The nicotinic acetylcholine receptor subunit family expressed in the central nervous system of the freshwater snail Lymnaea stagnalis: Molecular and functional diversity of the neuronal nicotinic acetylcholine receptors in a molluscan species

Smit, A.B. [Promotor

Distributed SUSY Breaking: Dark Energy, Newton's Law and the LHC

We identify the underlying symmetry mechanism that suppresses the low-energy effective 4D cosmological constant within 6D supergravity models, leading to results suppressed by powers of the KK scale relative to the much larger masses associated with particles localized on codimension-2 branes. In these models the conditions for unbroken supersymmetry can be satisfied locally everywhere within the extra dimensions, but are obstructed by global conditions like flux quantization or the mutual inconsistency of boundary conditions at the various branes. Consequently quantities forbidden by supersymmetry cannot be nonzero until wavelengths of order the KK scale are integrated out, since only such long wavelength modes see the entire space and so know that supersymmetry breaks. We verify these arguments by extending earlier rugby-ball calculations of one-loop vacuum energies to more general pairs of branes within two warped extra dimensions. The predicted effective 4D vacuum energy density can be of order C (m Mg/4 pi Mp)^4, where Mg (Mp) is the rationalized 6D (4D) Planck scale and m is the heaviest brane-localized particle. Numerically this is C (5.6 x 10^{-5} eV)^4 if we take m = 173 GeV and take Mg as small as possible (10 TeV corresponding to KK size r < 1 micron), consistent with supernova bounds. C is a constant depending on details of the bulk spectrum, which could be ~ 500 for each of hundreds of fields. The value C ~ 6 x 10^6 gives the observed Dark Energy density

Gravitational Forces on a Codimension-2 Brane

We compute the gravitational response of six dimensional gauged, chiral supergravity to localized stress energy on one of two space-filling branes, including the effects of compactifying the extra dimensions and brane back-reaction. We find a broad class of exact solutions, including various black-brane solutions. Several approximate solutions are also described, such as the near-horizon geometry of a small black hole which is argued to be approximately described by a 6D Schwarzschild (or Kerr) black hole, with event horizon appropriately modified to encode the brane back-reaction. The general linearized far-field solutions are found in the 4D regime very far from the source, and all integration constants are related to physical quantities describing the branes and the localized energy source. The localized source determines two of these, corresponding to the source mass and the size of the strength of a coupling to a 4D scalar mode whose mass is parametrically smaller than the KK scale. At large distances the solutions agree with those of 4D general relativity, but for an intermediate range of distances (larger than the KK scale) the solutions better fit a Brans-Dicke theory. For a realistic choice of parameters the KK scale could lie at a micron, while the crossover to Brans-Dicke behaviour could occur at around 10 microns. While allowed by present data this points to potentially measurable changes to Newton's Law arising at distances larger than the KK scale.Comment: 31 pages + appendices, 2 figure

Running with Rugby Balls: Bulk Renormalization of Codimension-2 Branes

We compute how one-loop bulk effects renormalize both bulk and brane effective interactions for geometries sourced by codimension-two branes. We do so by explicitly integrating out spin-zero, -half and -one particles in 6-dimensional Einstein-Maxwell-Scalar theories compactified to 4 dimensions on a flux-stabilized 2D geometry. (Our methods apply equally well for D dimensions compactified to D-2 dimensions, although our explicit formulae do not capture all divergences when D>6.) The renormalization of bulk interactions are independent of the boundary conditions assumed at the brane locations, and reproduce standard heat-kernel calculations. Boundary conditions at any particular brane do affect how bulk loops renormalize this brane's effective action, but not the renormalization of other distant branes. Although we explicitly compute our loops using a rugby ball geometry, because we follow only UV effects our results apply more generally to any geometry containing codimension-two sources with conical singularities. Our results have a variety of uses, including calculating the UV sensitivity of one-loop vacuum energy seen by observers localized on the brane. We show how these one-loop effects combine in a surprising way with bulk back-reaction to give the complete low-energy effective cosmological constant, and comment on the relevance of this calculation to proposed applications of codimension-two 6D models to solutions of the hierarchy and cosmological constant problems.Comment: 42 pages + appendices. This is the final version which appears in JHE

Accidental SUSY: Enhanced Bulk Supersymmetry from Brane Back-reaction

We compute how bulk loops renormalize both bulk and brane effective interactions for codimension-two branes in 6D gauged chiral supergravity, as functions of the brane tension and brane-localized flux. We do so by explicitly integrating out hyper- and gauge-multiplets in 6D gauged chiral supergravity compactified to 4D on a flux-stabilized 2D rugby-ball geometry, specializing the results of a companion paper, arXiv:1210.3753, to the supersymmetric case. While the brane back-reaction generically breaks supersymmetry, we show that the bulk supersymmetry can be preserved if the amount of brane-localized flux is related in a specific BPS-like way to the brane tension, and verify that the loop corrections to the brane curvature vanish in this special case. In these systems it is the brane-bulk couplings that fix the size of the extra dimensions, and we show that in some circumstances the bulk geometry dynamically adjusts to ensure the supersymmetric BPS-like condition is automatically satisfied. We investigate the robustness of this residual supersymmetry to loops of non-supersymmetric matter on the branes, and show that supersymmetry-breaking effects can enter only through effective brane-bulk interactions involving at least two derivatives. We comment on the relevance of this calculation to proposed applications of codimension-two 6D models to solutions of the hierarchy and cosmological constant problems.Comment: 49 pages + appendices. This is the final version to appear in JHE

Transcriptome analysis of the central nervous system of the mollusc Lymnaea stagnalis

