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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.
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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 ...
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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 ...
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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 ...
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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...

Model Organisms in Biomedical Research
2008-01-22 12:32:00
The term “model organism” is often used in research, to describe species that are extensively studied to understand particular biological phenomena. We say “model,” because there is usually the expectation that discoveries made in the organism model will be representative of related taxonomic groups. In particular, model organisms are widely used to explore potential causes and treatments for human disease when human experimentation would be unfeasible or unethical. For instance, a it may be difficult or impossible to visualize cellular processes in mammalian embryos; and the manipulation of human subjects is tightly regulated for obvious reasons. This strategy is made possible by the common descent of all living organisms, and the conservation of metabolic and developmental pathways and genetic material over the course of evolution. (more…)
More About: Research , Model , Organ

Preps in the Zyppy: How I Changed my DNA Miniprep, Gel Extraction and Conce
2008-01-21 10:47:00
After years of loyalty, our relationship was becoming stale - things just weren’t the way they used to be. I was putting in more than I was getting back and complaining about it didn’t seem to help. I just got the same old answer thrown back at me… “it’s not our problem, it’s yours”. Then things ...
More About: Services , Kits , Reagents , Prep

Around the Blogs
2008-01-18 14:38:00
It’s Friday again, and time to recap some recent and relevant posts around the rest of the blogs:
More About: Blogs

BioPop: 10 Songs That Should Be On Every Biologist?s iPod
2008-01-18 07:56:00
The late Francis Crick once said that “Trying to determine the structure of a protein by UV spectroscopy was like trying to determine the structure of a piano by listening to the sound it made while being dropped down a flight of stairs.” But, if you thought that protein structure determination was the closest that biologists ...
More About: Songs , Ipod

In Which I Agree with the Corporations
2008-01-17 13:03:00
In Deserting the hungry?, a Nature essay argues today that “Monsanto and Syngenta are wrong to withdraw from an international assessment on agriculture.” The assessment, titled the International Assessment of Agricultural Science and Technology, is an ambitious, 4-year, US$10-million project that aims to do for hunger and poverty what the Intergovernmental Panel on Climate ...
More About: News , History , Corporations , The Corporation

Ligation Independent Cloning Protocol
2008-01-17 10:43:00
A while back I wrote a post on a T4 DNA polymerase dependent ligation independent cloning method. In the comments, Max asked if anyone had a protocol. Since there does not appear to be a simplified protocol available on the web, I thought I would post mine for reference. It is adapted from a 2006 Organic ...
More About: Independent , Protocol , Cloning , Proto

Deserving of More Media Attention
2008-01-16 16:14:00
It’s no secret that science journalism is, with a few notable exceptions, very lackluster in general. It seems to a lot of biologists whom I speak to that cell and molecular biology, genetics, and related fields, are especially underrepresented in the press. Yesterday, Alex vented a bit on this, reflecting on the capacity ...
More About: Media , Communication , Attention

Who Else Thinks Biology Teaching Methods are Wrong?
2008-01-16 10:27:00
I shudder to think of the way I was taught about metabolic pathways as an undergrad. Lists of mysterious names connected by arrows - all to be memorized, with little reference to how the processes actually worked on a chemical basis. Even worse - and perhaps embarrassingly for me - I was almost at the end ...
More About: Biology , Teaching , Learning , Methods , Wrong

Closer to the Genetic Roots of Autism
2008-01-15 18:36:00
To go with this past Friday’s post on Alzheimer’s, recent progress is being made in understanding Autism . That’s the claim coming from an initial identification of a gene called CNTNAP2, which when mutated, this gene indicated a predisposition to autism in a specific population of Old Order Amish children from Pennsylvania. Three separate ...
More About: News , History , Roots , Closer

No more white elephants! - consider this before buying a real-time PCR cycl
2008-01-15 07:48:00
Does your lab have a closet full of white elephants; once expensive instruments that are no longer fit for purpose, or have broken down? In many cases, all of that wasted money and resource could have been saved if the buyers had made smart choices about matching the instrument more closely to their needs. A real-time ...
More About: Buying , Time , White , Real , Real Time