Tag: fungi

New publication from Cassie Ettinger (aka @casettron) and others: Fungi in the Marine Environment: Open Questions and Unsolved Problems 

New paper from Cassie Ettinger in the Eisen Lab:

Full citation:
Amend A, Burgaud G, Cunliffe M, Edgcomb VP, Ettinger CL, Gutiérrez MH, Heitman J, Hom EFY, Ianiri G, Jones AC, Kagami M, Picard KT, Quandt CA, Raghukumar S, Riquelme M, Stajich J, Vargas-Muñiz J, Walker AK, Yarden O, Gladfelter AS. 2019. Fungi in the marine environment: open questions and unsolved problems. mBio 10:e01189-18. https://doi.org/10.1128/mBio.01189-18.

Abstract:

Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far. To date, a relatively small percentage of described species are associated with marine environments, with ∼1,100 species retrieved exclusively from the marine environment. Nevertheless, fungi have been found in nearly every marine habitat explored, from the surface of the ocean to kilometers below ocean sediments. Fungi are hypothesized to contribute to phytoplankton population cycles and the biological carbon pump and are active in the chemistry of marine sediments. Many fungi have been identified as commensals or pathogens of marine animals (e.g., corals and sponges), plants, and algae. Despite their varied roles, remarkably little is known about the diversity of this major branch of eukaryotic life in marine ecosystems or their ecological functions. This perspective emerges from a Marine Fungi Workshop held in May 2018 at the Marine Biological Laboratory in Woods Hole, MA. We present the state of knowledge as well as the multitude of open questions regarding the diversity and function of fungi in the marine biosphere and geochemical cycles.

Definitely worth a look if you are interested in fungi and/or marine microbes.

 

Microbe-themed art of the month: Seung-Hwan Oh portraits w/ mold

OK this is pretty cool (from a microbe-art-science point of view): An Artist Who Paints Portraits With Mold | WIRED.  Seung-Hwan Oh “had to set up a micro-fungus farm in his studio” and he puts film in a warm wet environment (note to self – there could be a new human microbiome aspect of this project depending on what warm wet environment is chosen) and sometimes seeds the system with some mold.  And then he lets nature do its work.

See more about his Impermanence works here. (Really – check out the works – they are wild).

At that site the work is described in the following way:

The visual result of the symbiosis between film matter and organic matter is the conceptual origin of this body of work. The process involves the cultivation of emulsion consuming microbes on a visual environment created through portraits and a physical environment composed of developed film immersed in water. As the microbes consume light-sensitive chemical over the course of months or years, the silver halides destabilize, obfuscating the legibility of foreground, background, and scale. This creates an aesthetic of entangled creation and destruction that inevitably is ephemeral, and results in complete disintegration of the film so that it can only be delicately digitized before it is consumed.

Also see his Tumbl page where one can find many other images like this one:

Hat tip to Kate Scow for posting about this on Facebook.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Mendeley groups on environmental PCR, metagenomics, and microbial eukaryotes

As part of my NSF Research Coordination Network grant (RCN EukHiTS), I am currently managing a number of Mendeley groups that amalgamate relevant journal articles on different topics related to environmental PCR, metagenomics, and microbial eukaryotes. These groups are open (anyone can join with a Mendeley account), and I’m trying to keep them regularly updated with new articles (Mendeley members can also add articles, which I strongly encourage!):

  • Eukaryotic HTP Studies – Publications relevant to high-throughput environmental sequencing approaches focused on microbial eukaryotes. Articles will include any type of -Omic methods (marker gene amplicons, metagenomics, metatranscriptomics, etc.), eukaryote-focused tools/pipelines, and review/opinion pieces.
  • rRNA in Eukaryotes – Literature related to the ribosomal repeat array in eukaryotic genomes – variation in rRNA gene copy number, intragenomic polymorphisms, concerted evolution, transposable elements and their evolutionary and ecological implications.
  • Environmental PCRs – primer sets and bias – Literature related to primer set usage and bias across all taxonomic groups (bacteria, archaea, fungi and microbial eukaryotes) – includes primer sets and methods focused on 16S, 18S, ITS, other rRNA, COI, and other marker genes used for environmental sequencing.
  • eDNA in aquatic ecosystems – This group focuses on environmental DNA (eDNA) applications in aquatic ecosystems, include use of eDNA in bioassessment and environmental monitoring. Literature collection covers methods, analytical tools, and empirical studies (both basic and applied science).

