E. B. Fred

Bacteriology at U.W. – Madison

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Albino deer photos are below.


E. B. Fred Hall (Click on image
for 16 pages of demolition photos.)



aka "Reelin' John"

John A. Lindquist

Lab Instructor

SCHOLASTIC BACKGROUND:

Blair Elementary School and Hayward Community Schools way up in Hayward, Wisconsin where you may find my official headquarters off in the hinterlands – a genuine old-growth forest and partly-navigable wetland, filled with a variety of forest and swamp creatures. (See photos of some of them below.) Class of '63.

University of Wisconsin-Eau Claire and the Pigeon Lake Field Station – B.S./Biology, 1967. Click here for a wintery late afternoon view of the lower campus of UWEC.

University of Wisconsin-Madison – M.S./Bacteriology, 1975.

And a 3rd class FCC License (Chicago), 1976.

«– Here I am between classes at the SCHOOL OF ROCK & ROLL: The Surf Ballroom in Clear Lake, Iowa – site of Buddy Holly's last show. (Photo by Rockin' John McDonald.)

I am still here!

Thru thick and/or thin. Counting summer sessions as semesters, I finished up (in May, 2006) the last in a series of 113 consecutive semesters on the instructional laboratory staff of the Bacteriology Department. Right now I am taking a short break from here and spending a good part of the summer teaching and learning elsewhere. I think my favorite lecture of all time was on and off the Portage Trail between the St. Croix and Brule Rivers – a spontaneous "seminar" which included a retracing of part of the route that Schoolcraft & Allen (our own Lewis & Clark) took after making the first correct map of the source of the Mississippi River. Fascinating stuff one never learns about in geography courses. Anyway, I'll be back here for at least the coming school year.

Occasionally I get asked about my various activities over the decades including lab instruction, carnivorous plants, real alternative radio, and all those dozens of soil & water samples, and also why I felt I had to retire a few years ago whether or not I really wanted to. I am always happy to find a time to discuss the real substance involved for each of these things, much of which is revealed elsewhere in my collection of web pages which apparently continues to be one of my best-kept secrets around here. I am very grateful for the support and encouragement that I have gotten e-mailed to me over the years about my web efforts, and – of course – I am most grateful for the chronic cheerleading going on back home concerning the job overall. I could repeat this paragraph but let's move on.

As far as the webworks are concerned, I am still doing HTML the old-fashioned way, building on what I taught myself back in 1997 when I discovered it was fun, easy and intuitive. My favorite HTML-checking web browser suggests that I move up to stylesheets. Here are a couple ancient items from the archives, rendered with the old state-of-the-art, speech-capable and still-available browser NCSA Mosaic 3.0beta4 for the Mac: The HTML Page and The Web's First Splammo Page. The latter – viewed not so well with Netscape Mosaic 0.93beta – is shown here.

Most semesters over the past 20 years or so, I have been teaching Bacteriology 102 – the general lab course for non-majors – where we indulge in a fair amount of real hands-on microbiology such as the enrichment, isolation and identification of bacteria and also dilution theory, growth curves and many other things. We consider various aspects of bacterial nutrition and the related topics of catabolism, differential media and the cycles of elements – in both theory and practice. How does our catabolism page rank with search engines? Check it out on Google and Yahoo. One of the things we realize is that the concept of "oxygen relationships" does not classify living things as comprehensively as one might expect, and we work with organisms that can grow anaerobically for any of three reasons related to catabolism. We occasionally discuss bacterial identification by the use of nucleic acid analysis; the enteric bacteria are great models when it comes to learning about base-sequencing and the generation of phylogenetic trees. (Scroll up and down the 16S rRNA gene here and also here.) Our collection of "thought questions" should be a breeze for any thoughtful 102 student.

Check out the general list of Bact. 102 topics and a commentary on teaching an introductory bacteriology lab course. With a solid foundation and a sensible blueprint, one does not have to be memorizing a lot of disjointed trivia (i.e., micromanaging a house of cards) in an introductory bacteriology course.

