Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro

BACKGROUND: Mycobacterium bovis, the causative agent of bovine tuberculosis, is an intracellular pathogen that can persist inside host macrophages during infection via a diverse range of mechanisms that subvert the host immune response. In the current study, we have analysed and compared the transcriptomes of M. bovis-infected monocyte-derived macrophages (MDM) purified from six Holstein-Friesian females with the transcriptomes of non-infected control MDM from the same animals over a 24 h period using strand-specific RNA sequencing (RNA-seq). In addition, we compare gene expression profiles generated using RNA-seq with those previously generated by us using the high-density Affymetrix® GeneChip® Bovine Genome Array platform from the same MDM-extracted RNA. RESULTS: A mean of 7.2 million reads from each MDM sample mapped uniquely and unambiguously to single Bos taurus reference genome locations. Analysis of these mapped reads showed 2,584 genes (1,392 upregulated; 1,192 downregulated) and 757 putative natural antisense transcripts (558 upregulated; 119 downregulated) that were differentially expressed based on sense and antisense strand data, respectively (adjusted P-value ≤ 0.05). Of the differentially expressed genes, 694 were common to both the sense and antisense data sets, with the direction of expression (i.e. up- or downregulation) positively correlated for 693 genes and negatively correlated for the remaining gene. Gene ontology analysis of the differentially expressed genes revealed an enrichment of immune, apoptotic and cell signalling genes. Notably, the number of differentially expressed genes identified from RNA-seq sense strand analysis was greater than the number of differentially expressed genes detected from microarray analysis (2,584 genes versus 2,015 genes). Furthermore, our data reveal a greater dynamic range in the detection and quantification of gene transcripts for RNA-seq compared to microarray technology. CONCLUSIONS: This study highlights the value of RNA-seq in identifying novel immunomodulatory mechanisms that underlie host-mycobacterial pathogen interactions during infection, including possible complex post-transcriptional regulation of host gene expression involving antisense RNA

Data regarding transplant induced germinal center humoral autoimmunity

This data is related to the research article entitled “Germinal center humoral autoimmunity independently mediates progression of allograft vasculopathy” (Harper et al., 2016) [2]. The data presented here focuses on the humoral autoimmune response triggered by transferred allogeneic CD4 T cells and includes details on: (a) the recipient splenic germinal center (GC) response; (b) augmentation of humoral autoimmunity and accelerated heart allograft rejection following transplantation from donors primed against recipient; (c) flow cytometric analysis of donor and recipient CD4 T cells for signature markers of T follicular helper cell differentiation; (d) in vitro donor endothelial cell migration in response to column purified autoantibody from recipient sera; (e) analysis of development of humoral responses in recipients following adoptive transfer of donor CD4 T cells and; (f) the development of humoral autoimmunity in mixed haematopoietic chimeric mice

The Conformal Sector of F-theory GUTs

D3-brane probes of exceptional Yukawa points in F-theory GUTs are natural hidden sectors for particle phenomenology. We find that coupling the probe to the MSSM yields a new class of N = 1 conformal fixed points with computable infrared R-charges. Quite surprisingly, we find that the MSSM only weakly mixes with the strongly coupled sector in the sense that the MSSM fields pick up small exactly computable anomalous dimensions. Additionally, we find that although the states of the probe sector transform as complete GUT multiplets, their coupling to Standard Model fields leads to a calculable threshold correction to the running of the visible sector gauge couplings which improves precision unification. We also briefly consider scenarios in which SUSY is broken in the hidden sector. This leads to a gauge mediated spectrum for the gauginos and first two superpartner generations, with additional contributions to the third generation superpartners and Higgs sector.Comment: v2: 51 pages, 2 figures, remark added, typos correcte

Anomalous U(1) Mediation in Large Volume Compactification

We study the general effects of anomalous U(1)_A gauge symmetry on soft supersymmetry (SUSY) breaking terms in large volume scenario, where the MSSM sector is localized on a small cycle whose volume is stabilized by the D-term potential of the U(1)_A. Since it obtains SUSY breaking mass regardless of the detailed form of K\"ahler potential, the U(1)_A vector superfield acts as a messenger mediating the SUSY breaking in the moduli sector to the MSSM sector. Then, through the loops of U(1)_A vector superfield, there arise soft masses of the order of m_{3/2}^2/8\pi^2 for scalar mass squares, m_{3/2}/(8\pi^2)^2 for gaugino masses, and m_{3/2}/8\pi^2 for A-paramteres. In addition, the massive U(1)_A vector superfield can have non-zero F and D-components through the moduli mixing in the K\"ahler potential, and this can result in larger soft masses depending upon the details of the moduli mixing. For instance, in the presence of one-loop induced moduli mixing between the visible sector modulus and the large volume modulus, the U(1)_A D-term provides soft scalar mass squares of the order of m_{3/2}^2. However, if the visible sector modulus is mixed only with small cycle moduli, its effect on soft terms depends on how to stabilize the small cycle moduli.Comment: 28pages, no fi

Sparticle Spectrum of Large Volume Compactification

We examine the large volume compactification of Type IIB string theory or its F theory limit and the associated supersymmetry breakdown and soft terms. It is crucial to incorporate the loop-induced moduli mixing, originating from radiative corrections to the Kahler potential. We show that in the presence of moduli mixing, soft scalar masses generically receive a D-term contribution of the order of the gravitino mass m_{3/2} when the visible sector cycle is stabilized by the D-term potential of an anomalous U(1) gauge symmetry, while the moduli-mediated gaugino masses and A-parameters tend to be of the order of m_{3/2}/8pi^2. It is noticed also that a too large moduli mixing can destabilize the large volume solution by making it a saddle point.Comment: 29 page

