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 (TM) by Fluidigm (R). 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

Tidally Triggered Star Formation in Close Pairs of Galaxies: Major and Minor Interactions

We study star formation in a sample of 345 galaxies in 167 pairs and compact groups drawn from the original CfA2 Redshift Survey and from a follow-up search for companions. We construct our sample with attention to including pairs with luminosity contrast |\Delta m_R| >= 2. These 57 galaxies with |\Delta m_R| >= 2 provide a set of nearby representative cases of minor interactions, a central feature of the hierarchical galaxy formation model. Here we report the redshifts and positions of the 345 galaxies in our sample, and of 136 galaxies in apparent pairs that are superpositions. In the pairs sample as a whole, there are strong correlations between the equivalent width of the H\alpha emission line and the projected spatial and the line-of-sight velocity separation of the pair. For pairs of small luminosity contrast, |\Delta m_R| < 2, the member galaxies show a correlation between the equivalent width of H\alpha and the projected spatial separation of the pair. However, for pairs with large luminosity contrast, |\Delta m_R| >= 2, we detect no correlation between the equivalent width of H\alpha and the projected spatial separation. The relative luminosity of the companion galaxy is more important in a gravitational tidal interaction than the intrinsic luminosity of the galaxy. Central star formation across the entire pairs sample depends strongly on the luminosity ratio, |\Delta m_R|, a reasonable proxy for the mass ratio of the pair; pairs composed of similarly luminous galaxies produce the strongest bursts of star formation. Pairs with |\Delta m_R| >= 2 rarely have EW(H\alpha) >~ 70 Ang.Comment: Minor revisions following journal proof

Induced Gamma-band Activity Elicited by Visual Representation of Unattended Objects

Peer reviewedPostprin

Evolutionary adaptations of ruminants and their potential relevance for modern production systems

Comparative physiology applies methods established in domestic animal science to a wider variety of species. This can lead to improved insight into evolutionary adaptations of domestic animals, by putting domestic species into a broader context. Examples include the variety of responses to seasonally fluctuating environments, different adaptations to heat and drought, and in particular adaptations to herbivory and various herbivore niches. Herbivores generally face the challenge that a high food intake compromises digestive efficiency (by reducing ingesta retention time and time available for selective feeding and for food comminution), and a variety of digestive strategies have evolved in response. Ruminants are very successful herbivores. They benefit from potential advantages of a forestomach without being constrained in their food intake as much as other foregut fermenters, because of their peculiar reticuloruminal sorting mechanism that retains food requiring further digestion but clears the forestomach of already digested material; the same mechanism also optimises food comminution. Wild ruminants vary widely in the degree to which their rumen contents ‘stratify', with little stratification in ‘moose-type' ruminants (which are mostly restricted to a browse niche) and a high degree of stratification into gas, particle and fluid layers in ‘cattle-type' ruminants (which are more flexible as intermediate feeders and grazers). Yet all ruminants uniformly achieve efficient selective particle retention, suggesting that functions other than particle retention played an important role in the evolution of stratification-enhancing adaptations. One interesting emerging hypothesis is that the high fluid turnover observed in ‘cattle-type' ruminants - which is a prerequisite for stratification - is an adaptation that not only leads to a shift of the sorting mechanism from the reticulum to the whole reticulo-rumen, but also optimises the harvest of microbial protein from the forestomach. Although potential benefits of this adaptation have not been quantified, the evidence for convergent evolution toward stratification suggests that they must be substantial. In modern production systems, the main way in which humans influence the efficiency of energy uptake is by manipulating diet quality. Selective breeding for conversion efficiency has resulted in notable differences between wild and domestic animals. With increased knowledge on the relevance of individual factors, that is fluid throughput through the reticulo-rumen, more specific selection parameters for breeding could be defined to increase productivity of domestic ruminants by continuing certain evolutionary trajectorie

The Radio Properties of Composite LINER/HII Galaxies

Arcsec-resolution VLA observations -- newly obtained as well as published -- of 40 nearby galaxies are discussed, completing a study of the radio properties of a magnitude-limited sample of nearby galaxies of the composite LINER/HII type. Our results reveal an overall detection rate of at least 25% AGN candidates among these composite sources. The general properties of these AGN candidates, as compared to non-AGN composite sources and HII galaxies, are discussed.Comment: Accepted for publication in ApJ

In B-CLL, the codon 72 polymorphic variants of p53 are not related to drug resistance and disease prognosis

BACKGROUND: A common sequence polymorphism at codon 72 of the p53 gene encoding either arginine or proline was recently shown to be functionally relevant for apoptosis induction in vitro. In B-type chronic lymphocytic leukemia (B-CLL), p53 gene mutations occur in a subset of patients and are associated with impaired survival and drug resistance. Here, we address the functional relevance of the codon 72 single nucleotide (SNP) polymorphism for cell death sensitivity following exposure to clinically employed cytotoxic drugs and gamma-irradiation. METHODS: 138 B-CLL samples were analysed by SSCP-PCR and sequencing for single nucleotide polymorphism at codon 72 of the p53 gene. The in vitro cytotoxicity assay (DiSC-assay) was performed with 7 drugs (chlorambucil, mafosfamide, fludarabine phosphate, methylprednisolone, doxorubicin, vincristine) or gamma-irradiation. RESULTS: Of the 138 B-CLL samples, 9 samples were homozygous for proline (Pro/Pro), 78 samples homozygous for arginine (Arg/Arg), and 49 samples heterozygous (Arg/Pro). No differences were found for patient survival and cell death triggered by 7 cytotoxic drugs or gamma-irradiation. CONCLUSION: These data indicate that polymorphic variants of p53 codon 72 are not clinically relevant for apoptosis induction or patient survival in B-CLL

