Wednesday, February 26, 2014

On Molecules, Mycota, and Metazoa

Ctenophore (Image: John Wollwerth)
A recent discovery in animal evolution underscores the need to look at the findings of molecular phylogenetics with a critical eye. A couple months ago, a paper by Ryan, et al. was published in Science with well-supported molecular phylogenetic evidence that the group of animals to branch first from the common animal ancestor are the Ctenophora (comb jellies) (left). (A very good summary in structured abstract form can be found here.) Other molecular studies from the last few years, also with fairly strong support, support the traditional morphologically-based view that Porifera (sea sponges) branched first. A news article in Science summarizes the findings here. (Note: the link should be accessible by non-subscribers to Science and can be paged through. The article is 3 pages long.)

The confounding problem in animal evolution is that the many branches of the Metazoa evolved during a relatively short period prior to the Cambrian explosion, and then underwent a great deal of evolution and change since then. Hence, getting "phylogentic signal" for the early branching of animals can be difficult. On the other hand, there are some pretty clear morphological affinities in animals that have been understood fairly well since Darwin and Haeckel's time, many of which has held up when looked at molecularly.

There are many analogies here to the current understanding of fungal relationships, and relationships within groups of fungi, some of which are pretty confounding. The relationship of the microsporidia to the other fungi is something that's still being worked out for example, as are the relationships among the organisms that used be lumped in to the Zygomycota. For several years, the Glomeromycota (arbuscular mycorrhizal fungi) have come up in phylogenetic trees as a sister group to the Asco- and Basidiomycota line (supporting the hypothesis of a grand fungal radiation diverging with early plants), but on the other hand at least one phylogeny published in the last few years has grouped the Glomeromycota with the Mucoromycota and other core "zygos", supporting the classification that was largely abandoned at least a decade ago (and supporting alternate hypotheses of mycorrhizal evolution).

What to make of all this? Basically that while molecular phylogeny is wonderful and revolutionary, and has really deepened our understanding of the relationships and evolution of organisms, the information content can be as contradictory and unclear as any other method of understanding evolutionary relationships among organisms, and hence can't necessarily be treated as the final word on the matter. And this is why morphological, developmental, and ecological data, in other words, the stuff of old-fashioned natural history, is still critical to understanding evolutionary relationships and much else about the living world.

Addendum: I didn't think to have a look at Jerry Coyne's take on the Ryan, et al. paper until after I'd written the article, but probably should have - his perspective on these kind of discoveries is always valuable, and of course, I defer to his knowledge on anything to do with the subject of evolution, speciation, etc. That said, I'm not sure I entirely agree with him on this. His take is that the quality of molecular phylogenetic work in this paper is the best to date for the deep phylogeny of Metazoa, and that while the implications about evolutionary morphology in animals has some odd implications (notably, that the earliest ancestor living animal groups already had a simple nervous system, possibly some degree of bilateral symmetry, etc) but these should be accepted and studied within the evolutionary framework that this study suggests. I'm less sure given that so many prior studies have supported the idea of Porifera as the earliest metazoan branch, and morphological evidence, notably the strongly choanoflagellate-like collar cells in sponges, lends support to the sponge-like common ancestor hypothesis as well. Also, I've seen papers before that seemed to strongly support some kind of odd relationship between organisms, only to be falsified by the next paper that comes along. I reserve judgement on this matter until, as is bound to happen within a few years, one of these hypotheses becomes settled science.

Friday, January 17, 2014

More on hyphae and fungal evolution

Primary references:

Harris SD. (2011.) Hyphal morphogenesis: an evolutionary perspective. Fungal Biology 115(6):475-484. doi:10.1016/j.funbio.2011.02.002. 

Sekimoto S, Rochon D, et al. (2011.) A multigene phylogeny of Olpidium and its implications for early fungal evolution. BMC Evolutionary Biology 11:331. doi:10.1186/1471-2148-11-331. Available from: 

Stajich JE, Berbee ML, et al. (2009.) The fungi. Current Biology 19(18):R840-845. doi: 10.1016/j.cub.2009.07.004. Available from:

More soon.

Saturday, November 19, 2011

More on mycorrhizas

Well, I was hoping to have this up before the article was published, but it simply didn’t work out that way. In any event, better late than never. In the process of preparing for a Myco Digest article, I always read far more than I can cover in any kind of “further reading” list, and often must for reasons of space put aside information on the subject that I think would be interesting to include. But thankfully, I do have a blog (that unfortunately has gone largely unused for several years now), that serves as the perfect place for such addenda.

