Questions related to Mycology
Dear Research Gate hivemind,
assuming, that liquid culture is not an option and you can not easily scrape mycelium off the surface without getting agar in your sample, because the fungus grows mainly in the medium.
Is there an established method for extraction of DNA for further PCR or even direct sequencing purposes?
Maybe using filtration with a mesh of a certain size, freeze drying, ultrasonic baths, centrifuges or a combination of that...
If we have written the article with mentioning the genus level identification in fungi allow it to publications or not? If they are allowing please let me know the journal, probably we thought that the publication need thorough identification, but here my article is based on the rare distribution with ecological connection has been discussed. The article content the newly analyzed data where the unrecorded list found in collection of evidences or article analysis says..
I inoculated a 200 ml minimal medium with 50g/L glucose with an unknown yeast (shown in figures).
After an incubation of 72 hours, at 180 RPM and 28 C, the broth containing the yeast turned very viscous, slippery liquid. In HPLC, using H column with 5mM Sulphuric Acid as mobile phase and RID as well as UV detector, nothing was detected.
The colour of the yeast is not cream or white, but its like cantaloupe colour.
Any type of help in identifying this yeast or the viscous product shall be highly appreciated.
I am currently studying fungal endophytes and I am utilising both culture dependent and high throughput methods to do so.
When culturing I understand it is common practice to use leaf press controls and/or plating up wash water to make sure that the surface sterilisation was successful and that in fact anything that grows is a fungal endophyte.
I have been wondering what controls people are using to check the same thing when using high throughput approaches? There doesn't seem to be too much in the literature talking about this. I have started to collect "dirty" samples which I will not sterilise but will sequence for fungi - I expect that these dirty controls will contain more species than sterilised leaves, but this still doesn't feel like a true test of the surface sterilisation process.
Interested to hear what controls you may be using!
Would the dominance of one of the microbes in the gut change if we give different foods to insects or larvae? Suppose the insect is supplemented with amylase-producing bacteria, fed with carbohydrates such as rice, corn, and other sources.
Hello! I am a new PhD student and unfamiliar to the mycology world, yet my current project requires a decent amount of work in it. I would like to isolate total protein from Aspergillus fumigatus and then probe it with various antibodies we have to check for binding. However, I am unfamiliar with culture and lysis techniques for fungi. I have heard of a couple freezing and grinding techniques, but haven't found many established techniques. Can anyone recommend their favorite protocol that could help me? We have also discussed looking at hyphae and mycelium, so perhaps one protocol for each would be best. Thank you!
Is there anybody working on fungus? I am facing a problem in identification of fungus under microscope. I use lactophenol cotton blue flooding over slide where fungus is placed from fungal plate. Then i use cover slip on it. But the mycellium is not clear under microscope, i mean it shows a bizarre condensed growth.
Hello, I am currently an undergraduate student at Purdue. I am currently looking at potential research topics to get into during graduate school. Right now I work in a botany lab studying ABA levels in deciduous trees. However, in my own free time, I have been obsessed with the interaction between tree species through different mycorrhizal networks. I have a decent list of researchers working on this topic (I will put their names below), but I was wondering if there are any schools or individuals I should strongly consider and reach out to before applying.
1. Rolf Geisen (Max Rubner-Institut, Germany)
2. Marc Stadler (Helmholtz Centre for Infection Research, Germany)
3. John Pitt (Australia)
4. Jens Frisvad (Technical University of Denmark)
5. Vit Hubka (Charles University Prague, Czech)
6. State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences http://english.im.cas.cn/rh/rd/Mycology1/
7. Keith Seifert (Agriculture and Agri-Food Canada, http://www.agr.gc.ca/eng/science-and-innovation/agriculture-and-agri-food-research-centres-and-collections/ontario/ottawa-research-and-development-centre/scientific-staff-and-expertise/seifert-keith-phd/?id=1181921509394
8. Dr. Catherine Aime (Purdue University)
9. Songlin Fei (Purdue University)
10. Peter Kennedy (University of Minnesota)
Our Burkard 7 Day Volumetric Spore Sampler is not registering 10 litres/minute air according to the flow meter. The motor is running but the flow meter is showing no air coming in. A piece of kim wipe does hover at the orifice so some air is going in, but not enough. We have already replaced the motor, and tried sealing up any area where air could be leaking. Nothing is dirty or blocked. Has anyone experienced this issue?
