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 ...
For the past few days I've been avidly following Daniel MacArthur's tweets from the Personal Genome Conference at Cold Spring Harbor( @dgmacarthur #cshlpg). The Personal Genomics tweets aren't just interesting because of the science, they're interesting because MacArthur and others have started to take on the conventional dogma in genetic ...
In simple Mendelian genetics, a single change in one gene can produce a large change in mortality. The National Human Genome Research Institute (NHGRI) will be funding genomics studies on Mendelian traits using a similar strategy. NHGRI will fund a small number of centers, dominant centers you might say, and ...
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 ...
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 ...
Cofactor Genomics is offering to sequence a genome for a few classes for free using Next Generation DNA Sequencing technology (either Illumina GA or via AB SOLiD). Quoting from their site: Cofactor will ask course organizers for a 1 page description of how their ~700Mb sequencing project could be used ...
Maybe you did it for the extra cash. Maybe you wanted to be part of the sperm cube public art project. Whatever the reason, it's possible, just possible, your sperm took on a life of it's own, once you left it. And now that a genome is no longer an ...
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 ...
A simple web search says biotech is really big. One estimate indicates that the industry will have $400 billion in sales in 2017 with growth to over $775 billion by 2024 [1]. Another report suggests there are over 77,000 employers [2]. That’s big, but is it real, and what you ...
A key concept in science is molecular scale. DNA is a fascinating molecule in this regard.
While we cannot "see" DNA molecules without the aid of advanced technology, a full length DNA molecule can be very long. In human cells, other than sperm and eggs, six billion ...
A key concept in science is molecular scale. DNA is a fascinating molecule in this regard. While we cannot "see" DNA molecules without the aid of advanced technology, a full length DNA molecule can be very long. In human cells, other than sperm and eggs, six billion base pairs of ...
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 ...
Are 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 ...
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 ...
Last week, while attending the ISB " DNA of Innovation" symposium in honor of Lee Hood's 70th birthday, I decided to try live-blogging for the first time. Unbeknownst to others in the audience, except my husband, I quietly typed away, collecting notes and uploading impressions. But battery power has its ...
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?
National DNA Day has a fun challenge for teachers and classrooms using Pinterest. Your class can join a larger, national, effort to create a National DNA Day Pinterest board by making your own class Pinterest board on DNA, genetics, and genomics. Some possible topics are: Things to do with DNA ...
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 ...
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 ...
I had the good fortune on Thursday to hear a fascinating talk on deep transcriptome analysis by Chris Mason, Assistant Professor, at the Institute for Computational Biomedicine at Cornell University. Several intriguing observations were presented during the talk. I'll present the key points first and then discuss the data. These ...
If you like ham and bacon, you might be interested in this. GenomeWeb reports that researchers at the University of Barcelona have developed an assay that tests 46 SNPs and can be used to trace the origin of your pork dinner. According to GenomeWeb, the test identifies both the breed ...
Bacteria can cause other epidemics, why not obesity? Is there a relationship between our body weight and our bacterial inhabitants? Two reports in Nature (1, 2) suggest that bacterial populations differ between people who are obese and people who not, and that the bacterial inhabitants of their guts, may be ...
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 ...
Warfarin, a commonly used anti-clotting drug, sold under the brand name of Coumadin, has a been a poster child for the promise of pharmacogenomics and personalized medicine. The excitement has come from the idea that knowing a patient's genotype, in this case for the VKORC1 and CYP2C9 genes, would allow ...
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 ...
We have lots of DNA samples from bacteria that were isolated from dirt. Now it's time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we're using many ...
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 ...
" 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 ...
How did the human genome ever get finished if every one of the three billion bases had to be reviewed by human eyes? In the early days of the human genome project, laboratory personnel routinely scanned printed copies of chromatograms, editing and reviewing all DNA sequences by eye. For more ...
Have you ever wondered how people actually go about sequencing a genome? If they're sequencing a chicken genome, do they raise chickens in the lab and get DNA from the eggs? Does the DNA sequence come out in one piece? Why is there so much talk about computers? What are ...
A few years ago, the General Biology students at the Johns Hopkins University began to interrogate the unseen world. During this semester-long project, they study the ecosystems of the Homewood campus, and engage in novel research by exploring the microbial ecosystems in different sections of the campus. Biology lab students ...
Watching the chIPs roll in, then I watch them roll away again, I'm just sitting on the DNA, wasting time (sung to the tune of "Sitting on the dock of the bay" by Otis Redding) Hesselberth et.al. recently published a paper about digital genomic footprinting that blew me away because ...
After leading the Human Genome Project and the National Human Genome Research Institute at the NIH for many years, Francis Collins is retiring. No matter what you think of Francis Collins, he's been successful in getting the genome project done and he's done some amazing things during the 15 years ...
Genome Web's Daily Scan noted an interesting blog post today from John D. Halamka, one of the people to get his genome sequenced through the personal genome project. I was interested to see his post since Genome Web wrote that he was discussing data standards and we have been writing ...
The genie is out of the bottle. Personal genomes are not just for Venter and Watson anymore. Three competing companies, 23andme, Decode, and Navigenics are betting that you want to do a little better than reading your horoscopes and playing with tea leaves. They think that you want to know ...
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 ...
@synbiobeta concluded it’s #sbbsf17 annual meeting on synthetic biology Oct 5, 2017. The progress companies are making in harnessing biology as a platform for manufacturing and problem solving is world changing. Locations of Synbio Companies What is Synthetic Biology? Synthetic biology is a term that is used to describe the ...
Computers, biological data (molecular sequences, structures, and other data), websites, and databases are integral to modern research. Innovations like precision, or personalized medicine, expect a certain level of patient participation, and our future food and environmental sustainability will require that society can access a multitude of computer-based resources. Thus, higher ...
April 25th (4/25) is national DNA day. Digital World Biology™ celebrates by sharing some of our favorite DNA structures. We created these photos with Molecule World™ Molecule World is a tools for exploring molecular and chemical structures on an iPhone or iPad.
Today (4/25) is national DNA day. Digital World Biology™ is celebrating by sharing some of our favorite structures of DNA. We created these photos with Molecule World™ a new iPad app for viewing molecular structures. As we are taught in school, the double stranded DNA molecule is a right-handed helix ...
Good news! Good news! Last week the Senate passed the Genetic Nondiscrimination Act (GINA). This week it was passed by the House. It only needs one signature and GINA will become law. For years, those of us who teach genetics have had to caution students about genetic testing. The biggest ...
Scale, proportion, and quantity belong to one of the cross cutting concepts in the next generation science standards (NGSS). According to Volume 2 of the NGSS, "in engineering, no structure could be conceived much less constructed without the engineer's precise sense of scale." The authors go on to note that ...
Okay OpenOffice fans, show me what you can do. Earlier this week, I wrote about my challenges with a bug in Microsoft Excel that only appears on Windows computers. Since I use a Mac, I didn't know about the bug when I wrote the assignment and I only found out ...
