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	<title>Study abroad in Japan</title>
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	<link>http://blogs.monm.edu/jgodde</link>
	<description>In celebration of havng my first advisee spend a semester in Japan-  I am rehashing my own experience from 6 years ago...</description>
	<lastBuildDate>Wed, 19 Jun 2013 01:51:17 +0000</lastBuildDate>
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		<title>From the Valley to the Mountain</title>
		<link>http://blogs.monm.edu/jgodde/2013/06/19/from-the-valley-to-the-mountain/</link>
		<comments>http://blogs.monm.edu/jgodde/2013/06/19/from-the-valley-to-the-mountain/#comments</comments>
		<pubDate>Wed, 19 Jun 2013 01:51:17 +0000</pubDate>
		<dc:creator>James Godde</dc:creator>
				<category><![CDATA[Study abroad in Japan]]></category>

		<guid isPermaLink="false">http://blogs.monm.edu/jgodde/?p=366</guid>
		<description><![CDATA[I left the house a little after 8 and went to Umeda to pick up my camera. Once again, I arrived an hour before the shop opened, so I wandered around and tried to learn how to navigate the area &#8230; <a href="http://blogs.monm.edu/jgodde/2013/06/19/from-the-valley-to-the-mountain/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
				<content:encoded><![CDATA[<p>I left the house a little after 8 and went to Umeda to pick up my camera.  Once again, I arrived an hour before the shop opened, so I wandered around and tried to learn how to navigate the area better.  I walked to the end of the underground sidewalk and then tried to find my way to the camera shop above ground.  I was able to find it without much problem, so I sat on some steps and read for a while until it opened.  When the time came, my camera was ready to pick up.  I think the man told me that they had to replace the lens.  All I knew was that it worked again and that they charged me the price they had quoted the previous week.  I took the train to church and still arrived a little early.  Kira, the American student, gave the communion message and one of the Japanese brothers gave the main message.  After the main service, the kids came down from their classes and sang a few songs for the fathers, since it was Father’s Day.  Each child had made a craft with a picture of themselves, along with their father, in it.  One of the sisters who had taught the kid&#8217;s class had made one with just my picture in it.  I thanked her, and joked that I could add my kids&#8217; pictures to it when they come.  I left soon after the service was completed because I had an agenda planned for the afternoon.</p>
<p>I had decided to go into the mountains again, but this time further away, to Nose (No-seh, not like on your face), at the end of the train line into the mountains.  I had seen on a map where they ran a cable car to the top of Myokenzan Mountain and had confirmed this fact on the internet, although none of the Japanese people I had mentioned it to had actually been there.  I took the train for two stations past my usual stop and switched to the Nose line.  I began to realize how far off the beaten path I was getting when the trains at this station started displaying their destination exclusively in kanji, as did the fare chart for the tickets.  No problem, I knew enough kanji at this point to get by.  I had switched trains at Kawanishi Station (“western river”, a picture of a river followed by the symbol for &#8220;west&#8221;) and had to switch again at Yamashita (“bottom of the mountain”, a picture of a mountain and the symbol for &#8220;bottom&#8221;) to get to Myokenzan Station (“marvelous view”, a little more complicated).  </p>
<p>By the time I made it to Nose, I was very hungry.  I had left church around 1:30, it was now 3.  I decided to eat at a restaurant near the train station, as there was no guarantee I would find another closer to the mountain.  The restaurant was pleasant and had a small town diner-like atmosphere.  The menu, of course, was entirely in Japanese.  The menu was divided into udon dishes and those that were served over rice (don), I had learned that kanji from my lunches at the university.  What I didn&#8217;t know the kanji for, however, were most of the things being put on the noodles or the rice.  The only dish I was completely sure about was curry udon, which sounded just fine.  I ate my udon and walked to the bus stop just in time to catch the next bus from the station.  The internet said I had to take the “Cable-mae” Bus.  This was not difficult, since it seemed to be the only bus leaving from the station.  The bus drove for 15 minutes or so and dropped me off in front of the cable cars.  It had passed many rice fields, and fewer and fewer houses on the way as the bus had headed further into the country.</p>
<p>I bought a cable car ticket for 270 yen and waited until the next one left, at 4 pm.  This slowly climbed its tracks, and eventually deposited me at on the side of the mountain, where there was a path heading further up the slope.  After walking for a while, I came to a chair lift.  I had noted that 6 pm was the final cable car back down, but I wasn&#8217;t sure how far I still was from the summit.  For 250 more yen, I rode the chair lift further up the mountain.  At the top of the lift was a small shrine, as well as a path that continued to climb.  After another 20 minutes of walking, I came to a stone gateway that led to an array of statues, sculptures, temples, and shrines.  The entire top of Myokenzan Mountain seemed to be one big shrine!  I climbed the steps which led amidst the stone figures until I finally reached the summit.  On the summit stood a very modern looking temple made of steel and glass, which stood in stark contrast to the ancient statues which were scattered everywhere.  The mountain did live up to its name, however, it had a marvelous view of the valley below- I could see Osaka filling the valley in the distance.</p>
<p>I had noticed once I reached the top of the mountain that there was the option of walking back down it, by passing both the chair lift and the cable car.  Walking down the entire mountain made a lot more sense that walking up, but I wasn&#8217;t sure how long it would take or where the foot trail ended exactly, so I opted for going down the slope the same way I had gone up.  However, when I arrived at the bus stop at 5:20, I saw that there wasn&#8217;t another bus for an hour!  I decided that I would walk back to the station, and hoped I had paid sufficient attention on the way to the cable car to retrace the bus route back.  I ended up finding the station without any problems, and was on the train home by 6:20.  At home, I ate the bento that had been prepared for me on Friday, and then went to work on the final weekend chore that I had to accomplish- whacking the yard!  It is a good thing that I did, for later that evening it started to rain.  At least the weather had cooperated for my mountain top adventure!</p>
