Antibiotics are molecules of biological warfare. Produced by bacteria and some fungi, in response to extracellular signals, antibiotics represent a diverse group of compounds that inhibit bacterial growth at different points and different stages of the life cycle. We will get around to antibiotic resistance, but in these few words ...
This is a multi-part series on antibiotic resistance in bacteria. Eventually, we'll reach the ways in which bacteria develop antibiotic resistance, but before we get there, we'll spend a little more time on antibiotics themselves. What have we learned so far? 1. Antibiotics are natural products, made by bacteria and ...
The wind storms and heavy rains that hit Seattle a few years ago, and flooded the Battery Street tunnel, demonstrated why a bypass mechanism can be a helpful thing - for both bacteria and motorists. When the weather is nice, I bike to work. But when the weather gets bad ...
What's the difference between a synthetic drug and an antibiotic? Sometimes there's no difference at all. Let's take a look at chloramphenicol and couple of pencillins. Chloramphenicol kills many different kinds of bacteria by interfering with their ability to make new proteins. Here's a point where language gets tricky. Originally ...
Do other organisms make antibiotics? As far as I can tell, most of the commercially produced antibiotics are made by bacteria, fungi, and a bit chemistry (more on that in a moment). It appears, however, that compounds with antimicrobial properties are made by just about everything. Just to make things ...
This is a video that a friend made that shows, very clearly, how to pour an agarose gel, load the samples and run it. I especially like the way he used a bit of time lapse photography to show the dyes separating as the gel ran.
Considering that several genomes that have been sequenced in the past decade, it seems amazing in retrospect, that the first complete bacterial genome sequence was only published 12 years ago (1). Now, the Genome database at the NCBI lists 450 complete microbial genomes (procaryotes and archea), 1476 genomes from eucaryotes ...
"How much do I love you? I'll tell you no lie. How deep is the ocean? How high is the sky?" - Irving Berlin The other installments are here: Part I: Introduction Part II: Sequencing strategies Part III: Reads and chromats Part V: checking out the library We all know ...
About a week ago, I offered to answer questions about subjects that I've either worked with, studied or taught. I haven't had many questions yet, but I can certainly answer the ones I've had so far. Today, I'll answer the first question: How do you sequence a genome? Before we ...
Shotgun sequencing. Sounds like fun. Speculations on the origin of the phrase I think that this term came from shotgun cloning. In the early days of gene cloning before cDNA, PCR, or electroporation; molecular biologists would break genomic DNA up into lots of smaller pieces, package DNA in lambda phage ...
Vizzini: He didn't fall? Inconceivable! Inigio: You keep using that word. I do not think it means what you think it means. - William Goldman, The Princess Bride Excuse me while I temporarily interrupt the genome sequencing series to define a word. Artifacts in the classroom It's disorienting. You learn ...
There are five ways that I know of that allow bacteria to escape death. I call these t he five paths to antibiotic resistance 1. Persistence is resistance: Most antibiotics kill by acting on the metabolic pathways needed for bacteria growth. Ironically, bacteria can survive by not growing. Read more ...
If you've read any of the many stories lately about Craig Venter or Jim Watson's genome, you've probably seen a "SNP" appear somewhere. You may be wondering, and rightly so: just what is a SNP? Never fear, hopefully this post will answer some of those questions. SNP stands for Single ...
RFLP is an acronym that stands for "Restriction Fragment Length Polymorphism." That's quite a mouthful and once you've said this phrase a few times, you realize why we use the initials instead. I know a Restriction Fragment Length Polymorphism sounds like something that must be impossibly complicated to understand, but ...
I love the way you show me secret things. All I do is type: Select * from name_of_a_table And you share everything with me. Without you, my vision is obscured, and all I see is the display on the page. In fact, this was the push that finally made me ...
This morning I had a banana genome, an orange genome, two chicken genomes ( haploid, of course), and some fried pig genome, on the side. Later today, I will consume genomes from different kinds of green plants and perhaps even a cow or fish genome. I probably drank a bit ...
Science labs are not for all people. I've always enjoyed teaching lab courses, so some of you might find it strange that I agree with some of the comments from Steve Gimbel and fellow Sb'ers on the questionable benefits of laboratory courses in introductory physics. But you see, I wasn't ...
The general steps in genome sequencing were presented in the earlier installments ( there are links at the bottom of the page), but it's worth repeating them again since each of the earlier steps has a bearing on the outcome of those that come later. These are: Break the genome ...
To the ancient Greeks, a chimera was a kind of monster, with the body of a goat, the tail of a dragon, and a lion's head. To geneticists, a chimera can be an animal that's derived from two embryos, such as a transgenic mouse. Or if the organism is a ...
How to win the X PRIZE in genomics In October, 2006, the X PRIZE foundation announced that second X prize would focus on genomics. The first team to successfully sequence 100 human genomes in 10 days will win $10 million dollars. And I would venture to guess, that the winning ...
In which I present a quick guide for the omically challenged and a defense of 'arth and "ome." Other SciBloggers have shared their thoughts on the use of ome here and here. Sometimes I get frustrated too, with the way language is abused and tweaked by those around me. So ...
Vaccines work by stimulating the immune system to respond to a specific thing. Most of the vaccines we use are designed to prime the immune system so that it's ready to fight off some kind of disease, like whooping cough, polio, or influenza. Some vaccines can have more specialized functions ...
"Beware the Jabberwock, my son! The jaws that bite, the claws that catch! Beware the Jubjub bird, and shun The frumious Bandersnatch!" - from Jabberwocky, by Lewis Carroll I'm certain that if we ever sequenced DNA from the frumious Bandersnatch it would match hypothetical and putative proteins. Why? Because we ...
In the effort to help us define a few basic concepts, PZ started out by giving us a nice simple definition of a gene, but as he, rightly noted: I tell you right now that if I asked a half dozen different biologists to help me out with this, they'd ...
How do microbiologists determine which microbe caused a disease? As Tara has eloquently described ( I, II), we are covered with bacteria and other microbes. A reasonable question then, is when we get sick, how do we which little devil deserves the blame? In many cases, pathogens ( disease-causing organisms) ...
