Friday Five # 9 - Back to Normalcy, somewhat.

Here is the weeks top 5 things I found of interest cruising around the web.

1) Ultradeep Sequencing of a Human Ultraconserved Region Reveals Somatic and Constitutional Genomic Instability: This is one of the titles you go "what is this" and then realize that the methodology is pretty interesting. The idea in the article is to look at ultraconserved regions in the genome and then compare them to DNA from cancer cells to see if mutations in these regions cause cancer. Here is the abstract.

Early detection of cancer-associated genomic instability is crucial, particularly in tumour types in which this instability represents the essential underlying mechanism of tumourigenesis. Currently used methods require the presence of already established neoplastic cells because they only detect clonal mutations. In principle, parallel sequencing of single DNA filaments could reveal the early phases of tumour initiation by detecting low-frequency mutations, provided an adequate depth of coverage and an effective control of the experimental error. We applied ultradeep sequencing to estimate the genomic instability of individuals with hereditary non-polyposis colorectal cancer (HNPCC). To overcome the experimental error, we used an ultraconserved region (UCR) of the human genome as an internal control. By comparing the mutability outside and inside the UCR, we observed a tendency of the ultraconserved element to accumulate significantly fewer mutations than the flanking segments in both neoplastic and nonneoplastic HNPCC samples. No difference between the two regions was detectable in cells from healthy donors, indicating that all three HNPCC samples have mutation rates higher than the healthy genome. This is the first, to our knowledge, direct evidence of an intrinsic genomic instability of individuals with heterozygous mutations in mismatch repair genes, and constitutes the proof of principle for the development of a more sensitive molecular assay of genomic instability.

2) 'Junk DNA' Could Spotlight Breast and Bowel Cancer: Continuing with the cancer theme, this is an interesting news article investigating the relationship between cancer and non-coding regions of the genome.

3) My Oh Mayan! 2012 may indeed be the end of the world as we know it: This is an older article on 2012 and the impending apocalypse (not!). An interesting read on the schism between new age believers. It however would be nice if people included the actual Maya in the conversation (sort of a point of contention with me). Do you think the Maya get anything from the profits of the movie 2012.

4) Homemade 365 : The challenge - every day for one year, make something homemade - not just cook dinner, but usually make the homemade version of something that is usually purchased whole. Want to play along? J's new blog getting a shameless plug from her husband.

5) Science 2.0? A good blog post from fellow refuge from the LBA at KU. Kris is a way more informative blogger than me, which is of course why I now tweet.

Maya STRs

This article abstract is for early view article from AJPA. This is actually a fairly important article as few studies have investigated the genetic structure of Mayan populations even though as the abstract says there are 7.5 million living inhabitants speaking 28 languages throughout Central America. The typical view of individuals is to assume that the Maya are an extinct culture and not a modern vibrant culture that is suffering from a number of hardships suffered by indigenous groups throughout the region.

Delineating genetic relationships among the Maya
Lisa Ibarra-Rivera, Sheyla Mirabal, Manuela M. Regueiro, Rene J. Herrera

Abstract
By 250 AD, the Classic Maya had become the most advanced civilization within the New World, possessing the only well-developed hieroglyphic writing system of the time and an advanced knowledge of mathematics, astronomy and architecture. Though only ruins of the empire remain, 7.5 million Mayan descendants still occupy areas of Mexico, Guatemala, Belize, El Salvador, and Honduras. Although they inhabit distant and distinct territories, speak more than 28 languages, and have been historically divided by warfare and a city-state-like political system, and they share characteristics such as rituals, artistic, architectural motifs that distinguish them as unequivocally Maya. This study was undertaken to determine whether these similarities among Mayan communities mirror genetic affinities or are merely a reflection of their common culture. Four Mayan populations were investigated (i.e., the K'iche and Kakchikel from Guatemala and the Campeche and Yucatan from Mexico) and compared with previously published populations across 15 autosomal STR loci. As a whole, the Maya emerge as a distinct group within Mesoamerica, indicating that they are more similar to each other than to other Mesoamerican groups. The data suggest that although geographic and political boundaries existed among Mayan communities, genetic exchanges between the different Mayan groups have occurred, supporting theories of extensive trading throughout the empire. Am J Phys Anthropol, 2007. © 2007 Wiley-Liss, Inc.

Maya Manioc

ScienceDaily is reporting the discovery of ancient manioc cultivation site in El Salvador, this site is important is because it was previously unknown how the large Maya cities (like Tikal or Copan) were able to support their populations on only beans and corn. Manioc is an excellent source of nutrition and would have been useful in feeding a large number of people. I do have some issues with this article, it does not refer to an article (if there is one, it would be nice to know), which means the discovery may not have been published in a scientific venue. This seems to be increasingly common among archaeological sites. This is unfortunate because there may be issues with the site and its impact. The other thing is manioc is a South American domesticate so there had to be some interaction between groups through trade 1,400 years ago.

This discovery does go a long when in increasing our understanding of agriculture in Mesoamerica. There is often a misconception regarding the complexity of agricultural development in the region, where new dates have pushed back to approximately 8,000 to 10,000 years before present for a number of new world domesticates in South America including arrowroot, squash, gourds (Cooke, 2005) and years for maize (Pipererno et al. 2007). This places the origins of agriculture near the early domesticates in the old world. This is actually an exciting area of study and I'm sure several new discoveries will come out over the next decade.

References

Cooke R. 2005. Prehistory of Native Americans on the Central American Land Bridge: colonization, dispersal, and divergence. J Archaeological Res 13:129–187.

Piperno DR, Moreno JE, Iriarte J, Holst I, Lachniet M, Jones JG, Ranere AJ, Castanzo R. 2007. Late Pleistocene and Holocene environmental history of the Iguala Valley, Central Balsas Watershed of Mexico. PNAS. 104(29)11874-81.