I recently started a project to investigate some murine mice models of C.albicans association and infection models. Reading original articles and reviews is quite helpful but I want to understand this fungus more in depth. so I would deeply appreciate a good text book(s) to read about morphology , growth and culture of this organism..
Hope you are doing well.
I'd kindly like to ask if anyone may have any available internships/apprenticeships with regards to the field of research. I am a volunteer with IAESTE Malta and am currently in my second year completing a Bachelors of Science (Honours) with Chemical Technology where I place as one of the highest students in my class. I am looking for a 1-3 month period that focus' on spectroscopic technics or anything mycology and/or chemistry related.
I am asking here since I would like to have an experience outside of my country that would be both educational and enjoyable.
Anyone that may know of any offer and/or is offering one please leave a comment or email me through my student email: firstname.lastname@example.org.
Thank you for your time and considerations.
I want to study the interactions between some putative fungal endophytes and model plants related to valuable crops. As far as I know nothing is known about their possible interactions with plants. I was thinking of using either Lotus Japonicus or Medicago truncatula.
What model plant would you recommend and why?
I am currently pursuing my research in Bioactivity of Lichens . I'd like to know if this particular genus has any anticancer activity.
I observe strange dark brown segments of mycelium on my fungus (L. maculans) grown in vitro, the fungus is otherwise white. I wonder whether this morphological change is connected with mycelial viability.
So far I have not been able to find a camera lucida that fits a low range microscope.
I have an obstacle in the isolation of Colletotrichum gloeosporioides. I used PDA medium for the isolation. I got a colony of fungal, but I could not make them sporulate (producing the spores). Does anybody know how to obtain spores of this pathogen?
I recall reading a publication where the authors estimated (or was it speculated on) a ) the proportion of fungi that cannot be kept in culture and b) the proportion of fungi that do not seem to produce fruiting bodies. I cannot remember what publicaiton it was though. Does anyone know?
I am a member of a group of veterinarians who all became ill within about a years time of each other, and who all were employed in the same physical location. Some of the affected veterinarians also had human and/or canine family members who also went on to develop a very similar illness to that seen in the cluster of veterinarians. The practice facility was inspected by OSHA and traditional medical work-up was done on all of those affected. No unifying etiology could be determined for the "syndrome" of illness described by those affected, but environmental chemicals and psychiatric causes were ruled out. As veterinarians and other types of scientists (affected family members), we recognized that the pattern of illness development appeared most consistent with some type of infectious process (possibly with genetic predispositions to resistance/succeptibility to the agent). The illness appeared to develop in unrelated people who worked at a common site initially, then multiple family members of some affected veterinarians developed a similar illness. Our familiarity with collecting/interpreting FNA/cytology samples allowed us to do some diagnostic tests that are not available in human reference laboratories, and with the encouragement of infectious disease physicians at Mayo and UCD medical centers we began some carefully controlled cytology tests on samples provided by those affected with the "syndrome" of illness, as well as samples from healthy control family members/colleagues.
What we have found is an incredibly consistent pattern of fibers/filaments, copiously present in the urine of those affected individuals, and completely absent in the healthy controls. Initially we suspected the filaments to be a possible nematode, but further tests demonstrated that there were also more fragile yeast-like objects and highly organized fruiting-body-like structures associated with the filaments. We also found the filaments and "spores" in subcutaneous nodules, cyst fluid, sputum, and blood cultures from those affected. These details, along with positive staining for chitin by lactophenol cotton blue and calcofluor-white, and positive staining for a thick mucopolysaccharide coat by Alacian Blue- led us to modify the hypothesis and consider that these objects could indicate a fungal or pseudofungal infection.
