Associated Chromosome Trap for Identifying Long-range DNA Interactions

Genetic information encoded by DNA is organized in a complex and highly regulated chromatin structure. Each chromosome occupies a specific territory, that may change according to stage of development or cell cycle. Gene expression can occur in specialized transcriptional factories where chromatin segments may loop out from various chromosome territories, leading to co-localization of DNA segments which may exist on different chromosomes or far apart on the same chromosome. The Associated Chromosome Trap (ACT) assay provides an effective methodology to identify these long-range DNA associations in an unbiased fashion by extending and modifying the chromosome conformation capture technique. The ACT assay makes it possible for us to investigate mechanisms of transcriptional regulation in trans, and can help explain the relationship of nuclear architecture to gene expression in normal physiology and during disease states

A Context-based Approach to Robot-human Interaction

AbstractCARIL (Context-Augmented Robotic Interaction Layer) is a human-robot interaction system that leverages cognitive representations of shared context as a basis for a fundamentally new approach to human-robotic interaction. CARIL gives a robot a human-like representation of context and an ability to reason about context in order to adapt its behavior to that of the humans around it. This capability is “action compliance.” A prototype CARIL implementation focuses on a fundamental form of action compliance called non-interference -- “not being underfoot or in a human's way”. Non-interference is key for the safety of human-co-workers, and is also foundational to more complex interactive and teamwork skills. CARIL is tested via simulation in a space-exploration use-case. The live CARIL prototype directs a single simulated robot in a simulated space station where four simulated astronauts are engaging in a variety of tightly-scheduled work activities. The robot is scheduled to perform background tasks away from the astronauts, but must quickly adapt and not be underfoot as astronaut activities diverge from plan and encroach on the robot's space. The robot, driven by CARIL, demonstrates non-interference action compliance in three benchmarks situations, demonstrating the viability of the CARIL technology and concept

Polarization simulations of stellar wind bow shock nebulae. II. The case of dust scattering

We study the polarization produced by scattering from dust in a bow shock-shaped region of enhanced density surrounding a stellar source, using the Monte Carlo radiative transfer code SLIP. Bow shocks are structures formed by the interaction of the winds of fast-moving stars with the interstellar medium. Our previous study focused on the polarization produced in these structures by electron scattering; we showed that polarization is highly dependent on inclination angle and that multiple scattering changes the shape and degree of polarization. In contrast to electron scattering, dust scattering is wavelength-dependent, which changes the polarization behaviour. Here we explore different dust particle sizes and compositions and generate polarized spectral energy distributions for each case. We find that the polarization SED behaviour depends on the dust composition and grain size. Including dust emission leads to polarization changes with temperature at higher optical depth in ways that are sensitive to the orientation of the bow shock. In various scenarios and under certain assumptions, our simulations can constrain the optical depth and dust properties of resolved and unresolved bow shock-shaped scattering regions.Constraints on optical depth can provide estimates of local ISM density for observed bow shocks. We also study the impact of dust grains filling the region between the star and bow shock. We see that as the density of dust between the star and bow shock increases, the resulting polarization is suppressed for all the optical depth regimes.Comment: 21 pages, accepted for publication in MNRA

Individual and joint trajectories of change in bone, lean mass and physical performance in older men.

BackgroundDeclines in bone, muscle and physical performance are associated with adverse health outcomes in older adults. However, few studies have described concurrent age-related patterns of change in these factors. The purpose of this study was to characterize change in four properties of muscle, physical performance, and bone in a prospective cohort study of older men.MethodsUsing repeated longitudinal data from up to four visits across 6.9 years from up to 4681 men (mean age at baseline 72.7 yrs. ±5.3) participating in the Osteoporotic Fractures in Men (MrOS) Study, we used group-based trajectory models (PROC TRAJ in SAS) to identify age-related patterns of change in four properties of muscle, physical performance, and bone: total hip bone mineral (BMD) density (g/m2) and appendicular lean mass/ht2 (kg/m2), by DXA; grip strength (kg), by hand dynamometry; and walking speed (m/s), by usual walking pace over 6 m. We also described joint trajectories in all pair-wise combinations of these measures. Mean posterior probabilities of placement in each trajectory (or joint membership in latent groups) were used to assess internal reliability of the model. The number of trajectories for each individual factor was limited to three, to ensure that the pair-wise determination of joint trajectories would yield a tractable number of groups as well as model fit considerations.ResultsThe patterns of change identified were generally similar for all measures, with three district groups declining over time at roughly similar rates; joint trajectories revealed similar patterns with no cross-over or convergence between groups. Mean posterior probabilities for all trajectories were similar and consistently above 0.8 indicating reasonable model fit to the data.ConclusionsOur description of trajectories of change with age in bone mineral density, grip strength, walking speed and appendicular lean mass found that groups identified by these methods appeared to have little crossover or convergence of change with age, even when considering joint trajectories of change in these factors

