Genetics & Molecular Biology

I want my genome sequenced, too! Apparently, it's become a popular thing to get your genome sequenced. Craig Venter was the first. Jim Watson's genome (of Project Jim) was ceremonially released this morning (courtesy of 454), and now George Chuch, Larry King, cosmologist Stephen Hawking, Google co-founder Larry Page, Microsoft co-founder Paul Allen and former junk-bond trader Michael Milken want theirs done, too (1). Two articles from different GenomeWeb releases made a strange combination this morning when I turned on my computer. In one release, GW mentioned that NHGRI (the National…
The first research assignment for our Alaska NSF Chautauqua course has been posted. Your task is to find a wound-inducible plant gene, learn something about it, and post a description in the comment section. We've already had one excellent answer, but I know there are at least 54 wound-inducible genes, so I expect to see more. Once we get our genes in order (and possibly before), we'll talk more about designing an experiment for detecting gene expression. In the meantime, I have some pre-course reading assignments to help you prepare. tags: plants, Alaska, NSF Chautauqua courses,…
Is the case for open access truly "open and shut"? Will open access impede science by limiting genetic studies with families? tags: genetics, genetic privacy, bioethics, open access Microsoft's brave new world The April ALPSP conference began with songs for the open access choir. Microsoft's Lee Dirks painted visions of a utopian future where everything will be open, labs shall be judged by the worthiness of their databases, and even scientists will learn to share. According to Dirks, "Open access to scientific content, specifically data, will become the norm." Since I've had a few data…
An introduction to our Alaskan NSF Chautauqua course and a pre-course assignment. I don't know how well this will work, but I thought it might be interesting this year to experiment with blogging about our course and sharing some of our experiences with the rest of the world. Here's your chance readers, if you'd like to do some of the assignments, you are very welcome to follow along and give it a try. tags: plants, Alaska, NSF Chautauqua courses, bioinformatics, sequence analysis, evolution, wound inducible genes, moose I'm not likely to get all the assignments or course info posted on-…
Sometimes I think the field of biology suffers from collective amnesia. Like the girl in the movie "50 first dates," we discover things over and over and every time we find something, we forget that it's ever been found before. This is especially true if a phenomenon has been discovered in a biological subfield, like microbiology or virology. Over 26 years ago, microbiologists found that Bacillus subtilis uses different DNA signals (alternative promoters) to control the expression of genes related to development (1). Now, it turns out that this phenomenon is widely employed in the human…
`When I make a word do a lot of work like that,' said Humpty Dumpty, `I always pay it extra.' -Through the Looking Glass by Lewis Carroll In biology, we often ask our words do a lot of work. In what other field would we write direction like this "Transfer 10 lambda of lambda phage DNA into a cuvette and determine the lambda max."
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 rip into it and add a thousand qualifiers, and it would never get done. Well, okay, technically speaking he didn't ask me for help. But, since I'm a biologist, as soon as I looked at the definition that he chose, from Modern Genetic Analysis (by Griffiths, Lewontin, Miller, and Gelbart), I couldn't help but find something wrong. The definition from…
The American Society for Human Genetics is sponsoring the second annual DNA Day Essay contest. If you are a high school teacher here's your chance to combine an interesting assignment along with a contest. This year's essay questions are: If you could be a human genetics researcher, what would you study and why? In what ways will knowledge of genetics and genomics make changes to health and health care in the US possible? The rules are here at GenEdNet.org I also have an animated tutorial at Geospiza Education that might be of some help. The tutorial is titled Allelic Variants of Human…
Her name is Flora and she is a single parent. Born in Miami, Flora moved to Chester, UK, as a toddler. Now, she's almost 8 years old and starting a family, all on her own. Literally. Four eggs have hatched and another eight are ready to go. Yet, Flora has never gotten cozy with another male dragon. How did Flora accomplish this feat and how do we know that she's not just good at keeping secrets? Flora's not the only one Parthenogenesis -- reproduction without the need for fertilization by a male -- has been observed before in about 70 vertebrate species, including snakes and monitor…
Five Bulgarian nurses and a Palestinian doctor (dubbed the Tripoli six) may be executed soon by the Libyan government for the crime of deliberately infecting over 400 children with HIV. If they did infect the children, this would be a horrendous crime. If they did not infect the children, it's the Libyan government that will be killing innocent people. The clock is ticking. Some of you might be wondering (I know I was): How exactly is molecular sequence data being used to solve the crime? Why are scientists and science bloggers claiming that the Tripoli six are innocent? Let's begin by…
