November 2007
What is in that cabinet? →
October 2007
Streaming Video - Geoduck Research Program -... →
The Basics: How Does DNA Ligation Work?
It takes a real effort to keep your basic knowledge of molecular and cell biology fresh, in addition to everything else you have to do. Wouldn’t it be great to if there was a place where you could find easy-to-read articles that allow you to brush-up on those basics in just a couple of minutes?
…I hope you said “yes”, because this is the aim of my “The Basics:” series of articles, which I will be...
Firefox Add-ons for Molecular and Cell Biologists
Firefox is the most popular browser on the web. This in large part due to the vast array of free add-ons that allow you to customize the browser and add features that will help your everyday work. And molecular and cell biologists are not left out. In this article I have compiled a list of Firefox add-ons for bioscientists. Some specifically help with things like bioinformatics and information...
The Fall 2007 Fish-Ocean News →
Time to Think
Spare a thought for your poor over-worked neurons. In the information age, they are bombarded with input from the moment they are dragged into consciousness by the radio alarm clock each morning then throughout the day by e-mail, Google searches, RSS feeds, mobile phones, newspapers, books, blogs and more. In the post genomic era, it’s even worse if you are a bioscientist. The amount of data...
update
Hello- I’m Stephannie, a new Capstone student. I’m working on a Rickettsia Like Prokaryote. I’m looking into genes that might be responsible for it’s virulence. Today I got two sets of primers for possible gene candidates. Cool for me because I made them up. Don’t tell Steven but I just threw a bunch of nucleotides in a bag and pulled them out and wrote down what I...
5 Ways to Clean Up A DNA Sample
One of the most common tasks in molecular biology is cleaning up DNA from aqueous solutions to remove buffer salts, enzymes or other substances that could affect downstream applications. Examples include cleaning up PCR reactions, digests or other enzymatic treatments and cleaning up genomic or plasmid DNA contaminated with cellular proteins/debris. There are several ways to approach DNA clean-up,...
History of Molecular Biology
As a freshman biology major in undergrad, I was introduced to molecular biology with the following description: Molecular biology represents the intersection of genetics, biochemistry and cell biology. Some people, it turns out, add microbiology and virology into the mix. So molecular biology is often used as a catch-all, to describe a wide breadth of interests. (more…)
(via The...
The Invention of PCR
Few technical breakthroughs that have changed the face of their field like the Polymerase Chain Reaction (PCR). Gene cloning, sequencing of complex genomes, DNA fingerprinting and DNA-based diagnostics are just some of the techniques that were either inefficient, crude or plain impossible before PCR. The technique has revolutionized biological research and biotechnology to such an extent that it...
Welcome back, Sam!
Yes, I have started referring to myself in the third person. Except that last sentence. Whoops. It’s a new habit and is difficult to start doing. I guess that’s good. Anne’s pretty tired of it and most of the time I even forget to refer to myself (I mean, ‘Sam’) in the third person. Anyway, I am currently eating pickles and hotdogs in a 4:1 ratio and posting from...
Histone Methylation Determines Cell Fate
Gene expression is controlled at all sorts of levels in eukaryotic cells, and one of the hot areas is that of histone modifications and how they influence transcriptional accessibility on chromosomes - epigenetic regulation, as it’s called. Think of it as an analog annotation system for the cell’s genome, where each gene is wrapped up in such a way that it’s either accessible to transcriptional...
10 Tips on Writing a Research Poster
Poster presentations are a great way to show off your hard work, especially if you are just starting out in research. They are much less stressful than oral presentations, but still provide great networking opportunities and valuable practice at talking about your work. Follow these simple tips to create an attractive poster that will draw readers in and get people talking (to you!) Choose your...
Watch
Modeling Tertiary Structure
Predicting and modeling protein structure, making protein crystallography somewhat obsolete, has been an elusive science to date. Since Linus Pauling and others determined that the most favorable secondary structures are the alpha helix and beta sheet, molecular and structural biologists have sought a set of rules with which to predict a protein’s structure from its amino acid sequence.
...
10 Links: Cell and Molecular Biology Podcasts
Podcasts are great. I listen to podcasts every day during my commute and find them a great way to pick up information, whether it’s to learn about a new subject, brush up on something I have studied before or keep up with the news. Here are 10 molecular and cell biology related podcasts that I hope you will find useful. (more…)
(via The Molecular Biology Blog)
“I’m not sure if Steven mentioned this in class but I found a really...”
– Catalyst GoPost
EVERYONE
Everyone coming into the lab needs to add it to the calendar (accurately) particularly as SAM is on vacation next week and I am in and out. Otherwise the door might be locked, no direction, etc etc.
Degenerative_Primer_Assistor →
Need to review BLAST
Check out my lecture (pdf) and accompanying mp3.
