Looking at the tree of life, descent with modification is an obvious theme, where genes are passed on through ‘vertical’ lines of ancestry. It so happens though that genes can jump from one lineage to another, by a process called ‘horizontal gene transfer’ (HGT). Naked DNA uptake (transformation), viruses (transduction), and plasmids (conjugation) are the mechanisms by which the genetic units of heredity need not be inherited in the usual sense. HGT appears to blur the boundaries of what a species is, particularly for the bacterial domain of life. So the study published by Rotem Sorek, Edward Rubin et al.¹ on the determination of barriers to HGT is interesting from a couple different perspectives. Read more »

Here are the highlights of what I’ve been reading around the blogs this week: Read more »

I just came across a neat device now being offered by BioRad that may interest those of you who do a lot of electroporation of difficult-to-transfect mammalian cells, where tedious optimization of the electroporation protocol itself is required. Read more »

An essay in today’s issue of Nature struck a contentious cord at the intersection of modern science and politics: that of the ethical regulation of science. The context of ethics and science was succinctly summed up:

When in 1978 the first baby was born by in vitro fertilization (IVF) it was inevitable that there would be calls for the procedure to be prohibited. That science develops too fast for morality had become the cliché of the twentieth century.

Focusing on IVF in Britain, this essay by Mary Warnock is narrow in scope. The same principles can be applied to the use of recombinant genetics and embryonic stem cell research, to name a couple more. The instant that these breakthroughs hit the world stage, they have sparked uproars from “moral authorities,” but in the end, it is largely the scientists that regulate themselves. (the National Academies of Science have been the ones to issue the ethical guidelines on the conduct of all of the above forms of biomedical research, not any self-righteous elected authority) Read more »

In the early 1950’s so many new enzymes were being discovered in the burgeoning field of biochemistry that enzyme nomenclature was in danger of getting out of hand. With no guidelines on how to name enzymes, researchers simply chose their own. Some enzymes were given names, like diaphorase or Zwischenferment, that conveyed nothing about the reaction they catalyzed and enzymes with similar function were given names that implied they were different. It was all very confusing and clearly if the situation continued it would be disastrous for our attempts to study enzymes. Read more »

Science is an endlessly fascinating, challenging, and intellectually-satisfying endeavor. So it saddens me any time that I see someone mistakingly make claims about taking science on faith. This isn’t the forum for taking on religion - if you want that, more of my thoughts on that can be found at Migrations.

I have one request though, for us here at Bitesize Bio, and in particular, on our discussions of interesting and ground-breaking scientific studies:
Don’t take us on faith. Instead, ask questions. Scrutinize. Check out the data for yourself. Be skeptical. Be analytical. And reach your own conclusions. Catch me making a mistake, and demonstrate how a mistake was made. Read more »

Last month, Thomas C. Erren and colleagues published an editorial in PLoS Computational Biology entitled 10 simple rules for doing your best research, according to Hamming. The article provides some great philosophical guidance on setting out to do great research, drawing on advice given by the mathematician Richard Hamming during a Bell Communications Research Colloquium Seminar in 1986. Read more »

Here’s one of my favorite journal articles from the past year - an elegant study by Natalie Andrew and Robert Insall published in Nature Cell Biology: Chemotaxis in shallow gradients is mediated independently of PtdIns 3-kinase by biased choices between random protrusions. From the introduction:

We have made detailed, quantitative observations of Dictyostelium cells chemotaxing in shallow gradients, which contradict current models in several ways (see Supplementary Information, Fig. S1): first, new pseudopods are made in spatially restricted sites by splitting of the leading edge; second, the timing and direction of these new pseudopods are random, so they cannot correct the cell’s direction; and third, the survival and retraction of pseudopods are spatially controlled, suggesting an alternative mechanism of chemotaxis.

This model is very similar to the mechanism of growth cone guidance, where random protrusions are constantly exploring the cell’s surroundings, ‘tasting’ for attractant or repellant cues. These cues either stabilize or destabilize one side of the growth cone or pseudopod over the other side, causing the cell to turn one way or another. This isn’t a new concept (having been addressed in neutrophils previously - Arrieumerlou and Meyer, 2005), but Andrew and Insall formalize the case for biased choices in chemotaxis in Dictyostelium very nicely (Figure 1, below).

Read more »

In the budding yeast Saccharomyces cerevisiae, 59 of the 79 cytoplasmic ribosomal proteins are encoded by two genes, stemming from an ancient genome duplication event. Komili et al. (2007) now report that these paralogous genes are not functionally equivalent, suggesting the possible existence of a “ribosome code.”¹

Yeast and mammalian genomes are riddled with apparently duplicated genes, differing in only a few amino acids from one paralogue to its clone. Because they’re so nearly identical, most researchers assume some degree of redundancy in such circumstances, and attempt to ascertain the function of only one of the two. If there is any difference in function between two paralogues, the difference might be unimportant, or just too difficult to tease apart experimentally.

As we gain more and more insight into how the cell works, such minutiae might be a curious area to study up on. In the case of the yeast S. cerevisiae, it turns out that 59 of their 78 ribosomal proteins have doubles that differ by only a few amino acids. Suzanne Komili, Pamela Silver (Harvard Medical School, Boston, MA), and colleagues² make an intriguing argument that only rarely are individual members of a paralogous gene pair functionally identical, despite this strong sequence similarity. Read more »

As a product manager, one of my responsibilities is to exhibit at various scientific conferences to promote and advertise products for genomic DNA extraction. Less than three months into the job, I attended the American College of Medical Genetics (ACMG) conference to promote a new product we had just launched for DNA extraction from blood and cells. After hours of talking to people about the features and benefits of my fancy new kit, a gentleman walked by my booth, looked at the demo on the table, and asked me to explain how it worked. Excited that I finally found an interested scientist, I enthusiastically went into my spiel, but as it turned out, I was the one who did most of the listening.

Read more »