Aspects of the Modular Symmetry Approach to Lepton Flavour

A new bottom-up approach to the flavour problem based on modular invariance has been recently proposed and has gained considerable attention in the literature. In the present thesis we develop basic aspects of the requisite modular symmetry formalism and explore its application to the lepton flavour problem. After introducing the relevant notions (the modular group, the modulus field and modular forms), we concentrate on the theoretical tools required for model-building such as explicit construction of the modular forms, the interplay of modular and CP transformations and of the related symmetries, classification of residual symmetries and their possible relation to the observed hierarchical flavour patterns. Armed with these tools, we construct and discuss three examples of viable models of lepton flavour: a simple predictive model depending on a small number of parameters, a model with an unbroken residual symmetry which leads to trimaximal neutrino mixing, and a model with a slightly broken residual symmetry which explains the observed pattern of charged-lepton masses without fine-tuning

Spinning waveforms from KMOC at leading order

We provide the analytic waveform in time domain for the scattering of two Kerr black holes at leading order in the post-Minkowskian expansion and up to fourth order in both spins. The result is obtained by the generalization of the KMOC formalism to radiative observables, combined with the analytic continuation of the five-point scattering amplitude to complex kinematics. We use analyticity arguments to express the waveform directly in terms of the three-point coupling of the graviton to the spinning particles and the gravitational Compton amplitudes, completely bypassing the need to compute and integrate the five-point amplitude. In particular, this allows to easily include higher-order spin contributions for any spinning compact body. Finally, in the spinless case we find a new compact and gauge-invariant representation of the Kovacs-Thorne waveform.Comment: 7 pages, 1 figure; v2: minor improvements, references adde

PHOG: a database of supergenomes built from proteome complements

BACKGROUND: Orthologs and paralogs are widely used terms in modern comparative genomics. Existing procedures for resolving orthologous/paralogous relationships are often based on manual revision of clusters of orthologous groups and/or lack any rigorous evolutionary base. DESCRIPTION: We developed a completely automated procedure that creates clusters of orthologous groups at each node of the taxonomy tree (PHOGs – Phylogenetic Orthologous Groups). As a result of this procedure, a tree of orthologous groups was obtained. Each cluster is a "supergene" and it is represented by an "ancestral" sequence obtained from the multiple alignment of orthologous and paralogous genes. The procedure has been applied to the taxonomy tree of organisms from all three domains of life. Protein complements from 50 bacterial, archaeal and eukaryotic species were used to create PHOGs at all tree nodes. 51367 PHOGs were obtained at the root node. CONCLUSION: The PHOG database demonstrates that it is possible to automatically process any number of sequenced genomes and to reconstruct orthologous and paralogous relationships between genomes using a rigorous evolutionary approach. This database can become a very useful tool in various areas of comparative genomics

Finite Feynman Integrals

We describe an algorithm to organize Feynman integrals in terms of their infrared properties. Our approach builds upon the theory of Landau singularities, which we use to classify all configurations of loop momenta that can give rise to infrared divergences. We then construct bases of numerators for arbitrary Feynman integrals, which cancel all singularities and render the integrals finite. Through the same analysis, one can also classify so-called evanescent and evanescently finite Feynman integrals. These are integrals whose vanishing or finiteness relies on properties of dimensional regularization. To illustrate the use of these integrals, we display how to obtain a simpler form for the leading-color two-loop four-gluon scattering amplitude through the choice of a suitable basis of finite integrals. In particular, when all gluon helicities are equal, we show that with our basis the most complicated double-box integrals do not contribute to the finite remainder of the scattering amplitude.Comment: 35 pages, 8 figures, 5 table

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.

