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Zebrafish: Making Development Transparent
2008-02-19 10:58:00
With the recent development of transparent Zebrafish, allowing scientists to directly view its internal organs, and observe processes like tumor metastasis and blood production after bone-marrow transplant, it seems appropriate to describe Zebrafish as a model organism. (more…)
More About: Development , Transparent

Ligation Independent Cloning Primer Design
2008-02-18 13:46:00
Since I wrote about the wonders of ligation independent cloning a while back, several people have contacted me to say they were confused about how to design primers for this application. It can be a bit confusing, so here I’ll give a quick overview on how to do it.
More About: Design , Independent , Cloning

Around the Blogs
2008-02-15 11:43:00
This week, around the blogs is a bit heavy on the science posts, and light on the meta-science. First though, by way of Jake at Pure Pedantry, is an attractive visual demonstration of the cell cycle, from Sakaue-Sawano et al.:
More About: Blogs

The Best Polymerases of 2008
2008-02-14 12:55:00
Yawn…. The awards season is upon us once again. Overpaid, under-worked and over-ego’d celebrities get together to slap each other’s backs and tell each other how great they are. But little do they know where the real party is in town. The 2008 Thermostable Polymerase Awards (the THEPA’s) are underway and you have a front row seat. ...
More About: Services , Kits , Reagents

Critical Learning Habits
2008-02-13 13:53:00
One view on the aim of graduate studies towards a PhD is to foster critical learning and thinking habits, much more so than to simply learn facts. You’re supposed to learn how to “think like a scientist,” or develop and mature your intellectual behaviors in the discussions of difficult concepts (AKA, problems). “Habits of Mind ...
More About: Learning , Critical

The Basics: How Phenol Extraction Works
2008-02-12 16:10:00
Phenol extraction is a commonly used method for removing proteins from a DNA sample, e.g. to remove proteins from cell lysate during genomic DNA preparation. It’s commonly used, but not commonly understood. If you want to know how it works so you can show off to all of your friends… read on.
More About: Works , Basics , The Basics

GenePaint: Visualizing Developmental Expression
2008-02-11 12:03:00
In fields describable as functional or experimental biology, one tool that could be both useful and beautiful is a digital atlas of gene expression patterns in a representative mammal during development. That’s just what GenePaint represents. In studying any individual gene product, its global function in the whole organism needs to be addressed. ...
More About: Expression

Wrapping up a Week of Just FAK
2008-02-08 11:55:00
Just Science week has been fun, reading four recent journal articles on focal adhesion kinase (FAK). It has helped me refresh myself on FAK as I got back to writing fellowship applications - although it had the added effect of taking time away from said writing activities. So today I thought a recap ...
More About: Week

Around The Blogs
2008-02-08 11:55:00
Movie stars in the lab, debates and the destruction of creationism. There’s lots going on in the science blogs this week… here are the best bits…
More About: Blogs

FAK and Phosphatidyl Inositol in Cell Polarity
2008-02-07 12:07:00
After the past three days of blogging focal adhesion kinase (FAK), each focusing on an important regulator of cell adhesion dynamics and cell motility, I’m going to turn my attention to phosphatidyl inositol-3 kinase (PI3K). PI3K has a regulatory subunit (p85), and a catalytic subunit (p110) capable of catalyzing the phosphorylation of the D3 ...
More About: Cell

Could You Learn Better?
2008-02-07 07:27:00
Are you a visual, aural, read-write or kinesthetic learner? If you don’t know, it could be a good idea to find out. Changing the way you learn, study and take notes to suit your learning tendencies can allow you to learn faster and make your newly-acquired knowledge stay with you for longer.
More About: Learn

Dissecting Molecular Interactions Between FAK and Paxillin
2008-02-06 12:27:00
In keeping with this week’s trend of just science blogging on FAK, let’s take a look at another critical protein-protein interaction - this time with the scaffolding protein Paxil lin. Specifically, how do FAK and Paxillin interact and why? Conveniently, there’s a recent paper by Danielle Scheswohl et al., from the Schaller lab: Multiple ...
More About: Interact

Defending A Giant
2008-02-05 12:57:00
The problem with being the big kid in the playground is that there will always want to be someone who wants to bring you down. And in the playground of stem cells and cloning, few come bigger than Professor Sir Ian Wilmut. In recent years, Prof. Wilmut has been hounded through the courts and in the ...
More About: News , History , Giant

FAK and Lamellipodia
2008-02-05 11:56:00
Yesterday, I ended a post about FAK, Pyk2 and regulation of RhoA activity by asking “So, what about Rac regulation by [FAK] and Pyk2?” Today, let’s discuss a paper relating FAK/Pyk2 function studies on Rac1: Regulation of lamellipodial persistence, adhesion turnover, and motility in macrophages by focal adhesion kinase. Katherine Owen, et al., focus ...

