these lipids will be important. You may also consider that the mechanism of action of plant defensins has no been investigated in much detail and that they may have other roles beyond a simple fungicidal activity (i.e. signalling). I think you have devised an interesting research programme with your questions and could spend many fruitful years providing a much more detailed understanding than what is currently available.
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Hi All, 
Please here are some other pictures that I got. May somebody help me with the name of this fungus? I am working on water hyacinth and these pictures come from damage leaves by pathogens
Thanks
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Dear Sonia is may be possible Rhizoctonia sp. The hyphae of Rhizoctonia have  the following characteristics: 1) some shade of brown; 2) a special type of cross wall within the hyphae, called a dolipore septum; 3) each cell is multinucleate (has many nuclei) rather than binucleate; 4) branches that are produced at right angles; 5) no asexual spores are formed by the mycelium. You can isolate DNA of your culture and test some primer for identification. 
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As I have found, endophytic fungi mostly belong to the phylum Ascomycota and Basidiomycota.Has there been any other report of endophytic fungi belonging to phylum other than these two?
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Yes, there are some. At first there are a lot of papers based on molecular data with large lists of endophytes. So among "endophytes" you can find Zygomycota, Glomeromycota, Oomycota. As for me these endophytes look a bit doughtful. But sometimes it looks like the truth. For example: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3659578/ There is a review: http://www.tandfonline.com/doi/pdf/10.1080/21501203.2012.656724
And there are some reports about Mucor (Zygomycota) as endophyte. For example: http://www.ncbi.nlm.nih.gov/pubmed/20956060
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Any one can discuss or suggest the role of reactive oxygen species and its production during such type of interaction.
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 Thanks Sudip..!
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.i am researcher student of M.phil.My field is Environmental microbiology.where i want to know that how digestate effects on plant growth and inhibiting effect on plant pathogen (fungus) in soil (drought condition)
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then you should make contact with my PhD Lennart Lehman who is working on a similar topic at JKI in Braunschweig: lennart.lehmann@julius-kuehn.de
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As we know that the Macrophomina is the pycnidial stage, so where exactly the pycnidial stage form naturally.
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Respected sir,
I know about this type sign frequently found on the stem of soybean. But this is not the pycnidial stage of Macrophomina. Phomopsis sp., Diaporthe phaseolorum var. sojae, and D. phaseolorum var. caulivora is responsible for this sign.
If you contradict my response then clarify please.
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I will start a work on plant-pathogen interaction and I want to know if biotrophic fungi can secret elicitors in order to modify the transcription factors in the host. I am reading some papers related to inactivation of MAPKs fo suppress PTI (Zhang et al., 2007 Cell Host and Microbe 1: 175-185) but I really want to learn if fungal elicitors can interfere in MYB or WRKY transcriptor factors. Can anyone help me with this topic?
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Dear João Paulo R. Marques
Thanks for you, some point you mentioned still under research, signaling, pathways and factors , The affected networks are wide and overlapping, and careful elucidation of their interactions is required to fully understand the interplay between host and  microorganisms
Pls. find the attached files answering your question,for further reading
Timothy R. Hughes   2011. A Handbook of Transcription Factors Subcellular Biochemistry Springer Science & Business Media,306Pp. ISBN904819069X, 9789048190690
Arunika N. Gunawardena, Paul F. McCabe 2015. Plant Programmed Cell Death Springer, 306 Pp. ISBN 3319210335, 9783319210339
Francis Martin, Sophien Kamoun 2012. Effectors in Plant-Microbe Interactions John Wiley & Sons,444Pp. ISBN 0470958227, 9780470958223
Regards
Prof. Houda Kawas
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As we know that charcoal rot appear during stress period. Afterall pest and disease creates stress to plant.
Is there any relation between them?
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Perhaps the most prevalent stresses which predispose plants to charcoal rot are drought and high temperatures which go together and the interaction with weeds. 
The heat and drought may not be always avoidable but irrigation critically can do wonders. 
