Genetics & Molecular Biology:
Dave Robinson and Joann Lau from Bellarmine College in Kentucky are going to be describing their student project in a free webinar next Friday, May 16th. Their students clone GAPDH (Glyceraldehyde 3-Phosphate Dehydrogenase) genes from new plants, assemble the DNA sequences, and submit them to the NCBI. Here's an example. Plus, since GAPDH is a highly conserved, it's a great...
Posted on May 8, 2008 7:36 PM • 3 Comments •
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 determined that the mixed bases mostly likely come from different...
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Posted on April 17, 2008 8:00 AM • 2 Comments •
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 in the sequences of 16S ribosomal RNA are related antibiotic...
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Posted on April 16, 2008 7:54 PM • 2 Comments •
You can find out. Blaine Bettinger, the Genetic Genealogist has a fun little quiz....
Posted on April 9, 2008 5:30 PM • 0 Comments •
Goodbye desktop, we're off to see the web. Both my students and I have been challenged this semester by the diversity of computer platforms, software versions, and unexpected bugs. Naturally, I turned to the world and my readers for help and suggestions. Some readers have suggested we could solve everything by using Linux. Others have convincingly demonstrated that Open Office...
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Posted on April 3, 2008 12:40 PM • 6 Comments •
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?...
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Posted on April 2, 2008 1:59 PM • 6 Comments •
I made this video (below the fold) to illustrate the steps involved in making a phylogenetic tree. The basic steps are to: Build a data set Align the sequences Make a tree In the class that I'm teaching, we're making these trees in order to compare sequences from our metagenomics experiment with the multiple copies of 16S ribosomal RNA (rRNA)...
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Posted on March 27, 2008 9:11 AM • 24 Comments •
A video tutorial on molecular structures.
Posted on March 19, 2008 5:37 PM • 1 Comments •
I read about this in Bio-IT World and had to go check it out. It's called the Genome Projector and it has to be the coolest genome browser I've ever seen. They have 320 bacterial genomes to play with. Naturally, I chose our friend E. coli. The little red pins in the picture below mark the positions of ribosomal RNA...
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Posted on March 11, 2008 12:00 PM • 6 Comments •
Here's a fun puzzler for you to figure out. The blast graph is here:...
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Posted on March 7, 2008 12:28 PM • 2 Comments •
What do you do after you've used DNA sequencing to identify the bacteria, viruses, or other organisms in the environment? What's the next step? This four part video series covers those next steps. In this part, we learn that a surprisingly large portion of bioinformatics, or any type of informatics is concerned with fixing data entry errors and spelling mistakes....
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Posted on February 26, 2008 10:19 AM • 0 Comments •
Getting paid to do it?
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Posted on February 12, 2008 1:39 PM • 2 Comments •
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 for kids with special needs. It's a fantastic program. The...
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Posted on January 10, 2008 12:00 AM • 13 Comments •
Two molecules are locked in a tight embrace. Who are they?
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Posted on December 28, 2007 10:12 AM • 0 Comments •
Genetics textbooks abound with stories of European royalty and the hazards of having children after you've married one of your cousins. It struck me as an interesting parallel that the lion is such a popular symbol in so many royal coats of arms. Like the royal families of Europe, certain lion populations have also suffered from a few too many...
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Posted on December 26, 2007 11:25 AM • 1 Comments •
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 those cash prizes! The Alliance for Science is pleased to...
Posted on December 20, 2007 9:29 AM • 0 Comments •
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 database that you'll be using at a later time, sometimes...
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Posted on December 19, 2007 9:13 AM • 0 Comments •
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 hanging out with his friends. Somewhere in the movie, the...
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Posted on December 18, 2007 9:45 AM • 1 Comments •
If we suspected a virgin birth, how could we prove it?
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Posted on December 3, 2007 9:00 AM • 13 Comments •
Sexual attraction is all in your brain. At least if you're a nematode....
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Posted on November 19, 2007 12:20 PM • 2 Comments •
You too, can compare chimp and human DNA.