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		<title>Saturday Setback</title>
		<link>http://blogs.monm.edu/jgodde/2013/06/18/saturday-setback/</link>
		<comments>http://blogs.monm.edu/jgodde/2013/06/18/saturday-setback/#comments</comments>
		<pubDate>Mon, 17 Jun 2013 22:26:49 +0000</pubDate>
		<dc:creator>James Godde</dc:creator>
				<category><![CDATA[Study abroad in Japan]]></category>

		<guid isPermaLink="false">http://blogs.monm.edu/jgodde/?p=363</guid>
		<description><![CDATA[I arrived at work by 8, wanting to get the H4 purification done and knowing that it would probably take most of the day. I took the protein extracts and loaded them onto a new column, which I had almost &#8230; <a href="http://blogs.monm.edu/jgodde/2013/06/18/saturday-setback/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
				<content:encoded><![CDATA[<p>I arrived at work by 8, wanting to get the H4 purification done and knowing that it would probably take most of the day.  I took the protein extracts and loaded them onto a new column, which I had almost finished washing by the time Kiyoe came in at 1 pm.  I had just finished a bento consisting of a chicken patty covered in mushroom gravy, along with an assortment of vegetables, bean salad, as well as the ever-present rice.  Some seafood ramen and an iced coffee rounded out my meal.  </p>
<p>There was a conference going on at the university that day and Kiyoe wanted to attend the poster session to see if anything was of interest.  The talks that were being given were of less interest to me since they were in Japanese, but I turned off my column pump for a while and accompanied Kiyoe to see the posters.  Some were in Japanese, others were in English, and most were a mix of both.  After looking at various ones for about an hour, someone that knew me approached us.  He said that he worked at NIH at the same time Kiyoe and I were there.  I had no recollection of this person however- I must have repressed all of my memories of what went on during my postdoctoral studies at NIH, after my fairly adversarial relationship with Alan Wolffe.  First, Kiyoe&#8217;s wedding, and now this!  He showed me his poster and we talked for a while.  Soon, Kiyoe wanted to hurry back to the lab to get her computer so she could show her work to an important professor from Tokyo U. who was interested in her studies.  After that, the talks were about to begin again.  I told her that I better return to the lab in order to finish my purification.  </p>
<p>The samples were done eluting from the column by 5 pm.  I probably could have left them until the following Monday, as I had done before, but I wanted to get a preview of whether the experiment had worked this time.  I started reading the protein concentrations of the fractions using the Nanodrop spectrophotometer.  The concentrations looked awfully low!  To make matters worse, the machine kept quitting on me and had to be rebooted every 6 samples or so.  I read the fractions until sample 30 or so, plenty far enough to where I should had seen a protein peak.  It appeared that the purification had failed once again!  This type of setback was to be expected in research.  After all, if it were easy- someone would have already done it!  But, given the success of my three other samples, I had hoped to wrap up my purifications on this, the one-month anniversary of starting my project at Osaka U.  </p>
<p>I took the 6:40 monorail home, feeling a little down.  I decided to have dinner at a family restaurant called &#8220;Friendly&#8221; that I passed everyday on the bus.  I figured that, with a name like that, I couldn&#8217;t go wrong and it was bound to cheer me up.  They were friendly at the restaurant, although they didn&#8217;t speak any English, as could be expected.  I had the &#8220;Italian long hamburger&#8221;, a patty in marinara sauce that came with a salad and a cold scoop of mashed potatoes.  As I left Friendly, I decided to walk to Kohnan to pick up some supplies I needed.  I was actually doing all right with food supplies, but I was need of toothpaste, dental floss, and conditioner.  From Kohnan, I took the long way home past the Ishibashi station, since I had never gone that way before.  During my walk, I noted the location of some more restaurants that I thought the family would like.  As I cut through campus, I ran into Siddick, my Bangladeshi friend and his family going for a walk.  Soon, I would have my own family in Japan!  This thought, along with the good food and pleasant weather, served to cheer me up considerably.  Monday was the start of a new week, my last one alone in Japan, and would be another chance to reach my goal.</p>
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		<title>Payday &amp; Potluck</title>
		<link>http://blogs.monm.edu/jgodde/2013/06/17/payday-potluck/</link>
		<comments>http://blogs.monm.edu/jgodde/2013/06/17/payday-potluck/#comments</comments>
		<pubDate>Sun, 16 Jun 2013 21:25:18 +0000</pubDate>
		<dc:creator>James Godde</dc:creator>
				<category><![CDATA[Study abroad in Japan]]></category>

		<guid isPermaLink="false">http://blogs.monm.edu/jgodde/?p=361</guid>
		<description><![CDATA[I decided to attempt to use the time delay feature on my rice maker for the first time. I wanted to serve my curry chicken over rice, but knew I wouldn&#8217;t have time to wait for it to cook after &#8230; <a href="http://blogs.monm.edu/jgodde/2013/06/17/payday-potluck/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
				<content:encoded><![CDATA[<p>I decided to attempt to use the time delay feature on my rice maker for the first time.  I wanted to serve my curry chicken over rice, but knew I wouldn&#8217;t have time to wait for it to cook after getting home from work.  At the church potluck, I had assumed there would be a big pot of rice to go with the dishes, but that ended up not being the case.  My dish was ok without rice but would be much better with.  I pressed a button until my screen read 10; I hoped that this meant that the rice maker would come on 10 hours later, at 5:30.  Only time would tell!</p>