First off, though I did briefly introduce the idea of mycorrhiza, I presumed a certain degree of familiarity with the idea, and didn’t spend a whole lot of time introducing the concept of mycorrhiza and explaining its various subtypes. Good intros can be found on Wikipedia and the wonderful CSIRO site, Mycorrhizal Associations: The Web Resource.

Also, both sites have good intros to AM fungi, here and here.

Similarly, a good introduction to myco-heterotrophs, that is, parasitic mycorrhizal “cheater” plants can be found in this Wikipedia article, plus this article by David Hibbett, and one I wrote for Myco Digest a few years back.

I can vouch for its accuracy of the Wiki article, having written the majority of the article and having had Martin Bidartondo, a leading researcher on the topic, proof it. The article could use some updating based on research that’s been done over the last several years (in particular, I know Nicole Hynson published quite a bit of work on various aspects of myco-heterotrophy when she was doing her grad work in the Bruns lab), but it’s a topic I need to get caught up on. (Of course, if there any volunteers, Wikipedia is open to all…).

On the topic of the multiple lines of evolution of myco-heterotrophic plants, including myco-heterotrophs parasitizing the AM fungi, a good review can be found here.

I also mentioned the fact that fossils that of fungal associations with the roots of the early plant Aglaophyton found in the Rhynie chert of the Early Devonian epoch (about 410 million years ago). Although the plant is quite different from modern vascular plants, the mycorrhiza is quite clearly identifiable as AM mycorrhiza (and with ancient plants responding to fungal symbiosis in much the same way as modern plants do), with the fungal component, Glomites, being noticeably similar to modern members of the Glomeromycota. This was quite a breakthrough discovery back in 1995, when it was first reported. Key papers on this topic can be found here, here, and here.

Another recent experiment that I did not have space to discuss might shed some light on how the plant may control its relationship with AM fungi at the level of gene expression. A hot-off-the-press paper by Gaude, et al. of the Max Planck Institute for Molecular Plant Physiology (news article here, abstract here) describes how plant cells penetrated by fungal arbuscules express (among many other things) a protein that is built into channels on the cell membrane that allow phosphate compounds to cross over from the fungal arbuscules into the plant cell itself. And while this is not surprising, it was also noted that nearby plant cells also strongly expressed this protein, as if the plant was priming those cells to actively engage in nutrient exchange once fungi show up. Although it is not mentioned in the article, such a strong priming on the part of the plant cell for active exchange with mycorrhizal fungi could be key to how plants regulate exchange with more- vs. less-cooperative Glomus partners.

What I find especially cool about how the research was done is the use of (pardon the pun, Sherman) cutting-edge laser capture microdissection techniques to isolate individual root cells (both with and without arbuscules) so that gene expression could be looked at on a cell-by-cell basis. Laser microdissection is done using a microscope with a built-in microlaser controlled from a computer screen. One selects an area of cells or tissue onscreen, much like drawing a selection in Photoshop, then a microlaser cuts that area out. One can isolate very tiny parts of the organism for further study or analysis.

Also worth a mention is another recent paper by Toby Kiers (lead author of the study I wrote about in the Myco Digest article), “Mutualisms in a changing world: an evolutionary perspective”. This paper is a review of examples of change in mutualistic relationships driven by global climate change and other anthropogenic changes to out environment. Changes include abandonment of established mutualistic relationships by one or both partners, mutualists turning to antagonists or exploiters, and switches to novel mutualistic partners, often invasive entrants to ecosystems. We can see this dynamic taking place in everything from the pollinator extinction crisis to the emergence of Amanita phalloides as one of the most common visible mycorrhizal partners of California oaks. It is driven by many of the same dynamics as the spread of novel pathogens I wrote about last year for Myco Digest. These are important environmental issues we must pay close attention to, and mitigate where we can.

Monday, November 15, 2010

More on emerging fungal pathogens

A placeholder for more sources and material for my most recent Mycena News article. (12/4/2011) As of this re-edit, it's been a year and I haven't added anything, so I truly did drop the ball on it. In any event, I'm going to keep the placeholder, as I really do intend to add more material at some point soon.

Wednesday, August 6, 2008

New imaging breakthrough: A lensless CCD-based microscope

I was just listening to NPR's Science Friday the other day and there was a really interesting story about the latest breakthrough in microscope technology. Its a tiny "on-chip" microscope, about the size of a dime, consisting of simply a CCD and an aperture, or array of apertures. No lenses at all, which is why it can be so small. The mini-scope can be easily linked to an LCD (either iPod size or a computer screen) or a digital camera to view or capture the image.

