Limitations of the Rhesus Macaque Draft Genome Assembly and Annotation

Finished genome sequences and assemblies are available for only a few vertebrates. Thus, investigators studying many species must rely on draft genomes. Using the rhesus macaque as an example, we document the effects of sequencing errors, gaps in sequence and misassemblies on one automated gene model pipeline, Gnomon. The combination of draft genome with automated gene finding software can result in spurious sequences. We estimate that approximately 50% of the rhesus gene models are missing, incomplete or incorrect. The problems identified in this work likely apply to all draft vertebrate genomes annotated with any automated gene model pipeline and thus represent a pervasive challenge to the analysis of draft genomes

Formation of pedestalled, relict lakes on the McMurdo Ice Shelf, Antarctica

ABSTRACTSurface debris covers much of the western portion of the McMurdo Ice Shelf and has a strong influence on the local surface albedo and energy balance. Differential ablation between debris-covered and debris-free areas creates an unusual heterogeneous surface of topographically low, high-ablation, and topographically raised (‘pedestalled’), low-ablation areas. Analysis of Landsat and MODIS satellite imagery from 1999 to 2018, alongside field observations from the 2016/2017 austral summer, shows that pedestalled relict lakes (‘pedestals’) form when an active surface meltwater lake that develops in the summer, freezes-over in winter, resulting in the lake-bottom debris being masked by a high-albedo, superimposed, ice surface. If this ice surface fails to melt during a subsequent melt season, it experiences reduced surface ablation relative to the surrounding debris-covered areas of the ice shelf. We propose that this differential ablation, and resultant hydrostatic and flexural readjustments of the ice shelf, causes the former supraglacial lake surface to become increasingly pedestalled above the lower topography of the surrounding ice shelf. Consequently, meltwater streams cannot flow onto these pedestalled features, and instead divert around them. We suggest that the development of pedestals has a significant influence on the surface-energy balance, hydrology and flexure of the ice shelf.Ia

Diurnal seismicity cycle linked to subsurface melting on an ice shelf

ABSTRACTSeismograms acquired on the McMurdo Ice Shelf, Antarctica, during an Austral summer melt season (November 2016–January 2017) reveal a diurnal cycle of seismicity, consisting of hundreds of thousands of small ice quakes limited to a 6–12 hour period during the evening, in an area where there is substantial subsurface melting. This cycle is explained by thermally induced bending and fracture of a frozen surface superimposed on a subsurface slush/water layer that is supported by solar radiation penetration and absorption. A simple, one-dimensional model of heat transfer driven by observed surface air temperature and shortwave absorption reproduces the presence and absence (as daily weather dictated) of the observed diurnal seismicity cycle. Seismic event statistics comparing event occurrence with amplitude suggest that the events are generated in a fractured medium featuring relatively low stresses, as is consistent with a frozen surface superimposed on subsurface slush. Waveforms of the icequakes are consistent with hydroacoustic phases at frequency ${\bf \gt} \bf 75\,{\bf Hz}$ and flexural-gravity waves at frequency $\bf {\bf \lt}25\,{\bf Hz}$. Our results suggest that seismic observation may prove useful in monitoring subsurface melting in a manner that complements other ground-based methods as well as remote sensing.</jats:p

Inter-Intra Molecular Dynamics as an Iterated Function System

The dynamics of units (molecules) with slowly relaxing internal states is studied as an iterated function system (IFS) for the situation common in e.g. biological systems where these units are subjected to frequent collisional interactions. It is found that an increase in the collision frequency leads to successive discrete states that can be analyzed as partial steps to form a Cantor set. By considering the interactions among the units, a self-consistent IFS is derived, which leads to the formation and stabilization of multiple such discrete states. The relevance of the results to dynamical multiple states in biomolecules in crowded conditions is discussed.Comment: 7 pages, 7 figures. submitted to Europhysics Letter