The saga of my pancreas..feet..microbiome ..blood.. liver – part 1

Well, this just keeps going – on and on and on.  I thought I would be able to write a post when it was all done.  But clearly not.  So below is part 1 of an ongoing tale about me – my microbiome – my pancreas – my feet – my liver – my blood – and more.

Medical Record from my being admitted to
the hospital in 1984.

This particular saga started – I guess – in 1984.  That was when, at 15 years old, I came pretty close to dying before being diagnosed with type I diabetes.

My immune system had betrayed me by killing the beta cells in my pancreas. Thanks a lot immune system. Anyway – this is not supposed to be a post about diabetes. So – flash forward to a few weeks ago. Diabetes for almost 30 years and no major complications to note. Many annoyances. Some minor complications. But overall, I am doing OK.  Obsessive checking of my blood sugar and trying to keep my sugar in control and trying to regularly exercise seems to have kept the diabetes gods appeased. Eyes generally always have looked good. Feet HAD always checked out. Kidneys always seemed good.  Knock on wood – all was as good as I could hope for.

But then … something came up.  A month and a half or so ago I kept noticing this funny feeling on the bottom of my right foot. Near the toes. Exactly the same kind of feeling one gets when one has a bandaid or tape stuck to my foot (which, given I have two kids both of whom put bandaids on every minor scratch and then leave them lying all over the house and our pool deck – is not too rare).  I thought – maybe the feeling will go away. But it didn’t. It was lurking there. And after a week or so I decided I should get my doctor to check it out. So I put in an electronic request for an appointment on 7/21:

Appointment request.

I love this MySutterOnline system. After a few messages back and forth I set up an appointment for 7/31. Seemed reasonable. Nothing here seemed urgent.

Appointment info.

I did not want to see another doctor since, well, my doctor is awesome.  Best doctor I have ever had.

And on 7/31 I headed on in.  First I saw my doc’s assistant.  She asked a lot of questions as always.  I tried to explain the feeling on my foot.  Not numb.  Not pain.  Just weird.  Like something was stuck there.  She did not quite get it.  Kept asking about whether it felt numb or not.  But eventually the doctor came in.  And he asked some questions with his assistant there and explained to her that what I was experiencing is actually a pretty common thing in diabetics – not pain – not numb – just weird.

So – on to the foot exam.  He did a series of tests of my feet – circulation – feeling – and more.  And all looked good.  No detectible issues.  Except one thing.  Dermatophytes.  Veritable bucketloads of them. One my toenails.  And in the cracks between toes.  And right at the spot where I was feeling the weird feeling.  Oh – I should explain.  Dermatophytes are a kind of fungus.  On one’s feet they are generally referred to as “Athlete’s Foot.”

Athlete’s Foot fungus.

And my doctor explained – I have a decent case of this Athlete’s Foot.  And the weird feeling I was having could be caused by these fungi rather than the thing I feared – diabetic neuropathy.  So he said – he recommended that we first try and treat the fungal infection and hopefully the weird feeling in my foot would go away.  And getting rid of the dermatophytes would probably be a good things anyway.

So – how to get rid of them?  Oral antifungals was what he recommended.  A long long dose – three months or so.  With one issue – the antifungals could damage my liver.  And thus it was a good idea to screen my liver before, during and after the treatment.  So he ordered a liver panel test and also sent off a prescription for the antifungal terbinafine.  So – I left the office and decided – this was not so bad.  If my foot issue was caused by the fungi then perhaps it could be eliminated.  But of course I was worried about the effects on my liver.  And I was also wondering – what happens to my microbiome (the fungi and the others) when one takes antifungal drugs.  So in the medical office parking lot I googled around looking for information on microbiome studies after antifungals.  And I could not find too much.  So I decided perhaps some microbiome researchers might want to study me while I went through the treatment.

So – I text messaged Rob Knight – the guru of all things related to the human microbiome and one of the key people behind the American Gut project.  And I asked:

Text messages with Rob Knight

And eventually he told me that there were some studied going on but unlikely to be able to enroll in them.  He then suggested perhaps I could sign up for the American Gut Project and collect some samples via them.  And so – after I series of emails I volunteered to sample my self.  All seemed good.

Finally got around to getting the blood drawn 8/8.

Yes, I had my blood drawn.

And when I got back from the lab I found a nice surprise waiting for me.  

Package from the American Gut project.

