Investigating the global dispersal of chickens in prehistory using ancient mitochondrial dna signatures

Data from morphology, linguistics, history, and archaeology have all been used to trace the dispersal of chickens from Asian domestication centers to their current global distribution. Each provides a unique perspective which can aid in the reconstruction of prehistory. This study expands on previous investigations by adding a temporal component from ancient DNA and, in some cases, direct dating of bones of individual chickens from a variety of sites in Europe, the Pacific, and the Americas. The results from the ancient DNA analyses of forty-eight archaeologically derived chicken bones provide support for archaeological hypotheses about the prehistoric human transport of chickens. Haplogroup E mtDNA signatures have been amplified from directly dated samples originating in Europe at 1000 B.P. and in the Pacific at 3000 B.P. indicating multiple prehistoric dispersals from a single Asian centre. These two dispersal pathways converged in the Americas where chickens were introduced both by Polynesians and later by Europeans. The results of this study also highlight the inappropriate application of the small stretch of D-loop, traditionally amplified for use in phylogenetic studies, to understanding discrete episodes of chicken translocation in the past. The results of this study lead to the proposal of four hypotheses which will require further scrutiny and rigorous future testingExcavations in Fais by MI were made possible by a Grant-in-Aid for Scientific Research from the Japan Society for the Promotion of Science. DB gratefully acknowledges support from the Marsden Fund, and the Allan Wilson Centre for Molecular Ecology and Evolution. During the course of this research AS was supported by a Postgraduate Scholarship from the University of Auckland and a Fellowship from the Allan Wilson Centre for Molecular Ecology and Evolutio

Identification of novel proteins differentially expressed in pluripotent embryonic stem cells and differentiated cells

Mammalian pluripotent stem cells possess properties of self-renewal and pluripotency. These abilities are maintained by the strict regulation of pluripotent stem cell-specific transcription factor network and unique properties of chromatin in the stem cells. Although these major signaling pathways robustly control the characteristics of stem cells, other regulatory factors, such as metabolic pathways, are also known to modulate stem cell proliferation and differentiation. In this study, we fractionated protein samples from mouse embryonic stem (ES) cells cultured with or without the leukemia inhibitory factor (LIF). Protein expression was quantified by 2-dimensional differential gel electrophoresis (2D-DIGE). In total, 44 proteins were identified as being differentially expressed in the pluripotent stem cells and the differentiated cells. Surprisingly, half of the identified proteins were the proteins localized in mitochondria, which supply cellular energy and regulate cell cycle, development, and cell death. Some of these identified proteins are involved in the metabolic function and the regulation of pluripotency. Further analysis of the identified proteins could provide new information for the manipulation of pluripotency in ES cells

The mouse C9ORF72 ortholog is enriched in neurons known to degenerate in ALS and FTD.

Using transgenic mice harboring a targeted LacZ insertion, we studied the expression pattern of the C9ORF72 mouse ortholog (3110043O21Rik). Unlike most genes that are mutated in amyotrophic lateral sclerosis (ALS), which are ubiquitously expressed, the C9ORF72 ortholog was most highly transcribed in the neuronal populations that are sensitive to degeneration in ALS and frontotemporal dementia. Thus, our results provide a potential explanation for the cell type specificity of neuronal degeneration caused by C9ORF72 mutations

Evaluating the use of HILIC in large-scale, multi dimensional proteomics:horses for courses?

AbstractDespite many recent advances in instrumentation, the sheer complexity of biological samples remains a major challenge in large-scale proteomics experiments, reflecting both the large number of protein isoforms and the wide dynamic range of their expression levels. However, while the dynamic range of expression levels for different components of the proteome is estimated to be ∼107–8, the equivalent dynamic range of LC–MS is currently limited to ∼106. Sample pre-fractionation has therefore become routinely used in large-scale proteomics to reduce sample complexity during MS analysis and thus alleviate the problem of ion suppression and undersampling. There is currently a wide range of chromatographic techniques that can be applied as a first dimension separation. Here, we systematically evaluated the use of hydrophilic interaction liquid chromatography (HILIC), in comparison with hSAX, as a first dimension for peptide fractionation in a bottom-up proteomics workflow. The data indicate that in addition to its role as a useful pre-enrichment method for PTM analysis, HILIC can provide a robust, orthogonal and high-resolution method for increasing the depth of proteome coverage in large-scale proteomics experiments. The data also indicate that the choice of using either HILIC, hSAX, or other methods, is best made taking into account the specific types of biological analyses being performed

Nuclear Pore Complex Protein Mediated Nuclear Localization of Dicer Protein in Human Cells

Human DICER1 protein cleaves double-stranded RNA into small sizes, a crucial step in production of single-stranded RNAs which are mediating factors of cytoplasmic RNA interference. Here, we clearly demonstrate that human DICER1 protein localizes not only to the cytoplasm but also to the nucleoplasm. We also find that human DICER1 protein associates with the NUP153 protein, one component of the nuclear pore complex. This association is detected predominantly in the cytoplasm but is also clearly distinguishable at the nuclear periphery. Additional characterization of the NUP153-DICER1 association suggests NUP153 plays a crucial role in the nuclear localization of the DICER1 protein

Ongoing Archaeological Research on Fais Island, Micronesia

The third season of archaeological research was carried out on Fais Island in the Caroline Islands at the end of 2005. A deep cultural deposit (more than 3.3 meters) was excavated along the southern coastal deposit from which a number of potsherds, shell artifacts, bone artifacts, and various kinds of natural remains were found. The constant recovery of artifactual remains supports the previous supposition that the island was continuously inhabited since the time of the first colonization. Pigs and dogs (and possibly chickens) have definitely existed on the island since about A.D. 400 afterward. Two charcoal samples obtained from the earliest cultural deposit were securely dated as A.D. 230-410 (Beta-21306) and A.D. 240-420 (Beta213061). These are the earliest dates obtained for the coral islands in the central Caroline Islands. The continuous appearance of potsherds and natural food remains throughout the culture sequence indicates that Fais was permanently settled for the last 1700 years and was not just occupied for a short period of time. On the basis of introduced pottery and domesticated animals, maintaining cultural contacts with high islands could have been a significant way to survive on such small coral islands with limited resources

Biogeography and Prehistoric Exploitation of Birds from Fais Island, Yap State, Federated States of Micronesia

Five archaeological sites on the remote, raised limestone island of Fais, Yap, Federated States of Micronesia, yielded nearly 200 identifiable bird bones from strata that range in age from about 400 to 1800 radiocarbon yr B.P. Represented are 14 species of seabirds, five species of migratory shorebirds, four species of land birds, and the introduced chicken. This is the most species-rich prehistoric assemblage of birds from any island in Micronesia. Because the "modern" avifauna of Fais never has been studied, it is difficult to determine which of the species from archaeological contexts still occur on Fais. Nevertheless, based upon modern distributions of birds from other islands in Yap and adjacent island groups, the environmental condition of Fais, and what is known about the relative vulnerability of individual species, it is likely that about nine ofthe seabirds (Pterodroma sp., Bulweria bulwerii, Sula dactylatra, S. sula, Sterna sumatrana, S. lunata, S.fuscata, Anous minutus, Procelsterna cerulea) and three of the land birds (Poliolimnas cinereus, Gallicolumba cf. xanthonura, Ducula oceanica) no longer live on Fais