641 research outputs found
DNA-Based Diet Analysis for Any Predator
Background: Prey DNA from diet samples can be used as a dietary marker; yet current methods for prey detection require a
priori diet knowledge and/or are designed ad hoc, limiting their scope. I present a general approach to detect diverse prey
in the feces or gut contents of predators.
Methodology/Principal Findings: In the example outlined, I take advantage of the restriction site for the endonuclease Pac
I which is present in 16S mtDNA of most Odontoceti mammals, but absent from most other relevant non-mammalian
chordates and invertebrates. Thus in DNA extracted from feces of these mammalian predators Pac I will cleave and exclude
predator DNA from a small region targeted by novel universal primers, while most prey DNA remain intact allowing prey
selective PCR. The method was optimized using scat samples from captive bottlenose dolphins (Tursiops truncatus) fed a
diet of 6–10 prey species from three phlya. Up to five prey from two phyla were detected in a single scat and all but one
minor prey item (2% of the overall diet) were detected across all samples. The same method was applied to scat samples
from free-ranging bottlenose dolphins; up to seven prey taxa were detected in a single scat and 13 prey taxa from eight
teleost families were identified in total.
Conclusions/Significance: Data and further examples are provided to facilitate rapid transfer of this approach to any predator.
This methodology should prove useful to zoologists using DNA-based diet techniques in a wide variety of study systems
Optically trapped bacteria pairs reveal discrete motile response to control aggregation upon cell–cell approach
Aggregation of bacteria plays a key role in the formation of many biofilms. The critical first step is cell–cell approach, and yet the ability of bacteria to control the likelihood of aggregation during this primary phase is unknown. Here, we use optical tweezers to measure the force between isolated Bacillus subtilis cells during approach. As we move the bacteria towards each other, cell motility (bacterial swimming) initiates the generation of repulsive forces at bacterial separations of ~3 μm. Moreover, the motile response displays spatial sensitivity with greater cell–cell repulsion evident as inter-bacterial distances decrease. To examine the environmental influence on the inter-bacterial forces, we perform the experiment with bacteria suspended in Tryptic Soy Broth, NaCl solution and deionised water. Our experiments demonstrate that repulsive forces are strongest in systems that inhibit biofilm formation (Tryptic Soy Broth), while attractive forces are weak and rare, even in systems where biofilms develop (NaCl solution). These results reveal that bacteria are able to control the likelihood of aggregation during the approach phase through a discretely modulated motile response. Clearly, the force-generating motility we observe during approach promotes biofilm prevention, rather than biofilm formation
Measurements in two bases are sufficient for certifying high-dimensional entanglement
High-dimensional encoding of quantum information provides a promising method
of transcending current limitations in quantum communication. One of the
central challenges in the pursuit of such an approach is the certification of
high-dimensional entanglement. In particular, it is desirable to do so without
resorting to inefficient full state tomography. Here, we show how carefully
constructed measurements in two bases (one of which is not orthonormal) can be
used to faithfully and efficiently certify bipartite high-dimensional states
and their entanglement for any physical platform. To showcase the practicality
of this approach under realistic conditions, we put it to the test for photons
entangled in their orbital angular momentum. In our experimental setup, we are
able to verify 9-dimensional entanglement for a pair of photons on a
11-dimensional subspace each, at present the highest amount certified without
any assumptions on the state.Comment: 11+14 pages, 2+7 figure
Soliton pair dynamics in patterned ferromagnetic ellipses
Confinement alters the energy landscape of nanoscale magnets, leading to the
appearance of unusual magnetic states, such as vortices, for example. Many
basic questions concerning dynamical and interaction effects remain unanswered,
and nanomagnets are convenient model systems for studying these fundamental
physical phenomena. A single vortex in restricted geometry, also known as a
non-localized soliton, possesses a characteristic translational excitation mode
that corresponds to spiral-like motion of the vortex core around its
equilibrium position. Here, we investigate, by a microwave reflection
technique, the dynamics of magnetic soliton pairs confined in lithographically
defined, ferromagnetic Permalloy ellipses. Through a comparison with
micromagnetic simulations, the observed strong resonances in the subgigahertz
frequency range can be assigned to the translational modes of vortex pairs with
parallel or antiparallel core polarizations. Vortex polarizations play a
negligible role in the static interaction between two vortices, but their
effect dominates the dynamics.Comment: supplemental movies on
http://www.nature.com/nphys/journal/v1/n3/suppinfo/nphys173_S1.htm
CP violation Beyond the MSSM: Baryogenesis and Electric Dipole Moments
We study electroweak baryogenesis and electric dipole moments in the presence
of the two leading-order, non-renormalizable operators in the Higgs sector of
the MSSM. Significant qualitative and quantitative differences from MSSM
baryogenesis arise due to the presence of new CP-violating phases and to the
relaxation of constraints on the supersymmetric spectrum (in particular, both
stops can be light). We find: (1) spontaneous baryogenesis, driven by a change
in the phase of the Higgs vevs across the bubble wall, becomes possible; (2)
the top and stop CP-violating sources can become effective; (3) baryogenesis is
viable in larger parts of parameter space, alleviating the well-known
fine-tuning associated with MSSM baryogenesis. Nevertheless, electric dipole
moments should be measured if experimental sensitivities are improved by about