<p>The bus pulled away at 8:03 for the second time in a row, I was convinced that someone would be losing their job over this fiasco!  I wondered if the bus snafu would be featured that night on the news.  Once I was at work, I spun down the large cultures of the slow growing bacteria for another try at purifying histone H4.  The complexes that had hopefully been forming overnight were also due for a spin in the centrifuge, followed by an enzyme treatment.  I was still waiting to receive the materials needed to make a different kind of column, called a size-exclusion column, in order to purify these complexes away from the proteins that did not associate.  I spent the morning back in my noisy alcove, breaking open the latest batch of cells.  While these cells were taking yet another spin in the centrifuge, I had lunch.  Rather than getting another hot lunch that I had already tried before, I opted for a set of sushi rolls, along with inari sushi, little bags made out of deep fried tofu which were filled with rice.  I also had some udon noodles topped with beef as well as grapefruit juice to drink.  By 12:30, I was back on the 8th floor, sonicating my cells once again.</p>
<p>I had to cut this particular session short, though, since I was supposed to meet with a student at 1 pm.  One of the medical doctors in our group, a cardiologist, wanted me to meet with one of his students each week so that I could learn what they are doing and, (more importantly, I suspected) so they could practice presenting their research in English.  I talked with this particular student for about 40 minutes, and then returned to my alcove.  </p>
<p>When I had finished with the cells and had them safely stirring in the cold room, the secretary stopped by with my first paycheck stub.  Now that I had more than 1000 yen in the bank, it was time that I found out how to withdraw it.  I asked Kiyoe if she would show me how to use the cash station, since I wasn&#8217;t convinced that it would be in English.  After all, I hadn&#8217;t seen any English on the one I had used to pay the rent the first time.  We went to the main entrance of the hospital, where my bank had a cash station.  Sure enough, I did not see any English on the screen!  We went through the process of which buttons I should press, with me taking careful notes.  However, after I had pressed the last button, nothing happened!  The screen then went to a new view, this time it had a button to press for English.  I went through the whole process again, using the English buttons as I tried to withdraw 10,000 yen.  The final screen said some English words that I did understand- &#8220;Insufficient Funds&#8221;.</p>
<p>Kiyoe was a little suspicious.  I had opened the account at the bank because the university said it was too late to deposit the money at the Post Office, she wondered if they had indeed been able to deposit it there anyway but had failed to tell me.  My check stub made no mention of where the money had been deposited.  We walked down the hall to the Post Office and I used the machine there.  This machine was even easier than the bank&#8217;s- it had a button for English right from the start and then proceeded to speak to me in English during my transaction.  I tried withdrawing 10,000 yen again, knowing that I had only opened the account with 1,000 in it.  Sure enough, the machine dispensed the cash and gave me a receipt with my account balance, which was exactly 9,000 yen less than what my pay stub read.</p>
<p>The materials that I needed to make my size-exclusion column were waiting for me when I returned, but Kiyoe had to hunt for a while to find the glass tube I would use as well as a plastic piece I needed in order to pour the material into the tube.  As I read the instructions, it was going to be at least 3 hours of preparation time, not to mention the actual experiment, to get this column going.  Since it was after 4 pm already, I decided to wait and to pour the column later.  My sample could wait in the cold room until I was able to assemble the column.</p>
<p>I left on the 5:55 bus so I could get home and finish preparing my dish for the “Konnichi wa” potluck.  As I walked into the house, I thought that I smelled rice cooking.  My rice maker had come through for me after all!  I spread the rice out on a large platter and covered it with the chicken, which I had warmed in the microwave, then I set out for my class.  The platter proved to be quite heavy, I was hoping that my dish went over well- if only to ensure that it would be much lighter on the walk home.  </p>
<p>There was quite a spread assembled that evening!  About 15 of us gathered for the class: six foreigners and the rest Japanese.  In addition to myself, being the lone American once again, there was a British man, a man from China, a Taiwanese girl, and a lady, along with her young daughter, who were from Korea.  We all sat around a big table, with the food in the middle.  In addition to the Japanese food (gyoza, sushi, shrimp in a red sauce, minced chicken, eggplant salad, etc.) there was also Korean kimchi and gim bahp (the Korean version of sushi rolls), as well as my Indian dish, of course.  Once again it received rave reviews, especially from the women, who couldn&#8217;t believe that a man could actually cook.  Five of the women even took their picture with me, and I promised to write down the recipe and share it with them.  I now had the reputation in Japan of being a marvelous cook, and would have to live up to high expectations if we had future potlucks.  There was so much food; everyone got a small bento box of leftovers to take home.  The lady that was one of my teachers the first time I had come to class fixed a box for me.  Since it was completely empty, my platter was much lighter on the way back home.</p>
<p>When I got home, I decided to do some of the household chores early instead of waiting until Saturday or Sunday.  I did a load of laundry and washed all the dishes, finally going to bed sometime after 11.</p>
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		<title>More Writing Assignments</title>
		<link>http://blogs.monm.edu/jgodde/2013/06/16/more-writing-assignments/</link>
		<comments>http://blogs.monm.edu/jgodde/2013/06/16/more-writing-assignments/#comments</comments>
		<pubDate>Sat, 15 Jun 2013 22:40:05 +0000</pubDate>
		<dc:creator>James Godde</dc:creator>
				<category><![CDATA[Study abroad in Japan]]></category>

		<guid isPermaLink="false">http://blogs.monm.edu/jgodde/?p=359</guid>
		<description><![CDATA[My internal clock was back on schedule again- I woke up at 6:20, as usual. It was drizzling as I left the house, so I brought my umbrella. When I got in, I started my bacteria on another race. I &#8230; <a href="http://blogs.monm.edu/jgodde/2013/06/16/more-writing-assignments/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
