June 25, 2013

I've migrated to Tumblr

I've decided to continue this blog, or whatever it is, under a different form, and for what I have planned the Tumblr interface and functionality works better. Please go to http://egosumdaniel-od.tumblr.com from now on.

I've migrated my favorite posts from here to the Tumblr page, but I'll keep this blogspot as an archive of the last 5-or-so years - a time that spans from me being accepted into the PhD program to finishing and defending my thesis.

June 18, 2013

Figshare update and sodium channel evolution

Figshare has just announced that they're allowing embeddable content via a handy widget. This seems like a natural step to promote the dissemination of open data and self-publishing of research data. I've tried out the widget on a previous post about the evolution of voltage-gated sodium channels - link here - and it fits really well with the blog format. You can also see it below. PLOS has started using the widget seamlessly in their journal websites as well - see for example this article. They've already been using figshare to deposit supporting information for a while now.

Speaking of voltage-gated sodium channels, my former colleague Jenny Widmark and our group leader Dan Larhammar have just published a short chapter on their evolution for eLS (Encyclopedia of Life Sciences), based on our work. I've included the link to the eLS chapter below.

Phylogenetic maximum likelihood analyses of the voltage-gated sodium channel α subunit (SCNα) gene family based on amino acid sequence alignments. The sequences and alignments described in Widmark et. al. (2011) Molecular Biology and Evolution 28(1):859-71 (1) were used to re-analyze the phylogenetic relationships of vertebrate SCNα subtypes with more powerful methods.

Widmark, J., & Larhammar, D. (2013). Evolution of Voltage-Gated Sodium Channels eLS John Wiley & Sons, Ltd DOI: 10.1002/9780470015902.a0024936

February 12, 2013

Darwin Day 2013

Darwin by G. Richmond The day is almost over, but it's still Darwin day! 204 years since the man was born and and an opportunity to "recognize the importance of scientific thinking in our lives and to honor one of humankind’s greatest thinkers", in the words of US Representative Rush Holt as spoken earlier today.

Usually on Darwin day I spend some time leafing through "On the Origin of Species" or "Voyage of the Beagle", or any other of his writings, to find an aspect about Darwin that is new to me. Here are my entries from 2012 - Darwin on cruelty - and 2011 - Mockingbirds and Darwin's original thought. But this year, since I don't have much time over and I've just finished writing my PhD thesis, I thought I'd share a quick quote from "Origin" that I used in the introduction.

November 17, 2012

Keeping calm

The reason I've neglected this page over the past year can best be described with the image below. I defend my thesis "Evolution of Vertebrate Endocrine and Neuronal Gene Families - Focus on Pituitary and Retina" on January 18 March 1.

May 30, 2012

Quote: Ramón y Cajal on the inconvenient diversity of nature

Doing science is walking the fine line between assuming the simplest possible explanation for your observations, and avoiding our human bias towards beauty, elegance and organization.

Unfortunately, nature seems unaware of our intellectual need for convenience and unity, and very often takes delight in complication and diversity.

- Santiago Ramón y Cajal, in his 1906 Nobel lecture "The structure and connexions of neurons".

... and he should know! Santiago Ramón y Cajal applied himself to revealing the immense and, at the time, almost inconceivable complexity and variation of cells in the nervous system.

February 21, 2012

An exercise in open science: The evolution of voltage-gated sodium channels

>> This post describes my re-analysis of the voltage-gated sodium channel α subunit (SCNA) gene family evolution, based on a previously published study. I have shared the improved results as well as all source files and datasets openly in Figshare, together with a description of the methods: link.

This is probably not my last re-analysis of the same dataset, and I'd want to encourage others to use other phylogenetic methods on our alignments, or use our alignments to analyse their own SCNA sequences.

ResearchBlogging.orgLast year my research group published a study on the evolution of voltage-gated sodium channel α subunits (see reference below) with me as one of the co-authors. Voltage-gated sodium channels are the proteins that permit the passage of positive charges, in this case sodium ions, across the cell membranes of neurons and thus make it possible for your nerve fibres to fire electrical signals. The α subunits are the very large proteins forming the actual pore that selects only sodium ions and allows them to pass. It's difficult to overestimate how essential they are for the function of the nervous system, and how important their evolution has been for the evolution of neuronal signaling.

Our published study used both sequence-based phylogenetic data and genomic data to clear up the muddled relationships between different subtypes of voltage-gated sodium channels in vertebrates. Us humans, and most other mammals, have ten different types of these α subunits, encoded by genes of the SCNA family. The different subtypes have acquired different properties and are expressed in different parts of the nervous system and some other tissues in the body where electrical signaling is necessary. One of the subtypes, the product of the SCN7A gene, has even evolved to such a degree that it's not a channel anymore. It's probably more like a sodium "sensor". There are also specific diseases, different types of epilepsy, seizures and paralyses, that are associated with mutations of the various subtypes.

