Eukaryotic Micro: Week 3 the last of the fungi

So this week (actually last week) we covered what is probably the last unit concerning fungi: Cryptococcus neoformans. The first two weeks covered two ascomycetes, Candida albicans and Fusaruim species, and now we move over to the basidiomycetes, otherwise known as 'if I asked you to draw a fungus this is what you would draw'.

The primary research papers were:

• Polyploid titan cells produce haploid and aneuploid progeny to promote stress adaptation. Gerstein AC, Fu MS, Mukaremera L, Li Z, Ormerod KL, Fraser JA, Berman J, NielsenK. MBio. 2015 Oct 13;6(5):e01340-15. doi: 10.1128/mBio.01340-15.
• Protein Composition of Infectious Spores Reveals Novel Sexual Development and Germination Factors in Cryptococcus. Huang M, Hebert AS, Coon JJ, Hull CM. PLoS Genet. 2015 Aug 27;11(8):e1005490. doi: 10.1371/journal.pgen.1005490. eCollection 2015 Aug.

This is an interesting point in the semester. Upon completion of this week, we are ~25% of the way through the semester and exactly 25% of the way through the 12 modules. This is the point where students have completed the short writing assignment four times now, so hopefully they are comfortable with what I am looking for. I lay out the guidelines on day 1, and then model what I expect. There are two difficulties. 1: Getting students to explain a dataset of their choosing such that someone would walk away knowing what was done, what it showed, and most importantly be able to ask informed questions about the data set. Students are reasonably good at explaining the data after a week or two, but struggle to give enough experimental information such that you would know how the data was obtained. 2: Identifying limitations with the data set. This is in fact difficult, but it is an important skill to foster if we really want people who are critical thinkers. I ask them that their limitation answers the question 'how does this affect the authors' conclusions or interpretations?' This latter issue usually takes a couple more weeks to get better at for most of the class.

Cryptococcus neoformans normal and titan cells

It's also interesting because Cryptococcus follows up the ascomycetes we already discussed extremely well. Like Candida albicans, C. neoformans is a budding yeast, which is distinct from Fusarium, which although more closely related to C. albicans, is a filamentous fungus. However, like Fusarium, C. neoformans forms dikaryotic filaments during sexual reproduction and grows in a filamentous form during asexual spore production. 

I like these two papers (this is the first year I've used the Gerstein paper) because they deal with different aspects of development/differentiation in different ways.  The Gerstein paper is focused on a role titan cells play using primarily genomic approaches; the Huang paper is focused on spore formation and development using classical genetic approaches.

Gerstein et al ties in conceptually with the Selmecki and Ma papers from the Candida and fusarium modules respectively. All are centered on the acquisition of additional genetic information and the outcomes of this. I'm certain creationists always talk about the inability for an organism to acquire new 'information'. Well here are three independent examples.

Huang et al ties in, slightly, with the Lui paper from the Fusarium module by dealing with cellular differentiation and development. This is something we will come back to in the future frequently and is a biological concept I think is often underappreciated in microbes.  

Thinking about the vagina

I spent the better part of several days last week discussing a fungus that lives in the vagina. I invited a seminar speaker, who studies Candida albicans colonization of mucosal surfaces, which includes the mouth, intestine, and vagina, among other sites. C. albicans is a normal part of the human flora that does not appear to be detrimental or beneficial (a commensal).  During our discussions, which usually took place a local watering holes, it became clear to me that different mammalian species can vary markedly when it comes to the indigenous flora and ultimately the physiology of the vaginal tract.

In women, the vagina is a fairly acidic environment. This is due to the action of Lactobacillus, a bacterium that grows well in the vaginal tract. Lactobacilli generates copious amounts of lactic acid from the metabolism of complex sugars. Lactic acid, as the name suggests, is acidic. The acidic pH in the vagina, due to lactic acid accumulation, inhibits the growth of most other microbes with the notable exception of C. albicans, a fungus. Fungi are extremely tolerant of acidic environments, at least in comparison to many bacteria.