Methionine synthase interreplacement in diatom cultures and communities : implications for the persistence of B12 use by eukaryotic phytoplankton

Author Posting. © Association for the Sciences of Limnology and Oceanography, 2013. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 58 (2013): 1431–1450, doi:10.4319/lo.2013.58.4.1431.Three proteins related to vitamin B12 metabolism in diatoms were quantified via selected reaction monitoring mass spectrometry: B12-dependent and B12-independent methionine synthase (MetH, MetE) and a B12 acquisition protein (CBA1). B12-mediated interreplacement of MetE and MetH metalloenzymes was observed in Phaeodactylum tricornutum where MetH abundance was highest (0.06 fmol µg−1 protein) under high B12 and MetE abundance increased to 3.25 fmol µg−1 protein under low B12 availability. Maximal MetE abundance was 60-fold greater than MetH, consistent with the expected ∼ 50–100-fold larger turnover number for MetH. MetE expression resulted in 30-fold increase in nitrogen and 40-fold increase in zinc allocated to methionine synthase activity under low B12. CBA1 abundance was 6-fold higher under low-B12 conditions and increased upon B12 resupply to starved cultures. While biochemical pathways that supplant B12 requirements exist and are utilized by organisms such as land plants, B12 use persists in eukaryotic phytoplankton. This study suggests that retention of B12 utilization by phytoplankton results in resource conservation under conditions of high B12 availability. MetE and MetH abundances were also measured in diatom communities from McMurdo Sound, verifying that both these proteins are expressed in natural communities. These protein measurements are consistent with previous studies suggesting that B12 availability influences Antarctic primary productivity. This study illuminates controls on expression of B12-related proteins, quantitatively assesses the metabolic consequences of B12 deprivation, and demonstrates that mass spectrometry–based protein measurements yield insight into the functioning of marine microbial communities.This work was supported by National Science Foundation (NSF) Antarctic Sciences awards 0732665, 1103503, and 0732822; NSF Division of Ocean Science awards 0752291, 0928414, and 1031271; The Gordon and Betty Moore Foundation; Center for Microbial Oceanography Research and Education; an NSF Graduate Research Fellowship (2007037200); and an Environmental Protection Agency Science To Achieve Results (EPA-STAR) Fellowship to E.M.B. (F6E720324)

Reflections: Academia's Emerging Crisis of Relevance and the Consequent Role of the Engaged Scholar

Universities are facing a crisis of relevance. While there are multiple reasons for this to be happening, one that deserves particular attention is the extent to which academic scholars do not see it as their role to engage in public and political discourse. However, increased engagement is unavoidable in an emerging educational context where the caliber of public discourse has become so degraded and social media is changing the nature of science and scientific discourse within society. Further, there is a demographic shift in play, where young scholars are seeking more impact from their work than their more senior colleagues. In this article, I begin the process of articulating what we know and what we don’t know about the evolving role of the engaged scholar by breaking the conversation into two parts. First, why should academic scholars engage in public and political discourse? Second, how can we structure a set of ground rules that could form what might be considered a handbook for public engagement? In the end, this article is about a reexamination of how we practice our craft, to what purpose and to which audiences.http://deepblue.lib.umich.edu/bitstream/2027.42/136168/1/1343_Hoffman.pd

A new short-faced archosauriform from the Upper Triassic Placerias/Downs’ quarry complex, Arizona, USA, expands the morphological diversity of the Triassic archosauriform radiation

The Placerias/Downs’ Quarry complex in eastern Arizona, USA, is the most diverse Upper Triassic vertebrate locality known. We report a new short-faced archosauriform, Syntomiprosopus sucherorum gen. et sp. nov., represented by four incomplete mandibles, that expands that diversity with a morphology unique among Late Triassic archosauriforms. The most distinctive feature of Syntomiprosopus gen. nov. is its anteroposteriorly short, robust mandible with 3–4 anterior, a larger caniniform, and 1–3 “postcanine” alveoli. The size and shape of the alveoli and the preserved tips of replacement teeth preclude assignment to any taxon known only from teeth. Additional autapomorphies of S. sucherorum gen. et sp. nov. include a large fossa associated with the mandibular fenestra, an interdigitating suture of the surangular with the dentary, fine texture ornamenting the medial surface of the splenial, and a surangular ridge that completes a 90° arc. The external surfaces of the mandibles bear shallow, densely packed, irregular, fine pits and narrow, arcuate grooves. This combination of character states allows an archosauriform assignment; however, an associated and similarly sized braincase indicates that Syntomiprosopus n. gen. may represent previously unsampled disparity in early-diverging crocodylomorphs. The Placerias Quarry is Adamanian (Norian, maximum depositional age ~219 Ma), and this specimen appears to be an early example of shortening of the skull, which occurs later in diverse archosaur lineages, including the Late Cretaceous crocodyliform Simosuchus. This is another case where Triassic archosauriforms occupied morphospace converged upon by other archosaurs later in the Mesozoic and further demonstrates that even well-sampled localities can yield new taxa