Web services application programming interface (API) was developed to provide a programmatic access to the regulatory interactions accumulated in the RegPrecise database (http://regprecise.lbl.gov), a core resource on transcriptional regulation for the microbial domain of the Department of Energy (DOE) Systems Biology Knowledgebase. RegPrecise captures and visualize regulogs, sets of genes controlled by orthologous regulators in several closely related bacterial genomes, that were reconstructed by comparative genomics. The current release of RegPrecise 2.0 includes >1400 regulogs controlled either by protein transcription factors or by conserved ribonucleic acid regulatory motifs in >250 genomes from 24 taxonomic groups of bacteria. The reference regulons accumulated in RegPrecise can serve as a basis for automatic annotation of regulatory interactions in newly sequenced genomes. The developed API provides an efficient access to the RegPrecise data by a comprehensive set of 14 web service resources. The RegPrecise web services API is freely accessible at http://regprecise.lbl.gov/RegPrecise/services.jsp with no login requirements

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

<p>Abstract</p> <p>Background</p> <p>An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). Rapid accumulation of genome sequences creates opportunities for refining COGs but also represents a challenge because of error amplification. One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes.</p> <p>Results</p> <p>New Archaeal Clusters of Orthologous Genes (arCOGs) were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon) using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for identification of remote orthologs. The annotation of arCOGs is a consensus between three assignments based on the COGs, the CDD database, and the annotations of homologs in the NR database. The 7538 arCOGs, on average, cover ~88% of the genes in a genome compared to a ~76% coverage in COGs. The finer granularity of ortholog identification in the arCOGs is apparent from the fact that 4538 arCOGs correspond to 2362 COGs; ~40% of the arCOGs are new. The archaeal gene core (protein-coding genes found in all 41 genome) consists of 166 arCOGs. The arCOGs were used to reconstruct gene loss and gene gain events during archaeal evolution and gene sets of ancestral forms. The Last Archaeal Common Ancestor (LACA) is conservatively estimated to possess 996 genes compared to 1245 and 1335 genes for the last common ancestors of Crenarchaeota and Euryarchaeota, respectively. It is inferred that LACA was a chemoautotrophic hyperthermophile that, in addition to the core archaeal functions, encoded more idiosyncratic systems, e.g., the CASS systems of antivirus defense and some toxin-antitoxin systems.</p> <p>Conclusion</p> <p>The arCOGs provide a convenient, flexible framework for functional annotation of archaeal genomes, comparative genomics and evolutionary reconstructions. Genomic reconstructions suggest that the last common ancestor of archaea might have been (nearly) as advanced as the modern archaeal hyperthermophiles. ArCOGs and related information are available at: <url>ftp://ftp.ncbi.nih.gov/pub/koonin/arCOGs/</url>.</p> <p>Reviewers</p> <p>This article was reviewed by Peer Bork, Patrick Forterre, and Purificacion Lopez-Garcia.</p

Distinct Patterns of Expression and Evolution of Intronless and Intron-Containing Mammalian Genes

Comparison of expression levels and breadth and evolutionary rates of intronless and intron-containing mammalian genes shows that intronless genes are expressed at lower levels, tend to be tissue specific, and evolve significantly faster than spliced genes. By contrast, monomorphic spliced genes that are not subject to detectable alternative splicing and polymorphic alternatively spliced genes show similar statistically indistinguishable patterns of expression and evolution. Alternative splicing is most common in ancient genes, whereas intronless genes appear to have relatively recent origins. These results imply tight coupling between different stages of gene expression, in particular, transcription, splicing, and nucleocytosolic transport of transcripts, and suggest that formation of intronless genes is an important route of evolution of novel tissue-specific functions in animals

RegTransBase—a database of regulatory sequences and interactions in a wide range of prokaryotic genomes

RegTransBase is a manually curated database of regulatory interactions in prokaryotes that captures the knowledge in public scientific literature using a controlled vocabulary. Although several databases describing interactions between regulatory proteins and their binding sites are already being maintained, they either focus mostly on the model organisms Escherichia coli and Bacillus subtilis or are entirely computationally derived. RegTransBase describes a large number of regulatory interactions reported in many organisms and contains the following types of experimental data: the activation or repression of transcription by an identified direct regulator, determining the transcriptional regulatory function of a protein (or RNA) directly binding to DNA (RNA), mapping or prediction of a binding site for a regulatory protein and characterization of regulatory mutations. Currently, RegTransBase content is derived from about 3000 relevant articles describing over 7000 experiments in relation to 128 microbes. It contains data on the regulation of about 7500 genes and evidence for 6500 interactions with 650 regulators. RegTransBase also contains manually created position weight matrices (PWM) that can be used to identify candidate regulatory sites in over 60 species. RegTransBase is available at