Although C. albicans can grow reasonable well at the pH found in the vagina, it’s growth is limited by the vast abundance of Lactobacilli. Nutrients are not unlimited, so the faster growing Lactobacilli outcompete the slower growing C. albicans. Not surprisingly, if the Lactobacillus population is reduced, for example by broad spectrum antibiotic use or douching, then C. albicans can flourish, which can result in a yeast infection. (It can also lead to bacterial vaginosis, but this is less common.)

What is interesting, at least to me, is that vaginal pH of a female mouse is neutral. Based on this bit of information, you may not be surprised to learn that the murine vaginal tract is not colonized by Lactobacillus (therefore no lactic acid made and no vaginal acidic pH). Since the murine vaginal pH is not as acidic as a woman’s, you might expect C. albicans to do well there (as observed in women with a less acidic vaginal pH). However, C. albicans is not a normal colonizer of the mouse vagina. That being said, we can infect the murine vaginal tract in the lab with C. albicans. Indeed, when we do this, it appears that mice respond similarly to C. albicans as women with a yeast infection. What this tells us is that in the vaginal trac, C. albicans does not appear to be concerned with the environmental pH in regards to disease symptoms. This actually makes sense as recent studies have shown that women who have recurrent vaginal yeast infections (3 or more incidents a year during their child bearing years (yes hormones play a big role here)), the problem is how their bodies respond to C. albicans not due to anything specifically the fungus is doing.

To someone who works on how C. albicans responds to environmental pH, these results may seem disappointing. However, I for one find them intriguing. One primary reason we study the C. albicans response to environmental pH is that environmental pH has a dramatic effect on how this fungus grows. In acidic environments, C. albicans grows as a yeast indistinguishable from the Bakers yeast (Saccharomyces cerevisiae) you can buy in the grocery store. In neutral or alkaline environments, C. albicans grows in the hyphal form (analogous to the hairy mold growing on the bread you baked but left sitting around too long). Besides being a striking phenotype, the transition between the yeast and hyphal growth forms is critical for disease and presumably for colonization as a commensal.

In summary, the ability to switch between the yeast and hyphal growth forms is critical for disease and environmental pH directly controls morphology. The problem or point of interest is that the environmental pH in the vagina of two distinct mammals varies markedly yet disease appears similar. This suggests that other environmental factors contribute to morphogenesis (true) and/or that within the vaginal tract C. albicans morphology is not important (potentially true). Support for this latter idea comes from Candida glabrata, a yeast that commonly colonizes the vaginal tract that is closely related to S. cerevisiae (the one you can buy in the supermarket). The key here is that C. glabrata only grows in the yeast form and is readily able to cause yeast infections.

A couple of accessory points. 1, A picture may be worth a thousand words, but some posts are not amenable to google searches; 2, You can get some interesting looks from patrons of the local watering hole discussing the microbial contingent of the vagina.

Its Official: Fungi Kick Mammalian Butt

Bats with WNS

Since 2006 certain species of hibernating bats have been dying off in dramatic fashion by what has been called White Nose Syndrome (WNS). It is named as such because of some fungal growth around the nose of many affected bats. In 2008, Blehert and colleagues identified the fungus as Geomyces destructans and showed in early 2009 that the fungus was widespread throughout affected populations. In previous posts on these issues, I raised concerns because there was no data demonstrating causation. In fact, while noting that G. destructans could indeed be the etiologic agent of WHS, I also noted that it could be an indirect effect of some underlying problem. For example, the bat immune system could be impaired by a biological or chemical agent that allows G. destructans to infect and ultimately kill the bats (akin to HIV in people).

Well Lorch et al report in Nature that G. destructans is directly causing WNS in bats. Lorch et al essentially test the third of Koch's postulates, which are:

1. The microorganism must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms.
2. The microorganism must be isolated from a diseased organism and grown in pure culture.3. The cultured microorganism should cause disease when introduced into a healthy organism.
4. The microorganism must be reisolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent.

