Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño.

BackgroundGene regulatory variation has been proposed to play an important role in the adaptation of plants to environmental stress. In the central highlands of Mexico, farmer selection has generated a unique group of maize landraces adapted to the challenges of the highland niche. In this study, gene expression in Mexican highland maize and a reference maize breeding line were compared to identify evidence of regulatory variation in stress-related genes. It was hypothesised that local adaptation in Mexican highland maize would be associated with a transcriptional signature observable even under benign conditions.MethodsAllele specific expression analysis was performed using the seedling-leaf transcriptome of an F1 individual generated from the cross between the highland adapted Mexican landrace Palomero Toluqueño and the reference line B73, grown under benign conditions. Results were compared with a published dataset describing the transcriptional response of B73 seedlings to cold, heat, salt and UV treatments.ResultsA total of 2,386 genes were identified to show allele specific expression. Of these, 277 showed an expression difference between Palomero Toluqueño and B73 alleles under benign conditions that anticipated the response of B73 cold, heat, salt and/or UV treatments, and, as such, were considered to display a prior stress response. Prior stress response candidates included genes associated with plant hormone signaling and a number of transcription factors. Construction of a gene co-expression network revealed further signaling and stress-related genes to be among the potential targets of the transcription factors candidates.DiscussionPrior activation of responses may represent the best strategy when stresses are severe but predictable. Expression differences observed here between Palomero Toluqueño and B73 alleles indicate the presence of cis-acting regulatory variation linked to stress-related genes in Palomero Toluqueño. Considered alongside gene annotation and population data, allele specific expression analysis of plants grown under benign conditions provides an attractive strategy to identify functional variation potentially linked to local adaptation

Room temperature "optical nanodiamond hyperpolarizer": Physics, design, and operation.

Dynamic Nuclear Polarization (DNP) is a powerful suite of techniques that deliver multifold signal enhancements in nuclear magnetic resonance (NMR) and MRI. The generated athermal spin states can also be exploited for quantum sensing and as probes for many-body physics. Typical DNP methods require the use of cryogens, large magnetic fields, and high power microwave excitation, which are expensive and unwieldy. Nanodiamond particles, rich in Nitrogen-Vacancy (NV) centers, have attracted attention as alternative DNP agents because they can potentially be optically hyperpolarized at room temperature. Here, unraveling new physics underlying an optical DNP mechanism first introduced by Ajoy et al. [Sci. Adv. 4, eaar5492 (2018)], we report the realization of a miniature "optical nanodiamond hyperpolarizer," where 13C nuclei within the diamond particles are hyperpolarized via the NV centers. The device occupies a compact footprint and operates at room temperature. Instrumental requirements are very modest: low polarizing fields, low optical and microwave irradiation powers, and convenient frequency ranges that enable miniaturization. We obtain the best reported optical 13C hyperpolarization in diamond particles exceeding 720 times of the thermal 7 T value (0.86% bulk polarization), corresponding to a ten-million-fold gain in averaging time to detect them by NMR. In addition, the hyperpolarization signal can be background-suppressed by over two-orders of magnitude, retained for multiple-minute long periods at low fields, and deployed efficiently even to 13C enriched particles. Besides applications in quantum sensing and bright-contrast MRI imaging, this work opens possibilities for low-cost room-temperature DNP platforms that relay the 13C polarization to liquids in contact with the high surface-area particles

Top pair Asymmetries at Hadron colliders with general Z′Z' couplings

Recently it has been shown that measurement of charge asymmetry of top pair production at LHC excludes any flavor violating $Z'$ vector gauge boson that could explain Tevatron forward-backward asymmetry (FBA). We consider the general form of a $Z'$ gauge boson including left-handed, right-handed vector and tensor couplings to examine FBA and charge asymmetry. To evaluate top pair asymmetries at Tevatron and LHC, we consider $B^0_q$ mixing constraints on flavor changing $Z'$ couplings and show that this model still explain forward-backward asymmetry at Tevatron and charge asymmetry can not exclude it in part of parameters space.Comment: 18 pages, 7 figure

Z' signals in polarised top-antitop final states

We study the sensitivity of top-antitop samples produced at all energy stages of the Large Hadron Collider (LHC) to the nature of an underlying Z' boson, in presence of full tree level standard model (SM) background effects and relative interferences. We concentrate on differential mass spectra as well as both spatial and spin asymmetries thereby demonstrating that exploiting combinations of these observables will enable one to distinguish between sequential Z's and those pertaining to Left-Right symmetric models as well as E6 inspired ones, assuming realistic final state reconstruction efficiencies and error estimates.Comment: 21 pages, 6 colour figures, 10 table

Predictions from Heavy New Physics Interpretation of the Top Forward-Backward Asymmetry

