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Showing posts from November, 2009

To Make Our Ancient DNA Work Much Authentic

In this section, we summarized our efforts for making aDNA work much authentic during the entire procedure from archaeological field to wet lab works. Please follow the links below.

Our Works in Archaeological Fields
We believe that most of debates on authenticity of aDNA work must have been settled if biologists and archaeologists could have collaborated to minimize the possible modern DNA contamination of samples in every procedure from archaeological fields to aDNA lab....,

Criteria ofAuthentication
There are many viewpoints on the Criteria of Authentication, espically about the needs of such Criteria in aDNA lab works. Someone think that it is really needed for authentic aDNA work; the others say this is just formalities, not needed for researchers. I do not want to make a comment on whether the Criteria is really helpful for authenticating our aDNA results or not. What we want to care about is making our aDNA results without possibility of contamination as possibly as we can. If we …

How can you access to us?

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1. Finding the lab in Google Map
Red arrow points to my lab.
Enlarge the Map

2. Searching the subway route

If you are staying in one of hotels in Seoul City, it would be convenient for you to access my lab by subway because of heavy traffic in this city. Subway in Seoul is clean, quiet, safe; and always takes you to any destinations exactly on time. The subway route could be searched at this site. To find the way to my lab, just select the name of your "departing" station; and choose "Hyehwa" for your "arrival station" ("departing" and "arrival station" bars on the left corner of the map page). The page will show you the shortest course to my lab. You can print it (See the print button in the upper right corner of the page). 

3. Buying the subway ticket

Most of Korean passengers pay their subway fares with credit or SMART card (exclusively for subway charge). Just contacting the cards on the gate is enough for them. However, you need to buy …

Finding Clothes Wrapping Mummy in Archaeological Field of Korea

Click for Movie file

The tomb encapsulated by Lime-soil Mixture Barrier (LSMB) was found in Seoul, Korea on October 25, 2007. Archaeologists joining in this case knew well about the importance in reducing the number of direct contacts with human samples for successful aDNA studies. When the inner coffin was opened, well preserved clothes were identified by us. Since we decided to collect human samples contained within the clothes under well-appointed condition, the dead body was moved to our lab without any derangements of clothes. Caption available in movie.

More about Korea

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The Jongmyo
World Heritage of UNESCO


Why Should Koreans Be So Obsessive for National Independence?
Some Talks on the obsession of us, Koreans, for National Indepence and our future

The Pages of Korea's Past
News clip on magnificent historic documents of Korea

My favorite Songs
Some music clips

A River Runs Through It
Story about Han river running through Seoul city

Structural Evidence of Days Gone By
Refections on the Old Seoul

Palace with chaotic past born again
Old Seoul: frame by frame 19. Gyeongbok Palace

A Travel Guide Fit for Your Coffee Table
It's not for the down-and-dirty information hunt often necessary on trips

Mother Africa
My experience on a visit to National Museum of African Art in Washington DC, US.

Fieldworks

Filed Works Geographic information on Korea Oh CS, Lee SJ. Paleoparasitological sampling in Seoul City Hall. Dec 8, 2009Shin DH, Oh CS. LSMB Tombs of Joseon Dynasty: Yongin, Gyeonggi Province. 2009.Shin DH, Oh CS. LSMB Tombs of Joseon Dynasty: Bumbak-Dong, Bucheon, Gyeonggi Province. 2009.Shin DH, Oh CS, Lee SJ. LSMB Tombs of Joseon Dynasty: Gwanggyo, Sowon, Gyeonggi Province. 2009.Shin DH, Oh CS, Lee SJ. LSMB Tombs of Joseon Dynasty: Gwangjin, Seoul. 2009.Shin DH, Oh CS, Seo M. Paleoparasitological investigaion on Seoul Metropolitan City. 2009.Shin DH, Oh CS, Kim MJ, Seo M. Medieval Korean Mummy from Hadong. 2009.Shin DH. Human Skeletons from Bronze Age Tomb in Sacheon, Korea. 2009.Shin DH. Goryeo Dynasty Tombs: Yongwol, Gangwon Province. 2008.Shin DH, Oh CS. LSMB Tombs of Joseon Dynasty: Eunpyeong, Seoul. 2008.Shin DH, Oh CS. Korean Mummy from Dangjin, Korea. 2008Shin DH, Lee SJ. LSMB Tombs of Joseon Dynasty: Waegwan, Chilgok, Korea. 2008.Shin DH, Oh CS, Seo M. Paleoparasitological in…

My Colleagues

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Myung Ho Shin He is a historian. Anyway, we desperately need him because he could provide us with invaluable historic information, very helpful for undestanding the health or disease of the dead individuals. According to him, Joseon is a well organized, highly developed society in medieval times of Korea. His viewpoint seems to fall in place because many unbelievalbly detaied informaton had been provided by him, which could be only available in societies with plenty of historical sources. A few years ago, we consulted with him for getting some historic information on oyster production during Joseon Dynasty. This was beacuse we found some parasite eggs in several hundred year old female mummy, and the immediate host of the parasite was oyster. For this, he showed what we want, the past record on oyster production of the time; and much astonishingly, was successful even in finding the candidate dishes which might cause the parasite infection, only by searching for the old documents of J…

Journal Homepages

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Links to Ancient DNA and Forensic Genetics Sites

Construction of Joseon tombs

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LSMB tomb looks like a concrete box. Coffin is seen within well-made LSMB.


