Precisely full length, circularizable, complementary RNA: An infectious form of potato spindle tuber viroid

The replication of many viral and subviral pathogens as well as the amplification of certain cellular genes proceeds via a rolling circle mechanism. For potato spindle tuber (PSTVd) and related viroids, the possible role of a circular (−)strand RNA as a template for synthesis of (+)strand progeny is unclear. Infected plants appear to contain only multimeric linear (−)strand RNAs, and attempts to initiate infection with multimeric (−)PSTVd RNAs generally have failed. To examine critically the infectivity of monomeric (−)strand viroid RNAs, we have developed a ribozyme-based expression system for the production of precisely full length (−)strand RNAs whose termini are capable of undergoing facile circularization in vitro. Mechanical inoculation of tomato seedlings with electrophoretically purified (−)PSTVd RNA led to a small fraction of plants becoming infected whereas parallel assays with an analogous tomato planta macho viroid (−)RNA resulted in a much larger fraction of infected plants. Ribozyme-mediated production of (−)PSTVd RNA in transgenic plants led to the appearance of monomeric circular (−)PSTVd RNA and large amounts of (+)PSTVd progeny. No monomeric circular (−)PSTVd RNA could be detected in naturally infected plants by using either ribonuclease protection or electrophoresis under partially denaturing conditions. Although not a component of the normal replicative pathway, precisely full length (−)PSTVd RNA appears to contain all of the structural and regulatory elements necessary for initiation of viroid replication.

Geochemistry of corals: Proxies of past ocean chemistry, ocean circulation, and climate

This paper presents a discussion of the status of the field of coral geochemistry as it relates to the recovery of past records of ocean chemistry, ocean circulation, and climate. The first part is a brief review of coral biology, density banding, and other important factors involved in understanding corals as proxies of environmental variables. The second part is a synthesis of the information available to date on extracting records of the carbon cycle and climate change. It is clear from these proxy records that decade time-scale variability of mixing processes in the oceans is a dominant signal. That Western and Eastern tropical Pacific El Niño-Southern Oscillation (ENSO) records differ is an important piece of the puzzle for understanding regional and global climate change. Input of anthropogenic CO2 to the oceans as observed by 13C and 14C isotopes in corals is partially obscured by natural variability. Nonetheless, the general trend over time toward lower δ18O values at numerous sites in the world’s tropical oceans suggests a gradual warming and/or freshening of the surface ocean over the past century.

A statistical mechanical model for β-hairpin kinetics

Understanding the mechanism of protein secondary structure formation is an essential part of the protein-folding puzzle. Here, we describe a simple statistical mechanical model for the formation of a β-hairpin, the minimal structural element of the antiparallel β-pleated sheet. The model accurately describes the thermodynamic and kinetic behavior of a 16-residue, β-hairpin-forming peptide, successfully explaining its two-state behavior and apparent negative activation energy for folding. The model classifies structures according to their backbone conformation, defined by 15 pairs of dihedral angles, and is further simplified by considering only the 120 structures with contiguous stretches of native pairs of backbone dihedral angles. This single sequence approximation is tested by comparison with a more complete model that includes the 215 possible conformations and 15 × 215 possible kinetic transitions. Finally, we use the model to predict the equilibrium unfolding curves and kinetics for several variants of the β-hairpin peptide.

Circuitry for color coding in the primate retina.