And I decided to post a bit about the whole saga.  I posted to FB rather than my blog for many reasons.  I did not yet feel comfortable making all of this fully public but I wanted friends and family to know.  And secretly I was hoping that one person who I knew – who was a family friend – who I knew read my FB posts – and who was a MD working on antimicrobial compounds – might see the post and offer some advice.  I did not want to ask directly I guess so this was a way of trying to get some input without asking.

Lemons to lemonade for summer 2013. 

Well, without making this a TMI post, let’s just say I am having some foot problems that I hope are NOT due to a serious type I diabetes complication (~30 years of type I and no known major complications – lots of minor annoyances but nothing major). So I am hoping that my issues are caused by athlete’s foot. And to try and deal with that I will be most likely be starting on a long term antifungal treatment next week. There are risks of side effects – such as liver damage – so I am getting some blood tests done first and will be monitored during the three months I will be on the AF.

So where you may ask is the lemonade? While on the way home from the doctor’s last week after deciding to do the AF treatment I volunteered to be considered to be a subject for a microbiome study of the effects of AFs on the microbiome. Still have to do some paperwork for that, go through informed consent, and such. But hopefully I will have my microbiome studied for the first time and with a real potential use other than microbiome gazing. Stay tuned for more details. Going to be documenting the whole thing.



So – I was going to finally study my own microbiome.  And I could do it with a cool project – the American Gut Project.  Seemed like a good thing.  And it is … but one minor complication.  I wanted to not yet start sampling myself until after getting the liver test done.  Seemed like a formality.  Except of course … it wasn’t.

On 8/11 or 12 I got a message saying the test results were back.  I was busy and did not check until on 8/13. I logged in to see what they were.  Lipid profile looked OK (well, LDL cholesterol was a little high but not much).  But the liver panel was disconcerting:

Liver Panel #1

Uggh.  I have had many liver panels done over the years.  And none showed any abnormalities.  Until now.  So – I spent the whole night googling and learning about what elevated ALT and AST could mean and what could have caused that.  And was mostly freaking myself out.  But I realized this meant I should probably not start on the antifungal drugs.  Which was probably good since 8/14 I headed out with my family on a camping trip.

Just before heading out I sent a message to my doctor.

Messaging my Doc.

And I tried to ignore the liver thing.  But I admit that the few times I turned on my phone I used it to google about ALT and AST.  And also so a message back from my doc’s office.

Message back.

And when I returned from the camping trip I scheduled a follow up appointment with my doc and before the appointment he had me do some additional tests – based in part on email discussions between us.  One test was for hepatitis – which could have caused the elevated liver enzymes.  And the other test was to redo the liver panel.

Yes .. had blood taken.

Outside of Sutter labs.

I had the tests done just before my appointment so we did not have results yet when I met him.  And at that appointment he also ordered an ultrasound test.  I scheduled that for 8/26 and went on in.

Waiting for the ultrasound.

I never had had an ultrasound done before.  It was weird in that it reminded me of all the ultrasounds my wife went through for pregnancies.  And I got that goo all over me and my clothing.  The technician was nice but would not give me any information on what she was seeing.  But she seemed so upbeat that all must be good right?

Then I got a bit of good news.  The hepatitis tests were all negative.  And strangely and nicely – the ALT and AST in the re-test were now in the normal range.

Liver Panel #2

Hmm.  Weird.  What did that mean?  Was it a bad test?  Or were my enzymes spiked temporarily?  So I spent a lot of time googling and looking around to try to understand the meaning of temporary increases in ALT and AST.  Not really helpful since I still did not know if the elevated levels were real or an error.  But I guess it was good news that the second test seemed normal and that the hepatitis tests were all negative.

But alas, the good news would not last. On 8/27 I got the following results: (with the text and the screen shot …)

Ultrasound results


PROCEDURE: US ABDOMEN COMPLETE, 8/26/2013 1:02 PM

COMPARISON: None

CLINICAL INDICATION: Elevated liver enzymes. 

TECHNIQUE: Transverse and sagittal transabdominal sonograms of the upper abdomen, aorta and IVC were performed in conjunction with color Doppler.

COMPARISON: None 

FINDINGS: 

Liver measures 134 mm in vertical dimension. There is a 19 x 18 x 21 mm hyperechoic focus in the right lobe of the liver. No intrahepatic biliary tree dilatation. CBD measures 2 mm in diameter. Gallbladder is unremarkable. No gallstone. No pericholecystic fluid. No ultrasonographic Murphy sign. Hepatopedal portal venous flow.