Molecular and genetic factors involved in olfactory and gustatory deficits and associations with microbiota in parkinson’s disease

Deficits in olfaction and taste are among the most frequent non-motor manifestations in Parkinson’s disease (PD) that start very early and frequently precede the PD motor symptoms. The limited data available suggest that the basis of the olfactory and gustatory dysfunction related to PD are likely multifactorial and may include the same determinants responsible for other non-motor symptoms of PD. This review describes the most relevant molecular and genetic factors involved in the PD-related smell and taste impairments, and their associations with the microbiota, which also may represent risk factors associated with the disease

A Close Look at Star Formation around Active Galactic Nuclei

We analyse star formation in the nuclei of 9 Seyfert galaxies at spatial resolutions down to 0.085arcsec, corresponding to length scales of less than 10pc in some objects. Our data were taken mostly with the near infrared adaptive optics integral field spectrograph SINFONI. The stellar light profiles typically have size scales of a few tens of parsecs. In two cases there is unambiguous kinematic evidence for stellar disks on these scales. In the nuclear regions there appear to have been recent - but no longer active - starbursts in the last 10-300Myr. The stellar luminosity is less than a few percent of the AGN in the central 10pc, whereas on kiloparsec scales the luminosities are comparable. The surface stellar luminosity density follows a similar trend in all the objects, increasing steadily at smaller radii up to 10^{13}L_sun/kpc^2 in the central few parsecs, where the mass surface density exceeds 10^4M_sun/pc^2. The intense starbursts were probably Eddington limited and hence inevitably short-lived, implying that the starbursts occur in multiple short bursts. The data hint at a delay of 50--100Myr between the onset of star formation and subsequent fuelling of the black hole. We discuss whether this may be a consequence of the role that stellar ejecta could play in fuelling the black hole. While a significant mass is ejected by OB winds and supernovae, their high velocity means that very little of it can be accreted. On the other hand winds from AGB stars ultimately dominate the total mass loss, and they can also be accreted very efficiently because of their slow speeds.Comment: 51 pages, including 27 figures; accepted by ApJ (paper reorganised, but results & conclusions the same

The Nature of Composite LINER/HII Galaxies, As Revealed from High-Resolution VLA Observations

A sample of 37 nearby galaxies displaying composite LINER/HII and pure HII spectra was observed with the VLA in an investigation of the nature of their weak radio emission. The resulting radio contour maps overlaid on optical galaxy images are presented here, together with an extensive literature list and discussion of the individual galaxies. Radio morphological data permit assessment of the ``classical AGN'' contribution to the global activity observed in these ``transition'' LINER galaxies. One in five of the latter objects display clear AGN characteristics: these occur exclusively in bulge-dominated hosts.Comment: 31 pages, 27 figures, accepted by ApJ

Infrared Spectroscopy of a Massive Obscured Star Cluster in the Antennae Galaxies (NGC 4038/4039) with NIRSPEC

We present infrared spectroscopy of the Antennae Galaxies (NGC 4038/4039) with NIRSPEC at the W. M. Keck Observatory. We imaged the star clusters in the vicinity of the southern nucleus (NGC 4039) in 0.39" seeing in K-band using NIRSPEC's slit-viewing camera. The brightest star cluster revealed in the near-IR (M_K(0) = -17.9) is insignificant optically, but coincident with the highest surface brightness peak in the mid-IR (12-18 micron) ISO image presented by Mirabel et al. (1998). We obtained high signal-to-noise 2.03 - 2.45 micron spectra of the nucleus and the obscured star cluster at R ~ 1900. The cluster is very young (4 Myr old), massive (16e6 M_sun), and compact (density ~ 115 M_sun pc^(-3) within a 32 pc half-light radius), assuming a Salpeter IMF (0.1 - 100 M_sun). Its hot stars have a radiation field characterized by T_eff ~ 39,000 K, and they ionize a compact H II region with n_e ~ 1e4 cm^(-3). The stars are deeply embedded in gas and dust (A_V ~ 9-10 mag), and their strong FUV field powers a clumpy photodissociation region with densities n_H >= 1e5 cm^(-3) on scales of up to 200 pc, radiating L[H_2 1-0 S(1)] = 9600 L_sun.Comment: 4 pages, 5 embedded figures. To appear in proceedings of 33d ESLAB Symposium: Star Formation from the Small to the Large Scale, held in Noordwijk, The Netherlands, Nov. 1999. Also available at http://astro.berkeley.edu/~agilber