Have you ever wondered how to view and annotate molecular structures? At least digital versions? It's surprisingly easy and lots of fun. Here's a movie I made that demonstrates how you can use Cn3D, a free structure-viewing program from the NCBI. Luckily, Cn3D behaves almost the same way on both ...
How do you go about researching a genetic disease? This multi-part series explores how digital resources can be used to learn about Huntingtin's disease. Reposted and updated from the original DigitalBio. A bit of background Alice's Restaurant is a movie with an unforgettable song that mostly revolves around Arlo Guthrie ...
In which we're reminded that database searches are experiments, too. One of the trickiest things with bioinformatics experiments is repeating them. This challenge isn't related to the validity of the original results, the challenge is that, unless you made your own database and kept it in the same state, the ...
But I'm certain that you will find some interesting things. Mendel's Garden will be ready for harvest, here on Sunday, October 7th, and I need your help. You won't need to stay on the path, but I would like you to submit your best genetics & molecular biology articles by ...
You can get a jump on the Darwin Day festivities. Once again the Alliance for Science is sponsoring an essay contest for Darwin Day. If you download their suggestions for good essay writing, you can get your essay done over winter break and have a good crack at winning on ...
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 ...
What do the missing Romanov children, genetically engineered humans, financial risk taking, and poop have in common? You can read about all these topics from this month's Gene Genie carnival at Mary Meets Dolly. Who would have thought that mutations could be so much fun?
We've been fans of the Molecule of the Month series by David Goodsell, for many years. Not only is Dr. Goodsell a talented artist but he writes very clear descriptions of the ways molecules like proteins, RNA, and DNA work together and function inside a cell. To learn about proteins ...
The New England Journal of Medicine published a study yesterday showing that small changes in the DNA in the long arm of chromosome 16 are associated with autism. I met a teenager with autism last summer, when I attended family night at the Seattle Park and Rec summer camp program ...
In the class that I'm teaching, we found that several PCR products, amplified from the 16S ribosomal RNA genes from bacterial isolates, contain a mixed base in one or more positions. We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and ...
Ribosomes are molecular machines that build new proteins. This process of synthesizing a protein is also known as translation. Many antibiotics prevent translation by binding to ribosomal RNA. In the class that I'm teaching, we're going to be looking at ribosome structures to see if the polymorphisms that we find ...
Welcome to the October 15, 2006 edition of Mendel's Garden. Join me as we walk through the fields and admire the harvest. Evolutionary genetics As 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 ...
My garden at home is looking a bit bleak after all the snow, Mendel's Garden is blooming wonderfully at Jeremy Cherfas' blog Another Blasted Weblog. Jeremy has prepared a nice collection of perennial favorites. I especially like the story about pea breeding and, if you view the post, there are ...
October is a month of darkness, mystery, and dread. Only one holiday brings joy in October and even then, October joy is distilled through fear and apprehension. In the early evenings the sun hurries home and once familiar objects loom ominously in the dark. Giant spiders appear out the fog ...
What tells us that this new form of H1N1 is swine flu and not regular old human flu or avian flu? If we had a lab, we might use antibodies, but when you're a digital biologist, you use a computer. Activity 4. Picking influenza sequences and comparing them with phylogenetic ...
You might think the coolest thing about the Next Generation DNA Sequencing technologies is that we can use them to sequence long-dead mammoths, entire populations of microbes, or bits of bone from Neanderthals. But you would be wrong. Sure, those are all cool things to do, but Next Generation DNA ...
Is the case for open access truly "open and shut"? Will open access impede science by limiting genetic studies with families? tags: 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 ...
We had a great discussion in the comments yesterday after I published my NJ trees from some of the flu sequences. If I list all the wonderful pieces of advice that readers shared, I wouldn't have any time to do the searches, but there are a few that I want ...
Have you ever wondered what kinds of viruses can be found in human waste? Mya Breitbart and team have been sequencing nucleic acids from fecal samples in order to find out. You might expect that we'd find viruses that infect humans or viruses that infect the bacteria in our gut ...
The New York Times had a great article a couple of days ago on the need for personalized medicine to become more than a catchy phrase. As we're learning more about the interaction between genes and drug metabolism, we're also learning that large numbers of people are either taking the ...
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 ...
Mosquito-borne diseases, like Dengue and Malaria, are serious problems in many parts of the world. While some people are working on treatments for mosquito-carried disease, others are looking at ways to treat the mosquitoes. Figure 1. Image of Aedes aegypti from the Public Health Library tags: , Controlling insect activities ...