Beside critical irrigation and the critical weeding can be very important for pathogen crop environmental interaction.
The Indian fungus Piriformospora indica might be very important related to both its ability to be cultured on common laboratory but also its demonstrated ability to infect soybean and also stimulate antibiosis and probiosis. In this way the fungus can attack the pathogen and predisposing physiolical condition for the severe damage. 
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Any ongoing research work on the use of mycoviruses in India for the biocontrol of plant pathogens?
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Dear  Kamesh Krishnamoorthy 
Hello
Several Books and articles mentioned the hypovirulence mycoviruses at the fungal-plant interface. I read about India research. you could read the following: may its help.
Regards
Houda
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Do essential oils cause leaf scorching on leaves of the plants? Or do they have certain mechanisms of somehow "burning" or causing scorch when applied on the leaves? Thank you!!! 
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While many secondary metabolites are found in cytosol or in plant tissue matrix, essential oils are generally present in specialised sturctures like the glandular trichomes - peltate glands, capitate glands.
As such, it is very likely that essential oils at certain concentrations should have cytotoxic activity - afterall you want them to be bioactive - defence compounds. They do inhibit HeLa cells -
Eucalyptus oil does show leaf scorching and stunted gowth at high conc.
I hope you will find some more references - try to find research where essential oils is used to control plant pathogens  - you will get some plant effect data also.
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In plant-pathogen interactions, horizontal/ lateral gene transfers are well known to challenge each other. But, these are results of 'transfer of biosynthetic machineries' (operons, gene clusters, repetitive elements etc.) as a result of 'physical transfer' during the course of evolution. But, does this interaction between  plant and it's pathogens leave 'signatures' (patterns that mimic a defense response, circadian patterns, adaptive mutations in genes, suppressions, leading to super-active promoters etc.) in genes, proteins, inter-genic regions in the forms of signatures that is tracable using molecular techniques or computational efforts ? If yes, then how to trace these signatures and assign them to specific interactions (beneficial vs. harmful bacteria/ fungi/ nematodes )?
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Biswapriya,
there were some ideas, not always supported by experiment (I mean it has been no experiment done) about regulation of gene expression in plant pathogenic bacteria on the level of DNA structure: a) different ration of nucleotide transversions with the same number of hydrogen bond to different number of ones. b) disappearance of hidden stop-codons in genes involved in pathogenesis, c) additional sequence with transcription termination point after pathogenesis - related genes and operons, d) long regulatory intergene regions with several TF-binding sites before pathogenesis - related genes and operons... 
Usual problem - such comparison works in one case, and fails in others...
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A hot wet season and some hornamental plants traded from central america to nederland and Apulia produced the conditions for spreading. A froghopper philaenus spumarius feeds on xylem and was the vector to the olivs. It is interesting to stress that many riparian plants are host to bacteriun without any damage. Apparently a Ph variation induced by drought makes the bacteria to aggregate in clumps that kill the tree. One possible way is clearing riparian hosts by raising their xylem pH (possibly).
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Plant nematology
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The fecundity rates of Meloidogyne females, both for sexual and parthenogenetic reproduction, depend on genetic plant-host resistance that varies with different pathogen-host combinations (See two references):
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I want to determine the resting spore population present in Barley roots. if anybody can suggest how a single resting spore of Polymyxa graminis looks like, while resting spore suspension prepared by crushing the roots.
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You may treat the roots with GAA for some time and stain them with CB. You may find the good results and observe under microscope.
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I have many isolates of Pyrenophora teres and i want to know the fsp for them, is ITS region sequencing give me a good results for that.
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Hi Oadi,
Due to the high similarity among P. graminea, P. teres f. teres and P. teres f. maculata, ITS is not reliable to differentiate amongst these pathogens. Housekeeping genes such as Btub, GPD or Actin are not suitable, either. EF1 might be similar (I have never tried).
You should use specific PCR primers. There are different primer sets available for PG, PTT and PTM. It is always useful to include PG as control.