Many permutations of cytology tests (always coupled with control studies of the same tissues in healthy counterparts) have led us to suspect that we may be seeing some type of oomycete, somewhat similar to Pythium or Lagenisma. We have attempted sequencing, but not gotten consistent results and/or have gotten reports of sequences that are either truncated or reported as different types of fungi, none of which are obviously close relatives of oomycetes. Since this research is unfunded, we have not been able to pursue as much molecular testing as would be ideal. The UCD infectious disease physician did agree that the images were compelling, but not his primary field of study. He/we filed a report with the CDC about the possiblity of this being an emerging/novel human pathogen, but the CDC has not replied to his follow-up requests for assistance in characterizing the findings.
I realize our involvement in this research is both non-traditional and that those of us doing it have motivations beyond that which drives most research. However, we have had enough independent scientists/physicians corroborate our perception that we are seeing something "not normal" in the tissues/fluids of those affected compared to the healthy controls, and encourage us to continue to try to find answers, that I feel compelled to post our findings thus far and ask for opinions and advice. We are hoping that someone, much more expert in mycology/protistology than us might be willing to review these images and offer their perspective. Also, if there is anyone actively pursuing ( or wanting to pursue) this line of research, we are happy to share all of our data gathered thus far, in hopes that it may lead to faster and more thorough characterization of what we have found, and hopefully application to determine which chronic diseases may have this putative infection as a component of their etiology.
i have a fluid sample of a plant extract that over the weekend grew a massive contamination (lab bench - room temperature).
So to find out which of the used ingredients (dry substances or water) might have caused this it would be great to know what genera this could be - as this info may be used to track back the origin.
I am aware of the difficulties of specie identification from macroscopic pictures only, but this is unfortunately all we have.
As part of my PhD program I would require some Verticillium dahliae for inoculations on olive plantlets, preferably VD pathotype D of known virulence.
Is there anyone working with this pathogen willing to share their isolates or perhaps to share an information on where to obtain them?
Would appreciate any information you can provide.
The fungus I am working on doesn't produce spores even after 10 days of inoculation. To make the spore suspension, i am using the protocol mostly suggested using tween 80 and distill water, but still under microscope I can't observe any spores. Is there any particular protocol to observe the difference phases of fungal growth phases?
I collected a cryopreserved culture of Colletotrichum sp. nearly 10 months ago. It used to take nearly 18 days to completely cover a 9 cm diameter petriplate with PDA as media for almost past 9 months. And in the last one month suddenly it started to grow really fast and took only 12 days to completely cover the plate. Please help me in this.
A question for Trichoderma specialists - has any research been done on the morphogenesis of conidiophores in Trichoderma and how that might relate to mycoparasitic structures? What I've noticed is that Trichoderma harzianum hyphae tend to form these dense branchlet structures that look a lot like developing conidiophores. However, they don't always develop to conidiophores, but often can meet an form anastomosing structures between the main-branch hyphae or even become the source of appresoria. In dual cultures with other species, Trichoderma seems to form a lot of these branchlets at the growth front compared to when it is growing alone.
If this is a widely-known phenomenon, could someone point me to literature on the topic? I'm not finding much via a Google Scholar search.
Has such a question been answered in a paper? Or does anyone have experience with that?
I'm looking for a good protocol for taking fungi (mostly conidial ascomycetes) growing on an agar plate and fixing them and ultimately staining and mounting them. Would one simply remove a plug of agar with the hyphae growing on the surface and submerge that in buffer + formaldehyde or other fixative? How do you do this while keeping the conidia + conidiophores intact?
How do you separate the hyphal layer from the agar underneath, or at least as much of as possible, and then mount the hyphal layer under a coverslip?
