Genome sequence of an Australian kangaroo

I have been going through a new paper that presents the genome sequence of tammar wallaby, a small species belonging to the Kangroo family (marsupial lineage). The tammar is unique in its unusual mode of reproduction and development. For one thing the breeding cycle of tammar is highly adapted and synchronized. Tammar is able to delay the embryonic development for a period of 11 months while the embryo is kept in suspended animation (diapause). The delivery of the young occurs always around the same date in January and follows a short period of gestation (26 days). After this the under-developed newborns are transferred to the pouch where they remain for a prolonged period of lactation and development (9-10 months). Therefore most of the development happens in the pouch while the young are exposed to deadly pathogens. During this stage, the composition of milk plays an important role in providing immunity to the young and has to adjust to the different stages of the development. These features make the tammar a unique model organism for genetic studies of reproduction, physiology, immunology and embryonic development.

The sequencing of the tammar was carried out using a combination of shotgun Sanger sequencing, and sequencing using next generation technologies. Whole-genome Sanger approach was used to generate enough sequences of large DNA fragments (2-6Kb) in order to assemble the contigs for de novo assembly. Then ABI SOLiD produced short paired-end reads with large insert sizes which were used to correct the contigs and create the super-scaffolds. The scaffolds were then anchored to markers of the conserved regions in the human genome and genome of a closer relative (Brazilian opossum) in order to construct the seven autosomes and the X, Y chromosomes. It was observed that the genome of tammar is riddled with wide-spread rearrangements compared to that of the eutherians and reptiles (which diverged from marsupials 150M years ago). For example chromosome three consists of genes that exists on nine human chromosomes. The centromere regions are also greatly reduced in size compared to those in the human genome.

The low coverage of the data means many genes in tammar were unsequenced or split in different scaffolds. In spite of this, annotation with Ensembl genebuild led to discovery of more than 18,000 genes and 10,000 GeneScaffolds. To alleviate the problem of missing data, a number of genes were re-sequenced including the HOX gene clusters, major histocompatibility complex (MHC) and the X chromosome, where they made interesting observations: It was observed that most gene families had undergone expansion compared to the eutherian lineage. This is expected since genes duplicate and diverge from each other. The histocompatibility complex which is critical in immunity and recognition of exogenous pathogens, was also found to be highly rearranged where class I genes where moved outside of the complex. The genes on the X chromosome were also extensively reshuffled, although a large number of the non-coding regions were conserved. One imprtant gene XIST was missing which controls the X inactivation in eutherians. It is unclear how this affects the evolution of reproduction as other orthologous genes involved in development were widely conserved. The genome sequence of the HOX genes which are involved in the evolution of morphology were also largely conserved in tammar compared with the humans. Given the strikingly different embryonic morphology between the two species, the question is whether the morphological differences could be attributed to the regulatory elements?

In addition to the genome data, they provide a transcriptome resource and a library of novel microRNAs discovered for tammar. I am still trying to digest all the extensive details. But overall the paper is an enjoyable read and accessible to layman.

 

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Marilyn B Renfree, et al. Genome Biology 2011, 12:R81 doi:10.1186/gb-2011-12-8-r81

Published: 19 August 2011

Abstract (provisional)

Background

We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development.

via Genome Biology | Abstract | Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

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Is Space Expanding?

The telescoper has an interesting post about how the expansion of the universe should be interpreted properly. The “expansion of space” in the framework of the Big Bang theory has been well described by both theory and observation, but when it comes to interpreting and visualizing the expansion, many cosmologists get confused.

First, I like Peter Cole’s allusion to ‘metaphors’ in physics. It is very brave to describe that teaching physics involves “ever-decreasing circles of deception”, and that some concepts are “more meaningless than incorrect”. But I’d prefer to describe it differently and associate these ‘metaphors’ with the reductionist approach inherent in physics. Although physics is one of the most exact and rigorous sciences whose predictions are widely reproducible and quantifiable in precise formulae, one has to remember that the real world is more complicated than could be described by simplistic theories. The reductionist approach in physics provides a way to make sense of complex systems by probing their fundamental constituents, however there also exists inhomogeneity and friction between those constituents which have to be taken into account before applying purely idealistic theories to the physical reality.

It was Hubble who first formulated his observations of the expanding universe in terms of the redshift of receding galaxies. Since then, cosmology has gone through a complete restructuring where steady-state models were abandoned in favor of the Big Bang scenario. Our current understanding of the universe is that we live in an expanding space-time which is isotropic and homogenous on very large-scales. But it is only a coincidence that in such conditions the geodesic of a test particle is described by the FLRW metric whose space and time components are independent so that the metric easily allows for an expansion factor while preserving the spatial geometry.