FOR PG:
Taylor EJA, Stevens EA, Bates JA et al. (2001) Rapid-cycle PCR detection of Pyrenophora graminea from barley seed. Plant Pathology 50:347–355.
FOR PTT and PTM:
Williams KJ, Smyl C, Lichon A, Wong KY, Wallwork H. (2001) Development and use of an assay based on the polymerase chain reaction that differentiates the pathogens causing spot form and net form of net blotch of barley. Australasia Plant Pathology 30:37–44.
Lu S, Platz GJ, Edwards MC, Friesen TL. Mating type locus-specific polymerase chain reaction markers for differentiation of Pyrenophora teres f. teres and P. teres f. maculata, the causal agents of barley net blotch. Phytopathology. 2010 Dec;100(12):1298-306. doi: 10.1094/PHYTO-05-10-0135.
 Leisova L, Kucera L, Minarikova V, Ovesna J. 2005. AFLP-based PCR markers that differentiate spot and net forms of Pyrenophora teres. Plant Pathology, 54  66–73 Doi: 10.1111/j.1365-3059.2004.01117.x
Hope this helps you.
cheers,
József
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Damaged were beech seedlings planted in the spring 2015. The bark and phloem were damaged mainly shallow, on the several places were feeding spots oval and deeper. The feeding (probably insects) was mainly in the root neck area, but so in higher part of the seedlings, approximately in 20-30 (40) cm above ground. We found in the old German books (Escherich, Altum, Nüsslin), that similar damage was created from European hornet (Vespa crabro).
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Yes could be Vespa crabro (European Hornet). A more recent (1980's) observation is published (see link) from the USA. The paper and researchers are on ResearchGate so you may be able to get some direct comment. The damage symptoms described are reasonably similar but their observations are on older trees and interestingly they observed no damage one one-year old wood just in branches that were a bit older with more bark. They chew bark to feed on sap.
I think if it was voles or mice the damage would be even more concentrated around the soil line and would have different shapes of damage.
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Is there a way to analyse any possible inhibition effects of one pathogen on the other or possibly any other interactions between them ? e.g. one pathogen might just weaken the plant defenses without causing any symptoms, therefore facilitating easiest infection of the symptom-causing pathogen...
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Ioannis, I agree with Alex. As you know, today we cannot talk about species, but complex species. Besides differences in virulence among the species which can infect potatoes, such as Alternaria alternata, A. grandis, and A. solani, we can find considerable differences among isolates of these species. Therefore, I suggest you choose a specific interaction to elucidade the infection process. Leaf age and nitrogen fertilization play an important role in disease establishment and evolution and might be considered, especially for a weak pathogen like A. alternata. 
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will it be easier to do with RACE?
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Dear Shikha,
I would say that the choice of the method depends on the situation you’re in. If you’re dealing with a potyvirus, which its full genome can be accessed on GenBank, I encourage you to go for Genome walking. In that case you may need to perform a 5’RACE to get the 5’end sequence.
If you’re dealing with a potyvirus that has no record on GenBank, you can start genome walking using Potyvirus degenerate primers, then cover the gap using specific primers. We found in our case that RT-PCR yielded better results using purified virus than using total RNA, especially for amplicons longer than 1500 bp. Alternatively, You could think of exploiting the benefit of Next generation sequencing (NGS).
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Nail polish can't be peeled off and the epidermal tissue doesn't come off that easily.
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Please have a look on the following publications which used indirect method for finding stomatal opening and closure (PSII efficiency under non-photorespiratory conditions). If you used this method the presence of hairs are not problematic and also it give you a whole picture for stomatal status of whole leaf
Aliniaeifard, S., Malcolm Matamoros, P., van Meeteren, U., 2014. Stomatal malfunctioning under low Vapor Pressure Deficit (VPD) conditions: Induced by alterations in stomatal morphology and leaf anatomy or in the ABA signaling? Physiol. Plant 152, 688-699.
