Month: February 2007

Are “Acid-Fast” bacteria Gram-positive or Gram-negative?

I was wondering what today’s post ought to be – but a Google™ search that reached the page posed an interesting question and made it easy.

Someone from a Miami, Florida college got to this site after asking Google:
“Assuming you could stain any cell, would an acid-fast [bacterium] be gram-positive or gram-negative?”

Therefore, today’s post will deal with some Microbial Physiology.

The easy answer is, of course, “no“.

A more useful answer, though, is that it depends on what you mean by “Gram-positive”.

If one takes the “Assuming you could stain any cell” part of the question to mean that you’ve done whatever it takes to get the Crystal Violet/Iodine into the cell wall, and you mean “will the cell still look purple instead of pink at the end of the Gram Stain process”, then I’m pretty sure the answer would be yes, that it would be “Gram Positive”. It actually IS possible to stain “acid-fast” bacteria with the Gram stain. The catch is that it takes 12-24 hours of staining (according to Gram’s original paper) rather than a minute or so. This still counts as Gram-positive, though, and in fact the whole Phylum of Actinobacteria (including the Mycobacterium genus) is considered “High G+C Gram-positive”. (If the query was for an exam or homework problem, this is probably the answer you’re looking for.)

On the other hand, if you mean “does the cell wall structure of an acid-fast bacterium better resemble Gram-positive or Gram-negative bacteria?”, you can make an argument that instead of a nice simple “inner membrane surrounded by a thick peptidoglycan-layer cell wall”, the “acid-fast” bacterial cell wall looks more like a complex gram-negative-type cell wall, having multiple layers, with special proteins that form channels through them to let substances in and out of the cell through the otherwise penetration-resistant outer layer, just as Gram-negative bacteria have through their outer membrane. (On yet another hand, those outer layers are tough like a gram-positive bacterium rather than fragile like a gram-negative bacterium’s outer membrane, and don’t dissolve in alcohol.)

Therefore, if you’re speaking in terms of taxonomy, and by “Gram-positive” you mean firmicutes which, as far as I know at the moment, are really the only class with the simple, officially-gram-positive-type cell wall structures and therefore are usually what is meant when someone says “Gram-positive” (someone please correct me if I’m wrong here), the obvious differences with “acid-fast” type cell walls can at least make a good argument that they are “not ‘Gram Positive’ bacteria”.

But if you put that on your homework or exam answers, don’t blame me if you get marked wrong…

I actually found a pretty nice illustration on the University of Capetown website showing the differences in cell wall structures here, which might help.

So, to summarize – Officially, they’re either “neither” or “Gram-positive”. Unofficially, you can probably argue either way. Hmmm. I should try to work in a post on bacterial taxonomy one of these days.

Actual Microbiology Post: some search queries

Before I embarass myself further trying to describe principles of Natural PhilosophyPhysics comprehensibly, I think I’ll do a post or two on things that I think I can more easily describe…

I will also remind everyone that I am merely an undergraduate, so if you happen to be speaking to a Ph.D. microbiologist and mention “some guy on the internet said…” and he or she tells you I’m full of it, I’d appreciate it if someone would tell me. (If they say “Wow, that guy’s a genius“, tell them I say “thanks” and ask if they’ve got any spare grant money or surplus equipment they could send me…)

I did some poking through the web server logs and noticed a few hits from search queries, looking for basic information about microbiology (and in particular, preparing and staining slides).

(I found it interesting that although most of the hits on this site are Mozilla Firefox, every single one of the search-engine-query hits were using Microsoft Internet Explorer. [Safari looks like it amounts to a little more than the number of MSIE hits.] Don’t know if it MEANS anything, but still interesting.)

Aside from a hit from someone looking for pictures of Gram-stained bacteria and, oddly, one person looking for information about the “No You Can’t Have (X), Not Yours” meme, here are the queries that have led to my page so far:

From somewhere in Kuwait: someone looking for “Gram (something) that stain red because”
From Toronto, Canada: “Gram Staining work”
Hopefully, I managed to explain whatever they were looking for back in my post about why the Gram Stain works.

