Blog of Parag

Mission Victory: almost complete

Kumble takes India to brink of historic win

Indian team is so close to winning the first test match with Pakistan. It may end on the first ball of the last day. Impressive performance by Kumble and what about that triple century by Sehwag.... Excellent.

Strange coincindence

V and I sneaked out to get lunch at a chinese restaurant near work. At the end, the freakiest thing happened... Both of us got the same fortune in our fortune cookies.

                   You will be travelling and coming into a fortune

Is this a sign of things to come???? Is this a sign that we are perfect together????

How many times does this happen? I have never seen cookies with the same fortune even in a big group of 8-10 people.

Parent's night out!

Saturday night was our first night out without Ashwini. It was also our first experience with babysitting. But, it was at her daycare with her usual teachers, so, not a big change for her and she was comfortable being there. That is what we liked about it.

The last time, V and I went out to a restaurant for dinner was sometime in Feb2003, i.e. before Ashwini's birth. We dropped Ashwini off at around 6pm and our dinner reservation was for 730. So, spent an hour at Borders to do something we like to do: browse books. Predictably, walked out of there with a couple of kid's books for Ashwini.

Dinner at the 'Real Seafood Company' was excellent. Here is what we had:
Me: New England Clam Chowder followed by Sashimi-grade yellowfin tuna, grilled medium-rare with a sauce made from wasabi and soy sauce. It was heavenly. V didn't appreciate the pink-red stuff inside the hunk of tuna, but, that was the best part in my opinion.
V: Crab cake appetizer followed by grilled Mahi Mahi with Mango Salsa. Her crab cake was tastier than the Mahi Mahi.

We had a bottle of Brancott Estates 2002 'Reserve' Sauvignon Blanc from Marlborough region of New Zealand and we liked it a lot. Should buy a case of it, if I find it at a local store. It was not very dry and was full of fruity flavours with high acidity and a lingering finish. I would recommend it to anyone, who is looking for a change from regular Chardonnays.

We wanted to get desserts at another place that has great desserts but, it was full and we didn't have enough time to wait. So, ended up eating a cheesecake at a small little chocolate shop that was not that great.

Picked up sleeping Ashwini at around 945pm. That was the end of our first dinner date after more than a year. Hopefully, we'll go out and do this more often now as we know that Ashwini is OK with babysitting in the evenings.

A big change in the morning routine

Bob Edwards dumped as host of NPR's 'Morning Edition'

This will be a big change in the mornings of many people. Although this may sound weird and my wife wouldn't agree, I'll definitely miss waking up to the rich baritone voice of Bob Edwards.

"Morning Edition," which is broadcast live from 5 to 7 a.m. and is rebroadcast throughout the morning, is the most listened-to morning radio program in the country, with 13 million listeners weekly

Thok de saale ko???

Watched 'ab tak chhappan' last night. It is just awesome. Nana Patekar plays an officer in the special operations division of Mumbai police that 'deals' with gangsters. Nana is great as a cool and calculating cop. He seems so unpredictable throughout the movie. It is hard to figure out what he'll do next. Nana's interaction with a new officer on his first day reminded me of 'The Training Day', another great must-watch movie. Denzel Washington in that movie is also a special operations cop who is as unpredictable as Nana.

'Ab tak chhappan' is a very well scripted movie; no loose ends. Again, no idiotic songs. I think I am going to watch all Ram Gopal Varma movies at least for that one reason. The story moves at a fast pace and it is over before one knows it. A nice completely unpredictable ending. There is some violence but it is not gory. No long drawn-out fight scenes or torture of prisoners. It is shown in a casual way, like 'Pulp Fiction'.

I highly recommend it to everyone. A must-watch for Nana fans like me. Finally a director who has used his talents properly. He is so much different than his crappy streak of 'Krantiveer'-like movies.

P.S. This must be some kind of record. First of all, watching 2 hindi movies in 2 weeks. That doesn't happen often... And liking them both. This is the first time ever.

New outsourcing opportunities

YEEESSS!!! Finally....

Finally, it is time to celebrate for the Indian Cricket team. It is such a sweet sweet victory. Congratulations!!!!!

Laxman and Pathan lead India to series win

My Recent Publication

Some of my work from a long time ago got published in Biochemistry recently. My name on a paper after 3 years. Drastic reduction in ability to publish results in scientific journals is the biggest disadvantage of leaving academia for industry. Here is the abstract of the paper if anyone wants to know more....

Biophysical characterization of the complex between double-stranded RNA and the N-terminal domain of the NS1 protein from influenza A virus: evidence for a novel RNA-binding mode.

Chien CY, Xu Y, Xiao R, Aramini JM, Sahasrabudhe PV, Krug RM, Montelione GT.

Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854-5638, USA.