Aliniaeifard, S., van Meeteren, U., 2014. Natural variation in stomatal response to closing stimuli among Arabidopsis thaliana accessions after exposure to low VPD as a tool to recognize the mechanism of disturbed stomatal functioning. J. Exp. Bot. 65, 6529-6542.
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I need sequence information of above genes in Nicotiana benthamiana but I could not find. Every time I look for nicotiana benthamiana NCBI giving info about Nicotiana tabacum. liitle confused.. please help
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thanks Artur and Adrian for replying
I am planning to use Nicotiana Tabacum genes info as they are 96% identical
thanks
kind regards
Pratima
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The main goals are to maintain vigor and pathogenicity of the isolates, avoiding contamination.
Thanks.
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Hi Pablo
We've had very limited success ourselves with P. infestans with freezing at either -20 or -80. It's important also to remember that freeze storage is usually meant for long term preservation - it won't be very practical to maintain a 'working collection' ( that is , isolatestyou need to manipulate very frequently  for experiments), except as a backup in case you loose some during the course of exeperimental work ( that happens!).
If you go the freezing routre, I suggest you follow the suggestion of Andreas to have a gradual process. Phytophthora has only plasma membranes (except in chlamydospores and oospores, of course), and is very sensitive to freezing. Colleagues in Scotland used to pack the samples in several layers of lab towel paper before putting them in the fridge at -20°C, to ensure a slower decrease of temperatue and a more gradual freezing process. They were quite happy with that.
Best
Didier
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I would like to simulate a fungal infection of Altenaria sp. because unfortunatelly we can not grow plants with the fungus. Any ellicitor to do? What do you think about mechanical injury?
Thank you in advance
Raquel
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Dear Raquel,
I upload a paper on gas diffusion in porous media and a PPT on gas diffusion in liquid that lead to convection for your reference.  You need to combine both concepts in one set up in FLUENT, and add reaction, but remove g force to stop convection.  You can estimate the time steps from the spreading rate of Altenaria sp.  kk
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I am having problems observing the inhibition effects of Leonurus sibiricus and L. japonicus extracts against crop pathogenic fungi by using the disk diffusion method.
Therefore, I plan to diffuse the extracts directly into the PDA, and then inoculate the fungi samples into the media. However, I am confused by the ratio between the volume of extracts and PDA that will be mixed together. Any suggestions?
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Actually, there is a problem that we also encounter in this method when using sporulating fungi - normally the disc method works well with bacteria. In case the fungi sporulates, colonies of fungi grow haphazardly and it is difficult to celarly demarkate zones. One good alternative is using PD broth - and quantify mycelia growth by taking dry weight. It gives more accurate results.
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e.g. high concentrations of SA or interaction with abiotic stress factors and promoting its negative effect? Many authors indicate that SA has a beneficial role in plant-pathogen interactions or exogenous application alleviate the negative effect of salt stress. I'm interested in different roles of SA, what happened with plants when overproduction of SA has taken place (except conversion to less toxic form)? Maybe you know some publications, I have problems with finding. I know that SA can cause oxidative stress, but maybe you can help me more in this area.
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Does anyone know whether sulfur, iron, or copper may play a role in corn plant chemical defenses?  Jasmonic acid, DIMBOA, or production of any other chemical compound?  I know that sulfur is important for glucosinolate production, but to my knowledge corn doesn't employ glucosinolates.  Any references would be much appreciated.  Thanks!
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    All of the elements in question play some role in plant chemical defense.  The exact physiological function varies but as S, Fe, Cu are all involved in the production of proteins they all will play a role.  As proteins (especially enzymes) are required for the production of phytochemicals such as Plant Growth Regulators (PGR's) and Secondary Metabolites it is likely that all the elements in question contribute at some stage in the metabolic production of corn plant chemical defenses.  As these are all required plant nutrients a deficit would inhibit any pathway requiring such enzymes.  Nutrient deficient plants are generally more susceptible to pests due in part to the inhibition of metabolic pathways required for normal plant defense.
