Spatially incoherent modulational instability in a non local medium

We investigate one-dimensional transverse modulational instability in a non local medium excited with a spatially incoherent source. Employing undoped nematic liquid crystals in a planar pre-tilted configuration, we investigate the role of the spectral broadening induced by incoherence in conjunction with the spatially non local molecular reorientation. The phenomenon is modeled using the Wigner transform.Comment: 13 pages with 4 figures included. To be published in Laser Physics Letter

Determining the Binding Between SAGA Subunits and Spliceosomal Components

Proper gene regulation is vital to the health and development of an organism. Determining the relationship between splicing, transcription, and chromatin structure is vital for understanding gene regulation as a whole. There have been previous studies linking these elements pairwise; however, no evidence exists for a direct link between all three. Recent data shows that splicing components of the U2 small nuclear ribonucleic protein (snRNP) co-purify with Spt-Ada-Gcn5-acetyltransferase (SAGA), a highly conserved transcriptional co-activator and chromatin modifier. We hypothesize that SAGA binds with splicing components through a multi-protein binding surface with certain core components based on preliminary yeast two-hybrid data. Here, we examine the specific binding partners between SAGA and splicing components utilizing the yeast two-hybrid system in spt7Δ Saccharomyces cerevisiae as a validation for the preliminary yeast two-hybrid performed, producing recombinant proteins through sequence and ligation-independent cloning (SLIC) and Baculovirus transfections to obtain purified proteins, and co-immunoprecipitation (co-IP) to detect specific protein-protein interactions from recombinant proteins. Yeast two-hybrid results reveal that Spt7 is necessary for the transcription of reporter genes used in this assay. Therefore, this assay cannot validate previous results or detect false positives. Currently, recombinant proteins are being produced to perform co-IPs to test direct protein interactions. The results from these experiments will demonstrate the type of binding between SAGA subunits and splicing factors and provide direct evidence of a link between all three of the elements of gene regulation

Altered gene expression associated with epizootic shell disease in the American lobster, Homarus americanus

Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Fish & Shellfish Immunology 29 (2010): 1003-1009, doi:10.1016/j.fsi.2010.08.008.Epizootic shell disease is a poorly understood condition that has significantly affected the American lobster fishery in New England (northeastern US) since the 1990s. Here we present the results of a study to identify changes in gene expression in lobsters exhibiting symptoms of epizootic shell disease. Suppressive subtractive hybridization (SSH) was used to compare gene expression between cDNA pools from diseased (symptomatic) and apparently healthy (asymptomatic) lobsters. Subsequently, quantitative real‐time polymerase chain reaction (qPCR) was used to measure expression of nine genes that were differentially‐expressed in the SSH analysis, in seven tissues (muscle, gill, heart, hepatopancreas, brain, branchiostegite, gonad) dissected from individual symptomatic and asymptomatic lobsters. Expression of arginine kinase (involved in cellular energetics) was significantly decreased in muscle of symptomatic lobsters. Expression of hemocyanin (a respiratory hemolymph protein involved in oxygen transport) was highest in hepatopancreas and showed highly variable expression with a trend toward higher expression in asymptomatic individuals. α2‐Macroglobulin (involved in the innate immune system) was most highly expressed in the ovary, particularly of symptomatic lobsters. The ESTs produced through this study add to the fledgling field of crustacean genomics and revealed three genes that could be further evaluated in lobsters of varying shell disease severity, molt stage, and reproductive condition, for possible implication in epizootic shell disease.Funding for this research was provided by the National Marine Fisheries Service as the ‘New England Lobster Research Initiative: Lobster Shell Disease’ under NOAA grant NA06NMF4720100 to the University of Rhode Island Fisheries Center

Coherently tunable third-order nonlinearity in a nanojunction

A possibility of tuning the phase of the third-order Kerr-type nonlinear susceptibility in a system consisting of two interacting metal nanospheres and a nonlinearly polarizable molecule is investigated theoretically and numerically. It is shown that by varying the relative inter-sphere separation, it is possible to tune the phase of the effective nonlinear susceptibility \chi^{(3)}(\omega;\omega,\omega,-\omega)$in the whole range from 0 to$2\pi$.Comment: 10 pages 5 figure

