Road blocks on paleogenomes - polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA

Although the last few years have seen great progress in DNA sequence retrieval from fossil specimens, some of the characteristics of ancient DNA remain poorly understood. This is particularly true for blocking lesions, i.e. chemical alterations that cannot be bypassed by DNA polymerases and thus prevent amplification and subsequent sequencing of affected molecules. Some studies have concluded that the vast majority of ancient DNA molecules carry blocking lesions, suggesting that the removal, repair or bypass of blocking lesions might dramatically increase both the time depth and geographical range of specimens available for ancient DNA analysis. However, previous studies used very indirect detection methods that did not provide conclusive estimates on the frequency of blocking lesions in endogenous ancient DNA. We developed a new method, polymerase extension profiling (PEP), that directly reveals occurrences of polymerase stalling on DNA templates. By sequencing thousands of single primer extension products using PEP methodology, we have for the first time directly identified blocking lesions in ancient DNA on a single molecule level. Although we found clear evidence for blocking lesions in three out of four ancient samples, no more than 40% of the molecules were affected in any of the samples, indicating that such modifications are far less frequent in ancient DNA than previously thought

Why Do Curly Tail Lizards (Genus Leiocephalus) Curl Their Tails? An Assessment of Displays Toward Conspecifics and Predators

Animal display behaviors are used to convey specific messages to other animals, including potential mates, rivals, and predators. However, because these different types of interactions can be mediated by a single behavioral display, or conversely, multiple signals can be used to convey one specific message, interpretation of any particular behavioral display can be difficult. Leiocephalus lizards (i.e., curly tails) provide an excellent opportunity to study the use of display behaviors across multiple contexts. Previous research has demonstrated that the use of tail curling in these lizards is associated with predation risk, but less is known regarding the use of this behavior in social interactions with conspecifics. The goal of this study was to determine the extent to which tail curling display behavior is used to mediate both social and predatory interactions in two species, Leiocephalus barahonensis and L. carinatus. We found that in lizards of both species, tail curling was used in interactions with both conspecifics and potential (human) predators. However, tail curl intensity did not differ between lizards involved in social encounters and solitary lizards, although L. barahonensis lizards performed more headbobs during social than non-social observations. Further, L. carinatus lizards exhibited greater intensity of tail curling upon fleeing from a human predator than during observations in which individuals interacted with conspecifics, and lizards that exhibited tighter tail curls fled from predators for a longer distance. Finally, tail curl intensity was not correlated with headbob displays in either species, suggesting that these two components of display communicate different information. Our results suggest that tail curling displays, while consistently a component of interactions with potential predators, are not a necessary component of social interactions. These data contribute to a more complete understanding of how and why visual signals evolve for use in communication across multiple contexts

The Evolution of Androgen Receptor Expression and Behavior in \u3cem\u3eAnolis\u3c/em\u3e Lizard Forelimb Muscles

The motor systems that produce behavioral movements are among the primary targets for the action of steroid hormones, including androgens. Androgens such as testosterone bind to androgen receptors (AR) to induce physiological changes in the size, strength, and energetic capacity of skeletal muscles, which can directly influence the performance of behaviors in which those muscles are used. Because tissues differentially express AR, resulting in tissue-specific sensitivity to androgens, AR expression may be a major target of selection for the evolution of behavior. Anolis lizards (i.e., anoles) provide a robust system for the study of androgen-regulated traits, including the behavioral traits that facilitate social display and locomotion. In this study, we examined six anole species that demonstrate significant variation in the behavioral use of the forelimbs to measure the proportion of myonuclei in the bicep muscles that express AR. Using phylogenetic comparative analyses, we found that species with a greater proportion of nuclei positive for AR expression in the biceps exhibited greater frequencies of locomotor movements and pushup displays. These results suggest that AR expression in skeletal muscles may influence the evolution of androgen-regulated behaviors in this group

Status report of the CMS superconducting coil project

The CMS superconducting coil is designed for one of the two large experiments of LHC at CERN. This coil 12.5 m long, 6 m diameter and 2.7 GJ stored energy is a common project of the CMS Collaboration. It is a four-layer coil, equipped with a self-supporting conductor capable of carrying 20 kA to reach the maximum potential field of 4 T. It has been designed with a considerable contribution from CEA- Saclay for the engineering, ETH-Zurich for the conductor, INFN-Genova for the winding and CERN for the general coordination and construction of the ancillaries. The project entered the construction phase one year ago. The civil engineering is well advanced and ready to accept part of the yoke components already built. The coil itself has finished the pre-industrialization phase and the construction is beginning in industry. Most of the important contracts have been awarded and the foreseen schedule is now based on contractual engagements. A quick overview of the features of the project as well as a status report of the main activities are given. (6 refs)

Risk Assessment Plan for Petroleum Underground Storage Tanks in Kentucky

This study addresses the development of guidelines for corrective actions to be applied to petroleum underground storage tanks (USTs) within the Commonwealth of Kentucky. The report presents findings and recommendations for gasoline, diesel fuel, heating oil, kerosene, jet fuel, and waste oil

Rational Design of a Chalcogenopyrylium-Based Surface-Enhanced Resonance Raman Scattering-Nanoprobe with Attomolar Sensitivity

High sensitivity and specificity are two desirable features in biomedical imaging. Raman imaging has surfaced as a promising optical modality that offers both. Here, we report the design and synthesis of a group of near infrared absorbing 2-thienyl-substituted chalcogenopyrylium dyes tailored to have high affinity for gold. When adsorbed onto gold nanoparticles, these dyes produce biocompatible SERRS-nanoprobes with attomolar limits of detection amenable to ultrasensitive in vivo multiplexed tumor and disease marker detection