The resolution capability on these first on-chip scopes is about equivalent to a mid-power objective, with a maximum resolution of about 0.8 µm. (None of the popular articles, and oddly, not even the original journal article, refer to the functional NA of the on-chip scope. Based on my calculations, and assuming predominance of "mid" visible light wavelengths of around 500-550 nm, the spatial resolution would be equivalent to an NA of about 0.4 – that's the resolving power of a typical 20x achromat lens.) Another restriction is that the objects viewed must be in the same fluid medium as the on-chip scope, and I believe the working distance is quite small.

The CalTech lab that invented this technology is now working on higher resolutions and believe they will actually be able to not only match, but surpass the present limits of light microscope resolution.

Interestingly, the inspiration for this new scope came from looking at the nature of "floaters" in our visual field. These are caused by small proteinaceous particles in the eye's vitreous humor that float right above the retina (our own organic CCD). Floaters, of course, are a familiar annoyance to any microscopist, particularly nearsighted ones like myself. What's particularly cool about this new research finding is how it starts with a visual problem and turns it into a solution – this is scientific creativity at its finest.

Another cool thing about this technology is that its cheap – Changhuei Yang, one of the CalTech scientists who discovered this technology, estimates the on-chip scope itself will only cost around $10 to manufacture, though, of course, it will still need to be attached to other LCD-based viewers to actually see the image. There are all kinds of applications for this new microscope technology – this kind of highly portable microscope can revolutionize medicine and public health in the developing world, not to mention make technology for things like routine blood screening more widely available, and, in combination with imaging software, may even be able to automate some of these tests. For people like myself who are very into field biology, having a portable high-resolution microscope would be an enormous boon – I could only imagine how much easier it would be to identify cryptic mushrooms right out in the field if I could see the spores and other microscopic features right then and there.

If you want to learn more, the Science Friday program can be found here. (The podcast is on the upper left side of the page, and there are also links to other articles on the scope.) The original abstract and journal article can be found here.

Wednesday, April 2, 2008

A Tale of Two Zeiss's

As promised in my Mycena News article, the story of how their came to be two Zeiss companies during the Cold War and what that means in terms of buying older Zeiss scopes. Its a rather intriguing bit of history.

There were several Zeiss companies after the Second World War, two of which manufactured microscopes. (There was also Zeiss Ikon, which made camera lenses.) This was the result of the race on the part of the Soviets and Americans for German technical, industrial, and scientific know-how and infrastructure following Germany's defeat.

At the end of the war, Jena, which had been the headquarters of the Carl Zeiss corporation from its beginnings, was occupied first by American troops, but was later claimed as part of the Soviet Occupation Zone in 1946. In response, the Americans stripped the Zeiss corporation of much of its technical equipment, documents, and patents, and evacuated 86 of its top scientists and officials to Oberköchen in the American Zone. Equipment and documents were supposed to be brought along as well and used to establish a new company, but much of this never reached Oberköchen and was instead taken to the US.

Meanwhile, in the Soviet Zone, the Soviets carried out a similar move vis-a-vis the remainder of Zeiss' infrastructure and staff. Soviet policy demanded that Germany pay reparations to the Soviet Union in the form of material and expertise. In practice, this meant entire factories were stripped of their equipment, which was hauled off to the Soviet Union. Scientists and technical experts were also taken to the Soviet Union by persuasion or force. In the case of the Carl Zeiss staff and equipment, they were taken to Leningrad and used to set up the Soviet state microscopy firm, Lomo. (Lomo is still in business in modern Russia and is generally considered to be a very good "second tier" microscope company.) After a few years in the Soviet Union, the Zeiss staff were rapatriated to Jena.

What took place then is that two "Carl Zeiss" companies emerged, one in Oberköchen and another East German state corporation in Jena. Both companies continued to call themselves "Carl Zeiss", and much to the chagrin of Zeiss Oberköchen, the East German company continued to stamp the historic "Carl Zeiss Jena" label on all of its products. This status quo was maintained for many years, with the two companies competing in the microscopy business. By the end of 1950s, Carl Zeiss Oberköchen had reestablished much of the reputation and historic continuity of the historic Carl Zeiss company. Carl Zeiss Jena had less of a reputaiton for quality, especially for entire microscope systems, however, they continued to be competive in the area of components, which were made to be fully compatible with western Zeiss scopes.

