Evolution of the Animal Apoptosis Network

1. Christian M. Zmasek and 
2. Adam Godzik

Cold Spring Harbor Perspectives in Biology - Cell Survival and Cell Death

Abstract: The number of available eukaryotic genomes has expanded to the point where we can evaluate the complete evolutionary history of many cellular processes. Such analyses for the apoptosis regulatory networks suggest that this network already existed in the ancestor of the entire animal kingdom (Metazoa) in a form more complex than in some popular animal model organisms. This supports the growing realization that regulatory networks do not necessarily evolve from simple to complex and that the relative simplicity of these networks in nematodes and insects does not represent an ancestral state, but is the result of secondary simplifications. Network evolution is not a process of monotonous increase in complexity, but a dynamic process that includes lineage-specific gene losses and expansions, protein domain reshuffling, and emergence/reemergence of similar protein architectures by parallel evolution. Studying the evolution of such networks is a challenging yet interesting subject for research and investigation, and such studies on the apoptosis networks provide us with interesting hints of how these networks, critical in so many human diseases, have developed.

http://cshperspectives.cshlp.org/content/5/3/a008649.abstract

The impact of free-ranging domestic cats on wildlife of the United States

from SR Loss, T Will, and PP Marra (2013) "The impact of free-ranging domestic cats on wildlife of the United States" Nature Communications 4, 1396:

"free-ranging cats cause substantially greater wildlife mortality than previously thought and are likely the single greatest source of anthropogenic mortality for US birds and mammals"

link: http://www.nature.com/ncomms/journal/v4/n1/full/ncomms2380.html

70% of all domain combinations present in the human genome appeared by convergent evolution in at least one other eukaryotic genome

Our paper, entitled "This déjà vu feeling — analysis of multidomain protein evolution in eukaryotic genomes" has been published in PLoS Computational Biology.

This is a continuation of our work on protein domain gain and loss and the evolution of eukaryote complexity, "Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires", published Genome Biology in 2011.

The main findings are that at least 70% of all domain combinations present in the human genome independently appeared in at least one other eukaryotic genome. Overall, over 25% of all known multidomain architectures emerged independently several times during eukaryote evolution. Our results stress a recurring theme — namely, that evolution is an exceedingly dynamic, and seemingly random, process. New domain combinations are being created and recreated throughout evolution. Each group of organisms (and probably even each organism) has their own solutions, based on a partially shared set of  domains to solve shared biochemical and regulatory needs.

As more and more genomes are being sequenced, the percentage of independent domain combination evolution is likely to grow even more. In fact, with sufficient data available, the following paradigm of evolution at the domain level will probably emerge: Major clades (such as animals) have a relatively small set of distinguishing core domain combinations that are essential and defining for members of that clade (such as developmental programs and cell–cell adhesion for animals). Outside of these hierarchical sets of core domain combinations, all domains are randomly undergoing reshuffling, and the vast majority keep reemerging and disappearing both over species space and over time.

2012 Computational Phyloinformatics Course

I am teaching the "Molecular Evolution and Comparative Genomics with Ruby and BioRuby" section at the Computational Phyloinformatics workshop 2012:

• http://academy.nescent.org/wiki/Moscow_2012
• https://www.nescent.org/wg_comphy2012/Main_Page

Reconciliotastic at Phylotastic Hackathon

At the NESCent Phylotastic Hackathon I was part of a group who, among other things, worked on a user friendly webserver for gene-tree/species-tree reconciliation (gene duplication inference). The resulting webserver is here.

Phylotastic Hackathon

Phylotastic hackathon will take place from Monday 4. June to Friday 8. June, 2012.

DUF Annotation Jamboree

I am currently participating in the DUF Annotation Jamboree (December 7-9, 2011 UC San Diego).
The goal of this workshop is to annotate a possibly large number of protein families that are being referred to as having unknown functions (terms like UPF or DUF) despite (often) having a significant amount of reliable predictions, or even experimental data, about them (see also: TOPSAN AFP-DUF Annotation Jamboree page).

Rejuvenating senescent and centenarian human cells by reprogramming through the pluripotent state

In this interesting work, the authors successfully reprogram somatic senescent cells from very old patients into induced pluripotent stem cells (iPSCs). They also show hat many of the old-age-related changes in cells (e.g. telomere length and gene expression profiles) are reversed in such reprogrammed pluripotent cells.

• Laure Lapasset et al. "Rejuvenating senescent and centenarian human cells by reprogramming through the pluripotent state" Genes & Development

Mollusc Phylogeny

• Smith et al. "Resolving the evolutionary relationships of molluscs with phylogenomic tools" Nature

Human Brain (Development) - Genetics and Transcription

Recently, three fascinating studies regarding the genetics and transcription of/in the human brain have been published:

• Baillie et al. "Somatic retrotransposition alters the genetic landscape of the human brain" Nature
• Kang et al. "Spatio-temporal transcriptome of the human brain" Nature
• Colantuoni et al. "Temporal dynamics and genetic control of transcription in the human prefrontal cortex" Nature