Human color vision starts with the signals from three cone photoreceptor types, maximally sensitive to long (L-cone), middle (M-cone), and short (S-cone) wavelengths. Within the retina these signals combine in an antagonistic way to form red-green and blue-yellow spectral opponent pathways. In the classical model this antagonism is thought to arise from the convergence of cone type-specific excitatory and inhibitory inputs to retinal ganglion cells. The circuitry for spectral opponency is now being investigated using an in vitro preparation of the macaque monkey retina. Intracellular recording and staining has shown that blue-ON/yellow-OFF opponent responses arise from a distinctive bistratified ganglion cell type. Surprisingly, this cone opponency appears to arise by dual excitatory cone bipolar cell inputs: an ON bipolar cell that contacts only S-cones and an OFF bipolar cell that contacts L- and M-cones. Red-green spectral opponency has long been linked to the midget ganglion cells, but an underlying mechanism remains unclear. For example, receptive field mapping argues for segregation of L-and M-cone signals to the midget cell center and surround, but horizontal cell interneurons, believed to generate the inhibitory surround, lack opponency and cannot contribute selective L- or M-cone input to the midget cell surround. The solution to this color puzzle no doubt lies in the great diversity of cell types in the primate retina that still await discovery and analysis.

Phylogenetic relationships of the hoatzin, an enigmatic South American bird.

The hoatzin (Opisthocomus hoazin) lives in the humid lowlands of northern and central South America, often in riparian habitats. It is a slender bird approximately 65 cm in length, brownish with lighter streaks and buffy tips to the long tail feathers. The small head has a ragged, bristly crest of reddish-brown feathers, and the bare skin of the face is bright blue. It resembles a chachalaca (Ortalis, Cracidae) in size and shape, but its plumage and markings are similar to those of the smaller guira cuckoo (Guira guira). The hoatzin (pronounced Watson) has been a taxonomic puzzle since it was described in 1776. It usually has been viewed as related to the gallinaceous birds, but alliances to other groups have been suggested, including the cuckoos. We present DNA sequence evidence from the 12S and 16S rRNA mitochondrial genes, and from the nuclear gene that codes for the eye lens protein, alpha A-crystallin. The results indicate that the hoatzin is most closely related to the typical cuckoos and that the divergence occurred at or near the base of the cuculiform phylogenetic tree.

No surviving evolved companions of the progenitor of SN 1006

Type Ia supernovae are thought to occur when a white dwarf made of carbon and oxygen accretes sufficient mass to trigger a thermonuclear explosion(1). The accretion could be slow, from an unevolved (main-sequence) or evolved (subgiant or giant) star(2,3) (the single-degenerate channel), or rapid, as the primary star breaks up a smaller orbiting white dwarf(3,4) (the double-degenerate channel). A companion star will survive the explosion only in the single-degenerate channel(5). Both channels might contribute to the production of type Ia supernovae(6,7), but the relative proportions of their contributions remain a fundamental puzzle in astronomy. Previous searches for remnant companions have revealed one possible case for SN 1572 (refs 8, 9), although that has been questioned(10). More recently, observations have restricted surviving companions to be small, main-sequence stars(11-13), ruling out giant companions but still allowing the single-degenerate channel. Here we report the results of a search for surviving companions of the progenitor of SN 1006 (ref. 14). None of the stars within 4 arc minutes of the apparent site of the explosion is associated with the supernova remnant, and we can firmly exclude all giant and subgiant stars from being companions of the progenitor. In combination with previous results, our findings indicate that fewer than 20 per cent of type Ia supernovae occur through the single-degenerate channel.

Ethnic Violence on Kenya's Periphery: Informal Institutions and Local Resilience in Conflict-Affected Communities

Deadly, inter-ethnic group conflict remains a threat to international security in a world where the majority of armed violence occurs not only within states but in the most ungoverned areas within states. Conflicts that occur between groups living in largely ungoverned areas often become deeply protracted and are difficult to resolve when the state is weak and harsh environmental conditions place human security increasingly under threat. However, even under these conditions, why do some local conflicts between ethnic groups escalate, whereas others do not? To analyze this puzzle, the dissertation employs comparative methods to investigate the conditions under which violence erupts or stops and armed actors choose to preserve peace. The project draws upon qualitative data derived from semi-structured interviews, focus group dialogues, and participant observation of local peace processes during field research conducted in six conflict-affected counties in Northern Kenya. Comparative analysis of fifteen conflict episodes with variable outcomes reveals the conditions under which coalitions of civic associations, including local peace committees, faith-based organizations, and councils of elders, inter alia, enhance informal institutional arrangements that contain escalation. Violence is less likely to escalate in communities where cohesive coalitions provide platforms for threat-monitoring, informal pact making, and enforcement of traditional codes of restitution. However, key scope conditions affect whether or not informal organizational structures are capable of containing escalation. In particular, symbolic acts of violence and the use of indiscriminant force by police and military actors commonly undermine local efforts to contain conflict. The dissertation contributes to the literatures on civil society and peacebuilding, demonstrating the importance of comparing processes of escalation and non-escalation and accounting for interactive effects between modes of state and non-state response to local, inter-ethnic group conflict.