Now even Koch realized his postulates are not universal laws. For example, asymptomatic carriers kind of screw over postulate #1 and non-culturable organisms make #2 an impossibility. However, when fulfilled even partially, these postulates provide powerful information in the etiology of disease.

In the case of G. destructans, postulate #2 was fulfilled previously. In the study by Lorch et al, postulate #3 is shown to be true. If you grow G. destructans in culture and then expose healthy (but susceptible) bats to the fungus, they get l00% infection (Treated in table below), but similarly treated, but without the fungus, control animals should absolutely no development of WNS. More than 95% of infected bats succumbed to WNS within 3 months on infection! (Although it sucks for the bats, this provides definitive evidence that the fungus is the causative agent of WNS!!!1111!

Nature Table 1 (partial)

Furthermore, the authors found the fungi in lesions on the wings where most of the disease damage is thought to occur (despite the 'nose' being part of the name). This helps fulfill postulate #4.

This work is important because it affixes a firm target on the culprit. We can rule out other biological or chemical agents causing susceptibility to WNS. This also helps deal with postulate #1. Postulate #1 has been a complete dick in the case of WNS. This is due to the fact that G. destructans is found associated with European bats that are healthy. What Lorch et al's work tells us is that the situation is more complex than initially realized (but the truth of the matter is that life is always more complex). Maybe European bat species have immune mechanisms that prevent WNS. Maybe the G. destructans strain in the US is more pathogenic than the European isolates. Regardless, these are testable hypotheses. We can also definitively add mammals to the animals fungi feed on. Happy Halloween!


Lorch, J., Meteyer, C., Behr, M., Boyles, J., Cryan, P., Hicks, A., Ballmann, A., Coleman, J., Redell, D., Reeder, D., & Blehert, D. (2011). Experimental infection of bats with Geomyces destructans causes white-nose syndrome Nature DOI: 10.1038/nature10590

Groom of Fungus vs. Hymenoptera OR Told you so

Honeycomb

Last Fall I posted on a paper "Iridovirus and microsporidian linked to honey bee colony decline." describing an association between a virus a fungus and the honey bee deaths (colony collapse disorder, CCD) occurring all over the world. At the time I raised several concerns and expressed my skepticism regarding the major conclusions.


One issue that concerned me was that proteins were identified by mass spectroscopy from healthy and sick honey bees. However, only non-honey bee proteins were described. One would expect the vast majority of identified proteins to be honey bee proteins. If we took a skin sample from someone and did mass spectroscopy to see what proteins were there, we would find a ton (figuratively) of human proteins and a pound of microbial proteins from microbes that were living on the piece of skin. A response from Leonard J. Foster highlights how excluding the vast majority of proteins (honey bee), one greatly increases the detection of false positives. This goes a long way to explaining why the most abundant viral proteins were rarely detected. The more a specific kind of protein is in a sample, the stronger the signal you get from the specific protein (actually we are dealing with protein fragments not entire proteins, but the point is the same).


The reason for this is a signal-noise problem. In these types of approaches, you want to remove the strong signals, which overwhelm the data set, to identify the weak signals. The problem is that as we get closer to the limit of detection the difference between a bona fide weak signal and garbage (aka noise) becomes negligible. Think of an eye chart. Your eye is the detector and you want to identify letters. At the top, most people can identify the 'E', which has a strong signal because its so damn big. As you go down the chart it becomes more difficult to identify the letters. With my glasses on I can identify all the letters with 100% accuracy. Without my glasses and from a distance of about 18 inches, I got 1 wrong on line 6 (~83% accuracy), 3 wrong on line 7 (~57% accuracy), and all wrong on line 8 (0% accuracy). So as the signal got weaker, smaller sized letters for my eye detector, my accuracy was less. Importantly, I could see there was something there, but what I interpreted the letter to be was wrong. So, if we asked a population of people to identify these letters, there would be a strong detection of 'E' 'F' and 'P' in lines 1 and 2 and poor detection of 'D' 'O' and 'C' in line 8. The noise comes in because if we ask people, our detectors, to come up with answers on line 8, instead of 'D' 'O' and 'C', we may often get 'P' 'Q' and 'O' respectively. This is our noise. There's something there and we know it, but it is below our ability to accurately figure out what it is. All those Iridovirus sequences identified by Bromenshenk et al may be noise.