Spleen measures 118 mm. No focal splenic lesion.

Midline structures including pancreas, IVC and abdominal aorta
are not well seen and grossly are unremarkable.

Right kidney measures 111 mm and left kidney measures 122 mm. No definite echogenic stone. No hydronephrosis. No definite focal renal lesion seen.

No ascites. 

IMPRESSION:
1. No gallstone. No biliary tree dilatation.
2. Hyperechoic lesion in the right lobe of the liver as discussed. Further workup with contrast-enhanced CT or MRI may be considered further characterization is of clinical interest.
3. No renal stone. No hydronephrosis.
4. No ascites.

Now I have never looked at ultrasound results before.  But certainly one thing in there caught my eye —  “There is a 19 x 18 x 21 mm hyperechoic focus in the right lobe of the liver.“

Well that did not sound good.  And googling did not make me feel any better.  And so …  Liver enzymes might be off. Or might have been off.  And I have a focus / lesion on my liver.  Fuck.

Today I talked to my doc and emailed with and talked to few others.  And the plan now is for an MRI or CT scan to look at the focus / lesion more carefully.  Could be nothing.  Could be something but mostly harmless.  Could suck.

So – this PM I had to go in for another blood test to check my kidneys to make sure they can handle the “contrast” dye to be used.  I await the results and tomorrow will be scheduling the imaging …

Another blood draw.

Sutter Lab

And STILL I have not sampled my microbiome.  But in emails with the folks from American Gut we decided that getting a good baseline of “before” before I go on any antifungal would be a good thing.  So I am going to start sampling, maybe tomorrow.

Oh – and I forgot to mention the parallel track here. Just after I made the Facebook post discussed above I did indeed get contacted by the family friend MD who had amazingly useful things to say and to do about the fungal infection.  But more on that later.  Probably soon.  I am not having an easy time sleeping.  So I write …

UPDATE 9/11/2013

Well, I had my liver MRI today.  It was pretty freaky – have never had an MRI before.  First, I had to fast for four hours, which was OK.  As a diabetic, I frequently don’t eat for long periods of time if my blood sugar is too high.  And then I went in to the Sutter Clinic in Davis.  I had pondered taking some sort of anti-anxiety medication or sedative as I can get claustrophobic but when I called the clinic they suggested I wait to do that until I talk to the MRI people because they might not recommend it.  Big mistake.  But I will get to that.

So I drove over to the clinic for my 11:40 AM appointment and parked and took a few pics on the way in.

Parking area at Sutter Davis

I had to fill out a collection of forms about medical background and whether I had any metal inside of me:

Forms

I asked again about the antianxiety meds at the front desk and they again said to wait until talking to the people doing the MRI.  As I pondered just taking something (I brought some lorazapam) anyway, I was called into the back within a minute or so.  Maybe I was out of order for the better:

Not everyone in order …

In the back they told me I could put on a gown and some very posh medical shorts in a little changing area and I could lock up all my stuff in a drawer in there.

In the MRI changing room

The MRI lockbox

And then I asked about the antianxiety meds and they said something like “well, you should have done that a while ago since they take thirty minutes to kick in and we are ready to go”. Hmm.  Then they told me that I would not be going completely into the machine – my arms would stick out.  And my head would be near the opening.  So it sounded OK.  So I lay on the table and they put in an IV (for the contrast dye) and they got me nice and comfy with all sorts of pillows.  And they gave me earplugs.  And then they slid me into the machine.  Something like what is in this picture (I did not take any pics in the machine …)

From http://www.hfmhealth.org/?id=2255&sid=1

but with my arms over my head and my head a bit further into the machine.  In one hand I had a little squeeze ball to use if I needed to come out or needed their attention.  I seemed fine and then made a big mistake.  I opened my eyes.  And I could see nothing but the inside of the tube.  I felt trapped.  I shut my eyes again.  I tried to think of something else.  Baseball.  Movies.  Homeland (I had watched an episode from Season 2 the night before).  Anything.  But all I could think about was how close the tunnel walls were.  So – I squeezed the ball.  It took a few seconds for them to start to get me out – which felt like an eternity.  And I said – I don’t think I can do it.  And they said, well it may not be possible to do it today since it would take a while for the drugs to kick in if I took them.  And so they tried putting me in again and I lasted seconds.  Back out.  Fuck.  I needed to get this done.  So I asked – what if I took the lorazapam and maybe they could fit me in if the schedule was light?  And kindly they said they would look into rearranging the schedule – and a few minutes later they came back and said that as long as I had someone who could pick me up afterwards, they should be able to “squeeze me in” (their words) in their schedule after 30 or so minutes (so the meds could kick in).