The “Purpose of Heat-Fixing Bacteria on a Slide” query (posted about here) came from somewhere at a major technology company in Texas (and, coincidentally, today from someone at a college in Florida). And for Norfolk, Virginia (who just reached the site as I was typing this) – “Fixing” just means to keep something from moving – in this case, it means making the bacteria “stick” to the slide. Though I suspect he or she already figured that out from the previous “heat-fixing” post. On a related note, someone at a community college in Texas wanted to know “what would happen if too much heat were applied in heat-fixing”. To answer that one is (to the best of my knowledge), that it depends on how much is “too much”. Comparatively fragile bacteria like Mycobacteria would, I assume, tend to fall apart in the heat relatively easily. A bit more heat would probably fry the Gram-negative type bacteria, and a little more would finally destroy the Gram-positives (don’t quote me on this, I’m guessing here). One trick I’ve picked up is to hold the slide with my bare fingers (on the edges of the slide as far from the smear as possible) and slowly pass the slide into and out of the Bunsen burner flame until the slide gets uncomfortably hot (but stopping before it starts actually burning my fingers). That seems to do the job reasonably well.

Someone from the Fresno, California area wanted to find out how negative staining works.
A “Negative” stain is like a “negative” of a photograph – you’re staining everything BUT the bacteria on the slide (ideally). This is useful if something about the bacteria you’re looking at keeps it from being easily stained, or in particular if you want to see if the bacteria produces a capsule. If you stain the slide with India Ink, it’ll make the slide itself black, but leave a clear spot where the encapsulated (or, conceivably, any other bacteria that won’t soak up the ink) are, so you can find them. They also apparently do something similar in some kinds of electron microscopy.

Someone in New Jersey wanted to know what the purpose of “Simple Stains” were. A “Simple” stain just means you’re putting one kind of dye on the slide to color the bacteria, and you don’t really care about the color. Unlike differential stains (like the Gram stain) or a diagnostic stain (like an Endospore stain), it doesn’t really tell you anything about the bacteria other than what you can directly see in the microscope – but if the relative size, shape, and arrangement of the bacteria is all you’re interested in, a simple stain may be all you need. It doesn’t matter too much what kind of dye you use for this – I know methylene blue is a common one for this kind of thing.

Someone at a facility in Wyoming was trying to figure out what an alcohol wash did to bacterial cell walls. Presumably he got directed to this site because of my Gram Stain post. It’s probably worth mentioning that I believe the alcohol wash doesn’t actually do much to the cell wall – but it does seem to remove the outer membrane that is outside of the cell wall, if the bacteria have one.

Someone in the Chicago, Illinois area appeared to be searching for general information on choosing a dye for staining – that one probably deserves a post of its own, but I’ll try to put something together on it.

Another query was someone from the Phillipines specifically looking for an article on Schizomycetes. I just notices something about that post – I actually forgot to add one useful note about “Fission Fungi”: That’s what “Schizomycete” actually means (Greek: Schizo-: split in two -mycetes: relating to fungus). Also, for those photosynthetic bacteria (“Fission Algae”) the contemporary term was “Schizophyte”.

Finally, I find myself intensely curious about the very focussed query originating from a healthcare product company in New York, looking for information about Gram Staining of Bacillus atropheaus, specifically. Maybe Willy Bacillus has found his first fan…

The Entire Universe Explained Part 2: The Most Fundamental Observation

“The Universe is Powered by Laziness”

(I obviously need more practice – I’m still not sure how coherent this explanation is to anyone but me. Comments welcome here – or if you prefer, you can contact me via XMPP (“Jabber”, “Google Talk”) at XMPP:epicanis@enzymestew.dogphilosophy.net )

There you have it, the big secret that is at the heart of every single thing that happens in the natural world. Everything is the result of the Universe’s laziness. This is more or less what the Second Law of Thermodynamics says. In more proper language, it’s the observation that the total “disorder” in the universe is continually and unstoppably increasing.

I like to think of the universe as a big, fat, obnoxious sports fan. Picture him slouching in his couch. In one hand he’s holding a gigantic can of the most awful “lite beer” you can think of – you know, the one that only losers like – and in the other he’s got a giant foam hand with the logo of that team that only complete weenies like. He doesn’t even bother cheering – he just sits there, slouching as much as possible, maybe drooling a little, and wishing he could relax until he was nothing but an ever-spreading lump of flab…

So, what does this mean? Firstly, that there are always some “losses” whenever something happens. Basically, the universe can never manage to open a fresh can of that awful Lite Beer that it drinks without spilling at least a little bit of it on the floor. Secondly, that any bit of the universe you might happen to look at always wants to slouch a little further if it can.

