Nucleic Acid Substrates: Investigation of Structural and Dynamic Features that Influence Enzyme Activity

The previous view of DNA as a linear sequence of bases is evolving to consider structure, topology and dynamics. Sequences surrounding damage lesions have been shown to effect enzyme recognition and processing. Here we present an in depth investigation of subtle structural and dynamical features imparted to nucleic acid duplexes by a designed modification or damage lesions. Highly restrained solution structures were generated and validated utilizing a range of NMR techniques. This allowed for the characterization of multiple features of the nucleic acid duplex; such as base pairing, backbone torsion angles, deoxyribose sugar pucker, and intra and inter nucleotide proton distances. Additional experiments provided insight into dynamic movements of the nucleic bases. These features are then correlated to enzyme data in order to explain the observed modulation of activity

Geographic Patterns of Early Holocene New World Dental Morphological Variation

Dental anthropology played a seminal role in early studies of the peopling of the New World, and was a foundation of the early three wave model proposed by Greenberg, Turner and Zegura. In recent years, however, developments in anthropological genetics, craniometry, and archaeological discoveries have largely omit-ted dental anthropology from debates regarding Native American origins. Here we consider this situation and reassert dental anthropology\u27s relevance to the topic by presenting an inter-individual analysis of Paleoindian and Paleoamerican dentitions. A small set of dental morphological variables was used to estimate Gower similarity coefficients between individual specimens. The resulting similarity matrix was ordinated using multidimensional scaling; all analyses were per-formed in Clustan v. 7.05. While results should be considered preliminary, patterns of variation suggest morphological similarity along both coasts of North and South America with a somewhat distinct grouping of North American Paleoindians deriving from more inland portions of the continent. This pattern is consistent with recent genetic scenarios, notably the bicoastal model presented by O\u27Rourke and Raff (2010), which indicates that Paleoindians may have taken multiple migration routes from Beringia, moving along both coasts as well as through the ice free corridor. Future studies may build on this work to reintegrate dental data and analysis into research concerning the peopling of the New World

The Light Curve of the Weakly-Accreting T Tauri Binary KH 15D from 2005-10: Insights into the Nature of its Protoplanetary Disk

Photometry of the unique pre-main sequence binary system KH 15D is presented, spanning the years 2005-2010. This system has exhibited photometric variations and eclipses over the last 50 years caused by a precessing circumbinary disk. Advancement of the occulting edge across the binary orbit has continued and the photospheres of both stars are now completely obscured at all times. The system is now visible only by scattered light, and yet it continues to show a periodic variation on the orbital cycle with an amplitude exceeding two magnitudes. This variation, which depends only on the binary phase, has likely been present in the data since at least 1995. It can, by itself, account for shoulders on the light curve prior to ingress and following egress, obviating the need for components of extant models such as a scattering halo around star A or forward scattering from a fuzzy disk edge. A plausible source for the variable scattering component is reflected light from the far side of a warped occulting disk. We have detected color changes in V-I of several tenths of a magnitude to both the blue and red that occur during times of minima. These may indicate the presence of a third source of light (faint star) within the system, or a change in the reflectance properties of the disk as the portion being illuminated varies with the orbital motion of the stars. The data support a picture of the circumbinary disk as a geometrically thin, optically thick layer of perhaps mm or cm-sized particles that has been sculpted by the binary stars and possibly other components into a decidedly nonplanar configuration. A simple (infinitely sharp) knife-edge model does a good job of accounting for all of the recent (2005-2010) occultation data.Comment: To appear in The Astronomical Journa

Unusual DNA Structure and DNA Damage Recognition: Structure and Dynamic Markers

Nucleic acids play a central role in many biological processes, including information storage, gene expression, serving as messengers or structural components and even catalysis. Their diverse roles have made them targets of interest to diagnose and treat an array of human disorders such as infections, degenerative diseases and cancer. Nature has evolved proteins and ligands that recognize specific nucleic acid sequences or structures and control their function, demonstrating that this can be efficiently accomplished. This has led to the development of wide variety of synthetic molecules that selectively bind to nucleic acids. In turn, this has precipitated numerous studies which showed that nucleic acid structures and their dynamic properties must be understood in order to efficiently target specific sequences or structures

