A new rapid diagnostic test...

There are illnesses that we take in stride (the common cold), and then there are the ones that scare us at a visceral level (Ebola). Sometimes, that fear is justified - some bacterial pathogens are both amazingly virulent and stunningly endurant (tetanus). Other pathogens are commonly misidentified at first, but frightening lethal in a very short time (Ebola again). However, sometimes the larger public panic about disease is a holdover from an older time. Leprosy, or Hansen's Disease, is mix of both. Misunderstood by most people, and nowhere near as contagious as feared, leprosy is certainly not the threat it is often portrayed to be. However, as another disorder that is often misdiagnosed and with terrible consequences, it certainly is terrible for the 200,000 people diagnosed each year and those living with it already. In this article from the BBC, a new rapid diagnostic test was discussed. This could allow for rapid and accurate detection of infection with Mycobacterium leprae, the bacteria which causes Hansen's disease. This could lead to earlier treatment with the cocktail of antimicrobial drugs needed to treat the disease. The sooner patients can be started on appropriate antimicrobials, the better their prognosis is: they are less likely to suffer the nerve damage that leads to tissue necrosis and disfigurement.

On Wikipedia

When I first started college, there was no wikipedia (yes, I did just date myself), and professors were still adapting to the existence of the internet. Today, they’re adapting to ubiquity of the internet and the ease of access. Nowhere is this more obvious than in their hesitation to accept wikipedia.I will admit that not all articles on wikipedia are rigorously reviewed or accurate. Worse, once you leave wikipedia.com and wander into other wiki-type sites, you find sites that have smaller populations to monitor content and thus correct mistakes. These mistakes are why professors are hesitant to accept wikipedia as resources for academic papers. I am, however, unwilling to reject wikipedia entirely, so this is my guide to intelligent use of wikipedia in academia. Please note that if your professor tells you not to use wikipedia as a source, you should treat these tips the way you would any other search engine - uncited. If, however, your instructor is willing to accept a wiki source, you might try printing out your article (or grabbing a pdf copy at the time you access it so that there’s no concern about later edits), then go ahead and cite away. I’ve not had instructors willing to accept wikipedia entries, but that hasn’t stopped me from using them the same way I use search engines. In fact, unlike many search engines, wiki has an advantage - it gathers useful information in a single location and then provides citations for that information. Following the links to those external sources is the way to use wikipedia as a source and still keep your professors happy. Let’s look at two different examples. This first picture is the wikipedia entry for Pseudomonas pseudoalcaligenes, the bacteria isolated in the petri plate in my avatar. As you can see, there’s not much information, but there are a lot of links to follow out, so once I go to this one page, it becomes much easier to find other, more authoritative sites from this one. Further, among those references are peer-reviewed articles: the fact that the link starts “doi” is a giveaway that they come from sources every professor will accept.

Next is another wikipedia entry, this time, for “Gram negative”. I got here just by following the link in the first article. Look at how much more detailed this article is: pictures, drawings, sections dividing the information. Note, too, that there’s a section that’s been flagged for review. Wikipedia isn’t a perfect source, and I’m not trying to suggest that it is: this should never be a final source for information. But there is a wealth of information here that you can mine, links to follow out to sources that you can consider adequately authoritative to cite. This actually brings me to an important point, one that I don’t think many professors stress enough when they make a blanket ban on information sources. In science classes especially, you’ll hear your professors stress the importance of critical thinking and applying what you learn over rote memorization. It’s the difference between knowing that gram positive cells stain violet, and understanding that they stain violet because their cell walls are thicker and thus retain more of the violet dye. It’s comprehension. That comprehension, application, and critical thinking also allows you to look at your sources and decide if they are acceptable or not. That’s the sort of skill that your professors are looking for when they assign those sorts of papers, and when they ban an entire source of information, the question becomes if they find the information that unreliable or your skills that untested. My guess is that it is a combination of both. However, until we, as a student body, can demonstrate that we are capable of discerning useful information from junk, then sites like wikipedia will continue to languish, unheeded and ignored, or at best, as search engines. So ask yourself: What am I looking for? Will this answer my questions? Can I find the answer to my questions by following the links provided? Are these sources reliable? Does this make sense? And the most important question, the one that all that makes a scientist: Why?

An introduction to metric prefixes

This won’t give all the metric prefixes to you, but then, you won’t generally need them all. Most of the time, you’re working with just a few basic prefixes: kilo-, centi-, milli-, and micro-. In the internet age, we’re also a little more familiar with mega-, giga-, and even tera- (some of you may even have heard of peta-). In microbiology, being familiar with nano- , pico-, and even the Angstrom are useful, but if you can remember how to do the basic format, then it’ll be easier to put all the rest of these into place.

I know this is a little much to take in at once, but I’ll walk you through it. Each vertical line on this longer horizontal one represents a power of 10, or 10 multiplied by itself a given number of times, which is the same this as 10 raised to a given power or 10 to a given exponent.. At the central point, marked by the U, 10 is multiplied by itself 0 times. 10 to the 0 power equals 1, so this represents the base unit. That’s what the U represents: Unit. That’s also what the b below it means: base. Move one space to the left, and you get 10 to the first power, or 10. Move one space to the right, and you get 10 raised to -1, or 0.1 (one tenth). This pattern continues: Two spaces to the left is 10 to second, or 100, two to the right is 0.01 (one one-hundredth). Three spaces take you to 1000 on the left and 0.001 on the right.

That’s what makes the metric system so simple - everything is a factor of 10. There are no quarters or eighths or other fractional measurements to figure out. It’s all about moving a decimal point back and forth, and if you can draw a number line and keep the prefixes straight, then the rest becomes gravy.

