Genome-wide SNP typing of ancient DNA: Determination of hair and eye color of Bronze Age humans from their skeletal remains.

OBJECTIVE: A genome-wide high-throughput single nucleotide polymorphism (SNP) typing method was tested with respect of the applicability to ancient and degraded DNA. The results were compared to mini-sequencing data achieved through single base extension (SBE) typing. The SNPs chosen for the study allow to determine the hair colors and eye colors of humans. MATERIAL AND METHODS: The DNA samples were extracted from the skeletal remains of 59 human individuals dating back to the Late Bronze Age. The 3,000 years old bones had been discovered in the Lichtenstein Cave in Lower Saxony, Germany. The simultaneous typing of 24 SNPs for each of the ancient DNA samples was carried out using the 192.24 Dynamic Array™ by Fluidigm®. RESULTS: Thirty-eight of the ancient samples (=64%) revealed full and reproducible SNP genotypes allowing hair and eye color phenotyping. In 10 samples (=17%) at least half of the SNPs were unambiguously determined, in 11 samples (=19%) the SNP typing failed. For 23 of the 59 individuals, a comparison of the SNP typing results with genotypes from an earlier performed SBE typing approach was possible. The comparison confirmed the full concordance of the results for 90% of the SNP typings. In the remaining 10% allelic dropouts were identified. DISCUSSION: The high genotyping success rate could be achieved by introducing modifications to the preamplification protocol mainly by increasing the DNA input and the amplification cycle number. The occurrence of allelic dropouts indicates that a further increase of DNA input to the preamplification step is desirable.

Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European.

Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe. The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet. However, the limited data available from earlier hunter-gatherers preclude an understanding of the selective processes associated with this crucial transition to agriculture in recent human evolution. Here we sequence an approximately 7,000-year-old Mesolithic skeleton discovered at the La Braña-Arintero site in León, Spain, to retrieve a complete pre-agricultural European human genome. Analysis of this genome in the context of other ancient samples suggests the existence of a common ancient genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Braña individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, we provide evidence that a significant number of derived, putatively adaptive variants associated with pathogen resistance in modern Europeans were already present in this hunter-gatherer.

[Study of Siberian population movements: use of multiple markers]. / Etude des migrations de populations sibériennes du passé: apport d'une approche multi-marqueurs.

To further explore early Eurasian steppe migration, we determined the Y chromosome and mitochondrial haplotypes of 26 ancient human specimens from the Krasnoyarsk area, dated between the middle of the second millennium BC and the fourth century AD. Our autosomal Y chromosome and mitochondrial DNA analyses reveal that, whereas few specimens seem to be related matrilineally or patrilineally, nearly all the subjects belong to haplogroup R1a1--M17, which is thought to mark the eastward migration of early Indo-Europeans. Our results also confirm that, during the Bronze and Iron Ages, southern Siberia was a region of overwhelming European settlement.

Protective effects of new medicinal mushroom, Grifola gargal singer (higher Basidiomycetes), on induced DNA damage in somatic cells of Drosophila melanogaster.

Grifola gargal is an edible mushroom with attributed antioxidant properties. Different sources of G. gargal materials, i.e., fruit bodies and mycelia grown in liquid or solid media, were used to study its potential protective capacity when somatic mutation and recombination is induced in Drosophila melanogaster using DMBA (7-12-dimethyl-benz(α)anthracene) as promutagen. Heterozygote larvae (white/white+) were grown in media with different concentrations of DMBA. Grifola gargal fruit bodies (GgFB) or mycelia from liquid culture (GgLC) or from solid culture (GgWG), i.e., biotransformed wheat kernel flour, were added to the culture media in combined treatments with DMBA. Water, DMBA solvent, or wheat flour (WF) plus DMBA solvent were used as negative controls. Larval mortality increased from 9% to 11% in negative controls to 31% to 36% in DMBA treatments. The addition of GgFB, GgLC, or GgWG materials produced a protective effect on 25 µmol/vial DMBA-induced mortality. Mutations observed in SMART, as light spots per 100 eyes (LS/100 eyes), increased with increasing doses of DMBA; this was also true when considering the mutation incidence expressed as percentage of eyes exhibiting light spots (% eyes with LS). Interestingly, mycelia from GgFB, GgLC, or GgWG, in the presence of 25 µmol/vial DMBA, showed lower values in SMART of both the total LS/100 eyes and the percentage of eyes with LS. Thus, Grifola gargal materials were not only nontoxic, but in combination with 25 µmol/vial DMBA lowered the mortality induced by the promutagen and showed antimutagenic effects. Protective effects of G. gargal against DMBA are discussed in terms of the onset of desmutagenic and/or bioantimutagenic mechanisms of detoxification in the host organism, probably due to some bioactive compounds known to occur in higher mushrooms.