Supersymmetry in the shadow of photini

Additional neutral gauge fermions -- "photini" -- arise in string compactifications as superpartners of U(1) gauge fields. Unlike their vector counterparts, the photini can acquire weak-scale masses from soft SUSY breaking and lead to observable signatures at the LHC through mass mixing with the bino. In this work we investigate the collider consequences of adding photini to the neutralino sector of the MSSM. Relatively large mixing of one or more photini with the bino can lead to prompt decays of the lightest ordinary supersymmetric particle; these extra cascades transfer most of the energy of SUSY decay chains into Standard Model particles, diminishing the power of missing energy as an experimental handle for signal discrimination. We demonstrate that the missing energy in SUSY events with photini is reduced dramatically for supersymmetric spectra with MSSM neutralinos near the weak scale, and study the effects on limits set by the leading hadronic SUSY searches at ATLAS and CMS. We find that in the presence of even one light photino the limits on squark masses from hadronic searches can be reduced by 400 GeV, with comparable (though more modest) reduction of gluino mass limits. We also consider potential discovery channels such as dilepton and multilepton searches, which remain sensitive to SUSY spectra with photini and can provide an unexpected route to the discovery of supersymmetry. Although presented in the context of photini, our results apply in general to theories in which additional light neutral fermions mix with MSSM gauginos.Comment: 23 pages, 8 figures, references adde

Positronium Portal into Hidden Sector: A new Experiment to Search for Mirror Dark Matter

The understanding of the origin of dark matter has great importance for cosmology and particle physics. Several interesting extensions of the standard model dealing with solution of this problem motivate the concept of hidden sectors consisting of SU(3)xSU(2)_LxU(1)_Y singlet fields. Among these models, the mirror matter model is certainly one of the most interesting. The model explains the origin of parity violation in weak interactions, it could also explain the baryon asymmetry of the Universe and provide a natural ground for the explanation of dark matter. The mirror matter could have a portal to our world through photon-mirror photon mixing (epsilon). This mixing would lead to orthopositronium (o-Ps) to mirror orthopositronium oscillations, the experimental signature of which is the apparently invisible decay of o-Ps. In this paper, we describe an experiment to search for the decay o-Ps -> invisible in vacuum by using a pulsed slow positron beam and a massive 4pi BGO crystal calorimeter. The developed high efficiency positron tagging system, the low calorimeter energy threshold and high hermiticity allow the expected sensitivity in mixing strength to be epsilon about 10^-9, which is more than one order of magnitude below the current Big Bang Nucleosynthesis limit and in a region of parameter space of great theoretical and phenomenological interest. The vacuum experiment with such sensitivity is particularly timely in light of the recent DAMA/LIBRA observations of the annual modulation signal consistent with a mirror type dark matter interpretation.Comment: 40 pages, 29 Figures 2 Tables v2: Ref. added, Fig. 29 and some text added to explain idea for backscattering e+ background suppression, corrected typos v3: minor corrections: Eq 2.1 corrected (6 lines-> 5 lines), Eq.2.17: two extra "-" signs remove

Dark Force Detection in Low Energy e-p Collisions

We study the prospects for detecting a light boson X with mass m_X < 100 MeV at a low energy electron-proton collider. We focus on the case where X dominantly decays to e+ e- as motivated by recent "dark force" models. In order to evade direct and indirect constraints, X must have small couplings to the standard model (alpha_X 10 MeV). By comparing the signal and background cross sections for the e- p e+ e- final state, we conclude that dark force detection requires an integrated luminosity of around 1 inverse attobarn, achievable with a forthcoming JLab proposal.Comment: 38 pages, 19 figures; v2, references adde

Calving and rifting on the McMurdo Ice Shelf, Antarctica

ABSTRACTOn 2 March 2016, several small en échelon tabular icebergs calved from the seaward front of the McMurdo Ice Shelf, and a previously inactive rift widened and propagated by ~3 km, ~25% of its previous length, setting the stage for the future calving of a ~14 km2 iceberg. Within 24 h of these events, all remaining land-fast sea ice that had been stabilizing the ice shelf broke-up. The events were witnessed by time-lapse cameras at nearby Scott Base, and put into context using nearby seismic and automatic weather station data, satellite imagery and subsequent ground observation. Although the exact trigger of calving and rifting cannot be identified definitively, seismic records reveal superimposed sets of both long-period (&gt;10 s) sea swell propagating into McMurdo Sound from storm sources beyond Antarctica, and high-energy, locally-sourced, short-period (&lt;10 s) sea swell, in the 4 days before the fast ice break-up and associated ice-shelf calving and rifting. This suggests that sea swell should be studied further as a proximal cause of ice-shelf calving and rifting; if proven, it suggests that ice-shelf stability is tele-connected with far-field storm conditions at lower latitudes, adding a global dimension to the physics of ice-shelf break-up.</jats:p