NCBI oh noes
I have been spending the past week wandering through the nifty little resource known as the NCBI website. NCBI’s (National Center for Biotechnology Information) goal is to provide public databases as well as provide information on genomic, molecular and biological sciences in reference to human health and disease. But golly, you can use it for shellfish too. One of the resources NCBI...
Watchback online with a new angle
Google Spreadsheets Adds Conditional Formatting →
Sam?
Have not seen a post from Sam recently, must be cranking out some serious science at the bench?
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how two [via 507a]
to make it simpler to navigate the sharespaces, any movie file that is named [filename]2.mov is a how-to.
5 Tips for Getting the Most Out of Undergraduate... →
Does tollip have introns? a how-to movie →
how I would mumble through finding the answer.
How to: Keep your data organized
Talented, enthusiastic scientist required. Must have good organizational skills.
Do you fit the bill? With the pace of molecular biology and biochemical research quickening year on year, the importance of good organization and planning skills for researchers is becoming increasingly important. Here are 5 ways to ensure that your data is organized and easily analyzed, samples are safe and...
Why Do Enzymes Have Optimal Temperatures?
Every biologist is familiar with the profile of the rate of an enzymatic reaction versus temperature as shown in the figure. We know that enzymes from E.coli or warm-blooded animals tend to have an optimum around 37°C while those from thermal vent bacteria have much higher optimal temperatures. Surprisingly, I find that many biologists don’t have a grasp of why enzymes have these temperature...
FileMaker Campus Productivity Kit →
University of Washington on ITunes U →
back in lab!
I don’t think this post is as exciting as the videos a few posts down, but I’ll try my best! So I resumed work back in the lab here. I’ll be diving into the abalone withering syndrome project and investigating toll interacting protein (tollip). Lately, I’ve been spending hours on either the NCBI website or in Geneious trying to figure out where on the chromosome tollip is...
sequence processing [via FISH507a]
I was not going to bring this up till later in the quarter, however with the interest in the topic I have generated a how-to movie on how I deal with chromatogram files, including phredding, phrapping, blasting etc. The file is also on sharespaces. We will use the scripts in class later on. SR
i'm in ur lab sumarizin ur interleukins
This week I was given the assignment to get a general idea of what an interleukin is (also spelled interleeukin and interleuken apparently) and report it to you, the general public. An interleukin is a cytokine, a type of protein secreted by certain cells (in this case, white blood cells). These proteins are specialized to help stimulate immunity in an organism and fight against various pathogens....
BLAST information →
Heterologous Gene Expression Problems?
When heterologous gene expression goes wrong it can be a real headache. Here’s my checklist for the steps to take when you encounter problems with protein expression. Check the construct by sequencing the expression cassette to make sure that everything is as you expect. A lack of expression could result from a stray stop codon. (more…)
(via The Molecular Biology Blog)
FedEx: Trout tissue →
Videos
Those are some great videos! SR
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WatchAnother music video showcasing more new lab members!
WatchMusic video of a new lab member!
UW envisions a new Environmental College →
Woods Hole Center for Oceans & Human Health: WHOI,... →
GFP Beach Scene
Just a bit of fun for a Friday… I’ve often thought that some of what we molecular biologists do with staining and things could easily pass for artwork, but I’ve never seen anything like this fantastic agar plate artwork posted on Wikipedia. It shows a San Diego beach scene drawn on an agar plate using an eight color palette of bacterial colonies expressing fluorescent proteins. (more…)
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quarter has begun
While it has been a busy week, the stress was somewhat relieved when I learned that sea level rise is not the due to global warming but rather sheer volume of ferry traffic. The hybrid scallop assays hit rock bottom due to maternal ignorance, however we hope to have that resolved by COB Friday. Getting geared up for exposing some oysters to bacteria, should be great fun. Tanks should be flowing by...
Plasmid archiving at Addgene
Addgene is a non-profit plasmid repository that stores and distributes plasmids for academic labs. It’s great if you work in an academic lab and they happen to have your plasmid - drop them an order and get your plasmid in the mail. I don’t work in an academic lab, but I still love addgene… here’s why… (more…)
(via The Molecular Biology Blog)
An Attractive Genomic DNA Isolation Kit
I was becoming a bit bored with the tedium of column-based kits, so when I had to isolate genomic DNA from a range of micro-organisms for a recent project I decided to try something new. Invitrogen’s ChargeSwitch genomic DNA isolation kit, which uses magnetic beads to separate the gDNA from the cell debris, seemed interesting so I thought I’d give it a go. (more…)
(via The Molecular...
more information for the students...
Everyone should get very familiar with Molecular Genetics Bioinformatics ESTs the lectures from Bioinformatics 507a (at least the first few) also read the post below
Undergraduate Researchers
Please let your undergraduates know of the opportunity to apply for Mary Gates Leadership and Research Scholarships this quarter. Following this message are the deadlines and scheduled information sessions for autumn quarter. Full-time students engaged in research guided by faculty are eligible for Mary Gates Research Scholarships. Full eligibility requirements, program information and...