I've looked through a lot of 'materials and methods' sections in papers on microscopy of these kinds of fungi, but these details are largely missing.
i have recently completed my ph.d from jilin agricultural university changchun China, with two SCI publications. i am seeking post doc position, if anybody can help me, thanks in advance.
i need good topics from general microbiology, virology, bacteriology, mycology, microbial food toxicity, any topics on public health. i would prefer the topics to suit developing countries. thanks in advance
Looking for any papers or information on examples from various environments (ie. arctic vs drier southern climates) of lichen symbiosis and how each symbiont benefits or not from the relationship in relation to its environment. Or just any papers or information in general on lichen symbiosis would be appreciated.
My family and I would like to welcome any and all responses, advice, and any additional information that you would like to share. We would also like to thank you from the bottom of our hearts (in advance) for taking the time to read our 'question' and for sumbitting an answer. Your participation, assitance, and expertise can never be respected enough!!!
I am growing them on PDA (potato dextrose agar) @ 25-27C, dark condition as suggested from most papers and websites found.
However they have been growing mycelia insted of spores (Metarhizium has green spores, but only white mycelia can be observed).
Is there anyway to induce spores formation? Thanks
The fungus was isolated from rotted structural wood in an ancient building. Small white/grey sphaerical structures were visible by naked-eye on the wood surface. They were sampled and inoculated on Malt Extract Agar, the vegetative mycelium developped after few days but no fruiting bodies were present (even after 15 days). Pieces of the vegetative mycelium were then inoculated on a piece of Pinus sylvestris sapwood placed on MEA. The attached microphotographs were taken after 10 days.
Isn’t it true: “Paradigm” is one of the most deeply useful and most used or abused term in the intellectual circles and discussions?
I used the term often, without fully comprehending its finer details. So, I started searching for comprehensive description to fully comprehend the meaning to gain deeper insights but could not reach the goal yet.
Hence, I decided to create one and share here for debate and discussion for improving my understanding by listening to different perspectives for gaining new insights. Let me share, my preliminary draft description and insights briefly:
Question: What is a scientific or technological Paradigm?
Answer: A Paradigm is a complex perception of reality painted by a huge BoK (Body of Knowledge) comprising thousands of pieces of Knowledge such as individual observations, experiences, shared background axiomatic-assumptions, values, theories, postulates and prevailing climate of opinions or thought patterns of a very large community or group of persons subscribed to the paradigm.
A paradigm can become a deeply entrenched paradigm, only if it attracts a very large community or groups of practitioners and researchers for expanding the paradigm and they together accumulate a huge BoK by acquiring knowledge for decades or even centuries. Each piece of knowledge in the BoK for a deeply entrenched paradigm is consistent and/or congruent with all the other pieces of the knowledge in the BoK and overall perception of reality painted by the BoK.
The Books and research publications for each discipline (e.g. Botany, Zoology, Chemistry, virology, mycology, parasitology, and bacteriology to name a few) comprises a huge BoK accumulated for decades, and the BoK paints a perception of reality, where the perception of reality is the “Paradigm”.
In other words, paradigm for a discipline is our understanding of the world or perception of reality painted by the BoK or Knowledge in text books and research papers. Every mature discipline must have a paradigm, which is nothing but a perception of reality painted by the BoK acquired and accumulated for the discipline.
Almost every discipline including soft-sciences (e.g. sociology, political sciences, psychology, economics or even each religion) having BoK that paints a perception, which may be referred to as a paradigm. My understating has few gray or blurred patches, so like to here other perspectives to improve clarity.
Our understanding of term “paradigm” can never be complete without knowing the state of Knowledge without a paradigm (e.g. during pre-paradigmatic state). The seminal and influential book “The Structure of Scientific Revolutions” By Thomas Kuhn (who coined the term “paradigm”) describes a period called pre-paradigmatic (or pre-science) state for each scientific discipline, when the scientific discipline is in its infancy (i.e. at the time of its inception).
