Macro/Micro/Myco

More on mycorrhizas

2011-11-19T13:28:00.000-08:00

(Still not in a finished state, but better a "Version 1.0" than nothing at all. Hope to revise this into something a bit more polished soon.)

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.

More on emerging fungal pathogens

2010-11-15T20:49:00.000-08:00

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.

New imaging breakthrough: A lensless CCD-based microscope

2008-08-06T11:37:00.001-07:00

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 spacial 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.

Yet more on microscopes

2008-04-22T09:44:00.000-07:00

Just a placeholder here for now – will be adding some more links and info to go with my latest Mycena News article.

A Tale of Two Zeiss's

2008-04-02T18:44:00.000-07:00

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.

By way of introduction

2008-03-28T21:10:00.000-07:00

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.

Bay Area Microscope Service and Repair

2008-03-28T20:42:00.000-07:00

I searched around the web and was surprised to find that there was no handy list of such services locally. Hence, I've put together one here based on individual hits I got with more thorough google searches. With most, I simply link to their web page, except for B&B, which doesn't have a page. There's a large concentration of such services around Silicon Valley, not surprisingly, but only one that I know of close to San Francisco. If there are any I've left off the list, please let me know (particularly ones that are oriented toward servicing old scopes owned by individuals).

The list:

Burlingame:

Technical Instruments

Silicon Valley:

AL-TAR Services
B & B Microscope Service (4057 Moreland Way, San Jose, CA 95130-1237. Phone: 408-988-8300)
Bi-Optic Microscopes
JH Technologies
Labtek
Peninsula Microscope Service
Scientific Equipment Repair
Silicon Valley Micro Service

Scotts Valley:

Optekusa.com

I'm going to get some preventative maintenance and fine tuning of my scope done pretty soon. I'll post here about who I decide to go with and what the results were.

More on microscopes

2008-03-22T13:30:00.000-07:00

Hello, and welcome to my blog. Many of you are probably coming here from the link I provided in my April 2008 Mycena News article about buying a microscope. There are so many good sources of information out there, that I simply couldn't fit an adequate link list in at the end of the MN article, so I decided to set up this blog page instead. That way, I could list all of the links I want to and even have room to introduce the links. (This, of course, is also a good way to plug my new blog. ;)

First off, I definitely want to point out Michael Kuo's excellent "Using a Microscope to Study Mushrooms", an outstanding set of pages on mycological microscopy and mushroom microanatomy.

As for introductions to the microscope itself, there's lots of stuff out there. An overview of basic light microscope types can be found here, while a good introduction to the compound microscope itself can be found here. This page provides a more detailed guide to compound microscope components (a subject I hope to cover in more detail in my next installment). The eBay guide, "Some Advice on Caring for Microscopes" provides a good overview of scope care and cleaning.

An illustrated step-by-step overview of Köhler illumination, the illumination and lens setup I mention in the article, can be found here, and another article that describes it in more gory detail, here.

For those of you with a little basic knowledge who want some more in-depth info on microscopy, you definitely need to check out the wonderful Molecular Expressions, an extensive website that amounts to an online textbook on microscopy, with lots of really nice interactive Java tutorials. The other site I highly recommend is Microscopy-UK, a site I find particularly useful because of its "hobbyist" orientation – it's oriented toward people like myself who have older research-quality scopes and use them for various kinds of natural history/taxonomic applications. (As opposed to biomedically-oriented sites that assume you're in a well-funded clinical lab with all-new multi-thousand dollar equipment.)

There are also a couple of discussion forums on Yahoo Groups on microscopy which are definitely worth a look if you want to delve more deeply into the topic. Even if you don't join the forum, both forums can be read by non-members, have searchable archives, and are really good sources of information on all manner of otherwise-obscure microscopy questions. The first is "Microscope", which is presently quite active. The other is "Microscopes", which is less active, but has a lot of useful information in its archive nevertheless.

On the topic of buying a microscope, I intend my present MN article and its next installment to be a good thorough overview. However, the following guides from eBay and from Microscopy-UK are also quite good and worth having a look at. Another article from Microscopy-UK that's particularly useful is "The Best 'Affordable' Petrographic Microscopes of the 1970s to 1990s". While the focus is on mineralogical scopes, every scope mentioned in the article comes in a more basic "biological" version.

This page on buying high school microscopes is also worth a look, but gives some advice I would not follow if you're looking for a decent biological research scope. Specifically, I strongly recommend ignoring the "no's" under "I see a lot of other features advertised; which ones are worthwhile?" These features are actually something you'd want and should only avoid in "child-proof" scopes for young students.

Finally, if you want to get your microscope serviced (something I always consider a good idea when buying an old scope without a clear service record or refurbishment) or have one that needs repair, I've put together another post with a listing of Bay Area microscope service shops.
Anyway, hope you found my Mycena News article and the supplementary info here useful. This blog does take comments, so if you have any questions or anything else to add, please post.

ADDENDUM: I realized that I also said in the article that I'd write something about the two different Zeiss companies. That grew into an article unto itself, which I've placed on this blog under the title "A Tale of Two Zeiss's".

ADDENDUM 2: There was some controversy on the Microscope list with my reference to a number of microscope manufacturers as "second tier", particularly in regards to Reichert scopes, which are highly regarded. I refer readers to the archived discussion here.