Tuesday, March 7, 2017

Ann Arbor to Chicago union station - a train journey via Amtrack

A train journey from Ann Arbor to Chicago is an easy way to travel. Amtrak runs multiple trains throughout the day on this route which actually starts from Pontiac. The journey of approximately 4 hours can frequently be delayed by upto 30 minutes. Apart from experiencing this first hand, I also overheard a very upset American complaining that this delay had resulted in him reaching 30 minutes late to his job interview. Hopefully, he will still get the job as the interviewer seemed sympathetic to his cause. 

Ann Arbor, Amtrak station, Front entrance in March 2017

The train route meanders down from Ann Arbor through Jackson, Battle creek, Kalamazoo, Niles, and New Buffalo before entering the state of Illinois. After stopping over at Michigan city, it heads into Chicago to stop at the union station.

Kalamazoo is approximately the mid-point (for travelers from Detroit) located 142 miles from Detroit and 138 miles from Chicago. The phrase Timbuktu to Kalamazoo (both real places) commonly used by English speakers to refers to journeys between exotic places. The word is thought to originate from native American's of the Hopewell culture. The journey ends at the historic Union station of Chicago.




Wednesday, January 25, 2017

The sun rises in the east

What you see here is the sun rising. It most definitely is rising in the east.


Let's hope it's not a sunset :) If it was not clear before, let me make myself clear (as if it matters), all views expressed on this blog are my own personal views and don't reflect the views of my employers.

Monday, December 26, 2016

Why god hates ring species?

If god has an inordinate fondness for beetles, then he must surely hate ring species. As eminent evolutionary biologist, prominent god denier and all round good guy retired Professor Jerry Coyne notes in his blog, there are no ring species. Atleast no ring species that meet the textbook definition. He describes how genetic evidence has shown that even the most well regarded ring species have been shown to have some levels of allopatry. 

Being a long time follower of his blog, why evolution is true as well as his numerous papers and books that have established the field of Speciation, i was over joyed to write a digest for journal Evolution around this topic. The other great name in Speciation, Trevor Price has worked on Ring Species making this one of those cool things that has captivated the imagination of very smart people. Barriers to gene flow and ring species formation is a recent article that uses agent based model simulations to show how ring species formation requires narrow corridors. These narrow corridors are highly susceptible to disruption due to local changes. Such disruption can result in allopatry. 

"Tiny" amounts of allopatry can lead to a ring species not meeting the textbook definition. So obviously, god hates ring species :) and that is why he "designed" such a characteristic feature. On a more serious note, this paper does highlight the importance of using simulations in the field of Evolution. Hopefully, we will see increasing use of such approaches in the future.


Thursday, November 17, 2016

Stable polypoidy in yeast identified through experimental evolution

The paper we discussed today in the journal club is a topic that has always been very fascinating. Polyploidy, especially speciation driven by polyploidy is thought to be very common among plants. Janaki Ammal, "attributes the higher rate of plant speciation in the northeast Himalayas compared to the northwest to polyploidy" in her paper : The effect of the Himalayan uplift on the genetic composition of the flora of Asia. Infact, a lot of work done by her revolves around polyploidy. Some of this work is fascinating and seems relevant even today. One could continue her research program today and still be very current.

Coming back to the paper, it is yeast not plants. It makes it easier to study due to the ease of manipulation. Title of the paper is "Experimental Evolution Reveals Interplay between Sch9 and Polyploid Stability in Yeast". After constructing the strains, experimental evolution was conducted for 1000 generations to evolve the required strains. All that is needed for figure 1 and 7 is flow cytometry. Figure 3 and 5 are both relative fitness assay's and seem doable but need a lot of work. However, figure 2 and 4 need a array platform and might be out of reach.

The fact that they are able to pin down the the Sch9 gene and the TORC pathway takes the paper to the next level. Although it is not clear what the mechanism is or how general and widespread this pathway can be in stabilizing polyploidy. It would of course be interesting to see if the natural polyplod isolates from the evolution canyon show changes in this very pathway.




Wednesday, November 9, 2016

Heterogeneous genome differentiation : crow hybrid zones

Our paper about the analysis (mostly characterization, with some new ideas) of the genome wide differentiation landscape in more than 100 crow genomes is now available to read. With a title that reads "Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex" we hopefully portray the appropriate message. The message would be that it is rather easy for a well managed and well funded lab to choose a study system and build it up to a level of a model system rather quickly. The uniqueness of the study is the presence of replicate hybrid zones, being able to contrast the phenotypes at different evolutionary distances and try and disentangle how selection acts across the genome.

We say "..parallelism by pathway rather than by repeated single-gene effects." I like this part in that it suggests multiple genes that can lead to the same phenotype. However, pinning down the actual genes and the causative variants is easier said than done. Systems that are easier to manipulate with much more historical context are still not resolved to this resolution. This is not to say that this work is not needed. It definitely is needed before we go to the next step. Numerous bird species have come to a stage where these resources have been developed. Integrating these data into a theoretical framework that spans multiple study systems will probably still take time.