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Posted on November 16, 2007 8:51 AM • 0 Comments •
Students at Soldan International High School are participating in an amazing experiment and breaking ground that most science teachers fear to tread. Soldan students, along with hundreds of thousands of other people, are participating in the National Geographic's Genographic Project. Through this project, students send in cheek swabs, DNA is isolated from the cheek cells, and genetic markers are used...
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Posted on November 14, 2007 4:04 PM • 9 Comments •
An evolution activity for the classroom.
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Posted on November 9, 2007 3:47 PM • 0 Comments •
Welcome Bio256 students! This quarter, we're going to do some very cool things. We are going to use bioinformatics resources and tools to investigate some biological questions. My goal, is for you to remember that these resources exist and hopefully, be able to use them when you're out working in the biotech world. I don't believe that bioinformatics is a...
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Posted on October 21, 2007 4:30 PM • 2 Comments •
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 what did it really cost?...
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Posted on October 16, 2007 8:06 AM • 8 Comments •
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, lurking on webs that span our walkways and doors. Even...
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Posted on October 14, 2007 5:32 PM • 0 Comments •
But I'm certain that you will find some interesting things....
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Posted on September 19, 2007 2:25 PM • 0 Comments •
Fun with molecular models!
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Posted on September 11, 2007 11:46 AM • 3 Comments •
During the past few Fridays (or least here and here), we've been looking at a paper that was published from China with some Β-lactamase sequences that were supposedly from Streptococcus pneumoniae. The amazing thing about these particular sequences is that Β-lactamase has never been seen in S. pneumoniae before, making this a rather significant (and possibly scary) discovery. If it's...
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Posted on September 7, 2007 8:43 AM • 5 Comments •
Adding the costs and doing the math.
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Posted on September 6, 2007 12:16 PM • 13 Comments •
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. (If you haven't read any of the stories, CNN has one here, and my fellow bloggers have posted several here, here, here, here, here, and here.) You may be wondering, and rightly so: just what is a...
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Posted on September 5, 2007 10:35 AM • 4 Comments •
We were all thrilled last spring when the Genetic Information Nondiscrimination Act passed the House by a vote of 420 to 3. When GINA gets through the Senate, this act will protect individuals against discrimination based on their genetic information with health insurance and employment. The promise of genomic project won't ever be achieved until individuals (besides Watson and Venter)...
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Posted on September 4, 2007 10:11 PM • 4 Comments •
"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....
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Posted on September 4, 2007 12:42 PM • 11 Comments •
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?...
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Posted on August 16, 2007 11:00 PM • 0 Comments •
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 Weds. and hear Debbie Nickerson talk about genetics and drugs....
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Posted on July 30, 2007 2:30 PM • 3 Comments •
BLAST has gotten harder.
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Posted on July 12, 2007 1:39 PM • 4 Comments •
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...
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Posted on May 31, 2007 1:36 PM • 9 Comments •
Assigned readings on BLAST and phylogenetics.
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Posted on May 29, 2007 9:19 AM • 0 Comments •
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...
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Posted on May 28, 2007 9:10 AM • 2 Comments •
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...
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Posted on May 27, 2007 10:34 AM • 13 Comments •
Human genes get turned on when DNA is touched in different places.
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Posted on February 16, 2007 4:20 PM • 1 Comments •
`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...
Posted on February 3, 2007 8:13 PM • 2 Comments •
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...
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Posted on January 21, 2007 3:44 PM • 7 Comments •
Start writing those essays! You could win cash and a chance to work in a lab!
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Posted on January 19, 2007 4:43 PM • 0 Comments •
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....
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Posted on December 21, 2006 2:43 PM • 3 Comments •
Who infected the children with HIV: Using the data to solve the puzzle.
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Posted on December 7, 2006 6:33 PM • 2 Comments •
A quick guide for the omically challenged.
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Posted on December 1, 2006 1:35 PM • 18 Comments •
Welcome to the October 15, 2006 edition of Mendel's Garden. Join me as we walk through the fields and admire the harvest....
