Friday, June 24, 2011



Almost 2.5 year in Japan has made my tongue get accustom with Japanese food (well, mostly). Like and dislike are common since I'm originally from a country where spices are abundant and Japanese food is very, how to say, plain?. Yes, I mean preserving its original taste (read: eat it raw and use minimum seasoning). 

However, if we talk about maccha or green tea, you will find my eyes full of enthusiasm :D I love green tea, in every form. I am happy to find green tea cream cake, green tea ice cream, green tea chocolate, including make my own green tea pudding. Seems my list (and my happiness) will still continue. Yesterday I found green tea purin. Very delicious and addicting. 

Today I bought another cup. Yummy.. 


As I register to Digital Photography School weekly newsletter, today I received this week's edition. Through one click to another click, I was surfing some professional photographer's site, admiring their works, and being even more curious of how they can produce such beautiful photos. And that happened to be poisonous. 

In my old blog in Multiply (, I highlighted my passion of being a women scientist in my current field. However, now it weakened. Shoo, I should have known myself who is easily bored. Being a scientist means firm goal, tons of hard work, eternal patient, wrapped with never-wilted enthusiasm. I'm not sure I have stock of energy to keep myself on track until I can reach the goal. Somehow I don't find the idea interesting any more. My visual brain always associated something with colour or light; I see grey or dim light. 

Maybe it's just a temporary feeling. Or on the other hand, a chance to choose other way? I have large interest in photography and it keeps growing. Not once thoughts of switching my path come across my mind. I remember a story of Bara Patirajawane who decided to become chef instead of building his career in diplomatic world like his father, because of his love and passion on cooking. The guts. That is the most important thing I don't have enough right now. 

Shourai ni dou naru ka na~ I still have to do my experiment and write my thesis for next month. Perhaps I would better finish those first.       

Friday, June 17, 2011

an old man and Clark statue

Last Tuesday morning was gloomy enough to start the day. Not just it was raining (and didn't stop even until night came), I woke up extremely late, around 10.45 am. In my lab, we have 'core time' from 10 am to 5 pm, when everyone should be 'around'. Guilt struck me although I don't know to whom should I address that feeling to. 

Then finally after taking a shower (not want to skip in these sweating days) and got dress, I rode my bike to school (with normal speed, surprisingly). On the way, inside the campus, while I was still on my bike, suddenly I heard someone said, "....doko desuka? (Where.... ?)". No one else was there on the side walk and no one else was riding beside me, that must be for me, so I pulled my break (suppose to say 'pull' for bike, right?). An old man approached, I pulled my jacket's hood a bit, and he asked, "Where is the Clark statue?". After I explain the direction, he looked across the road, likely to call for his wife who was looking at the campus map. And I left, with a smile, naturally. 

Helping an old couple, in the middle of light rain, 'lost' inside the campus to find a famous person's statue (and perhaps take a picture with it) scene was enough to lift my mood. Simple as it is. Sometimes (even most of the times) simple happiness is enough to warm your heart.  


William S. Clark was the one who found Sapporo Agricultural College in 1876, now Hokkaido University. He is famous for his words 'Boys, be ambitious', also his pointing posture. Hokkaido University has half body statue of him and it becomes quite famous photo spot for visitor. 

Thursday, June 16, 2011

from the core

Published online 15 June 2011 | Nature | doi:10.1038/news.2011.368


Genome study solves twins' mystery condition

Sequencing ends years of speculation over children's rare disorder.