The same gene family in true bony fishes (teleosts) encodes up to eight different subtypes, almost as many as the mammalian family. The funny evolutionary twist is that we have evolved almost the same amount of subtypes by completely different mechanisms! In tetrapods, the fleshy-limbed mostly terrestrial group that we belong to, local duplications of genes on the same chromosomes gave rise to new subtypes, while in teleost fishes it was their ancestral duplication of the whole genome that did the same on different chromosomes! You can see the difference in the image below.

Chromosome organization of the SCNA genes and some of their neighboring genes in humans and zebrafish. Each numbered line represents a different chromosome. The ten human genes are named in a series from SCN1A to SCN11A, skipping the number 6. The duplicates in teleost fish are denoted by the letters "a" and "b".

This means that when doing comparative studies, it's important to know that while all vertebrate voltage-gated sodium channels have a common origin, they're not always directly related to each other.

Using more powerful and careful methods than we'd used before, I made new evolutionary trees that agree even better with these conclusions. Most of all these new trees are better and clearer examples of the evolutionary relationships between different voltage-gated sodium channel subtypes. You can see figures of the new trees and access all the source files and datasets in Figshare.

February 13, 2012

Quote: A bee doubtless would...

Researching yesterday's post, I found this beautiful and (unintentionally?) funny quote searching for references to bees and wasps in Darwin's writing.

All animals of same species are bound together just like buds of plants, which die at one time, though produced either sooner or later. <...> It is absurd to talk of one animal being higher than another. — We consider those, when the intellectual faculties/cerebral structure most developed, as highest. — A bee doubtless would when the instincts were —

- Charles Darwin, "Notebook B" pages 73 and 74.

It is absurd to talk of one animal being higher than another. A bee would consider itself highest in many other respects.


February 12, 2012

Darwin Day: Darwin on cruelty

Darwin by G. Richmond Happy International Darwin day! It's been 203 years since the man was born. As usual, I'm taking the chance to open one (of my several) copies of "Origin" or "Voyage of the Beagle" more or less on a random page and bring out some Darwiniana to celebrate evolution. Check out my previous Darwin entries here.

So I've been spending the day reading some Darwin, and chapter eight of On the Origin of Species (first ed.), with the captivating title of "Instinct", caught my attention this time. Darwin has two great realizations in this chapter; first he lays out how behaviors can evolve just as physical structures can; how shared ancestry and descent with modification can explain how related species on different continents can exhibit the same or similar behaviors. The second insight lies in his explanation of the, to us, very cruel behaviors that you often find in nature. To people of Darwin's time, it would be a problem to consider that a benevolent creator would have put on the earth creatures that not only killed in order to survive, but that did it in almost unnecessarily horrific and macabre ways.

February 05, 2012

Online bioinformatics tools and resources

Online bioinformatics tools I've updated my collection of online resources for genomics, sequence analysis and phylogeny - click here or on the "BioInfo" tab above.

These are all the tools that I use regularly in my work, so they're geared towards comparative genomics (mostly vertebrates), gene and protein predictions, sequence alignment and editing as well as different methods and applications for phylogenetic analyses. If you think there's a great resource out there that's missing, let me know in a comment below! I first put the page together for the people in my lab so that we could share all the same tools, but now it's more or less our informal start page. It's fantastic that so many researchers have developed all these great methods and are willing to make them freely accessible online. My work would certainly be impossible without that spirit of cooperation and openness. It does warm the heart to be part of a scientific field and a culture where this is the norm rather than the exception.

November 30, 2011

Two ways of looking at the same proteins: Insulin-like Growth Factor Binding Proteins

ResearchBlogging.org Back in June I blogged about a research paper that we had just published with myself as the lead author. The subject of our paper was the evolution of the Insulin-like Growth Factor Binding Proteins (IGFBPs), and how this family of proteins has expanded in vertebrate evolution. Yesterday I noticed that this paper, "my" paper!, now has received its very first citation! This was a my first paper as lead author, so naturally I avidly checked it out.

The research paper that cites us is in press in the Journal of Biological Chemistry (reference below). While we were interested in finding as many IGFBP genes in as many vertebrates as we could, studying the characteristics of their genetic code and establishing their evolution, this study is more concerned with the biochemical structures of the actual proteins.

Molecular model of mouse IGFBP-5 (N-terminal), showing the locations of the cysteines that form disulfide bridges. Ref: M. Nili et. al. (see reference below).