The influenza virus nonstructural protein 1 encoded by influenza A virus (NS1A protein) is a multifunctional protein involved in both protein-protein and protein-RNA interactions. NS1A binds nonspecifically to double-stranded RNA (dsRNA) and to specific protein targets, and regulates several post-transcriptional processes. The N-terminal structural domain corresponding to the first 73 amino acids of the NS1 protein from influenza A/Udorn/72 virus [NS1A(1-73)] possesses all of the dsRNA binding activities of the full-length protein. Both NMR and X-ray crystallography of this domain have demonstrated that it is a symmetric homodimer which forms a six-helix chain fold, a unique structure that differs from that of the predominant class of dsRNA-binding domains, termed dsRBDs, that are found in a large number of eukaryotic and prokaryotic proteins. Here we describe biophysical experiments on complexes containing NS1A(1-73) and a short 16 bp synthetic dsRNA duplex. From sedimentation equilibrium measurements, we determined that the dimeric NS1A(1-73) binds to the dsRNA duplex with a 1:1 stoichiometry, yielding a complex with an apparent dissociation constant (K(d)) of approximately 1 microM. Circular dichroism and nuclear magnetic resonance (NMR) data demonstrate that the conformations of both NS1A(1-73) and dsRNA in the complex are similar to their free forms, indicating little or no structural change in the protein or RNA upon complex formation. NMR chemical shift perturbation experiments show that the dsRNA-binding epitope of NS1A(1-73) is associated with helices 2 and 2'. Analytical gel filtration and gel shift studies of the interaction between NS1A(1-73) and different double-stranded nucleic acids indicate that NS1A(1-73) recognizes canonical A-form dsRNA, but does not bind to dsDNA or dsRNA-DNA hybrids, which feature B-type or A/B-type intermediate conformations, respectively. On the basis of these results, we propose a three-dimensional model of the complex in which NS1A(1-73) sits astride the minor groove of A-form RNA with a few amino acids in the helix 2-helix 2' face forming an electrostatically stabilized interaction with the phosphodiester backbone. This mode of dsRNA binding differs from that observed for any other dsRNA-binding protein.

Ek Hasina Thi

Watched it over the weekend. It was a good thriller. I like Ram Gopal Varma movies. First attractive feature is that they get done in 2 hours. Mostly because, there are no useless songs. I am sure he saves a lot of money by not going to exotic locations to film something that has nothing to do with the story of the movie.

This one has a gripping story and is presented in a technically competant manner. Urmila does another role of a maniac and does a good job. "Phoolan Devi" Seema Biswas as a woman police inspector is excellent. Saif Ali Khan did well too. Did he really have to be unshaven throughout the movie? But, he is so much better than Amir I-am-so-good-kiss-my-feet Khan, Salman I-can't-act-but-look-at-my-body khan or Shah Rukh I-may-not-have-Parkinson's-but-I-like-to-shake-all-the-time Khan. Part of the movie is in a women's prison. I am not sure how real all that stuff was. Many women in there are shown mentally deranged and quite menacing. That would be quite realistic if same statistics are true in India as compared to US, where about 10% of prison population has some mental problems. The action scenes are quite believable and not the usual 20 villain lackeys attacking one hero but, get beat. The background score is quite good and not too loud.

Overall, I would recommend anyone to watch this movie.

Old friends

This is an overdue post. Wanted to write this since a long time.

Last year was very good in terms of meeting old friends. Three of my school buddies came to visit me. I started going to 'Shishoo mandir' (preschool) with 2 of them, oh, almost 29 years ago. This last meeting was after 4 years. In 2002, I got to meet two of my good buddies from College. This was after a gap of about 6 years.

It is so nice to meet old friends. Time just flies by talking about the good old days. There are still some friends out there whom I used to be with everyday, but haven't seen them in 12-13 years. Wonder who on that list is next to meet?

More choices at Starbucks

Do you know that there are about 19000 different ways of ordering a cup of coffee at Starbucks? Recently, they announced one more option: Extra Hot: the beverage will be hotter by about 30F compared to usual. This will increase the total number at least by 1.5 times considering some of the combinations are for iced coffees.

Vaccines and Autism

From Mar 15, 2004 issue of Time magazine:

British researchers caused a furor in 1998 when they published a controversial report suggesting a link between the growing number of autism cases and the standard childhood vaccine for measles, mumps and rubella (MMR). Although other physicians criticized the authors for jumping to conclusions, many worried parents stopped immunizing their children. Now 10 of the 13 original authors have decided to retract the paper, acknowledging that their data were not strong enough to support their incendiary conclusion.

This report had caused such an outrage, making people rethink the risk/benefits of vaccination. Hopefully, the retraction of this study will make as big a news as the original publication. When will these doctors realise that if one needs rigorous statistical analysis to prove something, it may be wrong.

I like this quote I heard somewhere...

There are three types of lies: lies, damned lies, and statistics.

Update: I do not mean to bash statisticians here. Statistics is a very powerful tool. The problem is that sometimes people bear it without realising its power. That leads to wrong conclusions and controversies like this one.

The Great Orion Nebula.

Compare this with this. Well, actually don't. It is hard to imagine that these photos depict the same object.

Antibiotics

Heard a really nice seminar by an eminent scientist, Dr. Alexander Mankin about how antibiotics have evolved and how they work. Want to jot down a few things that I learnt from it before I forget.