Paradise Birdwing, a lepidopteran

A recent paper in PLoS ONE by Tokarz et al, casts further doubt on the link between the virus, at least, and honey bee colony collapse. The virus in question is an Iridovirus family member, which is a poorly studied group of viruses. In this paper, the authors used PCR to detect Iridovirus in a collection of healthy and CCD suffering honey bees. An Iridovirus, IIV24, has previously been associated with disease in honey bees, although not CCD. However, the Bromenshenk paper identified protein sequences most similar to IIV6 and not IIV24. IIV6 infects lepidopteran species, not hymenopterans like honey bees.


So why was IIV6 identified Bromenshenk in the first place? In the October 2010 paper, mass spectroscopy was used to identify proteins. Basically, portions of the amino acid sequence that make up the protein were identified. With these amino acid sequence, we can search protein databases for things that match these sequences. The only genome (DNA) sequence for an Iridovirus that is available is for IIV6. Thus, we can deduce all the protein sequences encoded by this virus. So the amino acid sequences identified by Bromenshenk appear to be most closely related to IIV6 proteins, as opposed to octopus proteins. (see Foster's short rebuttal for why this may likely be an artifact).


To test the idea that IIV6 or an IIV6-like virus is associated with CCD, Tokarz et al tried to detect viral DNA in sick honey bees (and healthy bees, which are predicted to lack the virus if the hypothesis is correct). They made primers that would detect IIV6 directly as well as related viruses based on what we understand to be the most conserved viral proteins. They also made primers to detect IIV24 directly. What did they get? Nothing, Zip, Nada, Zilch. They detected a positive control for honey bee genomic DNA, but obtained nothing for the viral sequences. They also conducted positive controls to show that they could detect viral sequences if it was added to honey bee DNA prior to the PCRs. This sounds like a conclusive result that Iridovirus are not associated with CCD.


However, even though this dataset supports my trepidation of the Bromenshenk conclusions, I am concerned that this study lacks a critical control. I would be much more convinced if the authors were able to detect at least some kind of virus in any of the honey bee samples, even some unrelated endogenous retrovirus. Just something to show they could detect a viral signal from actual samples, not mocked infected samples. The authors did note that it's possible the sick honey bees are infected with an Iridovirus that cannot be amplified with the primers used, which is true.


Finally, I want to hit on an issue you often hear about in the sciences. The myth that 'you cannot publish negative results.' This paper is in fact nothing but a negative result. Yet it is published. Now the authors use other studies to bolster their conclusions, so in fact this work is not simply a negative result. It's a negative result in context. There are many papers that are essentially negative results, although they are cast in a way that is positive. Now you probably won't see papers like this in Science, Nature or Cell, but you also won't find them retracted as often either.


Tokarz R, Firth C, Street C, Cox-Foster DL, & Lipkin WI (2011). Lack of Evidence for an Association between Iridovirus and Colony Collapse Disorder. PloS one, 6 (6) PMID: 21738798

Fungal research does not need death threats

As scientists we have to sell our work. We need to make our ideas as compelling and WOW!!! as possible to obtain funding, get published in the S/N/C glamour journals, and justify ourselves to the greater community and our peers. But we should never jump the shark.


A recent paper from Fungal Biology proceeds to do just that (subscription required). The press glommed onto to this paper with such objective titles as "'My Dishwasher Is Trying to Kill Me': New Research Finds Harmful Fungal Pathogens Living in Dishwasher Seals" and let's not overlook "My dishwasher is trying to kill me! Deadly bacteria found in household appliances" (Really!?! bacteria!?! Really!?!) A reality based article can be found at MinnPost, for which I provided some thoughts.