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 many word pairs that once made phrases—;log in, data set, file name, set up, and pick up—;have been condensed into single words, that I've had to start using Google to double-check my editing. Perhaps it's surprising then, that I like "ome," "omics," and even Sydney Brenner's chief phrase-to-hate, "systems biology." I…
Welcome to the October 15, 2006 edition of Mendel's Garden. Join me as we walk through the fields and admire the harvest. Evolutionary geneticsAs we stroll into the evolutionary biology plot, we notice a shape in the ground that looks suspiciously like a footprint. Who walked this path before? Where did they come from? Today, we have some interesting tools for learning about ancient peoples and satisfying our curiosity about the paths they trod. Or do we? Inspector RPM, from Evolgen, turns his magnifying glass on those methods and asks if they really tell us what we want to know. Take…
Why is an eye, an eye and a nose, a nose? Why do different cells create different kinds of tissues when all the cells in a single organism start out with the same set of instructions (aka DNA)? Head, Shoulders, Knees, and Toes is a learning activity that helps students discover, for themselves, that certain genes are expressed in some tissues but not in others. My goal here, as part of our NSF-funded project, is to show how students can learn biology by doing science with bioinformatics tools. If you already know all about ESTs, you might want to jump ahead and read about the activity. If…
Mendel's garden in Bruno, CZ, may be too far for physical travel, but you can still imagine what Mendel might have thought if he'd gotten a look at this version of his vision. Maybe I'm taking alliteration a little too far, but that doesn't mean that you have to show any restraint. All you have to do is submit to me by late Saturday afternoon and sometime on Sunday, you can see the fruits of your labor posted here in technicolor. Send 'em in everyone - I want to see GENETICS at it's best: digitalbio at gmail dot com UPDATE: Just to be absolutely clear, Mendel's Garden is a carnival of…
Razib inspired me to share some of the story behind why white people are considered derivatives. Reposted from the Classic Digital Bio. No red herrings, here! Lamason et. al. found a single gene that controls human skin color while studying pigmentation in zebra fish (1). These zebra fish had an unusual golden color that turned out to be an important clue. Lamason and collaborators found that the golden zebra fish lost their normal color because of a mutation in the slc24a5 gene. When the zebra fish have the mutant form, they produce fewer melanosomes. A short language lesson Fewer…
If we compare sections 1, 2, and 3, we see that section 2 matches very well in a number of different samples, and that there are differences between the sequences in sections 1 and 3. We also learn something about the people who did the experiment. At first it appears somewhat odd that there are many matching sequences that are all shorter than the genome and all the same length. What's up with that? It turns out that information doesn't have anything to do with the fraction of the genome that matches our query. These short segments are PCR products. They're the same size because the PCR…
Like biology, all bioinformatics is based on the idea that living things shared a common ancestor. I have posted, and will post other articles that test that notion, but for the moment, we're going to use that idea as a starting point in today's quest. If we agree that we have a common ancestor, then we can use that idea as a basis to ask some interesting questions about our genomes. For, example, we know that genomes change over time - we've looked at single nucleotide changes here and here, and we've seen that large chunks of DNA can move around here. So, it's interesting to consider…
Did HIV become resistant to Atazanavir because of a genetic change? Was that genetic change inherited? Did HIV evolve? Can we explain why genetic changes at specific sites might help HIV escape the effects of the drug? Let's find out. All of the sequences in the image below (except for the first) come from HIV strains that were isolated from patients who took Atazanavir and no other protease inhibitors. All of the strains of HIV from patients were resistant to the drug. If an amino acid is different from other strains, the color at that position is changed. Since we see different…
In which we see the results and come to our own conclusions. If you want to let other people tell you what's right and what's wrong, they will surely do so. Turn on the TV and hordes of happy actors bounce around, only too happy to help you purchase the right deodorant. Open your e-mail and everyone wants to share the best on-line pharmacy and investment guide. Ugh. I prefer making my own decisions, thank you very much. So, I want to give you a chance to look at the data and decide for yourself, if the data show HIV protease sequences changing over time. Let's see the results. We're…
August is the time when gardens look their best. Fruit becomes showy, flowers abound, and plants are large and plentiful. Mendel's Garden #4, currently blooming at The Inoculated Mind, is no exception. Evolgen pointed this out, so I had to go take a look. I enjoyed this trip through the experimental garden at UC Davis. It's a nice change to see someone with a scientific bent planting such a spicy garden. It was interesting to learn about how genetic engineering saved the papaya industry in Hawaii and the strains of flood-resistant rice. Karl's own gardening experiences were…