It is very important for researchers studying on cultural or human remains from LSMB tombs to know how the tombs were constructed during Joseon Dynasty. This is because well preserved condition of LSMB tombs is closely concerned with the presence of LSMB around the coffin. The protocol for LSMB tomb construction has been well known to historians in Korea because Joseon people made the tombs according to the ritual codes of the Kingdom; thereby the information on it could be obatined in detal when historians searched for related historic documents of those times. The figure is a summary of the information. Anyway, the LSMB is completely encapsulating the coffin, like a kind of concrete box, cultural or human remains could be preserved well unless the LSMB was accidently broken before archaeological investigation began.

(A) Digging burial pit. (B) Forming LSMB on pit bottom. (C) Placing outer coffin upon LSMB bot…

The Criteria of Authentication

We tried to follow the instructions in Criteria of Authenticity (Hofreiter 2001). Briefly, in-laboratory procedures were performed in the rooms only devoted to aDNA work; any modern samples were by no means imported to the rooms. PCR reaction was repeated in our lab to show reproducibility of amplification, during which negative control was always used for excluding possible contamination of modern DNA during lab works.

Reference: Hofreiter, M., Serre, D., Poinar, H.N., Kuch, M. & Pääbo, S. (2001): Ancient DNA. - Nat. Rev. Genet. 2, 353-359.

Examples of Criteria of Authentication observed in my lab

Extraction controls and PCR controls: Mock extractions and PCRs without template DNA are elementary controls that should be carried out.

Inverse correlation between amplicon length and amplification efficiency: Generally, amplification of only short DNA pieces is possible.

Quantitation of numbers of template molecules: If the number of DNA molecules that initiate the PCR is less than ~1,00…

Links on Archaeology

Links on Anthropology

Lab Setting

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I have run my own lab for the past 10 years. Therefore, conventional setup for biological experiments is already available in my lab, i.e., microscopic observation, immunohistological studies, in situ hybridization, PCR, and Western or Norther blots. Sequencing is also available in IFM where a number of sequencers are in full operation. aDNA works are done on human mtDNA, autosomal STR and Y STR in my lab. PCRs for ancient parasite, viral or bacterial could be also performed. Though it might be too crampled for comport experiments, the instruments or reagents in my lab are arraned for effective experiment on ancient samples.


One of the most crucial points in our lab setting is making them fit for aDNA analysis, by following the Criteria of Authentication (Hofreiter et al. 2001, Marota & Rollo 2002, Willerslev & Cooper 2005). Briefly, the distance between aDNA extraction or PCR preparation rooms of Building A and main PCR lab in Building B is about 60 meters. On 4th floor in Bui…

Autumn in SNU

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When I was the medical student in SNU, about 22 years ago, the trees were also there, being ablaze with autumnal tints. After then on, I always have been fascinated by the beautiful fall foliage in SNU. Red and gold visits us again this year, in the deep autumn.

Archaeology Magazine

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We previously conducted a paleo-parasitological study on soil samples from the ancient moat ruins of Weolseong palace, of the Silla Dynasty (BC 57–AD 935) of Korea. Based on the cultural remains found in the mud-soil layer, the layer was precipitated onto the floor of a moat between the 5th and 8th centuries AD. We found Trichuris trichiura eggs only in that mud-soil layer, whereas no parasite eggs were identified in the other archaeological strata of the ruins. As T. trichiura eggs are shed only in human feces, we speculated that palace toilet contents were continually drained into the moat; therefore, at a certain point in time after construction, the moat finally became a ditch around the palace. Structures in the stone embankments of the moat, possibly designed to make the water flow continuously in one direction, might reflect the Silla people's efforts to alleviate the ever-increasing problems inherent in a moat.
The study could be published in Journal of Archaeological S…

Exhibition in Seoul Museum of History

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Anyway, human remains found in archaeological fields of Seoul could be moved to our lab for further anthropological study on them. Eunpyeong Site was one of these. The people buried in the place were thought to be living in Seoul City during 16th to 18th centuries. And sampling at the site was done by interdisciplinary work of archaeologists and anthropologists. Part of the samples from the site are currently maintaining in our Joseon Dynasty Human Sample Collection. Seoul Museum of History plan to held the exhibition for the site (Nov 4 2009 - Dec 13 2009); and our human remains were also displayed there as the examples of paleopathology cases (Kyphosis; Osteoma in the skull; Costovertebral joint fusion) found in the site. To see the news, Please click here!

Seoul Museum of History

Exhibition Room in the Museum

Exhibition Room in the Museum