one order of magnitude.Comment: 33 pages, 6 figure
The Relationship Between HR Practices and Firm Performance: Examining Causal Order
Significant research attention has been devoted to examining the relationship between HR practices and firm performance, and the research support has assumed HR as the causal variable. Using data from 45 business units (with 62 data points), this study examines how measures of HR practices correlate with past, concurrent, and future operational performance measures. The results indicate that correlations with performance measures at all three times are both high and invariant, and that controlling for past or concurrent performance virtually eliminates the correlation of HR with future performance. Implications are discussed
MEF2A regulates mGluR-dependent AMPA receptor trafficking independently of Arc/Arg3.1
© 2018 The Author(s). Differential trafficking of AMPA receptors (AMPARs) to and from the postsynaptic membrane is a key determinant of the strength of excitatory neurotransmission, and is thought to underlie learning and memory. The transcription factor MEF2 is a negative regulator of memory in vivo, in part by regulating trafficking of the AMPAR subunit GluA2, but the molecular mechanisms behind this have not been established. Here we show, via knockdown of endogenous MEF2A in primary neuronal culture, that MEF2A is specifically required for Group I metabotropic glutamate receptor (mGluR)-mediated GluA2 internalisation, but does not regulate AMPAR expression or trafficking under basal conditions. Furthermore, this process occurs independently of changes in expression of Arc/Arg3.1, a previously characterised MEF2 transcriptional target and mediator of mGluR-dependent long-term depression. These data demonstrate a novel MEF2A-dependent mechanism for the regulation of activity-dependent AMPAR trafficking
Parameter estimation for robust HMM analysis of ChIP-chip data
Tiling arrays are an important tool for the study of transcriptional activity, protein-DNA interactions and chromatin structure on a genome-wide scale at high resolution. Although hidden Markov models have been used successfully to analyse tiling array data, parameter estimation for these models is typically ad hoc. Especially in the context of ChIP-chip experiments, no standard procedures exist to obtain parameter estimates from the data. Common methods for the calculation of maximum likelihood estimates such as the Baum-Welch algorithm or Viterbi training are rarely applied in the context of tiling array analysis. Results: Here we develop a hidden Markov model for the analysis of chromatin structure ChIP-chip tiling array data, using t emission distributions to increase robustness towards outliers. Maximum likelihood estimates are used for all model parameters. Two different approaches to parameter estimation are investigated and combined into an efficient procedure. Conclusion: We illustrate an efficient parameter estimation procedure that can be used for HMM based methods in general and leads to a clear increase in performance when compared to the use of ad hoc estimates. The resulting hidden Markov model outperforms established methods like TileMap in the context of histone modification studies.13 page(s
Echoes from Ancient Supernovae in the Large Magellanic Cloud
In principle, the light from historical supernovae could still be visible as
scattered-light echoes even centuries later. However, while echoes have been
discovered around some nearby extragalactic supernovae well after the
explosion, targeted searches have not recovered any echoes in the regions of
historical Galactic supernovae. The discovery of echoes can allow us to
pinpoint the supernova event both in position and age and, most importantly,
allow us to acquire spectra of the echo light to type the supernova centuries
after the direct light from the explosion first reached the Earth. Here we
report on the discovery of three faint new variable surface brightness
complexes with high apparent proper motion pointing back to well-defined
positions in the Large Magellanic Cloud (LMC). These positions correspond to
three of the six smallest (and likely youngest) previously catalogued supernova
remnants, and are believed to be due to thermonuclear (Type Ia) supernovae.
Using the distance and proper motions of these echo arcs, we estimate ages of
610 and 410 yr for the echoes #2 and #3.Comment: 13 pages, 3 figures, 1 table. PDF format. Note: This paper has been
accepted by Nature for publication as a letter. It is embargoed for
discussion in the popular press until publication in Natur
Monkeys and Humans Share a Common Computation for Face/Voice Integration
Speech production involves the movement of the mouth and other regions of the face resulting in visual motion cues. These visual cues enhance intelligibility and detection of auditory speech. As such, face-to-face speech is fundamentally a multisensory phenomenon. If speech is fundamentally multisensory, it should be reflected in the evolution of vocal communication: similar behavioral effects should be observed in other primates. Old World monkeys share with humans vocal production biomechanics and communicate face-to-face with vocalizations. It is unknown, however, if they, too, combine faces and voices to enhance their perception of vocalizations. We show that they do: monkeys combine faces and voices in noisy environments to enhance their detection of vocalizations. Their behavior parallels that of humans performing an identical task. We explored what common computational mechanism(s) could explain the pattern of results we observed across species. Standard explanations or models such as the principle of inverse effectiveness and a “race” model failed to account for their behavior patterns. Conversely, a “superposition model”, positing the linear summation of activity patterns in response to visual and auditory components of vocalizations, served as a straightforward but powerful explanatory mechanism for the observed behaviors in both species. As such, it represents a putative homologous mechanism for integrating faces and voices across primates
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