				<content:encoded><![CDATA[<p>My internal clock was back on schedule again- I woke up at 6:20, as usual.  It was drizzling as I left the house, so I brought my umbrella.  When I got in, I started my bacteria on another race.  I needed 5 large flasks in order to attempt the purification again, not just one.  I spun down the cells that had lost the race the previous day and froze them for later use.  I then changed the buffer that my dialysis tubing was suspended in; I would change it twice more throughout the day to induce the slow process of complex formation.  Lunch was another dish I had gotten previously- hamburger over cabbage and rice.  I did try a different brand of wonton soup that had noodles and sesame seeds in it, though, as well as cold milky green tea to drink.</p>
<p>Kiyoe stopped by my desk in the afternoon; she said she had a big favor to ask of me.  She had been asked to write a review about histones for the Journal of Biochemistry.  She did not really have the time to write it, but felt that she couldn&#8217;t refuse, since the journal is published by a society that had given her a grant in the past.  She wondered if I could write the review instead.  I had just turned in my measly 500-word article on DNA fingerprinting two weeks prior to this, and had since agreed to write a 1400-word article on &#8220;Chromosomes and Cancer&#8221; for the Encyclopedia of Health and Medicine: Cancer.  Now I was faced with my biggest task ever: 4500 words on histones, their modifications, and how this affects chromosome structure.  I agreed, of course, not knowing when I would get another opportunity to write a review article in a prestigious journal.  These articles, along with my yet-to-be-started chapter on assessment for Monmouth College, mean that I had a lot of writing ahead of me.</p>
<p>When my bacterial race ended, there were two losers this time around, so I split them between the remaining 4 large cultures that I needed to grow.  When I left work, it was still raining and had been doing so for most of the day.  I had leftover lasagna for dinner, along with some rice.  </p>
<p>I then set about cooking a dish for the potluck they were having the next day at “Konnichi wa” class.  I had decided to make Indian Chicken again, since I had most of the ingredients on hand and since this would be for a different group of people who had not been exposed to this dish before.  Unfortunately, I hadn&#8217;t printed out the directions for the dish-I did not expect to be making it again so soon.  However, I had saved the email that Trudy had sent me which contained the needed recipe.  Unfortunately, as hard as I tried, I could not get onto the internet- probably because of the rain.  I finally decided that I could probably make it from memory since making it for church was still fresh in my mind and, besides, I had all of the ingredients lying around to remind me.  I didn&#8217;t end up putting the dish in the oven until about 9:45, it was finally ready by 10:30.  I let my chicken cool down until 11, and then tasted it.  I had remembered correctly- it was just fine!  I put it in the refrigerator and went to bed.</p>
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		<title>Off Schedule</title>
		<link>http://blogs.monm.edu/jgodde/2013/06/15/off-schedule/</link>
		<comments>http://blogs.monm.edu/jgodde/2013/06/15/off-schedule/#comments</comments>
		<pubDate>Fri, 14 Jun 2013 21:44:45 +0000</pubDate>
		<dc:creator>James Godde</dc:creator>
				<category><![CDATA[Study abroad in Japan]]></category>

		<guid isPermaLink="false">http://blogs.monm.edu/jgodde/?p=357</guid>
		<description><![CDATA[I sometimes think that I have an internal clock. Although I caught the bus at 8 am every day, I had never woken up to an alarm in Japan. I had set the alarm for the first few days I &#8230; <a href="http://blogs.monm.edu/jgodde/2013/06/15/off-schedule/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
				<content:encoded><![CDATA[<p>I sometimes think that I have an internal clock.  Although I caught the bus at 8 am every day, I had never woken up to an alarm in Japan.  I had set the alarm for the first few days I was there, since I was still unsure whether my internal clock had reset for the 14-hour time difference.  I stopped using it, however, since I had never slept long enough for it to go off.  Everyday I woke up at 6:20, lay in bed for 10 minutes or so, and then I got up and got ready to face another day.  This particular day I woke up as usual, glanced at the clock in the dark, and then got up and got ready.  I was just about to leave for the bus when I glanced at my watch- it was only 6:40!  I had awakened at 5:20 instead of 6:20 and not realized what time it was in the dark.  I only had two clocks in the house: the alarm by my bed, as well as my wristwatch.  Somehow, my internal clock was an hour off that day.</p>
<p>My clock was not the only thing that was off.  On this particular day, the unthinkable happened- the bus was three minutes late pulling out from campus.  In the month that I had lived in Japan, it had never left earlier or later than precisely 8:00.  At 7:55, I asked Lu, the Chinese guy standing in line next to me, &#8220;Where is the bus?&#8221;  It showed up soon after that, but was a few minutes late pulling out.  Something was amiss in Japan!</p>
<p>Hitoshi had given me an idea of how to get histone H4 purified.  He said that cells which contain the gene for the protein actually grew slower than other cells.  If I was getting a mix of cells that contained it and cells that did not, the solution might be to stage a race.  I took 20 different colonies from my Petri plates that I had grown overnight and inoculated them into 20 different tubes.  I let them grow most of the day and decided to choose the slowest growing ones to mix into my larger culture flasks.</p>
<p>For lunch, I returned to one of my favorite dishes so far- the gingered beef over rice with an egg on top.  I did try a new soup and drink, however.   I had a creamy soup with croutons and squash, along with an unidentifiable vegetable as well as one of the strangest drinks that I had found so far.  It was white, like Calpis water, and tasted slightly like coconut, but it had tiny squares of gelatin suspended in it.  The day before, I had chunky lemonade with plants in it, now these gelatin squares!</p>
<p>Soon after lunch, it was time for Kanji Table.  Once again it started off with someone giving a fairly lengthy speech.  This one was much better, however, since it was about Taiwanese food.  A girl from Taiwan gave a PowerPoint presentation with lots of pictures of food, so I paid close attention.  It all looked very good.  Then, Yoshinaka-san had me read about April, the season when new employees start work in their companies in Japan.  I told him that there was no such season in the U.S., that employees started jobs at all different times of the year.  I then wrote kanji for a while and headed back to the lab.</p>