So I took the lorazapam, and then spent thirty minutes in a side waiting room reading Sports Illustrated and trying to relax.  Actually, the 30 minutes of relaxation was possibly as useful as the drugs.  And then we started over.  Reconnected the IV.  Set me up on the ned.  And rolled me into the machine.  And I kept my eyes shut.  I thought nice thoughts.  And I made it.  An hour or so in the machine.  Breathing in and out.  Holding breath.  Over and over.  The technician was completely awesome – perfect soothing voice and soothing style.  Always telling me what was going on and how long each image run would take and asking how I was doing.  And then, as my arms started to get sore (they were awkwardly positioned over my head) it was over.  Phew.

Except, not phew.  Now I had to worry about the results.  I went home.  I worried.  I faded in and out (the lorazapam really did have some effect).  I napped.  My kids came home.  We hung out (though I was asleep through much of it).  And life went on.

UPDATE on 9/13/2013

Thursday I spent most of the day working on a grant proposal and waiting for a phone call from my MDs.  It never came.  I called the imaging center, sniffing around to see if I could get the results sent directly to me.  Nope.  I emailed my primary care doc’s office … and wrote

Email to my docs

I then puttered around and hoped for a return message.  Nothing that day.  Uggh.  So I spent Thursday night a bit stressed, shall we say.

Friday 9/13/2013

Tried to relax.  Biked with my kids to their school.  
Biking to school w/ kids & wife
Came back to the house.  Was going to call my doctor.  And then I got an alert saying I had a message from the health care team online.  So I logged in and found this:

1st message back
Not what I was looking for.  So I puttered around the house some more.  Pondered how to hack into the MRI database and download my results.  Decided that was a bad idea (for now).  And then I got another message a few minutes ago saying I had a notification online.  So I went and logged in again and got this:

The good news

Well.  WHEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE.  Certainly is good news.  Apparently. the MRI showed nothing wrong with my liver.  Not sure what was going on.  But boy this was much better news than I expected.  I figured I had some sort of problem at the least.  Maybe I still do.  But at least nothing apparently showed up in the MRI.  And now I can get back to what began this whole saga.  My feet.  Stay tuned.  Going to start some microbiome sampling today for the “before.”

UPDATE Sept. 17, 2013

Well, I suppose it was a bit premature to be perfectly content with the message from my doctor …  I wrote to my doctor’s office asking how I go about getting a copy of the actual MRI scan so I would look at it myself and share it with some other medical professionals (and possibly even post it here).

Asking for the MRI scan

I still have not gotten the scan, but they did post the official MRI report from the radiologist.  Not quite as clean as I had imagined …

The full results

The key part is here:

The key parts

So – apparently  – the ultrasound was actually spot on.  I have multiple foci that “show characteristics of benign hepatic hemangioma”.  And they certainly aren’t tiny.  Now if these really are benign that is fine.  But now I am obliged to start digging around to see how often things that seem to be benign hepatic hemangiomas end up being something else … Uggh … it continues …

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Thank you interwebs: help proving fungi are cool

Well, am teaching three lectures this week on Fungal Diversity for BIS002C at UC Davis. And I decided tonight to ask the internet for help finding cool new stories on fungi. And boy did the internet come through in the clutch. Thanks internet. See Storification of Twitter and Facebook discussions below:

http://storify.com/phylogenomics/fungi-are-cool.js[View the story “Fungi are cool” on Storify]