One has to remember that the FLRW metric is only relevant to test particles at very large scales where the cosmological principle is relevant. On smaller scales the equivalence principle of the special relativity requires the metric of freely-falling observers to follow a Minkowski metric which is void of any expansion parameter. Therefore it is utterly misleading to ask whether the earth is receding from the moon or if we will become taller as the universe expands as such assumptions don’t apply to our coordinate system. Thus asks Peter Coles mockingly, “what about a black hole? Do you think there’s a Hubble flow inside one of those, struggling to blow it up!?”. In scales of the solar system, galaxies or clusters of galaxies the gravitational collapse has long surpassed the Hubble expansion, therefore such systems should be studied as bound systems when considering the effect of Hubble expansion.

One has to also note that the expansion of space is supposed to be due to a primordial push at the time of the big bang. As Peter Coles puts it, galaxies ‘started out’ receding from us. This is our best understanding of the early motion of the large-scale structures. The evidence for this comes from the inflation paradigm which sets the initial conditions of the universe. Furthermore, in the above discussion, the “spatial expansion” due to inflation ignores the “acceleration of spatial expansion” which is associated to the dark energy. It has been observed that the expansion is actually accelerating. This has been presently attributed to the force exerted by the empty space (vacuum) itself on the space-time. This could further complicate the arguments, but it’s only relevant in even much larger scales!

In the Dark

A blog about the Universe, and all that surrounds it

Is Space Expanding?

I think I’ve just got time for a quick post this lunchtime, so I’ll pick up on a topic that rose from a series of interchanges on Twitter this morning. As is the case with any interesting exchange of views, this conversation ended up quite some distance from its starting point, and I won’t have time to go all the way back to the beginning, but it was all to do with the “expansion of space“, a phrase one finds all over the place in books articles and web pages about cosmology at both popular and advanced levels.

via Is Space Expanding? « In the Dark.

An Identity Crisis for the Variable ‘R’

An interesting article questions one of the fundamental parameters of the financial theory, specifically it questions the validity of assuming a `fixed’ risk-neutral rate of interest in calculations.

Of course it is misleading to assume anything in finance is static, however modern finance theory quite inevitably requires the premise of a fixed risk-free interest rate in order to explain the future cash flows of all self-financing trading strategies in a no arbitrage world.

Modern finance has brought about numerous financial products. However, according to the complete market theory, the majority of those products are artificial constructs of the more basic securities. For example, exotic derivatives are usually modeled as complex replicates of the vanilla options. Likewise the put-call parity implies that a put and call option can be interchanged with a portfolio of the underlying stock and cash. The value of the stock is variable with the market volatility which has been subject to modelling for long; however time value of cash has been relatively straightforward and determined by the risk-free interest rate.

For decades the yield on the US treasury bills has been used as a proxy for the theoretical risk-neutral rate of interest. But in the wake of the possibility of default of the US government, and a further downgrade of the US debt by the S&P, what can serve as a proxy for a safe return in an ideally perfect risk-free world?

 

An Identity Crisis for the Variable ‘R’

By Christopher Faille

It might be the subject of a Sesame Street episode. “R is an important letter. It stands for Rate and Return and Risk-Free and lots of other words!” Yet, like Oscar the Grouch if deprived of his garbage can, R has lost its fixed abode…

via AllAboutAlpha: Hedge Fund Trends & Alternative Investment Analysis» Hedge Fund Operations and Risk Management Performance, Analytics & Metrics Today’s Post » An Identity Crisis for the Variable ‘R’.

The Man from Earth (2007)

I admire the acting/making of this movie. It was challenging, even insulting, to my intuition. I wanted to stop watching it, but couldn’t resist! What if a man from the upper paleolithic could have survived until the present time?

My only objection is that its highly intellectual dialogue doesn’t add to the plausibility of the case it is trying to make. So, even though I liked its provocative side, I still gave it 6/10, because it doesn’t deliver on the point which I believe should be the objective of every fiction movie: that a movie should make unbelievable believable.

The Man from Earth (2007)

The movie begins with Professor John Oldman packing his belongings onto his truck, preparing to move to a new home.

Director: Richard Schenkman

Writer: Jerome Bixby

Stars: David Lee Smith, Tony Todd and John Billingsley

via The Man from Earth (2007) – IMDb.

Things Happen, Not Always for a Reason

Sean Carol is very perceptive in his notion of ‘radical contingency’. Perhaps the reason our pattern-seeking brain compels us to look for law and order in random phenomena is that we need to associate a cause to every event and it’s only through patterns that we can make sense of the causality.

This pursuit of the causal relations has been the main driving force for discovery of the laws of nature, however it has also hindered such discoveries whenever they were not contingent on having an explanation for why the laws exist in the first place.

Makes sense?

Things Happen, Not Always for a Reason

by Sean

Two stories, superficially unrelated, neatly tied together by a deep lesson at the end…

via Things Happen, Not Always for a Reason | Cosmic Variance | Discover Magazine.

DNA differences could be linked to diseases

This piece of news by BBC Look East explains what we do at the Sanger Institute.

DNA differences could be linked to diseases

Reseach at the Sanger Institute in Cambridgeshire has led scientists to believe diseases like cancer and diabetes could be linked to minute variations in DNA.

Scientists say minute differences in that pattern, shared by different people, could hold the clue.

via BBC News – DNA differences could be linked to diseases.