Now maybe this is the fault of the media, but maybe not. Actually it's not. Well it's both. As far as the media simply reporting what they were told, they are not at fault. As far as the media actually doing their damn job and not simply being a mouthpiece, they are at fault.

The actual title of the paper is "Dishwashers – A man-made ecological niche accommodating human opportunistic fungal pathogens." That seems fairly benign, although the authors are already introducing the "OMG! We're all going to die!!!" meme by focusing on human opportunistic fungal pathogens. (As an aside, I've always been torn by the phrase fungal pathogen. Is it a pathogen that's a fungus or a pathogen of fungi?)

Fungi live here

So the researchers swabbed dishwashers from all over the world, including the US, and found fungi. This is not interesting. Microbes are everywhere. I am not exaggerating, they are everywhere. The freaking original buildings in Antarctica are being destroyed by fungi. What is interesting is that they found certain fungi frequently, suggesting the environmental factors associated with the dishwasher is most favorable to these types of fungi.

E. dermatitidis

The most common fungus obtained was Exophiala  dermatitidis followed closely by Exophiala phaeomuriformis. As expected these yeast grow remarkably well at high temperature (>45°C), high pH (>10 and even up to 12.5), and high salt (17%). These are all conditions, and harsh ones by most accounts, found intermittently in your dishwasher. Personally, I do find this interesting, albeit descriptive. If you check out your dishwasher seals (or even your refrigerator seals), you can often find some dark gunk growing there. In the case of the dishwasher, you have an idea of what the main fungus might be. (I wonder what's growing on the frig, its certainly a different environment from the dishwasher.)


OK, so how is this related to human health, remember the article's title? Well, E.  dermatitidis has been associated with disease in humans, although it is extremely rare. The word 'opportunistic' in the article's title means something. In the case of E. dermatitidis it means there is something wrong with your immune system. Several studies demonstrate that E. dermatitidis colonizes the lungs of Cystic Fibrosis (CF) patients. However, finding something there does not mean that something is causing a problem. Indeed, the very first sentence of the most recent paper on E. dermatitidis and CF reads "The black-pigmented fungus Exophiala dermatitidis is considered to be a harmless colonizer of the airways of cystic fibrosis (CF) patients." (emphasis mine) Ooohhh, that's some scary shit.


Hopefully, I've noted how the media went off the rails here. The question now is why? Did they make this hype up? Let's see if the authors of the paper in question have anything to say on the topic. The following quotes are directly from the paper.


"The ability of opportunistic fungi to survive near-boiling temperatures needs special attention." Yeah, yeah, we all think our research needs special attention, but why do these authors think this? Is it because this potentially deadly fungus is coming to get us?


"Roughly one-third of sampled dishwashers was infested mostly with one of the two Exophiala species." Anyone else think the word 'infested' was used primarily to elicit an emotional response?


"The presence of such fungi in dishwashers increases the risk of infection through tableware or otherwise." Well that's pretty damned definitive! Im sure there's a reference with data backing that statement up. What? There's not?!? Well, we all know E. dermatitidis infections have increased markedly since the 1970s when dishwashers became common in US households, wait, we don't know that? How about E. dermatitidis infection rates correlate with number of dshwashers/capita, we don't know that either? Hmm, well are E. dermatitidis infection rates higher in employees how spend their days working with dishwashers than others, we don't know that either? Fine! Let's consider this latter sentence  Fonzi's shark.


You know what jerks my chain the most? This is interesting work. The authors have looked in a previously ignored niche and found some interesting bugs. They provide physiological evidence for why these organisms, and not other organisms, are there. This work provides a way to identify natural niches for E. dermatitidis, look for hot high pH high salt locales. This work also highlights how very little we actually know about the microbial world in which we live. There's no reason to pump up the volume with fear (don't believe there was fear, read the comments following the Daily Mail article).