Background: The freshwater snail Lymnaea stagnalis (L. stagnalis) has served as a successful model for studies in the field of Neuroscience. However, a serious drawback in the molecular analysis of the nervous system of L. stagnalis has been the lack of large-scale genomic or neuronal transcriptome information, thereby limiting the use of this unique model. Results: In this study, we report 7,712 distinct EST sequences (median length: 847 nucleotides) of a normalized L. stagnalis central nervous system (CNS) cDNA library, resulting in the largest collection of L. stagnalis neuronal transcriptome data currently available. Approximately 42% of the cDNAs can be translated into more than 100 consecutive amino acids, indicating the high quality of the library. The annotated sequences contribute 12% of the predicted transcriptome size of 20,000. Surprisingly, approximately 37% of the L. stagnalis sequences only have a tBLASTx hit in the EST library of another snail species Aplysia californica (A. californica) even using a low stringency e-value cutoff at 0.01. Using the same cutoff, approximately 67% of the cDNAs have a BLAST hit in the NCBI non-redundant protein and nucleotide sequence databases (nr and nt), suggesting that one third of the sequences may be unique to L. stagnalis. Finally, using the same cutoff (0.01), more than half of the cDNA sequences (54%) do not have a hit in nematode, fruitfly or human genome data, suggesting that the L. stagnalis transcriptome is significantly different from these species as well. The cDNA sequences are enriched in the following gene ontology functional categories: protein binding, hydrolase, transferase, and catalytic enzymes. Conclusion: This study provides novel molecular insights into the transcriptome of an important molluscan model organism. Our findings will contribute to functional analyses in neurobiology, and comparative evolutionary biology. The L. stagnalis CNS EST database is available at http://www.Lymnaea.org/. © 2009 Feng et al; licensee BioMed Central Ltd

Synaptic proteome changes in a DNA repair deficient Ercc1 mouse model of accelerated aging

Cognitive decline is one of the earliest hallmarks of both normal and pathological brain aging. Here we used Ercc1 mutant mice, which are impaired in multiple DNA repair systems and consequently show accelerated aging and progressive memory deficits, to identify changes in the levels of hippocampal synaptic proteins that potentially underlie these age-dependent deficits. Aged Ercc1 mutant mice show normal gross hippocampal dendritic morphology and synapse numbers, and Ercc1 mutant hippocampal neurons displayed normal outgrowth and synapse formation in vitro. However, using isobaric tag for relative and absolute quantification (iTRAQ) of hippocampal synaptic proteins at two different ages, postnatal days 28 and 112, we observed a progressive decrease in synaptic ionotropic glutamate receptor levels and increased levels of G-proteins and of cell adhesion proteins. These together may cause long-term changes in synapse function. In addition, we observed a downregulation of mitochondrial proteins and concomitant upregulation of Na,K-ATPase subunits, which might compensate for reduced mitochondrial activity. Thus, our findings show that under conditions of apparent intact neuronal connectivity, levels of specific synaptic proteins are already affected during the early stages of DNA damage-induced aging, which might contribute to age-dependent cognitive decline

Sculpting the Extra Dimensions: Inflation from Codimension-2 Brane Back-reaction

We construct an inflationary model in 6D supergravity that is based on explicit time-dependent solutions to the full higher-dimensional field equations, back-reacting to the presence of a 4D inflaton rolling on a space-filling codimension-2 source brane. Fluxes in the bulk stabilize all moduli except the `breathing' modulus (that is generically present in higher-dimensional supergravities). Back-reaction to the inflaton roll causes the 4D Einstein-frame on-brane geometry to expand, a(t) ~ t^p, as well as exciting the breathing mode and causing the two off-brane dimensions to expand, r(t) ~ t^q. The model evades the general no-go theorems precluding 4D de Sitter solutions, since adjustments to the brane-localized inflaton potential allow the power p to be dialed to be arbitrarily large, with the 4D geometry becoming de Sitter in the limit p -> infinity (in which case q = 0). Slow-roll solutions give accelerated expansion with p large but finite, and q = 1/2. Because the extra dimensions expand during inflation, the present-day 6D gravity scale can be much smaller than it was when primordial fluctuations were generated - potentially allowing TeV gravity now to be consistent with the much higher gravity scale required at horizon-exit for observable primordial gravity waves. Because p >> q, the 4 on-brane dimensions expand more quickly than the 2 off-brane ones, providing a framework for understanding why the observed four dimensions are presently so much larger than the internal two. If uplifted to a 10D framework with 4 dimensions stabilized, the 6D evolution described here could describe how two of the six extra dimensions evolve to become much larger than the others, as a consequence of the enormous expansion of the 4 large dimensions we can see.Comment: 27 pages + appendices, 2 figure

Concerted nicking of donor and chromosomal acceptor DNA promotes homology-directed gene targeting in human cells

The exchange of genetic information between donor and acceptor DNA molecules by homologous recombination (HR) depends on the cleavage of phosphodiester bonds. Although double-stranded and single-stranded DNA breaks (SSBs) have both been invoked as triggers of HR, until very recently the focus has been primarily on the former type of DNA lesions mainly due to the paucity of SSB-based recombination models. Here, to investigate the role of nicked DNA molecules as HR-initiating substrates in human somatic cells, we devised a homology-directed gene targeting system based on exogenous donor and chromosomal target DNA containing recognition sequences for the adeno-associated virus sequence- and strand-specific endonucleases Rep78 and Rep68. We found that HR is greatly fostered if a SSB is not only introduced in the chromosomal acceptor but also in the donor DNA template. Our data are consistent with HR models postulating the occurrence of SSBs or single-stranded gaps in both donor and acceptor molecules during the genetic exchange process. These findings can guide the development of improved HR-based genome editing strategies in which sequence- and strand-specific endonucleolytic cleavage of the chromosomal target site is combined with that of the targeting vector