Friday, November 27, 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 of Authentication
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 could guarantee the authenticity of our aDNA work just by following the Criteria, why shouldn't we do it? We have followed, and will follow this Criteria  until another persuasive way for making aDNA work much authentic could be discussed among related researchers.

Lab Setting
After the samples were moved to our lab, we should perform aDNA works in a lab, following Criteria of Authentication, which have been suggested by a number of aDNA researchers. Among them, we explain our lab setting for authentic aDNA work.

IRB Approval of Our aDNA Work
During our aDNA work, it has been needed that sequences or profiles from ancient samples should be compared to those of participants in our study. This is indispensable to show if any modern DNA contamination from researchers was occuring during aDNA work. We got IRB certification on genetic analysis of participants in our studies.

Thursday, November 26, 2009

How can you access to us?

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 the ticket for today's trip.

4. From Subway Station "Hyehwa" to Our lab

To reach my lab, you should be out of station via Exit No 3 where you can find the signboard for Seoul National University Hospital.


Signboard for Seoul National University Hospital at Exit No 3 of Hyehwa Station
The Gate to Seoul National University College of Medicine. You can find this after 1-2 min walk from the station.
You should enter the gate to find the main building of Seoul National University College of Medicine. At this point, turn to the right.....
And go ahead, please.
Turn to the left again
Yes, this is my office and lab (post PCR lab).

Wednesday, November 25, 2009

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.

Tuesday, November 24, 2009

More about Korea

World Heritage of UNESCO


Some Talks on the obsession of us, Koreans, for National Indepence and our future

News clip on magnificent historic documents of Korea

Some music clips

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

Refections on the Old Seoul

Old Seoul: frame by frame 19. Gyeongbok Palace

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
Case Reports
Legends: Serial Number/ Report Date/ Archaological Sites/ Client/ Results

  •  2009-0609/ 2010. 3. 23/ Skeletons from three LSMB tombs of Joseon Dynasty/ Hanwool Institute of Cultural Heritage/ Basic anthropological examinations
  • 2009-0626/ 2010. 3. 22/ Skeletons from three LSMB tombs of Joseon Dynasty/ Central Institute of Cultural Heritage/ Basic anthropological examinations
  • 2010-0106/ 2010. 3.19/ Gyeongju Gyerim-Ro No. 14 Tumulus/ Gyeongju National Museum/ Teeth recognition only
  • 2008-0624/ 2010.3.18/ Medieval Tomb for Lady of Sacheon Mok Clan (Josoen Dynasty)/ Gyeonggi Provincial Museum/ Finding parasite eggs in the feces
  • 2010-0222/ 2010. 3.16 (1st report)/ Lung Tissue, Hungarian Mummy/ Dr. Mark Spigelman/ Trying to confirm the presence of ancient DNA (cross-checking)

My Colleagues

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 Joseon Dynasty!!! We should cooperate with highly-reputed historians for our successful mummy works and paleopathological studies. Dr. Shin is the one. He is studying on Korean History (especially on Joseon Dynasty); and currently in Dept of History, Pukyung National University, Korea (Professor). E-mail to him




Eun Joo Lee
If there were not any textile researcher studying on the clothing of Joseon Dynasty, every cultural or human remains from medieval tombs could not be successfully secured. About 40 years ago, some pioneering textile researchers started to investigate into the clothes from the tombs; and maintained them in their labs or institutes. After then on, many textile researchers have tried to elucidate invaluable information whenever they found medieval clothes in the tombs. Anyway, their work is closely related with our works because interdisciplinary work from various research fields is needed for getting invaluable information from well preserved, mummified cases. Dr. Lee EJ is one of the leading figures of the young school textile specialists in Korea. Anyway, we should always cooperate with her lab and other colleagues whenever the mummified individual was found in archaeological fields. Since well preserved clothes were always wrapped around the Korean mummies, removal of clohtes should be done by close cooperation of both side labs; and during which, clues for reconstruction of textile history could be secured by her lab; and contamination minimized biological samples for our authentic aDNA analysis could be obtained by us. Dr. Lee is currently in Dept of Clothing and Textiles, Andong National University, Korea (Professor). Though there are many works for which we have collaborated, one of the most notable paper might be this published in AntiquityE-mail to her




Myeung Ju Kim
He was graduated from Gyeongsang National University College of Medicine; and got trained in Dept of Anatomy, Seoul National University (MD., PhD). When I was graduate student in SNU, he was also studying in the same department. And currently both of us are doing the same work on mummy studies and Paleopathology. As seen in the left figure, he is also a great singer. Dr. Kim MJ is currently in Dankook University College of Medicine (Associate Professor). E-mail to him




