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 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

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

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

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.


Filed Works Geographic information on Korea   Oh CS, Lee SJ. Paleoparasitological sampling in Seoul City Hall. Dec 8, 2009 Shin 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. 2008 Shin DH, Lee SJ. LSMB Tombs of Joseon Dynasty: Waegwan, Chilgok , Korea. 2008. Shin DH,

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

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

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 up

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

About Me

I graduated from a medical school in South Korea, trained as anatomist in graduate school, and currently majoring in paleopathology and biological anthropology as a professor in Seoul National University, South Korea. Over the years, my research interest has been mainly focused upon acquiring the scientific information of pre-modern people’s health and disease status in history. By research tools ranging from anatomical, histological techniques to various biochemical analyses, I tried to reveal the changing patterns of physical or pathological traits of our ancestors at each stage throughout history. My topics include the paleopathological works on ancient bones and researches of viral, bacterial, or helminthic pathogens remained in archaeological human specimens. The studies were fruitful in that a vivid glimpse of the pre-modern people’s lives could be successfully restored, and thus, their actual health status and disease pattern were interpreted in more detail from medical as well

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

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 floo

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.

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 Archae

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