In the spring semesters since 2001, I have been teaching the 6-week short course in Farm Microbiology. The recently tidied-up website for the 2006 term just completed starts here, and we also had a weekly lab that included the mass production of some very edible yogurt.

Way, way back in the 1900's I frequently taught Bacteriology/Food Science 324 – the food microbiology lab course which covers bacteria involved in the production and spoilage of food and also those which cause (or are associated with) food-borne diseases. Getting into practical microbiology – rather than the purely descriptive (for its own sake) sort – continues to be one of the real joys of teaching microbiology, and that aspect enters into the environmentally-oriented experiments we do in our lab courses when we ask (1) what is it about an organism's structure and physiology that adapts the organism to its environment, and (2) what function does the organism perform in this environment? One can think about how an organism can potentially endanger itself by producing a large amount of acid in an environment high in fermentable sugars. If it doesn't have inherent resistance to the low pH, perhaps it can raise the pH by deaminating or decarboxylating substrates that may be available. In the sauerkraut fermentation, the organisms may eventually kill themselves off by their own acid production. Besides pH, another major consideration in food microbiology is water activity and how it affects the growth of various types of microorganisms that use foods as their media. And in all aspects of food analysis (and preparation!) is aseptic technique.

As in Bacteriology 102, we hit the enterics fairly hard in the food microbiology course, exploiting their physiological variety to explain the workings of isolation and identification media which one is expected to understand fully when consulting federal and industry manuals regarding methods and regulations. Also from such studies, one can understand better the reasoning behind identification kits such as the API-20E system. Back in my food micro teaching days, we went pretty deep into Salmonella, sausage and sauerkraut. For a couple decades, a free lunch of lab-made sauerkraut (often acidic enough to make one's teeth itch!) was available to one and all at the annual Kraut-Fest – one of the milestones of the fall semester along with Bactoberfest and the EOD Party.

A group of microbes which have been fun to isolate are the purple non-sulfur photosynthetic bacteria which I have recovered easily from rain, snow, icicles and now hailstones, and they can achieve high populations in the water trapped by the leaves of bromeliads and pitcher plants!  Click on the image on the right for a photo from my masters thesis.  In the vial of water from this leaf of a pitcher plant, the density of Rhodopseudomonas is around two billion per milliliter.  There are also several dead little frogs stuck to the inside surface of the leaf (shown here split open and mounted). Something that Brad Roberts could probably write a song about. We enrich for and isolate purple non-sulfur photosynthetic bacteria in Bacteriology 102 but not just to see if they are in the water samples or not; we hope to demonstrate fully how their anaerobic growth is associated with anoxygenic phototrophy.

Their superficial appearance might be interesting sometimes, but what bacteria actually do is where the excitement is. An old attempt to outline many of the bacterial cell's activities that are covered in Bact. 102 is shown here.

There is no bacteriological activity that pains me more than the maintenance of the stock culture collection. (But someone's gotta do it.) At the last "official" count (the 2002 census) there were 241 strains of over 130 species, and the collection is presently due for a major overhaul and the completion of the current round of lyophilizations. There have been some relatively joyous moments, however. In the early to mid-1990s the collection became happily overrun with enteric isolates as a result of my interest in developing new selective-differential media to sort out relatively obscure yet important organisms such as Edwardsiella tarda, an enteric pathogen found in aqueous environments. Go to the on-line edition of The Prokaryotes and type "Edwardsiella AND isolation" in the search box (without the quotation marks), and you will find the formulation for "ET Agar" – a plating medium upon which I would place membrane filters prepared from environmental water samples. Alkaline colonies with large black centers would generally indicate E. tarda. What had existed in the 1980s as superficial interests in environmental microbiology, enteric bacteria, taxonomy and media really came together in this project which – in the years since then – helped to bring better focus to microbiological matters with consequently a lot more joy and substance to the workplace in general and lab teaching in particular.