During the pre-paradigmatic period, there exists a chaotic situation. There is a good summary for chaotic state during pre-paradigmatic (or pre-science) for any discipline in this informative video starting 1 minute 16 seconds for just two and half minutes: https://www.youtube.com/watch?v=JQPsc55zsXA (also next video may be interesting, which explains that creating a paradigm is essential to overcome such chaos: https://www.youtube.com/watch?v=sOGZEZ96ynI)
During the pre-paradigmatic (or pre-science) it is very hard to acquire knowledge. So, a basic foundation would be formed over the period for a paradigm by accumulating various theories, axioms, postulates that are created using reasoning and consensus and by relying on background assumptions, observations, prevailing climate of opinions or thought patterns.
For example, the pre-paradigmatic (or pre-science) period for basic sciences might be between 4th century BC and 1st century CE, during the many ancient philosophers (e.g. Plato, Aristotle, Pythagoras and Archimedes etc.) created the foundation for first scientific paradigm. This unfortunately also comprised a flawed axiomatic assumption or fallacy: The Earth is static. Exposing the fallacy resulted in a scientific revolution.
Likewise, even modern scientific disciplines would have a pre-paradigmatic (or pre-science) period. For example, the paradigmatic (or pre-science) period for computer science and software was approximately between mid-1950s and early-1970s.
For example, two NATO software engineering conferences 1st from 7th to 11th October 1968 and 2nd conference from 27th to 31st October 1969 defined (or coined) new terms such as “software engineering”, components and assembling etc., where the conferences were attended by many influential though leaders and researchers of computer science from almost all nations, which were engaged on computer science research at that period.
Although they became integral part of our vocabulary, the terms such as “software engineering” or “assembling” were perceived to be provocative or strange in 1968. There would be a period for transition from pre-science to normal science for such terms to become integral part of our vocabulary.
Also different groups may make the transition during different periods. It is also hard to know exact duration of transition, so my guess is that it happened between 1970 and 1975, but certainly culminated into a paradigm before 1979.
A paradigm would slowly become more and more entrenched (1) as more and more pieces of knowledge are accumulated and added to the BoK (Body of Knowledge), and (2) as more and more practitioners and researchers become subscribers to the paradigm. I think, software paradigm also has fallacies injected during pre-science period. Exposing those fallacies should result in a revolution.
According to the book “The Structure of Scientific Revolutions” By Thomas Kuhn (who coined the term “paradigm”): If any new piece of knowledge or fact is proposed or discovered for a deeply entrenched or dominant paradigm, it would face fierce resistance from the practitioners of the paradigm and they try their best to suppress the new piece of knowledge (e.g. even by resorting to attacks), if the new piece of knowledge is not congruent, but contradict or inconsistent with the perceptions or reality painted by the BoK for the dominant paradigm.
Normal science solves puzzles that are posed by the prevailing paradigm but does not challenge the paradigm's basic axiomatic tenets or postulates. But in fact, "normal science" will suppress novelties which undermine its foundations (i.e. the basic axiomatic tenets or postulates). If the fundamental axiomatic postulates are fallacies and exposing the fallacies would result in a revolution.
I want to compile some information about the leading universities or research centers in the field. Feel free to contribute.
I need some help in the identification of these fungal ascospores evidenced in a sediment originating from the "Caune Arago" cave (eastern Pyrenees, France) and dated to 400 000 years ago approximately. There are 2 types: Tauta 12 and Tauta 14. Please see attached files.
I really thank you for your help.
I’m looking for options to publish in Mycology (specific or non-specific Journals on Mycology). In 2011, Hyde and KoKo published a very interesting and applicable paper entitled “Where to publish in mycology?” where they provided information for the major journals that publish manuscripts entirely devoted to Mycology. However, were created new Journals in the last years and (unfortunately) open access has forced the author to choice Journals with very expensive publications fees and that yet charge for reads theirs access to our articles. Because of this, I would like to know where do you are publishing your papers? It is worth to publish without open access? Which Journals do you recommend most for fungal biology/ecology publication? I’m asking it just because I'm very worried with the elitism of scientific knowledge and how it can delay the science progress and the dissemination of “what we do in our labs/universities”.