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Posted on October 15, 2006 12:03 PM • 6 Comments •
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)?...
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Posted on October 10, 2006 11:41 AM • 0 Comments •
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...
Posted on October 9, 2006 9:15 PM • 0 Comments •
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)....
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Posted on September 26, 2006 8:58 AM • 3 Comments •
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....
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Posted on September 1, 2006 11:37 AM • 0 Comments •
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...
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Posted on August 25, 2006 8:10 AM • 2 Comments •
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....
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Posted on August 23, 2006 10:06 AM • 0 Comments •
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...
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Posted on August 21, 2006 10:00 AM • 0 Comments •
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...
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Posted on August 20, 2006 3:21 PM • 1 Comments •
Let the experiment begin....
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Posted on August 19, 2006 11:35 AM • 0 Comments •
The past few Fridays, we've been comparing human mitochondrial DNA with the mitochondrial DNA of different apes. We started doing this here, where you can find directions for getting started. And, we've found some interesting things....
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Posted on August 18, 2006 3:43 PM • 2 Comments •
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 clearly as HIV. In this series, I'm going to guide...
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Posted on August 17, 2006 11:59 AM • 2 Comments •
During these past couple of weeks, we've been comparing mitochondrial DNA sequences from humans and great apes, in order to see how similar the sequences are. Last week, I got distracted by finding a copy of a human mitochondrial genome, that somehow got out of a mitochondria, and got stuck right inside of chromosome 17! The existence of this extra...
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Posted on August 11, 2006 1:14 PM • 5 Comments •
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 from Yoshiura (and friends), this bit of fun just went...
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Posted on August 10, 2006 2:30 PM • 3 Comments •
Last week, we decided to compare a human mitochondrial DNA sequence with the mitochondrial sequences of our cousins, the apes, and find out how similar these sequences really are. The answer is: really, really, similar. And you can see that, in the BLAST graph, below the fold. A quick glance shows that the ape with the most similar mitochondrial sequence...
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Posted on August 4, 2006 1:39 PM • 3 Comments •
We've had a good time in the past few last weeks, identifying unknown sequences and learning our way around a GenBank nucleotide record. To some people, it seems that this is all there is to doing digital biology. They would, of course, be wrong. We can do much, much more than identifying DNA sequences and obtaining crucial information, like who...
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Posted on July 28, 2006 8:00 AM • 0 Comments •
I mean phone call. Because, if I thought he remembered me, I would call and say "thank you." Because of the time I spent in his lab, I know that cloning started long before Dolly. The first vertebrate animal was cloned over 50 years ago. And it wasn't a sheep....
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Posted on July 8, 2006 9:09 PM • 3 Comments •
My colleagues have come up will all kinds of interesting bloggy things to use as an excuse for Friday celebrations. Adventures in Ethics and Science has Friday Sprog Blogging for cute stories about her kids. A Blog Around the Clock considers Friday's the perfect day to write about weird sex. Pharyngula salutes the spineless with Friday Cephalopods. Good Math, Bad...
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Posted on July 7, 2006 9:00 AM • 2 Comments •
Past Favorites for the holidays: Now that the dog genome is done, maybe we need a new project in genetic variation. What genotypes make people look like their dogs? technorati tags: dogs, humor dog genome...
Posted on July 3, 2006 9:58 AM • 0 Comments •
Mendel's Garden, that is. Enjoy a quiet mental stroll among the shady trees where Hsien Hsien Lei from Genetics and Health has compiled perennial favorites and annual suprises. Even though the season is young, Mendel's Garden is clearly growing. This edition of Mendel's Garden is great spot to branch out and explore the natural world. Check out the garden tour...
Posted on July 2, 2006 1:17 PM • 1 Comments •
I am a microbiologist and molecular biologist turned tenured biotech faculty turned bioinformatics scientist turned entrepreneur. My passion is developing instructional materials for 21st century biology (Geospiza Education).
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