<p>It was time to see who had lost, and therefore won, my little race between bacteria.  Out of the 20 tubes, all but one had grown rapidly.  I chose this one, streaked it out onto a Petri plate, and used the rest to start a large culture.  It was also time to combine the two H2 histones and have them form a complex.  I mixed equal amounts of them in a bag made of a semi-permeable membrane and placed them in a high salt buffer to &#8220;dialyze&#8221; overnight.  By morning, the buffer would have exchanged through the membrane but the protein complexes would remain inside the bag.  This was my first step in building a chromosome from scratch!</p>
<p>I was determined not to eat my Wednesday meal within a 10-minute time frame again, so I left the lab at 6 pm, 30 minutes earlier than usual.  I traveled to Mikuni Station and went to a Chinese Restaurant which was located underneath, next to McDonalds.  This was my first sit-down restaurant where people actually waited on me, and it had only taken me a month to get there!  I order Peking Duck (with gyoza, of course).  It was delicious and the meal came to less than 1000 yen. </p>
<p>At church, along with the usual Japanese songs, we sang a song in English that was actually written by someone whose parents I know very well.  It&#8217;s a small world sometimes!  Fiona was sharing the message at the church service.  She was usually the one who translated for me, but this time she spoke in Japanese and a Japanese brother named Shohei translated instead.  As usual, people hung around and talked after the service.  I ended up catching a train home around 10 pm.  </p>
<p>I got home at 11 and wanted to try out a new trick that I had learned that day.  Anna had told me that there was usually a button on your remote control to turn off Japanese dubbing for the shows that are normally in English.  I had brought in my remote that day so she could show me what buttons to press.  &#8220;Without a Trace&#8221; was on T.V., with the characters speaking Japanese, as usual.  I pressed a few buttons and, sure enough, they started speaking English.  It was the first time I had heard English coming out of my T.V. set!  However, since I was by that time too tired to actually watch the show, I turned it off and went to bed.</p>
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		<title>Quantifying Histones</title>
		<link>http://blogs.monm.edu/jgodde/2013/06/14/quantifying-histones/</link>
		<comments>http://blogs.monm.edu/jgodde/2013/06/14/quantifying-histones/#comments</comments>
		<pubDate>Fri, 14 Jun 2013 05:29:05 +0000</pubDate>
		<dc:creator>James Godde</dc:creator>
				<category><![CDATA[Study abroad in Japan]]></category>

		<guid isPermaLink="false">http://blogs.monm.edu/jgodde/?p=355</guid>
		<description><![CDATA[Despite the fact that I still did not have one of the proteins that I needed, it was time to forge ahead with other experiments while I worked to obtain it. Since our planned experiment called for making complexes out &#8230; <a href="http://blogs.monm.edu/jgodde/2013/06/14/quantifying-histones/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
				<content:encoded><![CDATA[<p>Despite the fact that I still did not have one of the proteins that I needed, it was time to forge ahead with other experiments while I worked to obtain it.  Since our planned experiment called for making complexes out of the two H2 histones first, I could begin this process while I worked on getting H4.  The first step was to make sure the two were the exact same concentration before mixing them.  While the Nanodrop spectrophotometer was good at measuring concentrations, its readings were affected by contaminating proteins as well as some of the components of the buffer the proteins were suspended in.  The best way to determine the exact concentration was running the proteins on a gel, staining with a special fluorescent stain, and scanning them with yet another very expensive instrument called a Phosphoimager.  </p>
<p>I ran a gel as soon as I got in to work and put it in the stain during the lunch hour.  I had fried fish in a brown gravy over rice; the soup I chose was called &#8220;Brown Soup&#8221; according to the Japanese on the label, and was a mixture of tomatoes, mushrooms, and croutons in a brown broth.  Kiyoe showed me how to use the Phosphoimager after lunch, which was actually located on the 8th floor, not far from my sonication alcove.  Unfortunately, I had loaded too much protein for the machine to work correctly and had to start again with another gel.  I proceeded to load ten times less protein onto the next one.  </p>
<p>As it ran, I thought about what had gone wrong with the H4 purification.  I realized that the H4-containing bacteria had grown many more colonies than the other three.  Overloading the colonies onto plates allows other bacteria to grow, even if they do not contain the correct piece of DNA.  I had probably selected some of these intruding colonies and grown them in the large flasks, getting very little protein in the end.  I was sure that was what had happened, and was determined not to let it happen again.  I inserted more of the H4-containing DNA into bacteria and grew them on three different Petri plates, using different methods of distributing the colonies.  I then put these in the incubator overnight.</p>
<p>The second gel was done running at 6:40.  I went back down to the 8th floor to scan it- it looked much better!  I didn&#8217;t have a lot of time to pour over the results, though, since I needed to catch the last bus.  I made lasagna for dinner from a kit that included uncooked noodles, a bag of meat sauce, and Parmesan cheese that was the consistency of mayonnaise.  I looked at the pictures on the back of the package to figure out how to make it.  I must have guessed close to the correct way, since it turned out pretty good!</p>
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		<title>Three Out of Four</title>
		<link>http://blogs.monm.edu/jgodde/2013/06/13/three-out-of-four/</link>
		<comments>http://blogs.monm.edu/jgodde/2013/06/13/three-out-of-four/#comments</comments>
		<pubDate>Thu, 13 Jun 2013 00:27:03 +0000</pubDate>
		<dc:creator>James Godde</dc:creator>
				<category><![CDATA[Study abroad in Japan]]></category>

		<guid isPermaLink="false">http://blogs.monm.edu/jgodde/?p=352</guid>
		<description><![CDATA[The first thing I did once I arrived at work was to check my gel that had been soaking in stain for most of the weekend- there were faint bands on it but nothing that was helpful in knowing if &#8230; <a href="http://blogs.monm.edu/jgodde/2013/06/13/three-out-of-four/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