Thanks for your response!
Hyde & KoKo (2011): https://bit.ly/2IuUQrQ.
What are the black structures that appear on Botrytis cinerea mycellium after two weeks of in vitro culture??
I tried to observe them under binocular microscope and I think that they are fruiting bodies but I am not sure.
Can anyone cofirm this ??
I have started working on some edible mushrooms in Nigeria. I wish to join international mycological societies so as to widen my scope and broaden my experience.
Hi to all!
How to choose a good culture medium to grow fungi in laboratory?
I'd like to know which medium is recommended to growth of saprophytic fungi for isolation and enzymatic activity analysis purposes? Potato Dextrose Agar (PDA) with antibiotic is suitable to all fungi in these group? Do you have any recommendation of protocols to preparation of these medium?
Hello every body
I am interested in producing an antibiotic from Paecilomyces variotii, I recently isolated from soil, I understand from a literature search that an antibiotic from this fungus could be very effective against bacteria, but most references I come across are very old or offer little information. I need a step by step guide on how I can go about this. Can anyone share with me the steps involved and how I can go about it? Many thanks.
I'm at the University of Wisconsin in a group working on a experiment on how mechanical stress affects ectomycorrhizal interactions in poplar trees on petri dishes. We are using time-lapse photography to analyze the trees' growth after stress, but we are unsure if there is a way to quantify how the fungi is affected. Is there a way to measure the growth of the fungi using microscopy?
Hi! Who can direct me by the culture medium the most advantageous for the isolation of fungi from the soil ( sabouraud or PDA)?
I tried 2 methods:
1) Measuring the radial distance between point-of-origin (on the mating spot) of the hyphae to the tip. The shortcoming of this method, I find, is that it is prone to error on my part, especially when the filaments are slightly older and thus, more tangled and branched.
2) Converting the image to greyscale and measuring the intensity of the image. The idea behind this is that increased filamentation = decreased image intensity. However, it isn't very accurate as far as invasive growth in 3 dimensions is concerned, especially closer to the point of origin.
Does anyone know of a better method? Or can someone suggest an improvement on these 2?
Details that may be of use:
The fungus filaments only on a few particular types of solid media.
I image the periphery of my spots under 10x and stitch together the images of larger patches of filaments.
I am hoping to visit Ternate and nearby islands in January (if Agung volcano permits). As a keen mycologist with fair knowledge of Northern Temperate and South American tropical mycology I am looking for literature to help with field identification of fungi. I realise that your project is aiming to fill a gap in the literature but wonder if there is anything you can recommend already available.
This Aspergillus sp. has been isolated during indoor air sampling.
The major characteristic feature of this fungus is the presence of hulle cells in microscopic examination.
Please see the attached files.
figure 1 shows the macroscopic features of colony, two (left) and five (right) days after sampling.
Figure 2 shows the features of colony after 12 days of incubation (PDA).
Figure 3 shows the features of colony after 12 days of incubation (Czapek dox agar).
Figure 4 shows the microscopic features of colony.
Good day everyone! I am now working with Pestalotiopsis sp. causing Gray Leaf Spot of Mango. I would like to know books or journals that I can use for my cultural and morphological studies. It's hard for me to determine the exact color of the colony of fungi without a color chart of fungal colony. Furthermore, I would like to give the exact term for the shape of the conidia.
Hi. Can someone recommend a protocol oligonucleotide primers for PCR amplification of Fd and light chain genes of equine IgG and IgM immunoglobulins? Thanks in advance.
I’m planning to construct polyclonal Fab fragment antibodies of horse, using pComb3X vector and E. coli host. Although well-research, but I could not find a valid protocol and detailed list of primers for PCR amplification of Fd and light chain equine IgG and IgM genes. I am grateful if someone could guide me or recommend for a valid protocol/article
I am gathering different opinions regarding to DNA barcoding of fungi. Please enumerate the major obstacles we are currently facing. And if there is any recommendation?