Does a pleiotropic gene explain deafness and blue irises in white cats?

The prevalence of deafness is high in cat populations in which the dominant white gene is segregating. The objective of this study was to investigate whether there is a gene that is responsible for deafness as well as for blue eyes and to establish a plausible mode of inheritance. For this purpose, data from an experimental colony with deaf cats were analyzed. The hearing status was determined by acoustically evoked brain stem responses (BAER). Complex segregation analyses were conducted to find out the most probable mode of inheritance using maximum likelihood procedures. The prevalence of deafness and partial hearing in the experimental colony was 67% and 29%, respectively. The results of the bivariate segregation analysis support the hypothesis of a pleiotropic major gene segregating for deafness and blue iris colour. The high heritability coefficients for both traits, 0.55 and 0.75 respectively, indicate that beside the major gene there is an important influence of polygenic effects.

Prior topical anesthesia reduces time to full cycloplegia in Chinese.

PURPOSE: To investigate the effect of prior anesthesia on the time to full cycloplegia in young Chinese subjects. METHODS: The amplitude of accommodation was monitored over a 50-minute interval after the application of 1% cyclopentolate hydrochloride with a pretreatment of 0.4% benoxinate (oxybuprocaine) or 0.9% saline solution (control). Using a nonlinear mathematical model, the rate of accommodative loss (k) and the time required for 95% of total cycloplegia (T95%) were determined. RESULTS: Statistical analysis revealed a significantly faster rate of accommodative loss (P < .0001) after prior anesthesia (0.129 +/- 0.05) compared with the controls (0.103 +/- 0.04). T95% was noted at 26.43 +/- 10.22 minutes after prior anesthesia, which was significantly shorter (P < .0001) than that after the saline treatment (35.28 +/- 16.51 minutes). CONCLUSIONS: Prior application of topical anesthetic can shorten the time to full cycloplegia for people, such as the Chinese, with dark irides.

The Drosophila Polycomb group gene pleiohomeotic encodes a DNA binding protein with homology to the transcription factor YY1.

Genes of the Polycomb group (PcG) of Drosophila encode proteins necessary for the maintenance of transcriptional repression of homeotic genes. PcG proteins are thought to act by binding as multiprotein complexes to DNA through Polycomb group response elements (PREs); however, specific DNA binding has not been demonstrated for any of the PcG proteins. We have identified a sequence-specific DNA binding protein that interacts with a PRE from the Drosophila engrailed gene. This protein (PHO) is a homolog of the ubiquitous mammalian transcription factor Yin Yang-1 and is encoded by pleiohomeotic, a known member of the PcG. We propose that PHO acts to anchor PcG protein complexes to DNA.

Molecular characterization of the deep orange (dor) gene of Drosophila melanogaster.

Mutations of the dor gene of Drosophila melanogaster cause defects in different stages of development. Heterozygotes for lethal or viable dor alleles and the rearrangement T(1;2)dor(var7), which causes position effect variegation of dor, exhibit traits such as rough eyes, reduction of bristles on the thorax and scutellum and wavy wings. The dor gene was mapped to the proximal part of the 2B3-5 band or in the interband between 2B3-5 and 2B6 and localised within an interval of 5 kb on the physical map of the cloned 2B region. The 3.0-3.1 kb dor transcript was detected by Northern hybridization at all stages of development and is expressed in salivary glands of third instar larve. This RNA was not expressed in the dor mutants with insertions in the 5' part of the gene. The sequence of the 3180 bp (dor cDNA predicts a 115.3 kDa protein that contains a cysteine- and histidine-rich zinc finger-like motif CX2CX13CXHX2HX2CX2H at the C-terminus. The protein sequence reveals 23% identity to the Saccharomyces cerevisiae PEP3 protein. The most significant homology (57%) similarity and 32%, identity) between the DOR and PEP3 proteins is observed at the C-termini of the proteins.