Efficient and specific oligo-based depletion of rRNA

In most organisms, ribosomal RNA (rRNA) contributes to >85% of total RNA. Thus, to obtain useful information from RNA-sequencing (RNA-seq) analyses at reasonable sequencing depth, typically, mature polyadenylated transcripts are enriched or rRNA molecules are depleted. Targeted depletion of rRNA is particularly useful when studying transcripts lacking a poly(A) tail, such as some non-coding RNAs (ncRNAs), most bacterial RNAs and partially degraded or immature transcripts. While several commercially available kits allow effective rRNA depletion, their efficiency relies on a high degree of sequence homology between oligonucleotide probes and the target RNA. This restricts the use of such kits to a limited number of organisms with conserved rRNA sequences. In this study we describe the use of biotinylated oligos and streptavidin-coated paramagnetic beads for the efficient and specific depletion of trypanosomal rRNA. Our approach reduces the levels of the most abundant rRNA transcripts to less than 5% with minimal off-target effects. By adjusting the sequence of the oligonucleotide probes, our approach can be used to deplete rRNAs or other abundant transcripts independent of species. Thus, our protocol provides a useful alternative for rRNA removal where enrichment of polyadenylated transcripts is not an option and commercial kits for rRNA are not available

Exploiting CRISPR-Cas9 technology to investigate individual histone modifications

Despite their importance for most DNA-templated processes, the function of individual histone modifications has remained largely unknown because in vivo mutational analyses are lacking. The reason for this is that histone genes are encoded by multigene families and that tools to simultaneously edit multiple genomic loci with high efficiency are only now becoming available. To overcome these challenges, we have taken advantage of the power of CRISPR-Cas9 for precise genome editing and of the fact that most DNA repair in the protozoan parasite Trypanosoma brucei occurs via homologous recombination. By establishing an episome-based CRISPR-Cas9 system for T. brucei, we have edited wild type cells without inserting selectable markers, inserted a GFP tag between an ORF and its 3'UTR, deleted both alleles of a gene in a single transfection, and performed precise editing of genes that exist in multicopy arrays, replacing histone H4K4 with H4R4 in the absence of detectable off-target effects. The newly established genome editing toolbox allows for the generation of precise mutants without needing to change other regions of the genome, opening up opportunities to study the role of individual histone modifications, catalytic sites of enzymes or the regulatory potential of UTRs in their endogenous environments

Superconformal constraints for QCD conformal anomalies

Anomalous superconformal Ward identities and commutator algebra in N = 1 super-Yang-Mills theory give rise to constraints between the QCD special conformal anomalies of conformal composite operators. We evaluate the superconformal anomalies that appear in the product of renormalized conformal operators and the trace anomaly in the supersymmetric spinor current and check the constraints at one-loop order. In this way we prove the universality of QCD conformal anomalies, which define the non-diagonal part of the anomalous dimension matrix responsible for scaling violations of exclusive QCD amplitudes at the next-to-leading order.Comment: 30 pages, 2 figures, LaTe

The local symmetries of M-theory and their formulation in generalised geometry

In the doubled field theory approach to string theory, the T-duality group is promoted to a manifest symmetry at the expense of replacing ordinary Riemannian geometry with generalised geometry on a doubled space. The local symmetries are then given by a generalised Lie derivative and its associated algebra. This paper constructs an analogous structure for M-theory. A crucial by-product of this is the derivation of the physical section condition for M-theory formulated in an extended space.Comment: 20 pages, v2: Author Name corrected, v3: typos correcte

Gauge fields and infinite chains of dualities

We show that the particle states of Maxwell's theory, in $D$ dimensions, can be represented in an infinite number of ways by using different gauge fields. Using this result we formulate the dynamics in terms of an infinite set of duality relations which are first order in space-time derivatives. We derive a similar result for the three form in eleven dimensions where such a possibility was first observed in the context of E11. We also give an action formulation for some of the gauge fields. In this paper we give a pedagogical account of the Lorentz and gauge covariant formulation of the irreducible representations of the Poincar\'e group, used previously in higher spin theories, as this plays a key role in our constructions. It is clear that our results can be generalised to any particle.Comment: 37 page

Leading Order QCD Corrections to b→s γb\rightarrow s \, \gamma and b→s gb \rightarrow s \, g Decays in Three Regularization Schemes

We discuss in detail the calculation of the leading order QCD corrections to the Effective Hamiltonian which governs $b \rightarrow s\, \gamma$ and $b \rightarrow s \, g$ transitions in three different regularization schemes (HV, NDR and DRED). We show that intermediate stages of the calculation do depend on the regularization, but the same scheme independent coefficients can be obtained in all the considered schemes. A detailed discussion of the results already present in the literature is also given.Comment: 35 pp + 4 figs not included (available by anonymous ftp at amisan.iss.infn.it (141.108.15.215), directory /ftp/dred ), LaTeX, ROME 973/93, INFN-ISS 93/6, ULB-TH 15/9

Characteristic cohomology of pp-form gauge theories

The characteristic cohomology $H^k_{char}(d)$ for an arbitrary set of free $p$-form gauge fields is explicitly worked out in all form degrees $k<n-1$, where $n$ is the spacetime dimension. It is shown that this cohomology is finite-dimensional and completely generated by the forms dual to the field strengths. The gauge invariant characteristic cohomology is also computed. The results are extended to interacting $p$-form gauge theories with gauge invariant interactions. Implications for the BRST cohomology are mentioned.Comment: Latex file, no figures, 44 page

Twenty Years of the Weyl Anomaly

In 1973 two Salam prot\'{e}g\'{e}s (Derek Capper and the author) discovered that the conformal invariance under Weyl rescalings of the metric tensor $g_{\mu\nu}(x)\rightarrow\Omega^2(x)g_{\mu\nu}(x)$ displayed by classical massless field systems in interaction with gravity no longer survives in the quantum theory. Since then these Weyl anomalies have found a variety of applications in black hole physics, cosmology, string theory and statistical mechanics. We give a nostalgic review. (Talk given at the {\it Salamfest}, ICTP, Trieste, March 1993.)Comment: 43 page

Superconformal symmetry and maximal supergravity in various dimensions

In this paper we explore the relation between conformal superalgebras with 64 supercharges and maximal supergravity theories in three, four and six dimensions using twistorial oscillator techniques. The massless fields of N=8 supergravity in four dimensions were shown to fit into a CPT-self-conjugate doubleton supermultiplet of the conformal superalgebra SU(2,2|8) a long time ago. We show that the fields of maximal supergravity in three dimensions can similarly be fitted into the super singleton multiplet of the conformal superalgebra OSp(16|4,R), which is related to the doubleton supermultiplet of SU(2,2|8) by dimensional reduction. Moreover, we construct the ultra-short supermultiplet of the six-dimensional conformal superalgebra OSp(8*|8) and show that its component fields can be organized in an on-shell superfield. The ultra-short OSp(8*|8) multiplet reduces to the doubleton supermultiplet of SU(2,2|8) upon dimensional reduction. We discuss the possibility of a chiral maximal (4,0) six-dimensional supergravity theory with USp(8) R-symmetry that reduces to maximal supergravity in four dimensions and is different from six-dimensional (2,2) maximal supergravity, whose fields cannot be fitted into a unitary supermultiplet of a simple conformal superalgebra. Such an interacting theory would be the gravitational analog of the (2,0) theory.Comment: 54 pages, PDFLaTeX, Section 5 and several references added. Version accepted for publication in JHE