genomics
sporte | September 24, 2008Part IV. Assembling the details and making the case for a novel paramyxovirus
This is the fourth in a five part series on an unexpected discovery of a paramyxovirus in a mosquito. In this part, we take a look at all the evidence we can find and try to figure out how a gene from a virus came to be part of the Aedes aegypti genome.
image from the Public Health Library
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. Assembling the details of the case for a novel mosquito paramyxovirus
V. A…
sporte | September 23, 2008Part III. Serendipity strikes when we Blink
In which we find an unexpected result when we Blink while looking at the mumps polymerase.
This is the third in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes. And yes, this is where the discovery happens.
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. Assembling the details of the case for a mosquito paramyxovirus
V. A general method for finding interesting things in GenBank
To paraphrase Louis Pasteur,…
sporte | September 22, 2008Part II. What do mumps proteins do? And how do we find out?
This is the second in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes, and a general method for finding interesting things.
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. Assembling the details of the case for a mosquito paramyxovirus
V. A general method for finding interesting things in GenBank
In Part I, we looked at the NCBI SeqViewer, and found a new way to check out a genome map, and learn more…
sporte | September 21, 2008Part I. The back story from the genome record
Together, these five posts describe the discovery of a novel paramyxovirus in the Aedes aegyptii genome and a new method for finding interesting anomalies in GenBank.
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. Assembling the details of the case for a mosquito paramyxovirus
V. A general method for finding interesting things in GenBank
I began this series on mumps intending to write about immunology and how vaccines work to stimulate the immune…
mikethemadbiologist | September 9, 2008One of the reasons to study the human microbiome--the microbes that live on and in us--is that many diseases might have a microbiological component. One of the best examples of this are gastric ulcers, most of which are caused by an infection by the bacterium Helicobacter pylori. A recent report by the American Academy of Microbiology argues that Mycobacterium avium subspecies paratuberculosis, also known as MAP, may, in part, be responsible for Crohn's disease:
Because the bacterium Mycobacterium avium subspecies paratuberculosis (MAP) causes a Crohn's-like gastrointestinal disease in…
edyong | August 30, 2008
The complex cells that make up plants and animals only survive today because their ancestors formed partnerships with bacteria. In a previous post, I wrote about a microbe called Hatena, which provides us with a snapshot of what the early stages of this alliance might have looked like. Hatena swallows an alga which becomes an integrated part of its body.
Millions of years ago, the ancestors of complex cells did the same thing, taking in bacteria and merging with them to form a single creature. Today, these integrated bacteria are mitochondria, which provide us with energy, and…
mikethemadbiologist | August 21, 2008This is a good start:
The US Federal Bureau of Investigation (FBI) plans to publish in peer-reviewed journals much of the scientific evidence it used to pin the 2001 anthrax attacks on microbiologist Bruce Ivins....
In lieu of expert witnesses and cross-examinations, the FBI plans to offer the evidence for peer review and will keep much of the data quiet until they are published. FBI laboratory director Chris Hassell anticipates a dozen or so papers related to the case, in addition to those that have already been published. However, Hassell says, some details of the investigation will remain…
sporte | August 21, 2008One of the things that drives me crazy on occasion is nomenclature. Well, maybe not just nomenclature, it's really the continual changes in the nomenclature, and the time it takes for those changes to ripple through various databases and get reconciled with other kinds of information. And the realization that sometimes this reconciliation may never happen.
One of the projects that I've been working on during the past couple of years has involved developing educational materials that use bioinformatics tools to look at the isozymes that metabolize alcohol. As part of this project, I've been…
mikethemadbiologist | August 17, 2008Olivia Judson, in an excellent op-ed, lays out the utility argument for why students should learn evolution as part of biology:
The second reason for teaching evolution is that the subject is immediately relevant here and now. The impact we are having on the planet is causing other organisms to evolve -- and fast. And I'm not talking just about the obvious examples: widespread resistance to pesticides among insects; the evolution of drug resistance in the agents of disease, from malaria to tuberculosis; the possibility that, say, the virus that causes bird flu will evolve into a form that…
sporte | August 12, 2008Ancestry tests aren't just for humans anymore. We went to Petco this weekend to buy dog food and found brochures for doggy DNA testing. Now, those of you with dogs of uncertain parentage need puzzle no longer. According to Petco, their SNP test (what is a SNP?) can identify over 100 different breeds and they'll tell you which breeds are represented in your dog and whether your dog's breeding is mixed (or pure).