twinsGenome sequencing suggested a new approach to treatment for twins Noah and Alexis Beery, shown here with their parents.Life Technologies
Two years ago, 13-year-old Alexis Beery developed a cough and a breathing problem so severe that her parents placed a baby monitor in her room just to make sure she would survive the night. Alexis would often cough so hard and so long that she would throw up, and had to take daily injections of adrenaline just to keep breathing. Yet doctors weren't sure what was wrong.
In a paper published today in Science Translational Medicine1, researchers led by Richard Gibbs, head of the Baylor College of Medicine Human Genome Sequencing Center in Houston, Texas, describe how they sequenced the genomes of Alexis and her twin brother, Noah, to diagnose the cause of her cough — a discovery that led to a treatment. Today, Alexis is playing soccer and running, and her breathing problem has gone, says Alexis's mother, Retta.
"We honestly didn't know if Alexis was going to make it through this," Retta Beery says. "Sequencing has brought her life back."
At age 5, the Beery twins had already been diagnosed with a genetic disorder called dopa-responsive dystonia, which causes abnormal movements, and had been taking a medication that was apparently successfully treating the condition. When Alexis developed a worsening cough and breathing problem, the twins' neurologists did not think it was related to her dystonia.
The twins' mother Retta Beery, whose husband Joe is the chief information officer at Life Technologies, a biotechnology systems and services company headquartered in Carlsbad, California, pushed for the childrens' genomes to be sequenced to find a definitive answer. The company helped fund the study at Baylor, which used Life's SOLiD sequencing technology to find that the twins carry mutations in a gene called SPR that encodes the enzyme sepiapterin reductase, which was previously linked to some cases of dopa-responsive dystonia.
Sepiapterin reductase enables the synthesis of the neurotransmitters dopamine and serotonin. The twins were already taking a dopamine precursor for their dystonia. So the study suggested that they might benefit from taking a chemical precursor of serotonin, 5-hydroxytryptophan, as well. A month after starting the treatment, Alexis's breathing problem had disappeared. Noah's handwriting has improved and he is also able to concentrate more in school, Retta Beery says.

Chalking up a win

The discovery is a win for genome sequencing in the clinic, which has already been used to guide cancer treatment2 and to diagnose and treat a handful of rare diseases whose origins are difficult to discern, and so hard to treat3.
"This study represents a good example of how genetic diagnosis of a rare genetic condition directly impacts treatment," says Joris Veltman of Radboud University Nijmegen Medical Center in the Netherlands.
Indeed, work like this is giving scientists hope that they will soon be able to 'solve' the genetic origins of almost all rare diseases and conditions. This is important because the rarer conditions by definition afflict fewer people than major killers such as heart disease, and so attract little funding for studies. Nor is it possible to organize large clinical trials into conditions that affect so few people.
There are also relatively few medical doctors who are expert in diagnosing rare diseases, so these conditions are often undiagnosed or misdiagnosed, and available treatments go unused. This is something Retta Beery knows all too well. Her children were incorrectly diagnosed with cerebral palsy at the age of two, and did not receive their correct diagnosis — and first effective treatment — until the age of six, after being subjected to hundreds of tests. And Alexis endured six years of inconclusive tests before sequencing pinpointed the cause of her breathing problem, Retta Beery says.
The work published today suggests that sequencing could shorten diagnostic odysseys like these, because it tests for all possible genomic mutations at once, thereby guiding the way towards treatments aimed at particular biochemical pathways, and does not need to be ordered by specialists in rare diseases. Gibbs predicts that 90% of disorders caused by single gene defects will be solved in the next three to four years.

The big question is when whole-genome sequencing will be inexpensive enough for routine clinical use. Gibbs estimates that the study released today cost about US$100,000, including $30,000 to sequence each twin's genome, and took two months. But some companies are offering sequences for as little as $5,000 to $7,500. Researchers think that when sequencing drops to $1,000 per patient, it will become more widespread."The availability of unbiased whole genome or exome sequencing will make an enormous impact on our opportunity to diagnose and treat patients with rare disease," agrees Veltman, whose centre is now offering exome sequencing — sequencing just the coding regions of genes, rather than the whole genome — to patients with disorders including intellectual disability, blindness, deafness, movement disorders and hereditary forms of cancer.
Beery says that for other families who need it, that day cannot come soon enough.
"It's ridiculous to think of the amount of time and money that we and our insurance company have spent, and the amount of suffering our kids went through, when they could have had their blood drawn once and got the answer," Beery says.


  1. Bainbridge, M. N. et al. Sci. Transl. Med. 3, 87re3 (2011).
  2. Jones, S. J. et al. Genome Biol. 11, R82 doi:10.1186/gb-2010-11-8-r82 (2010).
  3. Worthey, E. A. et al. Genet. Med. 13, 255-262 (2011).

Solved from the core. Only hope that the excellency of this kind of method can reach common people. Hmm.. definitely not in the next 10 years.