I don't know if any DIY biologists are looking for projects, but I think engineering yeast with a gene to detect heavy metals might be a good DIY biology project and I have some ideas for how to do this. What are the advantages of using yeast and working on ...
It was a wet and rainy day yesterday, and we have a dissecting microscope, so I decided to see if I could find some tardigrades. Tardigrade photo by nebarnix Reposted from Nov. 2006 I went outside and scraped a bit of moss and some lichens off of our deck. Then ...
For the past few years, I've been collaborating with a friend, Dr. Rebecca Pearlman, who teaches introductory biology at the Johns Hopkins University. Her students isolate bacteria from different environments on campus, use PCR to amplify the 16S ribosomal RNA genes, send the samples to the JHU core lab for ...
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 ...
This is third video in our series on analyzing the DNA sequences that came from bacteria on the JHU campus. In this video, we use a pivot table to count all the different types of bacteria that students found in 2004 and we make a pie graph to visualize the ...
Conflicts between predators like cougars and coyotes and human companions like pets and small children are becoming more common as people move into areas that used to be wildlife habitat. The Seattle Times has a great story this morning about biologists in Washington who are studying cougars to learn if ...
If you're in Seattle, Dr. Bruce Alberts will be talking tomorrow night (Jan 5th) at the Seattle Aquarium on science education and the role that scientists play. There are also some really interesting talks at a day-long workshop, Wednesday (Jan 6th) at the UW South Campus Center. The details and ...
Next Saturday afternoon, at ScienceOnline2010, the science goddess, the chemspider, and I will be presenting a workshop on getting students involved in citizen science. In preparation, I'm compiling a set of links to projects that involve students in citizen science. If you know of any good citizen science efforts, please ...
Do citizen science efforts ever go beyond "feel good" contributions? Do the data get published in peer-reviewed journals? In an earlier post, I started a list of citizen science projects that allow students to make a contribution. Many commentors are graciously adding to that list and I thank you all ...
We always see interesting creatures whenever we walk on the beach. Now, a new program from the University of Washington and the state department of Fish and Wildlife is seeking to enlist beach walkers in a community science project where they can help monitor biodiversity. The program is called NatureMapping ...
Metagenomics is a field where people interrogate the living world by isolating and sequencing nucleic acids. Since all living things have DNA, and viruses have either DNA or RNA, we can identify who's around by looking at bits of their genome. Researchers are using this approach to find the culprit ...
"Digital biology," as I use the phrase, refers to the idea of using digital information for doing biology. This digital information comes from multiple sources such as DNA sequences, protein sequences, DNA hybridization, molecular structures, analytical chemistry, biomarkers, images, GIS, and more. We obtain this information either from experiments or ...
Here's a fun puzzler for you to figure out. The blast graph is here: The table with scores is here, click the table to see a bigger image: And here is the puzzling part: Why is the total score so high? If you want to repeat this for yourself, go ...
This 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 ...
A few days ago, I wrote about a cool project that some high school students did where they used DNA sequencing to identify seafood. One question that came up from one of my commenters was how a school would start a project like this. I'm totally biased, but I think ...
The University of Nevada in Las Vegas is looking for a few good undergraduates to come do research this summer in environmental microbiology. Environmental microbiology goes way beyond hot springs bacteria and Yellowstone Park. At UNLV, you can do science in the desert. It almost makes me wish I was ...
I think all of us; me, the students the OO advocates, a thoughtful group of commenters, some instructors; I think many of us learned some things that we didn't anticipate the other day and got some interesting glimpses into the ways that other people view and interact with their computers ...
Charles Darwin was so fascinated by beetles he paid people to help him build his collection. The Coleopterists Society and the Smithsonian Institute want to help kids explore the wonders of beetles, too. They're providing grants for kids, in grades 7-12 to work on beetle biology. Applications are due by ...
Two teenagers, Kate Stoeckle and Louisa Strauss, carried out their own science project over the past year. They visited 4 restaurants and 10 grocery stores and gathered 60 samples of fish and sent them off to the University of Guelph to get sequenced. I like this story. One of my ...
Grasses at Yellowstone National Park are able to grow temperatures (65°; C) that would toast most living things. Step right up! Watch original research, as it happens, on the web! I'm going to use bioinformatics to see if I can find that answer to the puzzle of heat-tolerant plants. Previous ...
Are viral and fungal infections always a bad thing? Maybe not if you're a plant. In fact, if you're a plant trying to grow in the hot (65°; C) soils of Yellowstone National Park, you're going to need all the help you can get. A new study by Márquez, et.al ...
We heard quite a bit about rainforest destruction in the 80's and 90's. Even the Grateful Dead joined the efforts to raise awareness and gather support for rain forest preservation. In the past, the Dead stayed away from political activism because ( quoting Jerry Garcia): Power is a scary thing ...
Your canopy is disappearing, you're likely to freeze. NASA's Earth Observatory reports that over 1,110 acres of forest were illegally logged, during the past four years, in the Monarch Butterfly Biosphere Reserve in central Mexico. Monarch butterflies travel here from all over the United States and Canada. Images from the ...
Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt? This quarter, my bioinformatics class, at Shoreline Community College, will be working with chromatograms that were obtained by students at Johns Hopkins University, and graciously made available by Dr. Rebecca Pearlman ...
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 ...
The simple fact is this: some DNA sequences are more believable than others. The problem is, that many students and researchers never see any of the metrics that we use for evaluating whether a sequence is "good" and whether a sequence is "bad." All they see are the base calls ...
A common theme I hear in talks on personalized medicine, is that increased access to genomic data and medical literature are changing the relationship between doctors and patients. Patients are through being passive recipients of paternalistic health care. They are demanding to participate and be treated as partners with health ...
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 ...
As they say, there's nothing like travel to learn new and unexpected things. Especially from cab drivers. One of my ScienceBlog Sibs, Shelly, spends time talking with cabbies about earwax, but I seem to invite other kinds of lectures. Often times, my driver are Sikhs. So perhaps you can guess ...
The NASA Earth Observing System is an incredible resource for both science and education. One of the amazing things about it is all the different kinds and quantities of data are assembled together into pictures that even grade school kids can immediately comprehend. How do they do it? Each of ...
Yesterday morning I was sitting at conference table, downing coffee to keep my eyes open, when I heard someone say that it's springtime now and the snakes are waking up. Well, those kinds of statements at the breakfast table do have a way of getting my attention. I turned sideways ...
"And it's a hard, and it's a hard, it's a hard, and it's a hard, And it's a hard rain's a-gonna fall. " - BoB Dylan Tired of Simpson reruns and the exploits of Friends? [From the WSTA] NOVA is broadcasting an entire series of shows on hurricanes, Katrina, and ...