That first part is what accounts for the “losses” in light of the “nothing magically disappears” observation previously mentioned. In the real world, no matter how carefully you build something, you can never quite get as much energy out of something as you put into it. You might get nearly all of it back out if you’re really careful, but no matter how carefully you hand 12 ounces of beer to the Universe, it always seems to end up with only 11.999999999 ounces of beer to drink. Or a lot less. It didn’t “disappear”, it just ended up soaked into the Universe’s filthy carpet where it is no longer available for anyone to drink. That beer-spillage is what physicists call “Entropy”. Or, “Heat no longer available to do Work“, if you want the proper physics definition.

The second part relates to the fact that there is a certain amount of “energy” inherent in the way any kind of matter is arranged. Matter, being part of the universe, is lazy, and doesn’t like having to hold onto all that energy. If you give it an opportunity, a piece of matter will tend to want to rearrange itself so that it’s not holding onto as much.

As an example, if you mix together some chemicals that will burn together if you light them, then seal them completely in a solid container, and set them off (by adding just a little bit of energy), you’ll find that the weight of the sealed container stays the same before and after…but it got really hot. That means there was energy released, and apparently a lot more than the little bit that started the whole thing – where did it come from?

The answer is that it was “built in” to the structure of the chemicals. Setting them off with a little bit of energy shoved the chemicals together just hard enough to let them recombine in a way that they didn’t have to hold on to all the energy they had up until then. All the energy the lazy chemicals let go showed up as heat. The little bit of energy you had to put in to get things started is what chemists call “activation energy”. It’s just there because those molecular slackers sure weren’t going to put out any extra effort to start rearranging – but once a couple of them are shoved together hard enough to make them get started, the energy they release is enough to shove a few more molecules together and get them to release more energy…and so on.

Because cool science types seem to avoid using whole words whenever possible, this energy that comes out is referred to as ?G. The total amount of energy that is “built in” to a particular molecule is referred to as “Gibbs’ Free Energy” (named after William Gibbs.)

So, for the last horrible analogy for now, let’s return to our big fat slob of a Universe slouching on his sofa. He’s been drinking that disgusting beer of his all night, and his bladder’s full. He’d really like to go to the bathroom but, eh, it’s too much effort to stand up. However, if you get behind him and shove hard enough to push him off of the sofa, then he figures while he’s up he might as well hit the bathroom before he sits back down. And, yes, I suppose that means it is my fault if next time you go camping, you end up waxing poetic and describing the nice, comfy campfire as “urinating heat and light on everybody”.

Microbiologically, that means that for a microbe to be able to live on some kind of “food”, it’s got to be possible to convert the food into substances with less energy built in, in such a way that it can capture and store some of the released energy in the process for its own use. It also means that if the microbe needs to make more of, say, some kind of enzyme (a more “ordered” combination of smaller molecules) it’ll have to shove in some energy to make up for the increased “order” while it assembles the parts.

Finally, what enzymes (or any other kinds of catalysts) do is reduce “activation energy” for a particular reaction, so bacteria don’t have to burst into flame in order to “burn” sugars for energy (for example).

And now I think I ought to go back to Microbiology posts before I get myself lynched by angry chemists and physicists for making a mess of this explanation…

Search Engines appear to have found me…

Quick update: I just checked my logs – I just realized there have been a number of hits from Google searches in the last couple of days, from people trying to find information about staining and such.  I’ll try to throw in a post on search query topics that showed up in the logs in the next day or two as well.  Stay tuned…

The Entire Universe Explained: Part 1. The Most Important Observation

This is just a downright flippant Gross Oversimplification™ of some things that I’ve noticed over the years which seem to come up in every science class, though occasionally they are described in slightly different ways or under different names. The more I’ve thought about it, the more I find these principles always buried, somewhere, in every observation of the natural world.