Fungi are cool

Storified by Jonathan Eisen · Sun, Nov 04 2012 23:13:14

Twitter Discussion after I asked for suggestions …
Prepping 3 lectures on Fungal Diversity for Intro Bio class at #UCDavis – looking for suggestions for coolest recent fungal stories/studiesJonathan Eisen
@phylogenomics Saccharomyces eubayanus & the new world origin of lager yeast…jashapiro
@phylogenomics well, in the news, jump in fungi in metagenome studies in gulf post BP spill.Kenneth Bruno
@phylogenomics the obvious 1 is the fungal meningitis outbreakKitt Klaiss
@jashapiro reference?Jonathan Eisen
@phylogenomics This looks cool. I’m concerned that intro bio doesn’t have more micro, earlier. Is your syllabus available?Mark O. Martin
@KSBruno9 reference?Jonathan Eisen
@phylogenomics you can discuss Aspergillus around those iatrogenic fungal meningidites…Doctor_Strange
@phylogenomics And I love the whole story on fungi developing ability to degrade lignin leading to end of coal deposits.Kenneth Bruno
@phylogenomics I posted on FB, will get.Kenneth Bruno
@StrangeSource already on the listJonathan Eisen
Microbe domestication and the identification of the wild genetic stock of lager-brewing yeastAbstract Domestication of plants and animals promoted humanity’s transition from nomadic to sedentary lifestyles, demographic expansion, …
UW-Madison: University Communications: News PhotosPhotographs are available to media organizations and University of Wisconsin-Madison departments for news, editorial and public relations…
PLOS ONE: Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil SpillPLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific stud…
@phylogenomics I’m fond of Scott Strobel’s endophyte course and the discoveries they’re making w undergrads: http://news.yale.edu/2012/10/25/science-magazine-lauds-yale-science-discovery-courseJeramia Ory
Science Magazine lauds Yale science discovery courseAn innovative Yale science course that encourages undergraduates to discover and study plant-associated organisms has been recognized by …
@KSBruno9 heh – that is by @dr_bik … post doc in my lab …Jonathan Eisen
@phylogenomics @Dr_Bik cool, thought it was a great story. I’m from Louisiana so it was all close to home for me.Kenneth Bruno
@phylogenomics Hey, thank you! My students get taught (not by me) that bacteria are simple, don’t have cytoskeletons, no compartments, etc.Mark O. Martin
@phylogenomics @Dr_Bik Not to say that such a huge shift is necessarily a good thing…Kenneth Bruno
Biodiversity of FungiBiodiversity of Fungi is essential for anyone collecting and/or monitoring any fungi. Fascinating and beautiful, fungi are vital componen…
@phylogenomics Other thing that comes to mind is huge trend toward genome mining for secondary metabolites. Chemistry and genetics.Kenneth Bruno
World’s unique battle -Powerful Arthobortrys fungal adhesive employed to capture soil nematodenandkamat
World’s First video on soil nematode trapped by Drechslerella anchonia mycoadhesivenandkamat
@phylogenomics the responses u r getting is why twitter is cool now will spend part of today reading bout cool fungal researchSponch
May show this video by Louie Schwartzberg on fungi for #UCDavis class this week http://www.youtube.com/watch?v=EDkR2HIlEbc&feature=plcp (although will probably use w/o sound)Jonathan Eisen
Fantastic Fungi: The Forbidden Fruitlouieschwartzberg
@Sponch2 ain’t that the truthJonathan Eisen
@phylogenomics Here is a paleontological fungal/liverwort controversy! http://rlebling.blogspot.com/2012/06/when-funguses-ruled-earth.htmlMark O. Martin
A Strange Manuscript: When Giant Funguses Ruled the EarthAbout 400 million years ago, during the Devonian period, the world was a very strange place. Green plant life had begun to cover the land…
@phylogenomics Not totally fungal, but horizontal transfer of carotenoid production from fungi to aphids is cool. http://www.ncbi.nlm.nih.gov/pubmed/20431015jashapiro
Lateral transfer of genes from fungi underlies carot… [Science. 2010] – PubMed – NCBIPubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citation…
@jashapiro already on my list to cover .. I taught about this last few years …Jonathan Eisen
@phylogenomics Great story for a diversity course…jashapiro
Fermentation Guru Seeks Out New (and Old) Flavors”Oh, this is nice kimchi,” he said on a summer afternoon at Momofuku Noodle Bar, using chopsticks to pull crimson-coated knuckles of Napa…
@DrLabRatOry @phylogenomics I know the TAs of the class. Could get you in touch for skyping them in or send you pics from the field tripsDenina Hospodsky
Natural Products Version 2.0: Connecting Genes to Molecules – Journal of the American Chemical Society (ACS Publications)Abstract Natural products have played a prominent role in the history of organic chemistry, and they continue to be important as drugs, b…
Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms : Abstract : Nature Reviews MicrobiologyOne of the most promising applications of synthetic biology is the biosynthesis of new drugs from secondary metabolites. Here, we survey …
Fasebook Discussion after I asked for suggestions …
Prepping 3 lectures… | FacebookJonathan Eisen wrote: Prepping 3 lectures on Fungal Diversity… Join Facebook to connect with Jonathan Eisen and others you may know.
I would go for toe jam–that’s always popular.Amy Propps
well, I already talked about fecal transplants a few weeks ago … I think I am going to avoid the gross/semi gross this timeJonathan Eisen
Other than the contaminated steroids?Joanne Manaster
Ooo, that’s a good one!Amy Propps
New Ancient Fungus Finding Suggests World’s Forests Were Wiped Out In Global CatastropheTiny organisms that covered the planet more than 250 million years ago appear to be a species of ancient fungus that thrived in dead wood…