Cardiovascular gene expression profiles of dioxin exposure in zebrafish embryos

Author Posting. © The Authors, 2005. This is the author's version of the work. It is posted here by permission of Society of Toxicology for personal use, not for redistribution. The definitive version was published in Toxicological Sciences 85 (2005): 683-693, doi:10.1093/toxsci/kfi116.2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a widespread environmental contaminant that causes altered heart morphology, circulatory impairment, edema, hemorrhage, and early life stage mortality in fish. TCDD toxicity is largely dependent upon the aryl hydrocarbon receptor, but understanding of the molecular mechanism of cardiovascular embryotoxicity remains incomplete. In order to identify genes potentially involved in cardiovascular impacts, we constructed custom cDNA microarrays consisting of 4,896 zebrafish adult heart cDNA clones and over 200 genes with known developmental, toxicological, and housekeeping roles. Gene expression profiles were obtained for 3-day old zebrafish following early embryonic exposure to either 0.5 or 5.0 nM TCDD. 516 clones were significantly differentially expressed (p-value < 0.005) under at least one treatment condition; 123 high-priority clones were selected for further investigation. CYP1A, CYP1B1, and other members of the AHR gene battery, were strongly and dose-dependently induced by TCDD. Importantly, altered expression of cardiac sarcomere components, including cardiac troponin T2 and multiple myosin isoforms, was consistent with the hypothesis that TCDD causes dilated cardiomyopathy. Observed increases in expression levels of mitochondrial energy transfer genes also may be related to cardiomyopathy. Other TCDD-responsive genes included fatty acid and steroid metabolism enzymes, ribosomal and signal transduction proteins, and 18 ESTs with no known protein homologs. As the first broadscale study of TCDD-modulated gene expression in a non-mammalian system, this work provides an important perspective on mechanisms of TCDD toxicity.This work was supported by funding from the National Institutes of Health

Multistep cascading and fourth-harmonic generation

We apply the concept of multistep cascading to the problem of fourth-harmonic generation in a single quadratic crystal. We analyze a new model of parametric wave mixing and describe its stationary solutions for two- and three-color plane waves and spatial solitons. Some applications to the optical frequency division as well as the realization of the double-phase-matching processes in engineered QPM structures with phase reversal sequences are also discussed.Comment: 3 pages, 3 figure

Smoothed Analysis of Tensor Decompositions

Low rank tensor decompositions are a powerful tool for learning generative models, and uniqueness results give them a significant advantage over matrix decomposition methods. However, tensors pose significant algorithmic challenges and tensors analogs of much of the matrix algebra toolkit are unlikely to exist because of hardness results. Efficient decomposition in the overcomplete case (where rank exceeds dimension) is particularly challenging. We introduce a smoothed analysis model for studying these questions and develop an efficient algorithm for tensor decomposition in the highly overcomplete case (rank polynomial in the dimension). In this setting, we show that our algorithm is robust to inverse polynomial error -- a crucial property for applications in learning since we are only allowed a polynomial number of samples. While algorithms are known for exact tensor decomposition in some overcomplete settings, our main contribution is in analyzing their stability in the framework of smoothed analysis. Our main technical contribution is to show that tensor products of perturbed vectors are linearly independent in a robust sense (i.e. the associated matrix has singular values that are at least an inverse polynomial). This key result paves the way for applying tensor methods to learning problems in the smoothed setting. In particular, we use it to obtain results for learning multi-view models and mixtures of axis-aligned Gaussians where there are many more "components" than dimensions. The assumption here is that the model is not adversarially chosen, formalized by a perturbation of model parameters. We believe this an appealing way to analyze realistic instances of learning problems, since this framework allows us to overcome many of the usual limitations of using tensor methods.Comment: 32 pages (including appendix