Everyday Indivisibility: How Exclusive Religious Practices Explain Variation in Subnational Violence Outcomes

This project explores the puzzle of religious violence variation. Religious actors initiate conflict at a higher rate than their secular counterparts, last longer, are more deadly, and are less prone to negotiated termination. Yet the legacy of religious peacemakers on the reduction of violence is undeniable. Under what conditions does religion contribute to escalated violence and under what conditions does it contribute to peace? I argue that more intense everyday practices of group members, or high levels of orthopraxy, create dispositional indivisibilities that make violence a natural alternative to bargaining. Subnational armed groups with members whose practices are exclusive and isolating bind together through ritual practice, limit the acceptable decisions of leaders, and have prolonged timeframes, all of which result in higher levels of intensity, intransigence and resolve during violent conflict. The theory challenges both instrumentalist and constructivist understandings of social identity and violence. To support this argument, I construct an original cross-national data-set that employs ethnographic data on micro-level religious practices for 724 subnational armed groups in both civil wars and terror campaigns. Using this data, I build an explanatory “religious practice index” for each observation and examine its relationship with conflict outcomes. Findings suggest that exclusive practice groups fight significantly longer with more intensity and negotiate less. I also apply the practice model to qualitative cases. Fieldwork in the West Bank and Sierra Leone reveals that groups with more exclusive religious practicing membership are principle contributors to violence, whereas those with inclusive practices can contribute to peace. The project concludes with a discussion about several avenues for future research and identifies the practical policy applications to better identify and combat religious extremism.

The many lives of magnetized neutron stars

The magnetic field strength at birth is arguably one of the most important properties to determine the evolutionary path of a neutron star. Objects with very high fields, collectively known as magnetars, are characterized by high X-ray quiescent luminosities, occurrence of outbursts, and, for some of them, sporadic giant flares. While the magnetic field strength is believed to drive their collective behaviour, however, the diversity of their properties, and, especially, the observation of magnetar-like bursts from “low-field” pulsars, has been a theoretical puzzle. In this review, we discuss results of long-term simulations following the coupled evolution of the X-ray luminosity and the timing properties for a large, homogeneous sample of X-ray emitting isolated neutron stars, accounting for a range of initial magnetic field strengths, envelope compositions, and neutron star masses. In addition, by following the evolution of magnetic stresses within the neutron star crust, we can also relate the observed magnetar phenomenology to the physical properties of neutron stars, and in particular to their age and magnetic field strength and topology. The dichotomy of “high-B” field pulsars versus magnetars is naturally explained, and occasional outbursts from old, low B-field neutron stars are predicted. We conclude by speculating on the fate of old magnetars, and by presenting observational diagnostics of the neutron star crustal field topology.

Desarrollo de un videojuego basado en procesamiento de imágenes

El objetivo del proyecto consiste en crear un videojuego cuyos niveles se generen a partir del procesamiento de imágenes que el usuario podrá capturar con la cámara del móvil, o que podrá obtener de la galería de fotos del dispositivo. Se realizará una segmentación de la imagen y se extraerán así los elementos a utilizar en el juego, como por ejemplo zonas por las que poder movernos con un personaje, o bien piezas de un puzzle que debamos volver a construir. El videojuego se implementará con el motor Cocos2d-x.