Joanne – will cover the steroids w/o a doubt .. but I want MORE …Jonathan Eisen
Tut Shares Tomb with Former Fungi: Scientific American PodcastBrown stains on the walls of Tut’s tomb are fungal mats, indicating a hurried burial. Cynthia Graber reports The tomb of King Tutenkhamen…
A lot of news coming out of the UK just now about threat to ash trees from Chalara: http://www.bbc.co.uk/news/science-environment-20128172.Neil Saunders
ooh – King Tut fungus ..Jonathan Eisen
Chalara ash dieback outbreak: Q&AThe recent confirmed cases of Chalara ash dieback means it has become the latest threat to UK trees. Within the UK’s woodlands, ash is th…
That article looks like a stub, don’t know if there’s more to it.Amy Propps
Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen – Olson – 2012 – New Phytologist – Wiley Online Library
It’s hard to go past the Cordyceps “zombie fungus” 🙂 Video – http://www.youtube.com/watch?v=XuKjBIBBAL8 and article – http://www.wired.com/wiredscience/2011/03/zombifying-ant-fungus/.Neil Saunders
4 New Species of Zombifying Ant Fungus Found | Wired Science | Wired.comSee Also: Citation: “Hidden diversity behind the Zombie-Ant fungus Ophiocordyceps unilateralis: Four new species described from Carpenter…
Cordyceps: attack of the killer fungi – Planet Earth Attenborough BBC wildlifebbcworldwide
Bacterial-Fungal Interactions: Hyphens between Agricultural, Clinical, Environmental, and Food MicrobiologistsSummary: Bacteria and fungi can form a range of physical associations that depend on various modes of molecular communication for their d…
I think mimicry examples are cool – fungus making a pheremone http://www.pnas.org/content/104/20/8374; Gibberellin, a plant hormone, is also produced by fusarium http://www.plant-hormones.info/gibberellins.htm; Carrion smelling fungi attract flies to spread spores http://www.mapoflife.org/topics/topic_422_Mimicry-in-fungi/;Jason Stajich
Multitrophic interaction facilitates parasite-host relationship between an invasive beetle and the honey beeInternational Centre of Insect Physiology and Ecology, P.O. Box 30772-00100, Nairobi, Kenya; ‡Institute of Food and Agricultural Sciences…
Plant Hormones GibberellinsGibberellins are diterpenes synthesized from acetyl CoA via the mevalonic acid pathway. They all have either 19 or 20 carbon units groupe…
“Mimicry in fungi” : Map of LifeMost of us are familiar with fungi in the form of mushrooms, some of which are brightly coloured and not likely to be mistaken for anythi…
Fungus + Virus = heat tolerance for thermophilic grasses http://www.ncbi.nlm.nih.gov/pubmed/12446900 and http://www.sciencemag.org/content/315/5811/513Jason Stajich
Thermotolerance generated by plant/fungal symbiosis. [Science. 2002] – PubMed – NCBIPubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citation…
A Virus in a Fungus in a Plant: Three-Way Symbiosis Required for Thermal ToleranceA mutualistic association between a fungal endophyte and a tropical panic grass allows both organisms to grow at high soil temperatures. …
It’s not new, but there’s a lot of good population biology/epidemiology on sudden oak death (Phytophthera ramorum)–especially the function of landscaping plants as vectors.If you want to use human health as a hook, you can’t go wrong with fungal sec…See MoreKen Callicott
Ken – phytophtera is not a fungus though …Jonathan Eisen
That’s right! I keep forgetting that work that showed them completely unrelated (well, you know what I mean) to the actual fungi–the curse of spending too much time around people who refer to them as water molds.Ken Callicott
look this video Jonathan Eisen….it’s amazing.. http://www.youtube.com/watch?v=Pq1x5V2-3w0Felipe Gainza Cortes
BBC Planet Earth Cordyceps Fungus Finding of the holy mushroom – Diknek lorrie’sdnlscratcher
The deadly chytrid fungus: a story of an emergin… [PLoS Pathog. 2010] – PubMed – NCBIPubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citation…
underwater fruiting Psathyrella in Oregon discoved 3 years ago: http://2pat.files.wordpress.com/2011/05/underwater-mushroom-oregon.jpgDamon Tighe
WordPress
From a business side of things: 1) Using Oyster mushrooms to treat terrestial oil spills 2) BTTR in Emeryville that uses the left over coffee grounds to produce oyster mushrooms from whole foods etc 3) Eben Bayer’s TED talk on using mycellium to make packaging materials 4) Staments TED talk…fungus as pesticide replacement. 5) Cordyceps sinensis – Asia’s viagra, easily one of the most expensive mushrooms in the world and the hunt for them is causing major environmental problems in India the past summers.Damon Tighe
Eben Bayer: Are mushrooms the new plastic? | Video on TED.comTED Talks Product designer Eben Bayer reveals his recipe for a new, fungus- based packaging material that protects fragile stuff like fu…
Paul Stamets: 6 ways mushrooms can save the world | Video on TED.comTED
John Taylor’s recent reverse ecology study of NeurosporaMatthew Kane
Cambridge librarian finds forgotten fungus Charles Darwin brought back on the Beagle (and it was still wrapped in his newspaper)Fungi and seaweed collected by Charles Darwin on the Beagle Voyage has been uncovered wrapped in newspaper in a Cambridge University libr…
Also James Scott’s work on the angel’s share fungus http://www.wired.com/magazine/2011/05/ff_angelsshare/ and for the future lawyers in the room, what happens when fungal growth can be attributed to the distillers and thus they can be sued for this as …See MoreJason Stajich
The Mystery of the Canadian Whiskey Fungus | Wired Magazine | Wired.comThe air outside a distillery warehouse smells like witch hazel and spices, with notes of candied fruit and vanilla-warm and tangy- mellow…
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Tom Bruns talk on fungal dispersal at #UCDavis 11/10/11 #ecology #fungi