Min Seo
He was one of my classmates in medical school. Anyway, during school days, he was famous for his unique inspiration, which is still his trademark even by this time. After graduated from SNU college of medicine, further studied in Dept of Parasitology of the same university (MD., PhD). All the parasitological samples obtained from archaeological fields in Korea were examined by him. Anyway, without his help, we could not make any paleoparasitological achievements until now. He dreamed of finding a extinct parasite species in ancient samples; and examined all the samples from the countries around the world (Please see him playing with camels in Mongolia!!!). I believe he could accomplish his dream. He is currently in Dept of Parasitology, Dankook University College of Medicine (Associate Professor). E-mail to him



Journal Homepages



Anthropology and Archaeology
*International Journal of Osteoarchaeology
*Anthropologischer anzeiger
*Journal of Archaeological Science
*Antiquity
*American Journal of Physical Anthropology
*Journal of Anthropological Archaeology
*Archaeology, Ethnology and Anthropology of Eurasia
*International Journal of Historical Archaeology
*Archaeological and Anthropological Sciences
*Journal of Field Archaeology
*Australian Historical Archaeology
*Archaeologies
*Journal of Archaeological Research
*Journal of Archaeological Method and Theory
*Global Archaeology and Theory


Medicine
*Journal of Anatomy
*Annals of Anatomy
*Journal of Parasitology
*Memorias do Instituto Oswaldo Cruz
*Lancet
*Archives of Oral Biology


Korean and Asian Studies
*Review of Korean Studies
*Asian Perspective
*Korea Journal
*Seoul Journal of Korean Studies
*Bulletin of Indopacific Prehistory Association





Links to Ancient DNA and Forensic Genetics Sites

Links on Ancient DNA and Forensic Genetics Sites
*STRBase: STR DNA Internet Database
*Mitomap: A Human Mitochondrial Genome Database
*mtDNA manager
*PhyloTree
*Mitowheel
*YHRD: Y-STR Haplotype Reference Database
*Armed Forces DNA Identification Lab (AFDIL)
*Y Chromosome Consortium
*Human Genome Project Information
*Landmark HGP Papers
*Phylogenetic Network Software Download
*Mammalian Genotyping Service
*International Society of Forensic Genetics
*Tel TTAGGG telomere length assay
*Telomeric 1.2 in Fox Chase Cancer Center Bioinformatics
*International HapMap Project
*Array Designer
*Primer 3
*AutoDimer Software



Links on Archaeology
*Archaeology Conferences Worldwide
*Indo-Pacific Prehistory Association
*Southeast Asian Archaeology Newsblog

*FDI World Dental Federation: Two-Digit Notation to identify teeth with a number

Monday, November 16, 2009

Construction of Joseon tombs


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 bottom. (D) Forming LSMB on side walls of outer coffin. (E) Constructing inner coffin in mourning place. Spread charcoal on floor of inner coffin; Laying basal plate on charcoal layer; Placing clothes-wrapped body within coffin; Putting covering lid on inner coffin. (F) Moving inner coffin to graveyard (funeral procession). (G) When the outer coffin is laid within the grave pit, a lime-soil mixture is poured into the space between the soil and the outer coffin walls; the inner coffin is laid within outer coffin. (H) Laying cross bars upon the coffin lid. (I) and (J) Forming the LSMB upon the cross bars.


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 ~1,000, at least three independent amplifications need to be analysed, and the products need to be cloned and several clones should be sequenced.

Amplification from a second extract: The reproduction of the results from a second, independent extract should show that the result is reliable.

Links on Archaeology

*Archaeology Conferences Worldwide
*Indo-Pacific Prehistory Association
*Southeast Asian Archaeology Newsblog
*FDI World Dental Federation: Two-Digit Notation to identify teeth with a number

Links on Anthropology

*Center for Human Bioarchaeology, UK
*Guidance for the Care of Human Remains in Museums, UK
*Hungarian Natural History Museum
*Paleopathology Association
*18th European Meeting of the Paleopathology Association
*Institute for Mummies and the Iceman
*Dieneke's Anthropology Blog

Sunday, November 15, 2009

Lab Setting

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 Building A, there is not any lab performing PCR amplification of modern DNA. The rooms for aDNA extraction or PCR preparation were separated from our main lab where we did PCR works. The rooms were equipped with night UV irradiation, isolated ventilation, or laminated flow hood. The researchers in our lab should follow instructions in Criteria of Authenticity (Hofreiter et al. 2001, Marota & Rollo 2002, Willerslev & Cooper, 2005). None could enter into aDNA extraction or PCR preparation rooms without permission.

Wednesday, November 11, 2009

Autumn in SNU




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.

Sunday, November 1, 2009

Archaeology Magazine


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 Science.
And the news was briefly reported in Archaeology Magazine (Volume 62, Number 6, Nov/Dec 2009). To see the news in Archaeology Magazine, the information is here. The same contents was also dealt in Discovery Channel.

Exhibition in Seoul Museum of History

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