Friday, June 27, 2014

The Elephant Catchers

It has been 6 years since i read and blogged about Subroto Bagchi's book Go kiss the world. As with the previous book, finished reading the book "The Elephant Catchers" in one sitting. The writing style is very captivating and keeps you reading. 

The Elephant Catchers is all about growing a company that is hunting rabbits (small game) into one that now catches elephants. While many people start a startup, very few can make it into a self-sustaining and growing company. The book deals with the mistakes that happen and how to go about "fixing" those mistakes. 

Many anecdotes from different points along the way makes for an interesting read. The use of personification at different points to explain very different stories is very appealing. For example, at one point the company wins a big client who could be persuaded to hire a dog that is loyal instead of cat that is pleasing. 

Dividing the book into 6 parts with sub-chapters keeps it well organized. All of them have one thing in common, it is about scaling things. Be it scaling ideas or infrastructure the wisdom of having been there and having done that shines through brilliantly.

Monday, June 16, 2014

Largest known protein - Titin

With a length of more than 30Kb Titin is the largest known protein in the Human genome. Due to its repeated use of the same domains, it is thought have undergone very unpredictable exon losses. 

Apart from the biological reality of exon loss, the incredible length of the gene makes it prone to annotation errors. Prevalence of such large scale annotation errors makes it impossible to study the intricacies of the biology of such a gene. This is an attempt to identify such potential errors in annotation. The hope is that it will contribute to improving the annotation. 

Mutations in the Titin gene have been implicated in many diseases. Being the longest gene also makes it interesting from an evolutionary point of view. 


The human version of the gene (located on chr-2) has 363 annotated exons as per Human release 75 of Ensemble. The chicken version of the gene (located on chr-7) has only 47 annotated exons as per Chicken release 75 of Ensemble. Flanking genes are PLEKHA3 and CCDC141. However, a new gene, "ENSGALG00000026366" has been annotated in Chicken between PLEKHA3 and TITIN. While it has a name like "gga-mir-7474" and a link to the mirbase, it has gene type as protein coding. If that was not confusing enough, this gene has an aminoacid length of ~30Kb (has 269 exons). Given its location and length, it appears that the Titin gene has been incorrectly split into two genes (Titin itself and gga-mir-7474). As expected, the two genes are connected by a chicken cDNA EST (see figure below).

This "gga-mir-7474" gene gets top blast hit from Titin. 

So based on EST data and blast data these two genes can be merged as part of the Titin gene. We are still short by 47 more exons.


The release 75 of Ensemble has a ~61Kb long TTN gene with 106 exons annotated in Flycatcher. Two very short genes (with 1 and 2 exons) downstream from this TTN gene, ENSFALT00000015943 and ENSFALT00000003626 also give top blast hit to the TTN gene.

Even with availability of EST evidence, some very good objective predictions, the annotation seems rather sketchy.  

Wednesday, June 11, 2014

European crow hybrid zone poem

A poem by Jochen Wolf, that describes the European crow hybrid zone.

Crows are generally believed to be black,
but some think that they are grey.

fact is, both parties are right,
and anyway all crows are black at night.

but during day they meet along a narrow hybrid zone
where they eat and play.
and sometimes mate, and assortatively clone.
black with black and grey with grey.
so the question is: why do black and grey stay away.

to answer this riddle we climbed many pines,
and raised a good deal of young, for food that they shout.
we sequenced genomes and programmed
until the keyboard shines

and kind of
figured it out.

Young crows eat a lot

Young crow chicks need to be fed a lot of food. Since, they are not able to feed themselves, food has to be almost pushed down their throats. They eat meat (ox heart is supposed to be their favorite), eggs, corn etc. Some crows prefer not eating anything other than meat and can spit out the egg and corn. As they grow older, they learn to eat meat and leave the corn in the bowls. Moving worms are a big hit with crows. Although keratin rich worms are not their primary diet, they do like eating a few worms.

So a lot of protein rich food laced with vitamins, calcium (chalk) and water. Its really amazing that such small birds can eat so much food within a day. The very young crows with very tiny throats can find it hard to swallow food. Meat can also be blended into a viscous paste and fed to the crows either with a spoon or a syringe of some sort. However, as the crows get older, this should be discontinued gradually to make sure that the crows learn to use their tongue and beak.

Apart from food, captive crows need medication. The stress of being kept captive seems to make them more prone to diseases. Veterinarians working with farm birds should be able to help. However, wild birds like the crows are definitely harder to breed in captivity. Given such hardship in breeding crows in captivity, the recovery in the population of the Hawaiian crow [Alalā (Corvus hawaiiensis)] is worthy of praise.

Pictures of crow claw (obtained from dead crows with appropriate permission for research)