				<content:encoded><![CDATA[<p>The first thing I did once I arrived at work was to check my gel that had been soaking in stain for most of the weekend- there were faint bands on it but nothing that was helpful in knowing if the purification had worked.  I then set about checking the new fractions for protein using the Nanodrop machine.  This was the sample that had refused to grow well, but the protein concentrations seemed right in line with the other two that had worked.  Since pouring my own gels had backfired over the weekend, Kiyoe suggested that I return to the pre-poured ones, at least long enough to get an answer as to whether the last two purifications had worked.  I set up four gels on three different apparatuses with six different wires coming from my power supply- it looked like I was doing some serious research on my bench!  </p>
<p>Just then, Kiyoe stopped by and suggested that I go with them to the animal facility.  Since I had finally received my university I.D. card, I could turn in my hard-earned form that said I had taken the mouse class and was approved for access.  In the facility&#8217;s main office, I held my finger on a scanner so they could identify me from my fingerprint when I entered the building from then on.  It took a combination of my specially keyed I.D. badge as well as a finger scan to enter the building.  They were serious about security in Japan!</p>
<p> By the time I prepped the 51 different samples and loaded them on the gels, it was time for lunch.  I bought broiled chicken over rice and seaweed, clam chowder, and a drink with a picture of a lemon on it.  &#8220;You drink that?&#8221; Kiyoe asked me at lunch.  &#8220;I guess so,&#8221; I answered.  My drink was made of aroi, the same plant I had eaten in yogurt during my first week in Japan, it also had some lemon in it as well.  Kiyoe said that it was very healthy but had never tried it.  I&#8217;d made a habit of trying all sorts of new things- the drink tasted like lemonade with tiny chunks of plant in it.</p>
<p>I finished running the gels and then began the process of staining them.  While I waited for the protein bands to show up, I purified DNA from the cells that I had been slowly stocking up which contained more histone H4 clone, just in case.  The purification of that sample ended up being just fine, but the third sample was still a problem.  The purification had actually worked, I had very faint bands of pure protein- unfortunately, it was only one tenth the concentration of the other samples.  I emailed Hitoshi ask him if there were any tricks to getting this particular sample to work.  He soon replied that I should call him to discuss it further- but since it was time to go to our group meeting, I was forced to put off calling him for a while.  Kiyoe and Keisukei each talked for half of the meeting; I followed their talks better than usual since I was already familiar with the topic.  The meeting ran for about 95 minutes, after which I called Hitoshi back.  He said that they sometimes got three quarters as much protein using this sample but never as low as a tenth.  He suggested that I try the whole process again with that particular sample.  I guess three out of four isn&#8217;t too bad!</p>
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		<title>Monkey Business</title>
		<link>http://blogs.monm.edu/jgodde/2013/06/12/monkey-business/</link>
		<comments>http://blogs.monm.edu/jgodde/2013/06/12/monkey-business/#comments</comments>
		<pubDate>Wed, 12 Jun 2013 01:06:59 +0000</pubDate>
		<dc:creator>James Godde</dc:creator>
				<category><![CDATA[Study abroad in Japan]]></category>

		<guid isPermaLink="false">http://blogs.monm.edu/jgodde/?p=350</guid>
		<description><![CDATA[Before church, I decided to go downtown to get my camera fixed. It had stopped working the previous Sunday. When I went to take a picture of the group at the conveyer belt sushi restaurant, it had said &#8220;lens error&#8221;. &#8230; <a href="http://blogs.monm.edu/jgodde/2013/06/12/monkey-business/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
				<content:encoded><![CDATA[<p>Before church, I decided to go downtown to get my camera fixed.  It had stopped working the previous Sunday.  When I went to take a picture of the group at the conveyer belt sushi restaurant, it had said &#8220;lens error&#8221;.  I tried to get it working again but it was unrelenting.  The owner&#8217;s manual said that particular error message means it was time to take it to get serviced.  I had found a Nikon service center on the internet that was open on Sundays in Umeda.  I left early and arrived in Umeda at 9 am.  Since the camera shop did not open until 10, I had some time to kill.  I decided to walk and to try to find the &#8220;Floating Garden Observatory&#8221;, which is suspended 600 feet in the air, between two skyscrapers.  It wasn&#8217;t going to open until 10 either, but I just wanted to find it so I could take the family there when they arrive.  I ended up taking the long way around, but I eventually found it and figured out the shortest way to get there from the train station.  </p>
<p>By then it was 9:40, and it was time to find the camera shop.  The internet said that it was a 10-minute walk west of the station.  I tried to cross a very busy street to the west but there were no crosswalks, I then noticed some stairs going down and thought that perhaps there was a walkway under the street.  Was there ever!  The underground passage led me west for the full 10-minute walk, there must be a mile of passages underground that led from the station.  I surfaced where I though the building should be.  I asked a policeman who was directing traffic if I was going in the right direction and he said I was. The Nikon store ended up being around the next corner.  I had not prepared a speech for dealing with a camera repair shop, so I had to improvis.  The following is a rough translation of what transpired:</p>
<p>Me- My camera died (I didn&#8217;t know the verb for &#8220;broke&#8221;), can you fix it?<br />
Man- (Something I couldn&#8217;t understand)<br />
Me- I only speak a little Japanese.<br />
Man- Hang on a second. (He goes in the back room)<br />
Man- Sorry, I couldn&#8217;t find anyone who spoke English.<br />
Me- That&#8217;s ok.<br />
Man- I&#8217;ll have to keep your camera for a while in order to repair it.<br />
Me- Ok, how much will it be?<br />
Man- 13,500 yen<br />
Me- Ok, how long will it take?<br />
Man- 1 week. (He has me fill out a form)<br />
Me- Are Roman letters ok?<br />
Man- Yes</p>