We derive generic predictions at hadron colliders from the large forward-backward asymmetry observed at the Tevatron, assuming the latter arises from heavy new physics beyond the Standard Model. We use an effective field theory approach to characterize the associated unknown dynamics. By fitting the Tevatron t \bar t data we derive constraints on the form of the new physics. Furthermore, we show that heavy new physics explaining the Tevatron data generically enhances at high invariant masses both the top pair production cross section and the charge asymmetry at the LHC. This enhancement can be within the sensitivity of the 8 TeV run, such that the 2012 LHC data should be able to exclude a large class of models of heavy new physics or provide hints for its presence. The same new physics implies a contribution to the forward-backward asymmetry in bottom pair production at low invariant masses of order a permil at most.Comment: 11 pages, 6 figures. v2: added remarks on EFT validity range, dijet bounds and UV completions; matches published versio

Chiral U(1) flavor models and flavored Higgs doublets: the top FB asymmetry and the Wjj

We present U(1) flavor models for leptophobic Z' with flavor dependent couplings to the right-handed up-type quarks in the Standard Model, which can accommodate the recent data on the top forward-backward (FB) asymmetry and the dijet resonance associated with a W boson reported by CDF Collaboration. Such flavor-dependent leptophobic charge assignments generally require extra chiral fermions for anomaly cancellation. Also the chiral nature of U(1)' flavor symmetry calls for new U(1)'-charged Higgs doublets in order for the SM fermions to have realistic renormalizable Yukawa couplings. The stringent constraints from the top FB asymmetry at the Tevatron and the same sign top pair production at the LHC can be evaded due to contributions of the extra Higgs doublets. We also show that the extension could realize cold dark matter candidates.Comment: 40 pages, 10 figures, added 1 figure and extended discussion, accepted for publication in JHE

Novel signatures for vector-like quarks

We consider supersymmetric extensions of the standard model with a vector-like doublet (T B) of quarks with charge 2/3 and −1/3, respectively. Compared to non-supersymmetric models, there is a variety of new decay modes for the vector-like quarks, involving the extra scalars present in supersymmetry. The importance of these new modes, yielding multi-top, multi-bottom and also multi-Higgs signals, is highlighted by the analysis of several benchmark scenarios. We show how the triangles commonly used to represent the branching ratios of the ‘standard’ decay modes of the vector-like quarks involving W, Z or Higgs bosons can be generalised to include additional channels. We give an example by recasting the limits of a recent heavy quark search for this more general case.The work of J.A. Aguilar-Saavedra has been supported by MINECO Projects FPA 2016- 78220-C3-1-P and FPA 2013-47836-C3-2-P (including ERDF), and by Junta de Andaluc a Project FQM-101. The work of D.E. L opez-Fogliani has been supported by the Argentinian CONICET. The work of C. Mu~noz has been supported in part by the Programme SEV- 2012-0249 `Centro de Excelencia Severo Ochoa'. D.E. L opez-Fogliani and C. Mu~noz also acknowledge the support of the Spanish grant FPA2015-65929-P (MINECO/FEDER, UE), and MINECO's Consolider-Ingenio 2010 Programme under grant MultiDark CSD2009- 00064

High contrast dual-mode optical and 13C magnetic resonance imaging in diamond particles

Multichannel imaging -- the ability to acquire images of an object through more than one imaging mode simultaneously -- has opened interesting new perspectives in areas ranging from astronomy to medicine. Visible optics and magnetic resonance imaging (MRI) offer complementary advantages of resolution, speed and depth of penetration, and as such would be attractive in combination. In this paper, we take first steps towards marrying together optical and MR imaging in a class of biocompatible particulate materials constructed out of diamond. The particles are endowed with a high density of quantum defects (Nitrogen Vacancy centers) that under optical excitation fluoresce brightly in the visible, but also concurrently electron spin polarize. This allows the hyperpolarization of lattice 13C nuclei to make the particles over three-orders of magnitude brighter than in conventional MRI. Dual-mode optical and MR imaging permits immediate access to improvements in resolution and signal-to-noise especially in scattering environments. We highlight additional benefits in background-free imaging, demonstrating lock-in suppression by factors of 2 and 5 in optical and MR domains respectively. Ultimate limits could approach as much as two orders of magnitude in each domain. Finally, leveraging the ability of optical and MR imaging to simultaneously probe Fourier-reciprocal domains (real and k-space), we elucidate the ability to employ hybrid sub-sampling in both conjugate spaces to vastly accelerate dual-image acquisition, by as much as two orders of magnitude in practically relevant sparse-imaging scenarios. This is accompanied by a reduction in optical power by the same factor. Our work suggests interesting possibilities for the simultaneous optical and low-field MR imaging of targeted diamond nanoparticles

Explaining the t tbar forward-backward asymmetry without dijet or flavor anomalies

We consider new physics explanations of the anomaly in the top quark forward-backward asymmetry measured at the Tevatron, in the context of flavor conserving models. The recently measured LHC dijet distributions strongly constrain many otherwise viable models. A new scalar particle in the antitriplet representation of flavor and color can fit the t tbar asymmetry and cross section data at the Tevatron and avoid both low- and high-energy bounds from flavor physics and the LHC. An s-channel resonance in uc to uc scattering at the LHC is predicted to be not far from the current sensitivity. This model also predicts rich top quark physics for the early LHC from decays of the new scalar particles. Single production gives t tbar j signatures with high transverse momentum jet, pair production leads to t tbar j j and 4 jet final states.Comment: 7 pages, 6 figures; v2: notation clarified, references adde