" By night all cats are gray" - Miguel Cervantes in Don Quixote I've always liked Siamese cats. Students do, too. "Why Siamese cats wear masks" is always a favorite story in genetics class. So, when I opened my January copy of The Science Teacher, I was thrilled to see ...
Sexual attraction is all in your brain. At least if you're a nematode. Ricardipus has a great image if you want to see a nematode picture. I always thought worms were hermaphrodites (both male and female) but the story, as usual, turns out to be a bit more complex. Researchers ...
In its simplest sense, we imagine that learning occurs through a series of positive and negative rewards. Some actions lead to pleasure, others to pain, and it seems reasonable to expect that people will repeat the actions with pleasurable results and avoid those that ended in pain. Yet, we all ...
Thanks to Steven Colbert you can hear about DNA directly from Dr. Spencer Wells from the National Genographic Project. I read about this video in the GenomeWeb Daily Scan and had to check it out. Who would have thought scientists could be so funny? Watch it quick! There was a ...
This morning I attended a "bloggers-only" conference call with Dr. Eric Green and the folks from the NIH Human Genome Research Institute (NHGRI) to hear about NHGRI's new strategic plan. The new plan represents a shift away from viewing the genome through a lens marked "for research use only" and ...
I got my copy of " A short guide to the human genome" by Stewart Scherer today from Cold Spring Harbor Laboratory Press (2008, ISBN 978-087969791-4). Usually, I would wait until after I've read a book to write a review, but this book doesn't require that kind of study. As ...
A couple of years ago, I answered a reader's question about the cost of genome sequencing. One of my readers had asked why the cost of sequencing a human genome was so high. At that time, I used some of the prices advertised by core labs on the web and ...
A few weeks ago, I did some "back-of-the-envelope" calculations to explain to a reader why genome sequencing costs so much. I estimated that, if JCV's genome were sequenced at the cost advertised by university core laboratories, his genome would cost about $128 million. That was an estimate, of course. But ...
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 ...
A few months ago I posed some questions about the regulations that might oversee personal genomics companies ( Who's your Daddy? and Step right up, get your very own DNA profile). Why? Because I am biased. At Geospiza, where I work, we make software products that help our customers, who ...
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 ...
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 ...
By now, many of you have probably seen the the new BLAST web interface at the NCBI. There are many good things that I can say about it, but there are a few others that caught me by surprise during my last couple of classes. tags: Because of these changes ...
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 ...
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 ...
When can a really bad virus be used to do something good? When we can use it to learn. The human immunodeficiency virus, cause of AIDS, scourge of countries, and recent focus of ScienceBlogs; like humans, evolves. As one of my fellow ScienceBloggers noted, few biological systems demonstrate evolution as ...
Let the experiment begin. We're experimenting with HIV in this series. And yes, you can try this at home! If you want to see where we've been and get an idea where we're going, here are the links. Part I. Meet HIV and learn how we're going to use it ...
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 ...
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 ...
In which we search for Elvis, using blastp, and find out how old we would have to be to see Elvis in a Las Vegas club. Introduction Once you're acquainted with proteins, amino acids, and the kinds of bonds that hold proteins together, we can talk about using this information ...
" Come quickly, Watson," said Sherlock Holmes, " I've been asked to review a mysterious sequence, whose importance I'm only now beginning to comprehend." The unidentified stranger handed Holmes a piece of paper inscribed with symbols and said it was a map of unparalleled value. Holmes gazed thoughtfully at the ...
It's hard sometimes when you're out of synch with the rest of the world. While my fellow ScienceBloggers have been obsessing about breasts, I've been really amused by the genetics of ear wax. Eh, what's that you say? Yes, it's true. Back in March, when Nature Genetics published this paper ...
If you're in Seattle this week, and you're not going to the zoo concert on Wednesday night, you might enjoy this lecture series from the UW Genome Sciences department. We missed the first two talks because of travel, but our college-age daughter and her friend persuaded us to go last ...
Well, probably getting a stipend to help you do it. And, the really cool thing is that's part of the deal! Hustle, hustle the deadline is March 7th, and all the contact info is below. The NSF Research Experience for Undergraduates program in Environmental Microbiology at UNLV is accepting applications ...
Replication fork - https://en.wikipedia.org/wiki/Telomere. Organisms with linear chromosomes have to solve the problem that DNA replication makes them shorter. This is due to the fact that DNA polymerase can only add bases to the terminal 3'-OH of a DNA chain. The DNA replication initiation complex uses RNA primers to provide ...
For the past few months, the shake-up that began with Next Generation DNA Sequencing has been forcing me to adjust to a whole new view of things going on inside of a cell. We've been learning things these past two years that are completely changing our understanding of the genome ...
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 ...