I present them here mainly for people who don’t have a background in science, though I’m hoping those who do will at least find this mildly amusing. Essentially, I just want to mention these things now on the assumption that it might help some people understand some of the basic reliable assumptions that science uses. Since they also then explain the underlying principles that drive the biochemistry that’s important to the microbiology that I want to get into, and I’d like as many people as possible to understand what I’m talking about when I do.

Therefore, I’m going to attempt to describe, using my Super Undergraduate Writing Skills, in very brief terms, everything you need to know to understand basic biochemical processes that I plan to try to explain to the best of my current ability later. I apologize in advance to any serious “hard science” types who may suffer blurred vision, seizures, dizziness, upset stomach, or psychiatric anaphylaxis from reading this.

(As always, if I get something outright wrong here, please say so…)

Part 1. The Most Important Observation of the Natural World: “You can’t get something from nothing – or vice versa”. Or in other words, nothing ever magically appears or disappears. If something appears where there previously wasn’t something, it came from somewhere. If something disappears, it went somewhere – it hasn’t simply ceased to exist. This is more or less all that is meant by “The First Law of Thermodynamics” in physics. In practice, this is what’s being invoked whenever you hear someone describing a scientific “Conservation of [whatever]”. You can still chemically combine things to make completely different substances, melt solids into liquids, bubble gasses away or dissolve solids, turn one kind of energy into another (like turning electrical force into light), and so forth, but in the end the amount of material and energy at the end should be the same as when you started. (It’s even possible to turn material directly into energy and energy into particles of matter, but as far as I know this only actually happens in conditions that matter to people like high-energy physicists and such, not in biological systems.)

This is a handy principle – it lets you measure things indirectly. If, for example, you’re studying some kind of chemical reaction that makes hydrogen gas, you can measure just the amount of hydrogen that comes out when you mix the chemicals together and be confident that this will tell you exactly how much hydrogen was chemically combined into the original ingredients that reacted. Or if you put a three-ounce cricket in a cage with a 12-ounce snake, then come back a few minutes later and discover that the cricket has “disappeared” but the snake now weighs 15 ounces, it should be obvious what’s happened without having to give the snake an MRI.

I’ll pause here for comments before I get to parts 2 (regarding the 2nd law of thermodynamics) and 3 (tying the first two parts together to make Equilibrium and such), both of which I’ll try to get to tomorrow, unless it turns out that I’m completely butchering this whole explanation and have to fill in with something else while I rework it…

Just a little over an hour…

“Just Science” blogging week starts tomorrow, which is to say, in a little over an hour where I am. Starting sometime in the next 24 hours or so, all of the participants are supposed to post at least once each day, and only about scientific topics, for the whole week. Of course, I intend to do my part.

I haven’t decided what to start with yet, though. Depending on how much time I can afford to devote to it, I may either make my ambitious attempt to, in one post, explain the workings of the entire natural world (in Grossly Oversimplified form, of course – e.g. “The Universe is Powered by Laziness“), or I may just start out with a simple post or two on staining methods or how to cheat and quickly identify the “Pseudomonas” cultures when you have to do the “Unknown” identifications in basic microbiology labs, or something like that.

If I can get through the Three Basic Observations that (I boldly claim) describe pretty much everything in the natural world, plus a Grossly Oversimplified explanation of how chemistry works (hint: it’s nothing more than the aforementioned Three Basic Observations plus electricity) then maybe I can get into things like the Electron Transport Chain, the Sulfur, Nitrogen, and Phosphorus cycles, why microbial fuel cells work, and things like that.

Any requests?

About this blog

(I’ve only got a couple more days before the start of “Just Science” week, so if I’m going to get this post up, I’d better get to it…)

Now that I’ve briefly explained who I am, here’s the bit about this blog itself.

My intended audience:
Anyone who’s interested. Okay, that’s kind of a cop-out. Essentially, I’m aiming at anyone who’s sufficiently scientifically-minded to be interested. I’m kind of assuming that if and when I’ve got enough readers to consider a “core audience”, it’ll be made up largely of interested science students, people who are inclined to read magazines like “Scientific American” or “Discover”, and just generally reasonably intelligent people with an interest in scientific matters, particularly but not only microbiology. I’m hoping that I’ll reach the point of being able to write so as to be interesting to some scientific professionals but still comprehensible to people without much of a scientific or technical background. This blog is, in part, an exercise in “public access to scientific information”, so if I write anything badly or fail to explain something, please comment and let me know.

