A few articles from around the blogosphere, relating to the molecular biology of the cell and the conduct of science.

Confocal Image of Cochlea Wins Art Prize - Stunning micrography!

Microbial Sociology - Detailed post on the molecular mechanisms of microbial communication.

The Selfish Gene Drives an Operon - What does horizontal gene transfer look like from the gene-centered view of evolution, or “selfish gene” model of evolution? Operons anyone?

The Growth Cone - Kickoff post to a short series on the neuron structure of the same name. Growth Cones are a fascinating topic for me, relating to both the brain’s wiring and how cells move.

The Origins of Genome Architecture - A review of Michael Lynch’s book, which reportedly could have been subtitled “Why R.A. Fisher was wrong.”

Authorship on Scientific Papers - Discussion of the rules of authorship, and handling disputes equitably.

Bringing Your Research Lab’s Web Site into the 21st Century - Scientists often aren’t the best communicators, but promoting one’s scientific interests can help careers.

DNA Network Members Discuss Personal Genomics Service Providers 23andMe, deCODEme, and Navigenics - The latest developments in personal genomics, and what companies are offering.

Some thoughts on the IPS cell findings - genes and the power to create “souls” - Alex takes a look at some big news in stem cell research, contrasts it with posts that he’s written previously on earlier papers, and ponders a philosophical implication of this field of research.

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Bitesize Bio has gained a lot of new readers over the past few months so I thought it would be a good idea to highlight some of the articles newer readers may have missed. I’ll do this periodically to make sure none of our readers miss any of our great content. So, here are the best of our tech tips articles so far: Read more »

I just came across an extremely nice piece of plasmid mapping and annotation software that I’d like to share with you. PlasMapper is a web-based application, created by staff from the University of Alberta, that automatically generates fully annotated plasmid maps from your raw sequence input.

Using a database containing the sequences of hundreds of features (replication origins, antibiotic resistance cassettes etc), as well as restriction enzymes, the program identifies each of the features in your inputted plasmid and renders them in a publication quality graphical or text map. The image on the right shows some examples of the output of the application - click the image to view a larger version. Read more »

Apoptosis, or programmed cell death, is an evolutionarily conserved and neatly orchestrated process important for tissue remodeling and safe elimination of severely damaged cells. Conducted by a caspase-mediated proteolytic cascade, the cell death program results in a series of cellular changes distinct from cellular necrosis. And one of the critical aspects that distinguish apoptosis from necrosis is that intracellular components of apoptotic cells are isolated, preventing membrane permeability and release of inflammatory molecules.

Just how do dying cells keep themselves from spilling out their materials into the surrounding tissues? And what role do the cytoskeleton components have in this process? Those are the questions that José Sánchez-Alcázar and colleagues¹ asked in a paper in July’s issue of the journal Apoptosis. Read more »

In any experimental procedure, getting the controls right can save you a lot of work when things go wrong by allowing you to pin-point the source of the problem. DNA ligation is no different. In this article I look at how to set up a ligation reaction with a complete set of controls, and use them to pin-point the cause of your ligation problems. Read more »

“How many genes are mutated in a human tumor?” That’s the question that a team of researchers at Johns Hopkins posed, and took a comparative genomic approach. By analyzing the sequences of 20,857 transcripts from 18,191 human genes, in 11 breast and 11 colorectal cancers, Wood et al. were able to generate a topographical representation of gene mutations. The average number of mutations per tumor was approximately 80, but ranged from 39 to 193.

Read more »

One of the neat tools in molecular biology is the ability to recombine parts of two proteins to create fusion or chimeras. They’re often extremely useful for simple experiments, some of the time for targeting protein domains to subcellular sites, or to isolate a structural component of a protein. The functional information is often quite interesting.

One manuscript recently in Nature Precedings used the chimeric molecule approach slightly differently. John Rossi and coworkers describe a aptamer conjugate for delivering anti-HIV siRNA specificially to infected cells. The aptamer in question is a gp120-interacting molecule. The envelope glycoprotein gp120 is expressed on the surface of HIV-1 infected cells, allowing binding and interalization of the whatever is conjugated to the aptamer, in concept. In this case, Rossi et al. have conjugated the chimera to an siRNA that releases an anti-tat/rev siRNA, which in turn inhibits HIV replication. Read more »

Here at Bitesize Bio we are very proud to have the chance to host our first ever blog carnival. Gene Genie brings together blog articles from an array of perspectives within the area of human genes, genetics and diseases. It has been a pleasure and an education reading through all of these great articles and I’d like to thank all of the authors for contributing, and Gene Genie founder Berci Mesko for allowing us to host the carnival. So lets get to the articles…. Read more »

This month’s Nature Genetics has an article introduced with the catchy title Aging and cancer: killing two birds with one worm. That’s referring to using C. elegans as a model organism, of course, due to its utility as a model organism for genetic research.

Pinkston-Gosse and Kenyon follow a C. elegans-ortholog of FOXO transcription factors, DAF-16, to phenotypes of manipulated lifespans and cancer susceptability. The pathway stems from the respective ortholog of insulin/insulin-like growth factor 1 (IGF-1) receptors, and FOXO transcription factors turn on genes involved in p53-dependent apoptosis, cell cycle arrest, and cellular stress resistance.
Read more »