Kahler Independence of the G2-MSSM

The G2-MSSM is a model of particle physics coupled to moduli fields with interesting phenomenology both for colliders and astrophysical experiments. In this paper we consider a more general model - whose moduli Kahler potential is a completely arbitrary G2-holonomy Kahler potential and whose matter Kahler potential is also more general. We prove that the vacuum structure and spectrum of BSM particles is largely unchanged in this much more general class of theories. In particular, gaugino masses are still supressed relative to the gravitino mass and moduli masses. We also consider the effects of higher order corrections to the matter Kahler potential and find a connection between the nature of the LSP and flavor effects.Comment: Final version, matches the version published in JHE

The Two Faces of Anomaly Mediation

Anomaly mediation is a ubiquitous source of supersymmetry (SUSY) breaking which appears in almost every theory of supergravity. In this paper, we show that anomaly mediation really consists of two physically distinct phenomena, which we dub "gravitino mediation" and "Kahler mediation". Gravitino mediation arises from minimally uplifting SUSY anti-de Sitter (AdS) space to Minkowski space, generating soft masses proportional to the gravitino mass. Kahler mediation arises when visible sector fields have linear couplings to SUSY breaking in the Kahler potential, generating soft masses proportional to beta function coefficients. In the literature, these two phenomena are lumped together under the name "anomaly mediation", but here we demonstrate that they can be physically disentangled by measuring associated couplings to the goldstino. In particular, we use the example of gaugino soft masses to show that gravitino mediation generates soft masses without corresponding goldstino couplings. This result naively violates the goldstino equivalence theorem but is in fact necessary for supercurrent conservation in AdS space. Since gravitino mediation persists even when the visible sector is sequestered from SUSY breaking, we can use the absence of goldstino couplings as an unambiguous definition of sequestering.Comment: 21 pages, 1 table; v2, references added, extended discussion in introduction and appendix; v3, JHEP versio

Single-Scale Natural SUSY

We consider the prospects for natural SUSY models consistent with current data. Recent constraints make the standard paradigm unnatural so we consider what could be a minimal extension consistent with what we now know. The most promising such scenarios extend the MSSM with new tree-level Higgs interactions that can lift its mass to at least 125 GeV and also allow for flavor-dependent soft terms so that the third generation squarks are lighter than current bounds on the first and second generation squarks. We argue that a common feature of almost all such models is the need for a new scale near 10 TeV, such as a scale of Higgsing or confinement of a new gauge group. We consider the question whether such a model can naturally derive from a single mass scale associated with supersymmetry breaking. Most such models simply postulate new scales, leaving their proximity to the scale of MSSM soft terms a mystery. This coincidence problem may be thought of as a mild tuning, analogous to the usual mu problem. We find that a single mass scale origin is challenging, but suggest that a more natural origin for such a new dynamical scale is the gravitino mass, m_{3/2}, in theories where the MSSM soft terms are a loop factor below m_{3/2}. As an example, we build a variant of the NMSSM where the singlet S is composite, and the strong dynamics leading to compositeness is triggered by masses of order m_{3/2} for some fields. Our focus is the Higgs sector, but our model is compatible with a light stop (with the other generation squarks heavy, or with R-parity violation or another mechanism to hide them from current searches). All the interesting low-energy mass scales, including linear terms for S playing a key role in EWSB, arise dynamically from the single scale m_{3/2}. However, numerical coefficients from RG effects and wavefunction factors in an extra dimension complicate the otherwise simple story.Comment: 32 pages, 3 figures; version accepted by JHE

New Constraints (and Motivations) for Abelian Gauge Bosons in the MeV-TeV Mass Range

We survey the phenomenological constraints on abelian gauge bosons having masses in the MeV to multi-GeV mass range (using precision electroweak measurements, neutrino-electron and neutrino-nucleon scattering, electron and muon anomalous magnetic moments, upsilon decay, beam dump experiments, atomic parity violation, low-energy neutron scattering and primordial nucleosynthesis). We compute their implications for the three parameters that in general describe the low-energy properties of such bosons: their mass and their two possible types of dimensionless couplings (direct couplings to ordinary fermions and kinetic mixing with Standard Model hypercharge). We argue that gauge bosons with very small couplings to ordinary fermions in this mass range are natural in string compactifications and are likely to be generic in theories for which the gravity scale is systematically smaller than the Planck mass - such as in extra-dimensional models - because of the necessity to suppress proton decay. Furthermore, because its couplings are weak, in the low-energy theory relevant to experiments at and below TeV scales the charge gauged by the new boson can appear to be broken, both by classical effects and by anomalies. In particular, if the new gauge charge appears to be anomalous, anomaly cancellation does not also require the introduction of new light fermions in the low-energy theory. Furthermore, the charge can appear to be conserved in the low-energy theory, despite the corresponding gauge boson having a mass. Our results reduce to those of other authors in the special cases where there is no kinetic mixing or there is no direct coupling to ordinary fermions, such as for recently proposed dark-matter scenarios.Comment: 49 pages + appendix, 21 figures. This is the final version which appears in JHE