On May 31, 1999 I presented a poster on a proposed new genotypically-distinct genus which emerged "by accident" during the Edwardsiella tarda isolations. ASM members can access the abstract to this poster presentation here. Several co-authors and I should be getting the official paper published at its proper time in the sequence of things. For the present, the organism is established as CDC Enteric Group 121. The first isolate came out of a sample collected from an unnamed Northern Wisconsin pond on June 25, 1993. (Two more views of this pond are here and here.) After publication of the official paper we will have info, photos and stories about it here on the web along with some appropriately spiffy songs and animations. In the meantime, GenBank has its 16S rRNA sequence on the web; go here and search Nucleotide for AF015258.

A special note: The Prokaryotes Online is presently the most comprehensive, reliable and updated web resource for information on how to isolate, grow, differentiate and identify bacteria. After a considerable delay, Volume 2 of the second edition of Bergey's Manual of Systematic Bacteriology finally came out in August, 2005 as three separate sub-volumes, and Volumes 3-5 should be out shortly. (Don't wait for the movie.)

One of the shining stars of our stock culture collection – and one we do not charge for – is a strain of Photobacterium which students isolated from shrimp about 15 years ago. If one were to almost totally immerse fresh (not frozen) marine shrimp in flasks of a 3% NaCl solution and then incubate them in a fairly cool room (15-20°C), there is a good chance that patches of bioluminescent bacteria will become visible within 24 hours. Streaking from these areas onto a plating medium containing 3% NaCl eventually yields isolated luminescing colonies. The method is explained here.

Our strain of Photobacterium shines brightest when well-aerated and incubated at 18°C. Click on the image above for a photo of a just-shaken flask culture which is exposing the film with its own light – easily bright enough to read by! One can also write cryptic messages on plates with these bacteria.

So where does the hardly-earned money go? Partly to pump a never-ending stream of film through my old Canon SLR camera – especially on my weekly "commutes" between Madison and Hayward. On the right are two views from the Black River Falls area: a sunset taken Sept. 13, 2001 from the top of Bell Mound, and a foggy early morning scene taken Dec. 13, 2002 on the edge of town. A couple pages of photos from Black River Falls begin here, and quite often I visit the Apostle Islands area.

Speaking of photos, click on the one below which shows some Lindquist generations (circa 1915) immediately preceding mine. Among the three kids in the front row, spot the future school principal and architect, the future farmer, and the future aerospace engineer. In 1920, my grandfather Clarn (on the far right) built a barn on his farm near Hayward; click here for a recent photo. He also sharpened the saws for a major logging operation on Outer Island in the 1920s which is shown here.

Relevant Publications:

  • Deibel, R. H. and J. A. Lindquist. 1981. General Food Microbiology Laboratory Manual. Pearson Education, Paramus, NJ. ISBN 0-8087-5559-5.

  • Lindquist, J. A. 1975. Bacteriological and Ecological Observations on the Northern Pitcher Plant, Sarracenia purpurea. M.S. Thesis, Department of Bacteriology, University of Wisconsin, Madison, WI. Before emailing me about this subject matter, please go here first. Personally I find mulleins a lot more fascinating.

  • Lindquist, J. A. 1991. Medium and Procedure for the Direct, Selective Isolation of Edwardsiella tarda from Environmental Water Samples. (Poster presented at ASM Meeting in Dallas on May 8, 1991.) Abstr. Annu. Meet. Am. Soc. Microbiol. 1991, C-303, p. 302.

  • Lindquist, J. A. 2006. General Microbiology: A Laboratory Manual, Fourth Edition. McGraw-Hill/Primis Custom Publishing. ISBN 0-07-339101-8. Despite its occasional revisions and the major overhaul of the early 1990s for the First Edition of the present series, there are elements in this manual that bear traces of its 70-plus year lineage. Grab a copy of any edition and check out the Acknowledgements section.