http://storify.com/phylogenomics/tom-bruns-talk-on-fungal-dispersal-at-uc-davis-11-10-11.js<a href=”http://storify.com/phylogenomics/tom-bruns-talk-on-fungal-dispersal-at-uc-davis-11-10-11″ target=”_blank”>View the story “Tom Bruns talk on fungal dispersal at UC Davis 11/10/11” on Storify</a>]

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Coming up on http://phyloseminar.org Jason Stajich (aka @hyphaltip) #fungi #genomics

Upcoming seminar on Phyloseminar.Org

Jason Stajich speaks Wednesday, June 29th at noon PST on “Fungal phylogenomics: Getting lost in the moldy forest.”
Fungi occupy diverse ecological niches in roles from nutrient cycling in rainforest floors to aggressive plant and animal pathogens. Molecular phylogenetics has helped resolve many of branches on the Fungal tree of life and enabling studies of evolution across this diverse kingdom. The genome sequences from hundreds of fungi now permit the study of change in genes and gene content in this phylogenetic context and to connect molecular evolution with adaptation to ecological niches or changes in lifestyles. I will describe our work in studies contrasting pathogenic and non-pathogenic fungi and efforts to unravel the evolution of multicellularity in fungi comparing unicellular basal fungi with multicellular mushrooms and molds.
The development of tools for data mining and use of fungal genomics is also driving the pace of molecular biology and genetics of fungi. I will highlight new approaches to make this easier and the ways data integration can inform and transform studies of functional biology of fungi.

Japan 04:00 (04:00 AM) on Thursday, June 30
New Zealand 07:00 (07:00 AM) on Thursday, June 30
West Coast USA 12:00 (12:00 PM) on Wednesday, June 29
East Coast USA 15:00 (03:00 PM) on Wednesday, June 29
England 20:00 (08:00 PM) on Wednesday, June 29
France 21:00 (09:00 PM) on Wednesday, June 29

Learn how to connect ahead of time. To hear about upcoming talks, send an email to phyloseminar+subscribe@googlegroups.com or follow @ematsen.
If you can’t make it, don’t fret– you can always watch the recording

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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