The brochure from Petco also claims that knowing something about your puppy's parentage could be helpful in understanding their behavior and potential health risks. That's probably…
mikethemadbiologist | August 11, 2008I realize science is hard and stuff, but there are serious problems with the evidence in the anthrax investigation. I'm not the only who thinks so: ScienceBloglings Tara and Revere think so too, along with most of the commentors. Thankfully, these problems are finally starting to enter the discussion. First, from Glenn Greenwald:
The NYT today has an excellent Op-Ed from a microbiologist (the former Chief of Fort Detrick's bacteriology division) pointing out the numerous deficiencies in the FBI's scientific assertions. Critically, that Op-Ed describes the properties of the high-grade…
mikethemadbiologist | August 7, 2008Yesterday, I mentioned my doubts about there being two anthrax strains used in the 2001 attacks. Thanks to an article identified by reader TomJoe, I'm convinced that there was only one anthrax strain involved, if the only evidence for the existence of two strains is that there is a DNA inversion.
Just to remind everyone, this is what I mean by a DNA inversion:
In many bacteria, inversions are used as regulatory mechanisms--when the DNA is in one direction, nearby genes are turned on, and when in the other, they're turned off. Like so (this is a made up example for illustrative purposes only…
mikethemadbiologist | August 6, 2008In reading this NY Times story about the anthrax investigation, this statement about how the presence of an inversion (a region of flipped DNA) puzzled me (italics mine):
The genome of various stocks of the Ames strain of anthrax used in the attacks were almost identical in all the 5 million chemical letters of their DNA. But researchers found enough differences in the attack strain to provide a reasonable chance of identifying its source.
The chief difference was that a stretch of DNA was flipped head to tail in some bacteria in the attack strain, but not in any other samples.
Further, the…
sporte | August 6, 2008This the third part of case study where we see what happens when high school students clone and sequence genomic plant DNA. In this last part, we use the results from an automated comparison program to determine if the students cloned any genes at all and, if so, which genes were cloned. (You can also read part I and part II.)
Did they clone or not clone? That is the question.
But first, we have to answer a different question about which parts of their reads are usable and which parts are not. (A read is the sequence of bases obtained from a chromatogram file.)
How does our data get…
sporte | August 5, 2008This the second part of three part case study where we see what happens when high school students clone and sequence genomic plant DNA. In this part, we do a bit of forensics to see how well their sequencing worked and to see if we can anything that could help them improve their results the next time they sequence.
How well did the sequencing work?
Anyone who sequences DNA needs to be aware of two kinds of problems that afflict their results. We can divide these into two categories: technical and biological.
Technical problems are identified using quality values and the number of bases…
sporte | August 4, 2008What happens when high school students clone and sequence genomic DNA?
Background
DNA sequencing is a wonderful tool for discovery and a great technique for getting students involved in molecular science. This fall, Bio-Rad will officially begin selling their DNA cloning and sequencing kit. Now, students across the country will have the tools in hand to begin their own projects cloning and sequencing plant genes.
Of course, without bioinformatics there's no way to know what's been cloned or sequenced.
This is where we come in. As part of an agreement with Bio-Rad, we adapted a version of…
mikethemadbiologist | July 10, 2008Jonathan Eisen has a paper in PLoS One describing software that he's developed for analyzing 16S rRNA sequence data. Rather than walk through everything, I've decided this post will be different: I'm going to treat this as a manuscript that I'm reviewing (there will be some differences, and it won't be as formally written as a 'real' review). But I wanted to phrase some 'real' questions, as opposed to extensively distilling it for the 'lay' reader so non-scientists could see what we really criticize each other about (hint: it's not whether evolution is real). Onto the review.
Eisen has a…
evolgen | June 30, 2008There's a post up at Pharyngula describing the concept of synteny in comparative genomics (Basics: Synteny). The definition given by PZ Myers will sound pretty familiar to those of you who have read some of the genomics literature. The problem: it's not quite correct. It's actually the definition that I think most comparative genomics folks would give if they were asked to define synteny. But they keep using that word, and I don't think it means what they think it means. What's the definition? Here it is in PZ's own words:
Synteny is the conservation of blocks of order within two sets of…
sporte | June 21, 2008Are you curious about Second Life?
Next week you can satisfy your curiosity and learn about the personal genomics frontier at the same time.
Bertalan Meskó announced that Erin Davis (science writer) and Joyce Tung (human geneticist) from 23andMe will be giving a presentation next week in Second Life on personalized genetics.
As travel costs rise and traveling becomes harder, I think we'll see many more things happening in alternative places like Second Life. Virtual environments like this can make on-line communication entertaining in ways that conference calls and webinars can't. I may…
sporte | June 4, 2008I'm in Berkeley right now at the annual Bio-Link Summer Fellows forum. We're getting to hear talks from people in the biotech industry, listen to enthusiastic instructors describe their biotech programs and ideas, and try out new educational materials.
Yesterday, two speakers (Damon Tighe and Jason Baumohl) from the Joint Genome Institute in Walnut Creek, CA, gave a fun talk about DNA sequencing and sequence assembly.
They also showed some very nice Flash animations, made by Damon Tighe, at the JGI, that illustrate how DNA sequencing is done. There's no sound, but the animations are…