For those who don't think about this everyday, here is some background. The basic paradigm of biology is:

DNA ==Transcription==> RNA ==Translation==> Protein

All the genetic information is stored in DNA, it is transcribed into RNA, and then translated to proteins that actually do the biochemical reactions necessary for life-functions. One copy of RNA can be used multiple times to make many copies of protein.

Some of the RNA is also catalytic, but mostly it works as a molecule that carries information for translation into protein. The most important catalytic RNA is in the protein synthesizing machineary, Ribosome.

Why target ribosome for antibiotic action?
Synthesis of proteins is an essential task for any living being, so, targeting it, is an obvious choice for killing an organism. But, the major problem is selectivity. All ribosomes are evolved from a common ancestor and hence it is very similar across different species. The ideal chemical should target protein synthesis of the unwanted organism but, should not affect the host (fungi or human) protein synthesis. This makes it difficult to keep making newer and newer antibiotics. Although, the current antibiotics take advantage of minute differences between the structures of human and bacterial ribosomes to be effective, they suffer from side effects due to the similarities.

Why do antibiotics work as well as they do?
There has been a lot of effort in mapping the sites on ribosome where the antibiotics interact. Most of the antibiotics interact with the RNA part of ribosome. The reason behind this is very clever.

About 2/3rd of ribosome consists of RNA. There are about 10,000 ribosomes in a given bacterial cell. To make that many ribosomes, there are multiple copies of genes coding for ribosomal RNA, but, a single copy of genes coding for the protein. Because, the cell has to go through multiple steps of transcription to make enough RNA, but, a single step transcription can be followed by multiple step translation can make enough protein to assemble all these 10,000 ribosomes.

This makes it possible for a mutation in the single copy of the protein gene to disrupt its interaction with the antibiotic and make the bacteria resistant to the antibiotic. But, a mutation in one of the copies of ribosomal RNA, can make only a small fraction of functional ribosomes immune from antibiotic action and that is not enough for the bacteria to survive. Thus, molecules that interact with RNA part of ribosome to stop protein synthesis are more effective in killing bacteria.

Can you guess when the ice melts?

West Danville, VT is gearing up for its 80 year annual tradition of betting on the exact date and time (hour and minute) when a local pond called "Joe's Pond" will thaw. They have an electric clock rigged up with a mechanical device that sinks when the ice melts to record the exact time of the thaw. Usually, the pond thaws between April 15th and May 15th. Last year, it was April 28th, 9:54 am.

Anyone can bet $1. The winner of the bet gets half the total money collected and the rest is used for 4th of July fireworks in town. Last year, they collected about $5000.

Check it out if you wish to bet.

Ikea and Diwali

I don't think Ikea has an operation in India yet, but, they have started targeting the population of Indian origin in USA. My favorite home furnishing store scores a few more brownie points. Check out the special section in their catalog during Diwali time.

Hubble Ultra Deep Field

The Hubble Space Telescope has just finished taking the Hubble Ultra Deep Field (HUDF), the deepest image of the universe ever taken in visible light. Pictured above, the HUDF shows a sampling of the oldest galaxies ever seen, galaxies that formed just after the dark ages, 13 billion years ago, when the universe was only 5 percent of its present age. The Hubble Space Telescope's NICMOS and new ACS cameras took the image. Staring nearly 3 months at the same spot, the HUDF is four times more sensitive, in some colors, than the original Hubble Deep Field (HDF). Astronomers the world over will likely study the HUDF for years to come to better understand how stars and galaxies formed in the early universe.

copied shamelessly from: Astronomy Picture of the Day

The double Helix

The double Helix: A Personal Account of the Discovery of the Structure of DNA
by James D. Watson

• Interesting book about how the structure of DNA was discovered. Describes the whole process very well without getting too deep in the science. The narrative does justice to a dramatic sequence of events.
• Maybe Watson is being modest, but, it seems like he didn't do much in discovering the structure. He was just there discussing things with Crick and others.
• Linus Pauling was subjected to harrasment by Sen. McCarthy. He was denied a passport to travel internationally to attend a meeting.

The Complete Far Side

I was just amazed by its sheer size. Didn't realise it would be this big and bulky when I ordered it. It is a set of two very high-quality hardbound volumes and probably weighs 20 pounds. It could be easily used as a weapon.

Gary Larson's wry humor is admired worldwide and his drawings have this surreal quality which makes them so enjoyable. In 1994, he decided never to make any more of those and has kept his word. I liked the first line of his introduction to the book.... "It has been seven years since I hung up the eraser."

I have been reading a month at a time when I get a chance. It is very enjoyable. I would highly recommend this to anyone who likes 'The Far Side".

Saturn on Feb. 27th, 2004

Half Moon

The Great Nebula in Orion (M42)

Nursery for new stars...

  

Check out these images of M42 taken by others. Please don't make any comparisons with my photo as it doesn't belong in the same category.

Pleiades (M45) again

Better photograph of Pleiades (M45), compared to my earlier attempt. Used the telescope driving mechanism this time to avoid the streaks caused by Earth's rotation.

The stars in this cluster are very young, only a few million years old. Long exposure photographs show nebulocity around them; the clouds that they were born from.