P. Zalara, M. Novak, G.S. de Hoog, & N. Gunde-Cimerman (2011). Dishwashers – A man-made ecological niche accommodating human opportunistic fungal pathogens Fungal Biology DOI: 10.1016/j.funbio.2011.04.007

Fungus vs. Hymenoptera (the honey bee edition)

A honeybee colony. Photograph: Haraz N Ghanbari/AP
from  The Guardian

I have already expounded on the awesome power of fungi against mammals (bats), amphibians (frogs), and nematodes (worm), now it is time for the insects to go down...well, maybe. Over the last five or so years, honeybee colonies have been dying off at a dramatic rate, this is referred to as colony collapse disorder (CCD). Basically the bees in a colony go all Roanoke and it is unclear why.

Several studies of CCD have reported viruses associated with bees from infected colonies, suggesting that the CCD is an infectious disease problem. However, a recent study by Bromenshenk and colleagues identified potential microbial agents associated with CCD. Of particular interest in the the approach that the authors took to identify microbial associations.  In short, bees suffering from CCD as well as healthy controls, were gathered and the proteins were isolated and digested using degradative enzymes. Peptide fragments were then identified by mass spectroscopy (MS). Once the peptide fragments are identified, the original protein can be inferred as well as the source of the protein by analyzing available protein databases. Now it amazes me that the MS data was able to identify microbial peptides from the massive amount of bee protein that must have been in the samples. There may have been steps taken to enrich for the microbial sequences, but I doubt it since most microbial species identified were viral, which I am assuming came from infected bee cells and not free virions (although I could be wrong about this).

From these analyses, the authors determined that CCD-affected colonies were associated with co-infection with a virus and a fungus. The less interesting virus appears to be an Iridovirus, but the more interesting fungus is a microsporidian.  The microsporidia used to be classified with the protists, but are clearly fungi. The microsporidians identified included Nosema apsis, which is known to be associated with honey bees, Nosema ceranae and several other Nosema spp. What is interesting is that the authors grouped the Nosema spp. into group 1 and group 2, but group 1, which contains N. apis, was correlated with CCD, whereas group 2, which contains N. ceranae, was not (Table 1, 3, and the discussion). Finally, CCD correlated with co-infection of the Iridovirus and group 1 Nosema, suggesting that one "pathogen" is not sufficient for CCD, but both cause collapse.

Now the authors take their studies further by testing whether co-infection with IIV-6 and N. ceranae promotes CCD-like disease. (The authors are clear that the cannot be sure IIV-6 and  N. ceranae are the actual causative agents since these organisms were implicated by peptide sequences which could easily be found in related but distinct spp.) Low-and-behold they find that co-infection with both spp. is more virulent than infection by either spp. alone or controls (Figure 3). However, looking at the 50% mean survival times, the results appear to be 9.5 days for co-infection, 11 days for either single infection, and ~16 days for uninfected bees (I extrapolated based on the data presented).

I want to point out that this latter experiment is important and is often not done in these kind of studies, so kudos to the authors. However, I am not yet an enthusiastic supporter of the Iridovirus + Nosema promotes CCD hypothesis. First, the data presented, up to Figure 2, is strictly correlative. Maybe honey bees suffering from CCD are more susceptible to viral and fungal infections or even overgrowth. Karposi-sarcoma viral infections in young men was not the cause of, but a symptom of AIDS. Fungi are decomposers, so if the bees are going south the fungi may just have a leg up by being already associated with the healthy honey bees. Second, I find it problematic that the authors used N. ceranae for their infection studies, since N. ceranae was a group 2 member, but group 1 Nosema spp. were more tightly coorelated with CCD. Maybe any number of co-infections would have similar effects. Clearly the control bees go south regardless of infection, so maybe any combination of stresses simply compounds mortality loss.

Regardless, an interesting paper working on a difficult research area (no petri dish cultures for easy manipulations).