The main result of the paper is basically figure 2, which tries to subtract out the background signals and find signatures that are unique to each hybrid zone. Similar attempts are underway in various other species with slightly more rigorous models. Some incorporate recombination rate maps, others use sequence conservation across species. A resolution of how common selective sweeps (hard, soft, partial etc.) are in natural populations as well as the methodology to detect them will probably still have to play out as functional validation methods are developed.


Saturday, September 24, 2016

Janaki Ammal's last day in the USA

A letter dated May 8th, 1931 from Cambridge (in USA) to Cobb Blanchard is a short letter. Janaki Ammal (JA for short), is happy to be spending her time in this "interesting part" of the country. She also refers to the fact that she has not had time to think about Ann Arbor after leaving and regrets at having "left many a thing unfinished and undone."

Just 3 days before this, May 5th, 1931 is a type written, unsigned letter sent to JA. The letter talks about Grace (Cobb's daughter) looking at JA's portrait and recognizing her. It has some more questions about what to do about some refunded money and type writer that was left behind. Cobb thanks JA for a homespun cover that she left for Cobb, remarking that it is "lovely". We further come to know that JA took a bus from Ann Arbor to Washington (for sight seeing) and then onto Cambridge and Boston.  It seems the May 8th letter is a response to the letter sent on May 5th.

On June 8th, 1931, Cobb writes a reply to the May 8th letter. In this they talk about Eileen's accident and hope for her recovery. Cobb talks about various things regarding her family. Its probably worth noting that she refers to her husband Frank being tired due to the extra duties of looking after the children. She also thanks JA for a postcard of sea gulls sent from New York. This letter talks about the third child (a boy) and his arrival into the family.

On June 28th, 1931 JA write a reply to this letter from John Innes Horticultural Institution. As a true cytologist she writes "I am so happy that atleast one of the three has the Y chromosome of the family".  Dorothy and Grace are the older girls referred to in the previous letters. JA is also very happy with atmosphere for working at John Innes. More than anything else, she is impressed by C.D Darlington and writes "is a really brilliant man with a delightful sense of humor and an infinite capacity for talk and discussion." At tea time and lunch, JA has heard about the two books being written by Darlington, one is a text book of cytology and another about travels in Persia.

In the same letter JA talks about having looked at root tips from her egg plants and seeing 46 to 48 chromosomes. She is excited to think that they are tetraploids. Her egg plants here of special importance as they are named "Janaki Brengal" and referred to as her first love in the Michigan Alumnus Volume 42, page 532, who's who. The article in the Michigan Almunus also notes that she lived in the Martha cook building.

Thursday, September 22, 2016

Janaki Ammal Correspondence with Cobb Blanchard - Part 1

Have managed to photograph all the correspondence involving Janaki Ammal from the Bentley archives. So i have around 150 pages worth of material to read through and discuss. So, this is going to be spread over numerous blog posts with my own comments and observations. Finally, i hope to put all this information together to paint a picture of Janaki Ammal as seen through these letters.

The first letter i am going to talk about is dated December 24th, 1931 from the Department of Botany, the Presidency college Madras. It is addressed to Frieda Cobb Blanchard, who along with Harley Harris Bartlett worked on evening primrose research. Cobb, earned her doctorate in 1920 while studying Mendelian inheritance in certain strains of Oenothera. This letter is written by Janaki Ammal, after she has returned to India and has taken up a position as a Research Fellow at the Presidency college.

The letter begins by thanking Cobb Blanchard for the data about her Egg plant cultures sent along with the letter. Then she inquires about the little girls (Cobb's daughters). As a Indian, i can appreciate the similarity of life back in 1930's to what we have now when she writes "I led a very gypsy life in Malabar visiting all the members of the E.K clan and being introduced to all the new arrivals". Its hard for me to decipher if this sentence reflects some amusement on her part at having to visit so many members of her Clan.

She writes "I have just fitted up a small cytological lab." Her teachers in Botany, Prof. Tyson and Dr Ekambaram are keen that they perform cytological studies. She is also supposed to guide 3 boys working for their Msc and give a few lectures in Cytology.

Apart from this position, she is also in contact with a Sugar cane expert at the agricultural station in Coimbatore who wants her help in studying the cytology of Indian sugar canes. In November she visited this cane station and fixed (for cytological examination) some material. She also talks about how life in Madras is very interesting and that they are having the "All India Women's Educational Conference". Most of the delegates are being house at the Queen Marry college where she is at that time. Its probably worth noting that the All India Women's Conference was formally registered in 1930. However, i did not find mention of this event in Madras in their history.