How it works:
It’s easy: I think of something that I find interesting and that I think someone else might also find interesting, and I post something about it here. I expect to focus primarily on microbiology-related science, but a wide variety of topics might come up. I have a particular fondness for subjects that I think are underappreciated or ignored in other venues. Comments on whether or not things I bring up are interesting or boring will help guide the topics. I’ll tend to focus more on informal and hopefully pleasant to read style rather than a dry but detailed technical discussion – though wherever possible I’ll include links to that kind of information for anyone who’s interested (or perhaps thinks I’ve gotten it wrong.).
I also try to make the postings somewhat interactive – at the very least, I try to add extra information, explanations, and comments wherever I think they might be helpful or just entertaining. If you see words or phrases with thick dotted underlining, you should be able to “hover” your mouse cursor over it and get a little bit more information. I generally try to do the same with links and pictures. Maybe once in a while I’ll get bored and plant an Easter Egg or two.
Comments are welcome and encouraged, other than “spam”. What little information you’re required to give in order to comment is entirely to discourage spammers.

But…Why?
Really, this is mainly for personal gratification – I like to write. I like science. I’d like to share this interest, and I think scientific information would be interesting to many more people if more of it was presented in an interesting and accessible manner without making it seem otherworldly or dumbing it down to the point of uselessness. This blog is a cheap and easy way to get practice.
It’s also a cheap and easy way to get free learning for myself – I find trying to explain something helps me recognize when I don’t know something as well as I thought, helps me understand things better, and occasionally is a handy way to find out when something that I think I know is wrong.

Addendum: Yes, my Mom reads my blog. No, she does not wear combat boots. No, she does not dress me funny.

About this blog, Part 1: Me.

I thought it’d be useful to do a couple of posts explaining who I am (this post) and what I’m hoping to accomplish with this blog.

Don’t worry, I’ll try to be concise.

In a metaphorical nutshell: I’m a general-purpose nerd with a 15-year history of being a reasonably hardcore computer geek. I’m now escaping that field, and am a continuing undergraduate (at least as of right now.) who’s been painfully puttering part-time through college for many years off and on until recently – they don’t seem to make much provision for ““Non-traditional” students in US colleges. I’m now hoping to actually finish and graduate this summer – and then find an appropriate graduate program in whatever part of the country I end up in afterwards.

My area of academic interest is Environmental and Industrial (“Applied”) Microbiology. Medical microbiology, which seems to get all of the attention and funding, is somewhat interesting, but I’d rather people be able to benefit from anything I learn without having to get sick first.

In particular, at the moment I’m interested in exotic modes of respiration in prokaryotes. Or, more colloquially, fun (and preferably useful) ways of playing with live bacteria and electricity at the same time.

I’ve also got some interest in science history, public policy, writing and other forms of mass communication, public access to science, travel, food and food science, and at least casual interest in a wide variety of other areas. As such, you can generally expect that most of this blog will focus on microbiology and microbial biotechnology related topics, but will occasionally veer off in odd directions.

I also hope very much that someone besides me will get some pleasant usefulness out of this blog, so I strongly encourage comments, suggestions, corrections, and so forth.

Wow, I guess everything IS bigger in Texas…

…including, at least for today, my audience.

After being linked to from The Tangled Bank I’ve gotten hits from all over. Mostly using Firefox, I notice, and a large number of Mac users (plus at least one and possibly two fellow Penguinistas.)

Hits coming from all over – A few from Canadian colleges, Michigan, California, New York, the U.K., the Sydney, Australia area [update: Oh, and now India – Hello, India!]…and a surprisingly large number from Texas.

Interesting selection of institutions, too. Colleges, research institutions, government agencies…I just want to assure the readers from the disease and mental-health organizations (there was at least one from each) that I’m perfectly healthy and sane. For certain values of “perfectly”, anyway. At least, I’m not 5150 nor afflicted with any sort of terminal condition.

Since at least a few people seemed to come back and look at the rest of the site, I’ll endeavor to put up a post tomorrow on what exactly I’m trying to do in this blog and such (in case anyone’s thinking “that’s nice, but does this get better?…”).

But for now it’s bedtime – early morning Pathogenic Microbiology Lab tomorrow. Goodnight, all.