Bromenshenk, J., Henderson, C., Wick, C., Stanford, M., Zulich, A., Jabbour, R., Deshpande, S., McCubbin, P., Seccomb, R., Welch, P., Williams, T., Firth, D., Skowronski, E., Lehmann, M., Bilimoria, S., Gress, J., Wanner, K., & Cramer, R. (2010). Iridovirus and Microsporidian Linked to Honey Bee Colony Decline PLoS ONE, 5 (10) DOI: 10.1371/journal.pone.0013181

A dearth of frogs and how to catch a mole you'ld rather just kill

I have a fairly generic house from the 1950s. A rambler, like all the other ramblers in the neighborhood. However, over its 60 years of existence previous owners have done some nice renovations, including completing a bedroom in the basement. This included putting in a wall to separate the bedroom from the rest of the finished part of the basement, adding a large cedar lined closet, and most importantly putting in an egress window. Yes, the egress window is the most important part, otherwise the bedroom is not legally a bedroom just a glorified storage room. Because this bedroom is in the basement, it happens to also be below the ground. So the window well outside the egress window is about 4 feet deep (in case of fire, you can open the window, climb into the window well and then hoist yourself out of the window well).

We can skip over the safety of having to climb out of the window well in case of emergency, just know that it is physically possible. The point is that we have a rather large and deep window well. Every year, starting around  mid-summer, moles and frogs decide to make the window well their home (read they fall in). Normally I wouldn't care too much, but there are always a few dry leaves in the window well and the moles really love to run over and through these dry leaves starting at about 2AM. Again, I wouldn't normally care, except said window well is directly below the bedroom window right next to my side of the bed. You might be surprised how much freaking noise a 20 gram mole can make using just a few dry leaves in the middle of the night. (Just for the record, frogs are good neighbors and either sleep normal hours or are scared of dry leaves.) So on a fair number of nights every summer, Ill be outside in my slippers and sweatpants (you hope) with a flashlight, a large box, and a small garden rake. One can easily jump into the well, place the box on its side along the wall of the window well (the important thing is to make sure the flaps are open and not bent backwards), then using the rake and flashlight scare the mole around the edge of the wall and into the box. Once in simultaneously close the flaps and tip the box upright (This is actually your second attempt, because the first time the mole went into the box, it escaped while you were dicking around with the flaps, which you left folded backwards). Ensure the mole is in the box by give it a gentle shake (gentleness is inversely correlated to the number of hours I had already been asleep). Of course, it will take several attempts to actually get the damn mole into the box because the flap won't be tight against the wall and the mole will go behind the box, or there will be a small gap between the flap or box and the gravel at the bottom of the window well and the mole will go under it (The number of failed attempts at catching said mole also affects the degree of box shaking gentleness).

Evil mole of satan

Once caught, lift the box up onto the lawn along with the flashlight and hoist you cranky and tired ass up out of the window well. You can then pick your favorite curse to mutter as you realize you left the rake at the bottom of the window well. Back in, and back out with the rake. Vigorously check to make sure the mole didn't go anywhere. Take said box to the woods up the street and dump said mole, feel free to explain to said mole that the Mrs. is the only reason said mole is actually still viable. Back to the house to put away mole catching equipment and drag your sorry ass back to bed.

American Toad

Now I have learned to check the window well occasionally during daylight hours and can often avoid the nighttime ritual of rodent hatred. Under these conditions, if a mole is there it is caught more easily. (Being awake almost certainly has nothing to do with that.) Further, any frogs in the well can be saved. We get american toads, wood frogs, and leopard frogs in the window well. The frogs are easy to catch and I know a 7 year old that I can lower into the window well to catch them.

So 2010 has been an interesting year. Weather-wise there has been nothing remarkable and I have had to capture several moles this year. However, there have been virtually no toads/frogs in the window well, in fact I can only recall a single one.

So what gives? Damned if I know, but one thing I thought about was the rampant world-wide decimation of frogs populations particularly in tropical climes. Entire ecosystems are being upended rapidly because once frogs are gone, animals that feed on frogs are not far behind, also animals that frogs feed on flourish (aka insects), which causes additional disruptions.

