Glueballs and Their Kaluza-Klein Cousins

Spectra of glueball masses in non-supersymmetric Yang-Mills theory in three and four dimensions have recently been computed using the conjectured duality between superstring theory and large N gauge theory. The Kaluza-Klein states of supergravity do not correspond to any states in the Yang-Mills theory and therefore should decouple in the continuum limit. On the other hand, in the supergravity limit g_{YM}^2 N -> \infty, we find that the masses of the Kaluza-Klein states are comparable to those of the glueballs. We also show that the leading (g_{YM}^2N)^{-1} corrections do not make these states heavier than the glueballs. Therefore, the decoupling of the Kaluza-Klein states is not evident to this order.Comment: 8 pages, LaTe

Holography in Superspace

The AdS/CFT correspondence identifies the coordinates of the conformal boundary of anti-de Sitter space with the coordinates of the conformal field theory. We generalize this identification to theories formulated in superspace. As an application of our results, we study a class of Wilson loops in N=4 SYM theory. A gauge theory computation shows that the expectation values of these loops are invariant under a local kappa-symmetry, except at intersections. We identify this with the kappa-invariance of the associated string worldsheets in the corresponding bulk superspace.Comment: 36 pages, LaTeX, references adde

String Theory on AdS_3

It was shown by Brown and Henneaux that the classical theory of gravity on AdS_3 has an infinite-dimensional symmetry group forming a Virasoro algebra. More recently, Giveon, Kutasov and Seiberg (GKS) constructed the corresponding Virasoro generators in the first-quantized string theory on AdS_3. In this paper, we explore various aspects of string theory on AdS_3 and study the relation between these two works. We show how semi-classical properties of the string theory reproduce many features of the AdS/CFT duality. Furthermore, we examine how the Virasoro symmetry of Brown and Henneaux is realized in string theory, and show how it leads to the Virasoro Ward identities of the boundary CFT. The Virasoro generators of GKS emerge naturally in this analysis. Our work clarifies several aspects of the GKS construction: why the Brown-Henneaux Virasoro algebra can be realized on the first-quantized Hilbert space, to what extent the free-field approximation is valid, and why the Virasoro generators act on the string worldsheet localized near the boundary of AdS_3. On the other hand, we find that the way the central charge of the Virasoro algebra is generated is different from the mechanism proposed by GKS.Comment: 22 pages, 4 figures, LateX; references added, minor correction

Evolution of the Influenza A Virus: Some New Advances

Influenza is an RNA virus that causes mild to severe respiratory symptoms in humans and other hosts. Every year approximately half a million people around the world die from seasonal Influenza. But this number is substantially larger in the case of pandemics, with the most dramatic instance being the 1918 “Spanish flu” that killed more than 50 million people worldwide. In the last few years, thousands of Influenza genomic sequences have become publicly available, including the 1918 pandemic strain and many isolates from non-human hosts. Using these data and developing adequate bioinformatic and statistical tools, some of the major questions surrounding Influenza evolution are becoming tractable. Are the mutations and reassortments random? What are the patterns behind the virus’s evolution? What are the necessary and sufficient conditions for a virus adapted to one host to infect a different host? Why is Influenza seasonal? In this review, we summarize some of the recent progress in understanding the evolution of the virus

Quantifying evolutionary constraints on B cell affinity maturation

The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through high-throughput sequencing. Here, we develop modern statistical molecular evolution methods for the analysis of B cell sequence data, and then apply them to a very deep short-read data set of B cell receptors. We find that the substitution process is conserved across individuals but varies significantly across gene segments. We investigate selection on B cell receptors using a novel method that side-steps the difficulties encountered by previous work in differentiating between selection and motif-driven mutation; this is done through stochastic mapping and empirical Bayes estimators that compare the evolution of in-frame and out-of-frame rearrangements. We use this new method to derive a per-residue map of selection, which provides a more nuanced view of the constraints on framework and variable regions.Comment: Previously entitled "Substitution and site-specific selection driving B cell affinity maturation is consistent across individuals

PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences

The purpose of the proposed web server, publicly available at http://paccmit.epfl.ch, is to provide a user-friendly interface to two algorithms for predicting messenger RNA (mRNA) molecules regulated by microRNAs: (i) PACCMIT (Prediction of ACcessible and/or Conserved MIcroRNA Targets), which identifies primarily mRNA transcripts targeted in their 3′ untranslated regions (3′ UTRs), and (ii) PACCMIT-CDS, designed to find mRNAs targeted within their coding sequences (CDSs). While PACCMIT belongs among the accurate algorithms for predicting conserved microRNA targets in the 3′ UTRs, the main contribution of the web server is 2-fold: PACCMIT provides an accurate tool for predicting targets also of weakly conserved or non-conserved microRNAs, whereas PACCMIT-CDS addresses the lack of similar portals adapted specifically for targets in CDS. The web server asks the user for microRNAs and mRNAs to be analyzed, accesses the precomputed P-values for all microRNA–mRNA pairs from a database for all mRNAs and microRNAs in a given species, ranks the predicted microRNA–mRNA pairs, evaluates their significance according to the false discovery rate and finally displays the predictions in a tabular form. The results are also available for download in several standard formats

A Recoding Method to Improve the Humoral Immune Response to an HIV DNA Vaccine

This manuscript describes a novel strategy to improve HIV DNA vaccine design. Employing a new information theory based bioinformatic algorithm, we identify a set of nucleotide motifs which are common in the coding region of HIV, but are under-represented in genes that are highly expressed in the human genome. We hypothesize that these motifs contribute to the poor protein expression of gag, pol, and env genes from the c-DNAs of HIV clinical isolates. Using this approach and beginning with a codon optimized consensus gag gene, we recode the nucleotide sequence so as to remove these motifs without modifying the amino acid sequence. Transfecting the recoded DNA sequence into a human kidney cell line results in doubling the gag protein expression level compared to the codon optimized version. We then turn both sequences into DNA vaccines and compare induced antibody response in a murine model. Our sequence, which has the motifs removed, induces a five-fold increase in gag antibody response compared to the codon optimized vaccine