FAK, Pyk2, and p190RhoGEF in Cell Motility
2008-02-04 10:56:00
Focal adhesion kinase is an important signaling molecule in integrin-mediated cell signaling and cell adhesion. In FAK genetic knockout (FAK-null) cells, its closely homologous relative proline-rich kinase (Pyk2) is upregulated in FAK-null fibroblasts to partially compensate, but the mechanisms of Pyk2 upregulation and compensation remain undefined1. A recent study by Yangmi Lim, David ...
More About: Cell

Love in Mendel?s Garden
2008-02-04 01:01:00
It’s February… the end of winter is in sight and with Valentine’s day approaching, romance is in the air in Mendel’s Garden . In case you don’t know it, Mendel’s Garden is a delicious box of brain candy - a phenylethylamine-packed, monthly collection of blog articles on gene expression, development and evolutionary genetics. This month we ...
More About: Love

Around the Blogs
2008-02-01 10:58:00
The Future of Scientific Publishing, and Bloggers talk to bloggers, scientists talk to scientists - How science is communicated is changing rapidly. Sometimes it is difficult to keep up with, in fact. 10 more interesting posts from around the blogs, below the fold…
More About: Blogs

17 Ways to Stop Pipetting Errors Ruining Your Experiments
2008-02-01 10:56:00
If you work at the bench, accurate pipetting is crucial — without accurate it your experiments would be non-reproducible, stock solutions inaccurate and assays would have such large errors that comparing them would be meaningless. But luckily, there’s no need to worry - your trusty, precision micro-pipettes take care of all that for you. Or do ...
More About: Experiments , Stop , Errors

A New Unnatural Base-Pair
2008-01-31 10:53:00
You know about adenine, thymine, guanine, cytosine. Now get used to SICS and MMO2. In this JACS article published this month, researchers at the Scripps Institute reported the identification of these two artificial bases. They are efficiently incorporated during in vivo DNA synthesis by the Klenow fragment of E.coli DNA polymerase and pair together with high ...
More About: Pair , Base

Fast restriction digests?
2008-01-30 11:40:00
In the old days, restriction digests were a great excuse for long lunch breaks. Come back 1-2 hours later and it’s done. But, just to ruin our fun, Fermentas then NEB started to offer ranges of restriction enzymes that do their job in 5 minutes. Nothing changed with these enzymes - someone just figured out that ...
More About: Fast , Strict

Metabolism as Biogenesis
2008-01-30 10:53:00
One of the several popular views regarding the origin of life stems from thermodynamics. Harold Morowitz refers to it as “Metabolism recapitulates biogenesis”. In PLoS Biology there’s an interesting essay that was submitted posthumously by the chemist Leslie Orgel on this subject - The Implausibility of Metabolic Cycles on the Prebiotic Earth. ...

Geometries of Cells
2008-01-29 11:23:00
Form follows physics in the fly eye, say Sascha Hilgenfeldt, Sinem Erisken, and Richard Carthew Simple forces, complex shapes: While most biological features appear complex in their geometries and varieties of components, appearances can be deceiving. That finding is supported by a recent modeling study by Hilgenfeldt, et al., looking at the arrangement of cone ...

Quickly Boost Your Writing Skills
2008-01-29 07:27:00
Reports, grant applications, theses, manuscripts, essays, patent applications, your Nobel Prize acceptance speech. As a scientist, there are so many things you have to write. And writing them well is important. Writing clearly and with structure allows you to get your message across and avoiding grammatical errors stops you looking stupid in front of your audience ...
More About: Books , Skills , Boost

Worms: Models of Development
2008-01-28 12:36:00
Continuing with the recent theme on model organisms, there is the nematode (roundworm) Caenorhabditis elegans. This organisms is particularly useful owing to the fact that it has very defined development patterns involving fixed numbers of cells, and it can be rapidly assayed for abnormalities. Further, strains are cheap to breed and can be ...
More About: Models , Development , Worms , The Basics

Warning: Dihydrogen Monoxide is Worse Than Ethidium Bromide
2008-01-28 08:08:00
Please read and pass this life-saving information on to your friends. A chemical that all of us use in the lab has turned out to be highly dangerous. It is an asphyxiant, can cause severe burns and is a contributor to the greenhouse effect. Medical organizations all over the world confirm it to be responsible for ...
More About: Safety , Warning

Around The Blogs
2008-01-25 15:10:00
There were some great posts in the science blogosphere this week… here are my favorites!
More About: Blogs

How Should We Customize Life?
2008-01-25 09:46:00
The big biotech news of the week has been the successful construction of an artificial bacterial genome by J. Craig Venter et al., chemically assembled from scratch. While the genome is little more than a watermarked version of the wild bacterium Mycoplasma genitalium, it is now technologically feasible to construct custom genomes for bacteria ...
More About: News , Life , History

Xenopus as a Model for Early Development
2008-01-24 10:35:00
Another popular model organism is the African Clawed Frog, Xenopus laevis, which is extremely useful for studying development and cellular physiology, owing to its particularly large and easy manipulable oocytes and embryo.
More About: Development , Model , Early , The Basics

The Essential PCR Troubleshooting Checklist
2008-01-23 15:10:00
Routine PCR? Let’s be honest, there’s no such thing. Even with the simplest PCR reaction things can go wrong, so you need to have a good checklist of ideas for troubleshooting and rectifying the problem. Today I have brainstormed all of the ways I can think of to approach problems with standard PCR reactions. I’ve inevitably missed some things out so please chip in if you can think of anything else to add. I will add your ideas to the list to make it a resource we can all refer to. (more…)
More About: Troubleshooting , The Essential , Essential

Dictyostelium as a Model
2008-01-23 11:00:00
As noted in the previous post on Model Organisms, Dictyostelium discoideum is a popular model for studying fundamental aspects of cell-cell communication and chemotaxis. This is a soil-living social amoeba grows as separate, independent cells that interact to form multicellular structures when challenged by adverse conditions such as starvation. Up to 100,000 cells signal each other by releasing the chemoattractant cAMP and aggregate together by chemotaxis to form a mound that is surrounded by an extracellular matrix. This mechanism for generating a multicellular organism differs radically from the early steps of metazoan embryogenesis. However, subsequent processes depend on cell-cell communication in both Dictyostelium and metazoans. Many of the underlying molecular and cellular processes appear to have arisen in primitive precursor cells and to have remained fundamentally unchanged throughout evolution. Basic processes of development such as differential cell sorting, pattern fo...