<p>I filled out the form and he entered the information into the computer.  Kiyoe had warned me that it would be expensive to repair a camera but I needed it done and had been really pleased with that camera.  The man gave me a work order, he had written my name as &#8220;jdns Gadde&#8221;.  I didn&#8217;t argue with him, I figured the chance of someone with that name coming in to pick up a camera within the next week was pretty slim.</p>
<p>I then took the passages back to the train station and rode the train to church.  A Korean man who has lived in Japan for the last 11 years was visiting from the church in Nagoya, Japan&#8217;s 4th largest city (Osaka is 3rd, behind Tokyo and Yokohama).  He spoke Japanese very well and gave his message using it.  The best news of the day was that Takashi was finally released after 10 days in jail.  They were still deciding whether to prosecute his case- so he was not completely in the clear yet, and everyone was still praying for him.  Afterwards, Florentine and his wife wondered if I wanted to go out for sushi.  We went to a different kaiten sushi restaurant; Nori, Fiona, and Bond joined us as well.  It was good- of course.  I had sea urchin along with my usual fare, I&#8217;m not sure if I had tried it before.  It was a little mushy, but otherwise tasty.  I got home at 4pm, and was ready for a little &#8220;monkey business&#8221;.</p>
<p>When we had gone to the grocery store the previous day, I had asked Kiyoe if there were places to go hiking in the mountains that surrounding Osaka.  She told me to take the train to the end of the line in Mino-o (where I had “Konnichi wa” class) and to walk to Mino-o falls.  She said there were wild monkeys who lived in the mountain forests there.  That was enough for me- I wanted to see a wild monkey and couldn&#8217;t believe they lived within 5 miles of my house.  </p>
<p>It was threatening rain as I arrived home and I could hear rumbles of thunder to the south, over Osaka.  But to the north, in Mino-o, the sky looked clear, and nothing was going to dissuade me from my goal.  The train station in Mino-o was a 15-minute walk from my house and I took the train for just 2 stops.  From there, a brick road led up the hill, though a very quaint shopping district, and into the park.  </p>
<p>Mino-o Park was beautiful!  It reminded me of Turkey Run in Indiana, a favorite hiking spot of ours when we lived in Champaign, Illinois.  It had a deep gorge with a river running through it, and trails going every direction.  Down various trails were temples and shrines to explore as well as various statues.  I imagined a person could spend the whole day exploring the park and not see all the neat things there.  The main trail was not hard to miss.  It would uphill for a mile and a half until it reached Mino-o Falls.  I had seen a half dozen smaller falls during the hour-long stroll to Mino-o Falls, but they did not compare to the 100-foot drop of the final waterfall.  There was a little Japanese bridge that crossed the river right below the falls, it was amazing!  What a time to be without a camera!  I figured that I would bring the family back to the park the first chance that I got, so I could snap some pictures then.</p>
<p>As I approached the falls, a monkey hopped across the boulders that spanned the river 20 feet in front of me and hoisted himself over the low railing that stretched along the trail.  He then ran up to a refreshment stand, grabbed two boxes of Pokey (Japanese cookie sticks which are dipped in chocolate), and bolted back across the river to eat them.  I walked down to the falls, admired them for a while, and then walked across the bridge and up the trail on the opposite side of the river from where I had come.  As I climbed a hill, there, in the middle of the trail, was the monkey, eating his treats.  The monkey was about two and a half feet tall, coming up to about my mid-thigh.  I stood about 10 feet away from him and watched him.  </p>
<p>&#8220;Oishi? (Is it delicious?)&#8221; I asked the monkey.  The monkey ignored me and kept eating.  &#8220;Do you speak English?&#8221; I asked the monkey.  Still, he ignored me.  I didn&#8217;t want to try to get past him on the trail in case he thought I was trying to steal his food.  I had heard that monkeys can be quite aggressive when it comes to their food.  Eventually, he finished eating and climbed further into the forest.  The hike down the mountain to the train station was much easier that going up, I was back there within 30 minutes.  As I walked home from the station, I saw a supermarket and decided to complete my final weekend chore that I had to accomplish- the shopping.  I spend 3,840 yen to stock up for another week and then returned home.  It never had rained on me, but I had brought my umbrella just in case.  Since it was shopping day, I had California rolls for dinner along with dim sum, mixing the Japanese and Chinese cultures once again.</p>
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		<title>Another Special Lunch</title>
		<link>http://blogs.monm.edu/jgodde/2013/06/11/another-special-lunch/</link>
		<comments>http://blogs.monm.edu/jgodde/2013/06/11/another-special-lunch/#comments</comments>
		<pubDate>Mon, 10 Jun 2013 23:36:30 +0000</pubDate>
		<dc:creator>James Godde</dc:creator>
				<category><![CDATA[Study abroad in Japan]]></category>

		<guid isPermaLink="false">http://blogs.monm.edu/jgodde/?p=347</guid>
		<description><![CDATA[I had a couple of cold egg rolls for breakfast and was on the monorail by 8 am. I wanted to get things done at work as soon as possible. I prepped the lysed cells for the column and got &#8230; <a href="http://blogs.monm.edu/jgodde/2013/06/11/another-special-lunch/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
				<content:encoded><![CDATA[<p>I had a couple of cold egg rolls for breakfast and was on the monorail by 8 am.  I wanted to get things done at work as soon as possible.  I prepped the lysed cells for the column and got my samples ready to run on the gel.  Kiyoe came in around 11, she had asked me over for lunch again that day, and we agreed to leave around 12:30.  I finished running my gel and put it into some water to soak.  I also had my column washing by the time we had to leave for lunch, so I turned off the pump- knowing that it would wait for me until we got back.  </p>