  • Lindquist, J. A. and J. J. Farmer III. 1999. Isolation and Characterization of a New Genus of Edwardsiella-like Bacteria from Wisconsin Lakes. (Poster presented at ASM Meeting in Chicago on May 31, 1999.) Abstr. Annu. Meet. Am. Soc. Microbiol. 1999, R-1, p. 616.

  • Lindquist, J. A. and J. J. Farmer III. 2005. Genus XXXVIII. Trabulsiella. In Brenner, Krieg and Staley (eds.), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, pp. 827-828. Springer, New York. ISBN 0-387-24144-2. (No, this isn't the new genus mentioned above. Stay tuned for that!)

Surf's Up!

Family and Medical Leave Act Information for UW Employees is here.
  • The General Microbiology manual listed just above (the one with an actual Acknowledgements section) is presently supplemented by my two main microbiology sites which will remain on the web in perpetuity – freely accessible as always:

    • The growing list of "GENERAL TOPICS" that are indexed here and had their origin in supplementary material given out as handouts in the Bacteriology/Food Science 324 lab course way back in the last millenium. In all my years here, I have not been able to come up with a stand-alone lab manual – i.e., one that does not require updated and better ways of explaining things for students and instructors. (A movie that demonstrates correct aseptic technique is coming soon!)

    • The BACTERIOLOGY 102 site which goes along with the course each semester that I teach it. The site's home page is here, and the updates page for the current semester gives some focus to the web resources and reiterates the announcements given in the lab.

  • The obligatory site outline, pets & links pages.

  • Some more things of possible interest:

Up in my neck of the woods, various interesting animals have been observed including Domino the black squirrel who could chew through wood and plastic and destroy all kinds of "squirrel-proof" bird feeders, Little Ollie the good-natured teddy-bear type who was unjustly accused of taking down our feeders, and a big mama bear with triplets who got caught in the act and then charged the camera with face flushed in fury! For photographing bears, I use a wide-angle camera with an automatic motion detector, so I really don't have to be present during these portrait sessions.

Delighting all who saw her strolling through her domain was Maureen II (caught here with the bear camera), the albino deer who popped out of the woodwork several years ago, replacing the first Maureen who appeared as big as a horse and was first seen in our woods in February 1999 prancing through the snow. A couple photogalleries of Maureen II are here and here (she loved walnuts), and one of the first Maureen is here. If presented with an apple and a similar-sized scoop of mashed potatoes, Maureen II would take the mashed potatoes every time and just sniff at the apple. We lost her in a car accident in early November, 2004, and whatever happened to her predecessor is a mystery. We always have a woods full of the "regular" kind of deer, but they tend to be quite tame and boring in comparison.

The ravens can put on a good show, sometimes spending a lot of time passing things real and imaginary from one to another. In the late summer of recent years, we have been seeing insects bouncing across the back yard like tiny blue balls of cotton, travelling in a small pack and landing preferentially on raspberry and black cherry leaves. Not finding a photo of such a thing anywhere, we determined that they shall be called blue fuzzy cherry gnats – although two authorities at UW-Madison have tentatively identified them as wooly alder aphids.

My mom used to love to watch the animals from the picture window and took this photo of twin bears resting in the back yard.

Email address:
 [email protected]
 or [email protected]

Snailmail address:
 John Lindquist
 120 Old Biochemistry   
 420 Henry Mall
 Madison, WI 53706

   Current Hayward Area Weather ––»
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Five photos taken at the edge of a
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This page was originally placed on the web 1/28/97,
and found sanctuary on jlindquist.com in 2001.
This is the July 12, 2006 edition of the homepage,
archived for "historical" (?) purposes here on the web.
All photos on these web pages are by myself unless they
are credited otherwise or are obviously old archive photos
such as this one (ha ha).

John Lindquist, Department of Bacteriology,
University of Wisconsin, Madison.

Weather Pixie transferred to current homepage.