The base unit of length in the metric system is the meter. If you’re used to working in the US system, then visualize a yard-stick. A meter is just longer than a yard - just over 39 inches (there’s also around 2 kilometers for every 3 miles, but I’m getting ahead of myself). We’ll start with the meter as our base unit and add our prefixes onto that. (The other units shown are L for liter, the measure for volume, and g for gram, which is the metric unit of mass. Note that in SI, which is the scientific standard, the basic unit of mass is actually the kilogram. However, for simplicity, we’ll just work with the meter).

1 meter (1 m) is just that, 1 meter. Since the metric system operates on a base 10 system, then moving the decimal right or left by one unit adds a prefix. Move the decimal one place to the left, and you have 10 meters (10 m) or 1 dekameter (1 dam). Move the decimal one place to the right, and now you have 0.1 meters (0.1 m) or 1 decimeter (1 dm). If you start 1 meter and move the decimal 2 units to the left, you have 100 meters (100 m) or 1 hectometer (1 hm). Go to the right instead, and you have 0.01 meters (0.01 m) or 1 centimeter (1 cm).

Continue following this pattern: 1000 meters are 1 kilometer (1 km). 1/1000 of 1 meter, or 0.001 meter is 1 millimeter (1 mm).

There are names for the prefixes for 10,000 and 100,000, as well as .0001 and .00001, but these are so rarely used that I must admit I don’t know them. Instead, we skip ahead to 1,000,000 meters or 1 megameter (1 Mm), 1,000,000,000 meters or 1 gigameter (1 Gm), 1,000,000,000,000 meters or 1 terameter (1 Tm), and 1,000,000,000,000,000 meters or 1 petameter (1 Pm). You’ll know that we really don’t use any of these prefixes with meters - once we get to lengths so vast that they are measured as millions, billions, trillions, and so on, of meters, we actually start moving over to different units, a derived unit, the light year (the distance light travels in one year).

On the other side of the decimal, however, in discussing fractions of a meter, 0.000 001 meters is 1 micrometer (1μm). This is sometimes also referred to as 1 micron.The next unit, 0.000 000 001 meters is 1 nanometer (1 nm) and 0.000 000 000 001 meters is 1 picometer (1 pm). Finally, there’s a very special unit of length, 0.1 nanometers or 0.000 000 000 1 meters that is equal to 1 Ångström (1 Å). Note: this is not Am, Angstrommeters, and there are no Angstromgrams or Angstromliters. This is the one little exception - it is a special unit of length named for a Swedish physicist. Officially, it should contain the dots (diacritics) over the o and the ring over the A, even though these are often omitted when being written in English.

So, to summarise:

I remember this with the following mnemonic:

King Henry died by drinking chocolate milk, mother. That sentence gives me the most frequently used prefixes, (kilo, hecto, deka, base units, deci, centi, milli, micro) which is enough to build the basic metric line. I use the comma to remind me to leave spaces between milli- and micro-, and for most things, that’s enough. Even working in microbiology, I really only need to learn the bottom half of the table, pictured below, and that’s a lot easier to learn once you have the basics mastered.

Do you have to use this? Not at all. If you have your own mnemonic, use that. If you can learn it another way, go with it. I’m just offering you the tools that have served me.

If nothing else, remember: once you start with length, mass, and time (meters, grams, and seconds) every other unit is derived (made) from that, and everything is in powers of 10. You may like ounces, pounds, tablespoons, inches, feet, yards, and so on, but keep in mind that there are more units and harder conversions between them than metric. At the very least, metric offers ease of use that the US system doesn’t. The more you use it, the more intuitive it gets. Also, if you’re in science or medicine, you MUST learn it.

I use the metric system

I grew up in the US. The US has not yet standardized on the Metric, or SI, system. However, science, medicine, and most of the world has. As this blog is focused on science and medicine, you’ll find things in metric on the site. Also, many science classes in the US wind up having to teach metric conversion so that students can be more comfortable working in it because that’s what science uses. As a result, there will be metric conversion reviews available as well. Also, as a displaced short yankee, I’d like to point out that use of the metric system means that: My mass is 2 digits (not 3!), my height is 3 digits (not 2!) and the temperature outside is NEVER 3 digits! In other words, by using kilograms, centimeters, and Celsius, all those units that we, as Americans, have an intuitive feel are large, feel smaller to me. :P

Metric System...

 

This is why I prefer the metric system: it's just easier.

Gladstone scientists map process by which brain cells form long-term memories

Gladstone scientists map process by which brain cells form long-term memories. Great discoveries are not made all at once, but rather in little steps, one at a time. One such little step seems to have uncovered the pathway by which learning goes from temporary into long-term storage, thus establishing new pathways in the brain long into adulthood.

Getting Started

There are a million reasons to start blogs and websites, and many of them are awful. When I was trying to decide what I wanted to do with this one, I wanted to avoid all the awful reasons and actually do something interesting and useful. That’s when I remembered how I wanted to create a review for Introduction to Microbiology classes, and the articles that I find and that are shared with me. I realized how useful it is to find resources on a single topic in a single place, and I thought that perhaps, this tumblr could be that. So, the hope is to build reviews on microbiology, cell biology, biochemistry, and similar topics that can be used by students to study for exams. The hope is to gather articles of interest from all over the world related to microbiology, biochemistry, and immunology. I may include some pharmocology, I may not. I’ll try to tag things by discipline to make them easier to find.

If you find something worth sharing, please email it to heathermicrobiologyjackson@gmail.com and put “blog” in the subject line. I’ll try to add things as often as possible.