The question immediately on your mind Im sure is, "why are frogs populations crashing?" Great question, it turns out the culprit is a fungus called Batrachochytrium dendrobatidis. B. dendrobatidis is a member of the chytridiomycota, aka the chytrids. These are extremely cool fungi (apart from the killing all the amphibians part). They are quite distantly related to the fungi we commonly think about which are Ascomycetes (eg Bakers yeast) and Basidiomycetes (eg Shitake mushrooms). Moreover they are motile!! That's right these SoBs will come to you. Actually it is the spores (zoospores) that are motile via a flagella, not the vegetative cells, but still I expect people in general would state that fungi are non-motile (because most are), but biology is ripe with awesomeness because there is always an exception.

Ok, but Minnesota is generally not considered a tropical clime, so what's a single season lack of frogs in my window well got to do with B. dendrobatidis? Probably nothing, but thinking is fun. A quick google search for B. dendrobatidis and Minnesota came up with this paper (Prevalence of the pathogenic chytrid fungus Batrachochytrium dendrobatidis, in an endangered population of northern leopard frogs, Rana pipiens). It turns out B. dendrobatidis is associated with a reasonable number of frogs in Minnesota! Now at this point there is no indication that B. dendrobatidis is negatively affecting frogs here, but this may be something to keep an eye on.

Ultimate Death Match: Fungus vs Worm

As the newest penultimate addition to the FoS collective (should any group of bloggers ever use the term collective?), I thought I should introduce myself to the other bloggers here at FoS.

Hi, I'm Lorax. Nice to meet you.

Clearly, I am joining a great group of scientists and am happy to add my ramblings here. However, I am also a competitive jerk. So when I read this cool post over at Skeptic Wonder, where Psi Wavefunction waxes poetic about Theratromyxa, I felt a rush of testosterone course through my veins. Amoeba, like Theratromyxa, are basically just free living macrophage *yawn*. Theratromyxa crawls to their prey (nematodes, which are microscopic worms), engulfs it, and then proceeds to eat the nematode. On the plus side Theratromyxa has two things going for it: 1. A single celled organism eating a multicellular organism is inherently cool, 2. Theratromyxa belongs to a group called the Vampyrellid, I mean that is awesomely cool.

http://commons.wikimedia.org/wiki/
File:Arthrobotrys_spores_160X.png

However, if you want a truly amazing nematode hunter, let me introduce you to Drechslerella (previously called Arthrobotrys), a group of filamentous fungi that do something truly amazing! Drechslerella species grow as hyphae (the long spaghetti looking things) and can make spores (there's a collection of 5 cells that formed spores just North of center in the picture). OK, I'll admit that they are not much to look at. And unlike the amoeba, Drechslerella is non-motile, so it needs its food to come to it. If you are hunting prey that moves, but you do not, then you have a problem. Drechslerella deals with this problem in a way analogous to how we catch mice while we sleep, it traps it.

And this is where Drechslerella completely outcools Theratromyxa. I'll let the picture speak for me.

N. Allin and G.L. Barron

The above nematode has crawled into the fungal trap at two points. Along the hypha, a ring is formed by 3 cells. When a nematode enters the ring, these cells rapidly expand (~1/10th of a second) trapping the worm (see below, left and right top two pics). This effectively traps/crushes the worm, think about the last time you stuck your arm in a blood pressure sphygmomanometer (yes that's what those things are called). At this point, cells germinate, sending invasive hyphae into the worm which eats the worm from the inside (see below, right bottom two pics). 

This leads to some pretty interesting biological questions. For example, fungal cells are surrounded by a cell wall, how does this expansion occur so quickly? How is the worm detected, are there touch sensors (yes) and do they act like touch sensors in our cells? Are these "trap" cell structures made all the time or only when worms are around? With organisms like this, what does it mean to be multicellular? a differentiated tissue? etc.

Now I should point out that many nematodes are detrimental to plants and biocontrols are sometimes used, including the use of Arthrobotrys (commercially still using the old name).

To conclude: Drechslerella >> Theratromyxa >> Nematodes

UPDATE: Checkout the noob, who bumped me for newest addition. You can learn all kinds of cool things about how the environment affects physiology!