      Iron and Cu are both extremely important in the production and/or utilization of PGR's.  Cu is involved in both Abscisic Acid, and GA metabolism, Iron plays a role in Auxin metabolism.  These are just examples and the elements likely play a very widespread role in regard to PGR's.  As PGR's are extremely important in the regulation of plant metabolism, the influence of elements on the production of PGR's would directly influence the production,accumulation, and/or transport of phytoprotective chemicals  
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Suppose I want want to design ANN and SVM model for designing siRNA against plant pathogen. Is it possible to take Hueskan (2431) dataset for testing and training purposes because Huesken dataset is mammalian? Also, I want to know whether there is any standard siRNA plant dataset with respective efficacy. 
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Yes Madam, I got it. But I want to know whether this database are siRNA or not. If I click on http://smallrna.udel.edu/project_data.php?download=1 then some sequence would displayed. Now I am not getting whether this sequences are siRNA or miRNA. How can I distinguish them. Please assist me to clarify my doubt.
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Also if you know any procedure...
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If you are interested in the coat-protein genes for WMV-2 resistance, you can find more in Marc Fuchs' paper from Nature in 1995. (Attached)
There are also the naturally occurring genes Wmv from C. moschata and Wmvecu from C. ecuadorensis that have been introgressed into C. pepo. (see Paris and Brown 2005 HortScience link.)
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Hello,
I need to infect my plants with powdery mildew to check if they become more susceptible to the infection. Currently in my lab, we just drop spores and try to do it as evenly as possible. But I think it should be a more accurate method to infect plants. Do you know any protocols? Also, how do you check the results of the infection? 
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We don't use water for inoculation with powdery mildew as conidia break down in water. We use a inoculation tower for 'sedimentation' of the conidia in case we want to have inoculation done in a quantitative way. This is a simple method and works fine. Some people use a spray with conidia in water followed by high temperatures to dry the plants asap. I don't like this method very much.
Results we check by scoring area of leaf surface covered with mycelium and/or by scoring the sporulation or by plant responses in the leaves.
You can find details in our publications, for example: Moghaddam Hosseini H; Dewitte A; Van Bockstaele E; Van Huylenbroeck J & Leus L. 2014. Roses Exhibit Pathotype-specific Resistance Responses to Powdery Mildew JOURNAL OF PHYTOPATHOLOGY 162: 107-115
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Which soybean seedborne Fusarium species can we expect to find in a soybean seed lot? Do we actually know that? Are seedborne Fusarium species plant pathogens?
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How close related those species are? What about their pathogenicity to plants? 
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Hello Rodrigo,
Here is a very recent paper which might be helpful for you
Castella and Cabanes 2014, doi: 10.1007/s10482-014-0200-x. 
Phylogenetic diversity of Fusarium incarnatum-equiseti species complex isolated from Spanish wheat.
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Can anyone recommend where I can get (commercially for research purposes) nematodes (Meloidogyne spp) infecting Phaseolus vulgaris (bean) or any nematode infecting Helianthus annuus (sun flower)?
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by survay of cultivated fields which infested with root-knot nematode and make a culture for your work as well as isolate an egg mass (just one) in separate pot to identify it later by any of available methods to know the speices
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I want to test the genetic diversity between F. graminearum ? what is the best method and what is the best primers to use?
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If you are interested in being able to compare your isolates to material that has already been identified, the most widely accepted gene in Fusarium is the translation elongation factor 1-alpha.  For widely used genes and genetic regions for Fusarium, see the Fusarium-ID website (http://isolate.fusariumdb.org/index.php).
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I have been consistently observing that corn seedling radicles are much more extensively damaged by pathogens, compared to the seminal roots of the same seedlings. Can anyone point me to some literature on why this might be the case?
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Matthew, can be the temperature fluctuations, or more precisely the herbicide injury (this simptom I have in this year in the nursery).
BR,
Lucian.