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 bringing to you periodically (Feel free to let me know whether you think this is a good or bad idea either in a comment or by hitting the “contact” button above). This article explains the basics of DNA ligation. I hope you find it useful. Read more »

Perhaps the most fundamental aspect of migration of any kind is, how do you know which way to point yourself? Heck, this isn’t just about migration, it’s about how something is oriented in its immediate environment. For orientation, there’s magnetic North, gravity, or any conceivable cue that you might choose to face towards. How do cells orient themselves, however?

One of the primary ways in which cells orient themselves is by labeling regions of the cell membrane - by phosphorylating a type of lipid called phosphatidyl-inositol(4,5)bisphosphate [PI(4,5)P₂] (green), so that it becomes [PI(3,4,5)P₃] (purple), as shown by the image (Comer and Parent, 2007). As this reaction invovles the phosphorylation of the ‘3′ site of the inositol ring of carbon atoms, the enzyme which catalyzes this reaction is called PI-3 Kinase. (kinase = phosphorylating enzyme)
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In memorandum of one of the pioneers of molecular biology, who was awarded a Nobel Prize in medicine for the discovery of DNA polymerase. What molecular biology blog would this be if we didn’t honor his memory? Larry Moran presents a fine eulogy, as does the NYTimes:

Dr. Arthur Kornberg, a biochemist whose Nobel Prize-winning discovery of how DNA is assembled helped ignite the biotechnology revolution, died on Friday in Stanford, Calif. He was 89 and worked in his laboratory at Stanford University until a few days before his death.

The cause was respiratory failure, a spokesman for Stanford said.
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Now for a bit of light entertainment of the biological kind. Wash out your mind - I don’t mean that kind of biological entertainment Read more »

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 searches, while others provide more general support with PDF downloading and unit conversion and the like. Here they are: Read more »

Nature Precedings represents a step forward for disseminating experimental results in the internet age. Especially ‘negative’ results, that might not have gotten published otherwise, but is extremely helpful to other researchers in trying to avoid making the same mistakes. Refutation of a hypothesis, while not a discovery, is the goal of the well-planned experiment in the trenches of science.

An outstanding example of such a Preceding can be found in the manuscript Internal ribosomal entry site lacks secondary structure by Xuhua Xia of the University of Ottawa’s Department of Biology.
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10 links to some popular blogs of the molecular and cellular biosciences:

Bacillus? Acinetobacter? Thermus?!? - Rosie takes us through her thought process in developing an experiment on growth conditions, while she considers what organism to use.
These Cells are Left-Handed - Some comments on the influence of chirality on cell polarity.
Chlamydomonas Swims Across the Line - The plant that swims gets its genome sequenced.
TRPV1 Ion Channels - A student answers his professor’s question about a ligand-gated ion channel, and what was done to test its interactions with anesthetics.
Microcosm: Unveiling the New Book (Or At Least Its Cover) - Here’s teaser on a new book on the horizon.
MicrobeWorld: what have you done? - Sandra catches a bunch of microbiologists mistaking a bacterium for a virus.
Do Bacteria Age? - Well, do they?
A Fever for Enzymes - Explanations of how temperature relates to enzymatic reaction rates, sparked by one of our posts.
The Nobel Prize in Chemistry 1946 - “for his discovery that enzymes can be crystallized.”
5 Facts (and Caveats) About DNA Profiling - Commentary on five facts about DNA profiling that people should know.

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 available literally at your fingertips via BLAST searches and the like is staggering. In this environment it’s easy for your mind to become overloaded, and an overloaded mind is no good for the logical and creative thought processes that are essential for effective science. Read more »

The Public Library of Science (PLoS) defines the issue of Open Access Publication as:

An Open Access Publication[1] is one that meets the following two conditions:

1. The author(s) and copyright holder(s) grant(s) to all users a free, irrevocable, worldwide, perpetual right of access to, and a license to copy, use, distribute, transmit and display the work publicly and to make and distribute derivative works, in any digital medium for any responsible purpose, subject to proper attribution of authorship,[2] as well as the right to make small numbers of printed copies for their personal use.

2. A complete version of the work and all supplemental materials, including a copy of the permission as stated above, in a suitable standard electronic format is deposited immediately upon initial publication in at least one online repository that is supported by an academic institution, scholarly society, government agency, or other well-established organization that seeks to enable open access, unrestricted distribution, interoperability, and long-term archiving (for the biomedical sciences, PubMed Central is such a repository).

It is derived from the Creative Commons Attribution License, and can more simply be described as “scientific works gleaned from government funding should be publicly available.”

That’s not a radical idea. However… Read more »

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, here are five of them. Read more »