<p>Kiyoe once again hadn&#8217;t gotten a chance to go to the store, so we stopped there first.  We went to the same multi-level store as we did the last time I had lunch at her house.  Since it was Saturday, her husband Shinichi was off work.  I had met him a few times when Kiyoe and I worked together in Maryland, including when I was at their wedding, I suppose, but couldn&#8217;t distinctly remember him.  We ate raw chopped up tuna mixed with green onions, and rolled this up, along with rice and fish eggs, in a rectangle of seaweed.  Kiyoe also had picked up some sushi and raw scallops to go with it.  After lunch, she got out some green tea powder and made tea the way you would make it for a tea ceremony.  She said that she had studied the tea ceremony but wasn&#8217;t a very good student because she concentrated too much on science instead of the art of making tea.  The tea was still very good.</p>
<p>We didn&#8217;t get back to the lab until about 3 pm.  I turned the column pump back on and stained the gel.  After an hour of staining, it looked like nothing was on it!  I worried that I had no sample from that purification, but noticed that the standards on the gel did not stain either.  That would seem to indicate that the problem was with the gel and not necessarily my samples.  I left the gel to stain until Monday.  The column finished the elution process around 5:20; I decided to measure the protein in the fractions on Monday as well so I could get home at a decent time.</p>
<p>When I got home, I ate another hamburger over rice.  As I was cooking dinner, it started to rain.  The rain was coming down extremely hard, in sheets.  I pitied anyone caught out in it, realizing that someday my luck would run out and it would be me out there.  I opened my front curtains to watch the storm and remembered doing the same thing in Virginia, IL when Trudy and I were first married.  Anyway, it was better than anything on T.V.  After I ate, I did the laundry and the dishes.  There would definitely be no hacking the yard that day, since it was under an inch of water in some places.</p>
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		<title>Ear-Splitting Work</title>
		<link>http://blogs.monm.edu/jgodde/2013/06/10/ear-splitting-work/</link>
		<comments>http://blogs.monm.edu/jgodde/2013/06/10/ear-splitting-work/#comments</comments>
		<pubDate>Mon, 10 Jun 2013 02:41:13 +0000</pubDate>
		<dc:creator>James Godde</dc:creator>
				<category><![CDATA[Study abroad in Japan]]></category>

		<guid isPermaLink="false">http://blogs.monm.edu/jgodde/?p=345</guid>
		<description><![CDATA[I woke up early, so I decided to make crepes for breakfast. I had picked up some mix at the store in addition to what was most likely chocolate hazelnut spread, based on the pictures on the side of the &#8230; <a href="http://blogs.monm.edu/jgodde/2013/06/10/ear-splitting-work/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
				<content:encoded><![CDATA[<p>I woke up early, so I decided to make crepes for breakfast.  I had picked up some mix at the store in addition to what was most likely chocolate hazelnut spread, based on the pictures on the side of the package.  They turned out pretty well, and I had been right about the spread; I ate a crepe and put a couple more in the refrigerator for later.  At work, I got started on the purification of H2B as soon as I got in.  I didn&#8217;t have as many troubles with the fraction collector this time, so I had it washing by 11 am.  I then decided to break open the cells that were expressing histone H4 so the protein would be ready to purify on Saturday.  I returned to my alcove once again as the column continued its washing procedure.  I ate lunch as I spun down the latest batch of cells; I had pork (I think) and a soup that had pasta in a tomato base.  By 12:30, I had started the protein eluting from the column and was back at it at the sonicator.  </p>
<p>As I wrapped up the sonication, I hoped that it was the last time that I had to do this task.  I&#8217;m sure the rest of the building&#8217;s residents felt the same way!  I have failed to mention how loud the machine was that I used.  Sonication, as the word suggests, is a way of breaking open cells with sound waves.  Our machine on the 10th floor (which remained broken at this time) was kept in the cold room in a soundproof box.  The one I had been using was completely out in the open in its alcove next to the ladies&#8217; room.  When Kiyoe had come to the 8th floor to find me, she said that she could hear the machine going as she approached the stairwell on the 10th floor.  During my last run that day, I did an experiment and walked down the stairwell instead.  Sure enough, I could hear my machine as far down as the 5th floor.  Oops!</p>
<p>I measured the protein concentration in the fractions that had come off the column and was a little disappointed that they were rather low.  I half expected histone H4 to give me troubles, but had not counted on H2B messing up.  Kiyoe suggested that I run the samples on a gel to be certain what happened.  She told me that when she had done similar purifications, she didn’t always trust the machine to detect the protein.  I poured two gels, but one of them leaked all over my bench and needed to be redone.  By the time I had re-poured the offending gel, it was getting late and I decided to run the gels the following day, on Saturday.  I didn&#8217;t want to miss my &#8220;Konnichi wa&#8221; class again.</p>
<p>I caught the 6:15 bus and had 25 minutes to spare by the time I arrived back at my home campus.  Evgeni, a Bulgarian dentist I had met on the bus had told me about a short cut through campus to get to Mino-o, where the class was held.  I knew that by taking it I risked getting lost again, but  I decided, with my recent run of good luck, that it was worth a chance.  I found the way he had described, which happened to lead right past the McDonalds by the grocery store called Nissho, so I stopped there- it was 6:50.  It seemed to be a reoccurring theme in Japan that I had only minutes to find some food and then make it somewhere.  I ordered a teriyaki burger meal, something that I had first tried in Kyoto during my visit the previous year.  I got to the community center and sat outside on a park bench to eat my dinner, and then I went to class.</p>
<p>The same man was there as the previous time I had gone; he wanted to discuss everything from the cost of tuition in Japan to the percentage of foreign students at my home institution, all in Japanese.  We had a very nice talk but soon it was at 8:30 and I started walking home.  I tried to find a second-hand shop that another person on the bus had told me about, but after walking for a while without seeing it, I decided to turn around and make my way home.  I did find lots of interesting restaurants and bookstores on my walk, though.  I figured that I would return to some of these once the family arrived.  As I walked up to my house at 9 pm, it began to rain and then started pouring after I was safely inside.  I had timed that walk just right!</p>
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