Microbial updates

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This has been a pretty hectic week, and with lots of food for thought. The situation in the world concerns me, and also other issues of the bigger picture. But today I will focus on updates on bugs. Taking care of microbes growing has  a zen-like quality to it. Call me old-fashioned, but waiting for a hot loop to cool is relaxing.

One of the bugs I brought from Yale, a perky Pseudomonas, has proved to be a funky one. Last week I strode into the lab and decided to try everything available in the fridge, and inoculated all kinds of media to get more information. Results came out along the expected ways (negative fermentation and MR-VP among others), but the nitrate was negative. The sequence had been pointing at a weird fish-killing Pseudomonas, but  P.plecoglossicida is nitrate positive. My bug did not seem to be fluorescent under UV light, so P. fluorescens seemed to be out of question, but it is nitrate negative, so I inoculated a couple of gelatin deeps and am waiting for the results, gelatinase production being one of the distinguishing features. I have been around labs enough to not get too excited about weird stuff, and I just cannot believe that the soil at Yale University is harboring some kind of special bug. But at the end that is not so important…it is the antibiotic production that matters. So I am also repeating the spread/patch plate against four bugs, including E. coli & P. aeruginosa. After that, if things repeat, then I will have to make some decisions about what to do next.


West Coast & East Coast kombucha. Just refilled the East Coast one, that’s why it is in the bottom.

As for kombucha, as they say, no news is good news. It has been growing placidly in the corner, by now in its 3rd of 4th tapping. The first ones had 1/2 cup of sugar per liter, and were very sweet in the beginning and very tart at the end. Then I halved the sugar amount, and the resulting drink was way mellower but also bland. I had started experimenting with diluting the strong concoction with fruit juices, which seems to produce a pleasant flavor. Another option is to add chia seeds, which give a nice chewy quality to the drink not to mention the added protein. I finally relented and bought a set of big jars for the cultures. The West Coast one has been steadily growing, and I can see it becoming equal to the Yale one, especially after today as I started to give away babies (tearing away a layer). Next stage will be experimenting with different teas and sources of sugars.

My next post will be about scaffolding assignments for a General Bio class. I had a kind of epiphany about grading rubrics the other day while banging my head in frustration because of students not following instructions. Stay tuned!

Correcting course(s)

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I had seen it on the web some weeks ago and I covered my ears and sang “lalala.” But now that I have it in front of me, smiling smugly from the cover of Science magazine, I cannot ignore the giant Pandoravirus and its acolytes anymore.

Electron microscopy image of teh huge virus pandora

Enhanced transmission electron microscopy image of a “Pandoravirus” particle, from the cover of Science, July 19 2013.

Gosh, maybe Patrick Forterre is right after all, and we have to rewrite the three domains and invite viruses in? Consider them alive?

Please note that I am NOT a virus expert and I do not follow the field. However I did come across Forterre’s work quite a while ago, found it fascinating, and immediately tried to forget. Put my head in the sand. Because I have been there before, facing a group of non-majors who have to take a general biology class because they have to. And they find everything about biology complicated and tiresome, and they look at their textbooks as the source of all wisdom and then one does the science thing. The days I am more pacific I purr softly “There are new developments that question some aspects of this theory,” and may leave it there. Other days I may try to transmit the enthusiasm of new discoveries in science that challenge old paradigms. But few students share the joy, especially if they just got something and then I am ruining it for them.

It is interesting how the perception of changes is different when inside or outside the field. Inside a field, one is aware of the small changes due to minor discoveries that eventually may lead to a complete reevaluation of the existing knowledge. As an outsider to the virus field, I have been seeing only bits and pieces of discoveries, which now suddenly seem to be moving in a certain direction.

So I’ll wait and see. I still remember years ago, when the idea that the microbes living on our body could do something else that just try to invade us given the chance was novel and revolutionary. I went from the casual comment of “it seems like gut microbes can influence obesity” to the current discussion of microbiomes and their importance in health and disease. Maybe in a few years, those slides with the neat 3 domains will become something very different.

This reflection is coming of course from my non-majors general bio class that started yesterday. Even during our SWI discussions last week it was obvious that non-majors require an extra dose of fun and excitement in a science class to make it somehow memorable. That’s why I decided to go for the Phelan book, for several reasons: it reads easier, it has a great companion website, it has tons of real life examples and applications, it has lots of graphing examples and illustrations, it is cheaper than the one we used before, and overall it just seems to be more fitting the modern student. I am also drawing heavily from the ideas and rubrics of the Vision and Change report, which identifies a set of core concepts and skills that should be part of the undergraduate biology education.  It is nice to have some solid guidelines for the design of coursework.

Two glass containers containing kombucha

My kombucha cultures, day 3.

The kombucha mothers, by the way, have risen to the surface of the sugary tea, not completely yet, but exposing more “body” to the air. What a relief. Following the instructions, I have been tasting the drink daily, feeling a slight tanginess invading the sweetness of the original tea. It is very pleasant, and it is amazing how quickly the pH changes day after day. It should not take many more days to get to the right balance point.

Other than that, lots of catching up to do after the SWI week. My cultures should arrive tomorrow to campus, but will have to wait until next week in the fridge as I am out of town this weekend…again. Stay tuned!

Kombucha day 1

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Two starters cultures and tea. Kombucha time!

When I landed yesterday, one major issue was on my mind: my non-majors online General Bio course starting Monday. I had the website more or less organized, but I knew there were things to straighten up before the course shell opened on Sunday. As anybody who has taught online knows, the first week is the most critical: information has to be detailed and easy to find, instructions crystal clear, and instructor responses as fast as possible. So after some grocery shopping and catching up, I spent the night hours trying to tie up all the loose ends.

Two glass containers with kombucha cultures.

West Coast to the left, and East Coast to the right. Same tea. Curious how they will turn out!

In contrast Sunday was a mellower day. Short visit to the beach, coffee, more grocery shopping, and then housework, which these days counts almost as relaxation. Part of housework mixed with science was getting the East-West kombucha challenge. I had obtained a vial of local kombucha some weeks ago, and had it in a vase full of sugary water waiting for the biofilm to develop. Then I had Ashley Shade’s kombucha that traveled with me from Yale. She said it would be fun to compare the two, so I decided to get them started more or less in parallel. Needless to say, while the tea and sugar solution was the same, I cannot really say that the conditions are replicated, as  there is no way to say how many and what type of cells are in the two slimy films that landed in it. But for now my idea is just to get them started side by side. I boiled water and then poured it over the tea leaves (1 tsp/cup). After seeped, I added 1 cup of sugar/liter tea, and let it cool. Once at room temperature, I carefully let the biofilms slide in. Neither floated completely, and I hope they will straighten up eventually as they produce gas. Or not. Covered with double paper towels secured with rubber bands, and placed them on the counter, in a darker corner.

For now I do not intend to collect any samples, just to produce some kombucha and once I have more or less comparable “mothers,” then maybe starting a parallel experiment in earnest.

Oh and if you wonder why are the two containers different, there is a reason.

I could not find two large glass containers of matching size.

Time to visit a Goodwill store 🙂

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