On the work distribution for the adiabatic compression of a dilute classical gas

We consider the adiabatic and quasi-static compression of a dilute classical gas, confined in a piston and initially equilibrated with a heat bath. We find that the work performed during this process is described statistically by a gamma distribution. We use this result to show that the model satisfies the non-equilibrium work and fluctuation theorems, but not the flucutation-dissipation relation. We discuss the rare but dominant realizations that contribute most to the exponential average of the work, and relate our results to potentially universal work distributions.Comment: 4 page

Male-biased predation and its effect on paternity skew and life history in a population of common brushtail possums (Trichosurus vulpecula)

Differences in predation risk may exert strong selective pressures on life history strategies of populations. We investigated the potential for predation to shape male mating strategies in an arboreal folivore, the common brushtail possum (Trichosurus vulpecula Kerr). We predicted that possums in a tropical population exposed to high natural levels of predation would grow faster and reproduce earlier compared to those in temperate populations with lower predation. We trapped a population of possums in eucalypt woodland in northern Australia each month to measure life history traits and used microsatellites to genotype all individuals and assign paternity to all offspring. We observed very high levels of male-biased predation, with almost 60% of marked male possums being eaten by pythons, presumably as a result of their greater mobility due to mate-searching. Male reproductive success was also highly skewed, with younger, larger males fathering significantly more offspring. This result contrasts with previous studies of temperate populations experiencing low levels of predation, where older males were larger and the most reproductively successful. Our results suggest that in populations exposed to high levels of predation, male possums invest in increased growth earlier in life, in order to maximise their mating potential. This strategy is feasible because predation limits competition from older males and means that delaying reproduction carries a risk of failing to reproduce at all. Our results show that life histories are variable traits that can match regional predation environments in mammal species with widespread distributions.This work was supported by the Australian Research Council http://www.arc.gov.au/ Grant number DP0449621 to CNJ, DP0449544 to WJF. JLD was supported by an Australian National University Graduate School Scholarship

Complex Variability of the Hα\alpha Emission Line Profile of the T Tauri Binary System KH 15D: The Influence of Orbital Phase, Occultation by the Circumbinary Disk, and Accretion Phenomenae

We have obtained 48 high resolution echelle spectra of the pre-main sequence eclipsing binary system KH~15D (V582 Mon, P = 48.37 d, $e$ $\sim$ 0.6, M$_{A}$ = 0.6 M$_{\odot}$, M$_{B}$ = 0.7 M$_{\odot}$). The eclipses are caused by a circumbinary disk seen nearly edge on, which at the epoch of these observations completely obscured the orbit of star B and a large portion of the orbit of star A. The spectra were obtained over five contiguous observing seasons from 2001/2002 to 2005/2006 while star A was fully visible, fully occulted, and during several ingress and egress events. The H$\alpha$ line profile shows dramatic changes in these time series data over timescales ranging from days to years. A fraction of the variations are due to "edge effects" and depend only on the height of star A above or below the razor sharp edge of the occulting disk. Other observed variations depend on the orbital phase: the H$\alpha$ emission line profile changes from an inverse P Cygni type profile during ingress to an enhanced double-peaked profile, with both a blue and red emission component, during egress. Each of these interpreted variations are complicated by the fact that there is also a chaotic, irregular component present in these profiles. We find that the complex data set can be largely understood in the context of accretion onto the stars from a circumbinary disk with gas flows as predicted by the models of eccentric T Tauri binaries put forward by Artymowicz & Lubow, G\"{u}nther & Kley, and de Val-Borro et al. In particular, our data provide strong support for the pulsed accretion phenomenon, in which enhanced accretion occurs during and after perihelion passage.Comment: accepted to Ap

Simulated herbivory : the key to disentangling plant defence responses

Plants are subjected to a multitude of stimuli during insect herbivory, resulting in a complex and cumulative defence response. Breaking down the components of herbivory into specific stimuli and identifying the mechanisms of defence associated with them has thus far been challenging. Advances in our understanding of responses to inconspicuous stimuli, such as those induced by microbial symbionts in herbivore secretions and mechanical stimulation caused by insects, have illuminated the intricacies of herbivory. Here, we provide a synthesis of the interacting impacts of herbivory on plants and the consequential complexities associated with uncoupling defence responses. We propose that simulated herbivory should be used to complement true herbivory to decipher the mechanisms of insect herbivore-induced plant defence responses