Soon after German reunification in the early 1990s, Zeiss Oberköchen bought out Zeiss Jena, reuniting the microscopy divisions of both companies, and moving the microscopy division back to Jena, where it remains to this day. Zeiss Jena, however, had diversified into a number of technological areas not originally associated with Zeiss, at the behest of East German central planners, in large part because they wanted Zeiss to create high-tech equipment that were largely not manufactured in the Eastern Block. Carl Zeiss let go of these divisions, which became a company called Jenoptik, which no longer manufactures microscopes.

So what does this mean in terms of buying used microscopes? Basically, it means that one needs to be careful to distinguish the different Zeiss companies, becuase sellers don't always make the distinction. The website Zeiss Historica provides a rather useful guide to the alphabet soup of Zeiss companies and offshoots, though unfortunately, they leave out the more modern "ZEISS" logo found on Zeiss Oberköchen products from the 1960s onward. The logo "Carl Zeiss Jena" indicates either a pre-1945 or East German product. A logo that says "Zeiss Opton", "Carl Zeiss", or "ZEISS", typically with "Germany" or "West Germany" underneath is Zeiss Oberköchen. There was also briefly a "Zeiss Winkel" logo used in the mid-1950s after the merger of the Rudolf Winkel microscope company into Zeiss Oberköchen.

Postwar Zeiss Jena scopes and components, while less common than the West German ones, are still found for sale today. Zeiss Jena compound scopes are quite distinctive from West German Zeiss scopes, the 1970s Zeiss Jena scopes being true nightmares of modern industrial design. Zeiss Jena objectives are also pretty distinctive, often having a rather distinct simple one-piece and elongate shape compared to West German Zeiss objectives.

In terms of quality, Zeiss Oberköchen scopes of the 1960s to 1980s are of excellent build and optical quality, and often still in excellent shape to this day, even with minimal maintenance. I expect many such scopes will stay in use well into the 21st Century. Zeiss Jena scopes I've read mixed reviews of – I'm told that the build quality is not to as high of a standard and in some cases, metal components have begun to lock up. Then again, some people really like them. As for Zeiss Jena objectives, I've never seen them compared side-by-side with Zeiss Oberköchen objectives, so I can't say how the quality compares. Zeiss Jena objectives are not uncommonly found on Zeiss West Germany scopes from the same generation, in fact, the scopes I was trained on at the first lab I worked at at University of Washington had just such a setup. From what I remember, these lenses gave good clear images and nice phase contrast, though I really had nothing to compare them to at the time. I also have heard good things about high-end apochromat lenses from Zeiss Jena, and that they were of good quality and at the same time bargains compared to Zeiss West Germany apochromats. (Note: I've just read that Zeiss Jena condenser's are not compatible with Zeiss West Germany scopes, at least, not without special machining to make it fit the characteristic Zeiss West dovetail mount.)

Its also important to keep in mind that even within the Zeiss Oberköchen line, lens quality varied quite a bit over time, being much better in the 1970s than it had been in the 1950s. I discovered this the hard way, after buying an old Neofluor phase contrast 40X/0.75 NA objective for my scope. It was from, I believe, the 1950s, having a seven-digit serial number and a "Carl Zeiss/Germany" label on it (as opposed to a six-digit label and simple "ZEISS/West Germany" logo of later objectives). Comparing this to a 1970s/1980s simple achromatic 40X/0.65 NA lens, I found this the more modern yet entry-level lens to have better sharpness and resolution, and stronger phase contrast as well, on both a dry condenser and a high-end 1.4NA oil-immersion condenser. Needless to say, I'm wary of buying 1950s-era Zeiss lenses anymore.

If you want to know more about Zeiss history, besides the Zeiss Historica society site, there's a good page on the "History of optics at Jena" which gives a good overview. Also, Zeiss Jena vs Zeiss Oberköchen was used as a test case by a couple of economists who ask, "Did Socialism Fail to Innovate?". Their conclusions are rather interesting. Finally, the book Red Prometheus: Engineering and Dictatorship in East Germany, 1945-1990 (partly readable online) gives a really fascinating history of Zeiss Jena during the Nazi and Communist periods, and how the collegial culture of Zeiss responded to regimentation and heavy Stasi infiltration during the East German period.

Friday, March 28, 2008

By way of introduction

Your humble blog host is Peter Werner, of Bay Area mycological "fame" (such as it is). The scope of this blog will be about my three favorite "M's" – mycology, microscopy, and macrophotography, but branching out into plants, insects, and other areas of natural history, as well as biological photography and imaging, and environmental topics as I see fit.

I'll probably blog and post images intermittently at first, but if this blog proves to have a readership, I'll try and make it more active.