Assessing the robustness of parsimonious predictions for gene neighborhoods from reconciled phylogenies

The availability of a large number of assembled genomes opens the way to study the evolution of syntenic character within a phylogenetic context. The DeCo algorithm, recently introduced by B{\'e}rard et al. allows the computation of parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. Following the approach pioneered by Sturmfels and Pachter, we describe how to modify the DeCo dynamic programming algorithm to identify classes of cost schemes that generates similar parsimonious evolutionary scenarios for gene adjacencies, as well as the robustness to changes to the cost scheme of evolutionary events of the presence or absence of specific ancestral gene adjacencies. We apply our method to six thousands mammalian gene families, and show that computing the robustness to changes to cost schemes provides new and interesting insights on the evolution of gene adjacencies and the DeCo model.Comment: Accepted, to appear in ISBRA - 11th International Symposium on Bioinformatics Research and Applications - 2015, Jun 2015, Norfolk, Virginia, United State

The genome of the medieval Black Death agent (extended abstract)

The genome of a 650 year old Yersinia pestis bacteria, responsible for the medieval Black Death, was recently sequenced and assembled into 2,105 contigs from the main chromosome. According to the point mutation record, the medieval bacteria could be an ancestor of most Yersinia pestis extant species, which opens the way to reconstructing the organization of these contigs using a comparative approach. We show that recent computational paleogenomics methods, aiming at reconstructing the organization of ancestral genomes from the comparison of extant genomes, can be used to correct, order and complete the contig set of the Black Death agent genome, providing a full chromosome sequence, at the nucleotide scale, of this ancient bacteria. This sequence suggests that a burst of mobile elements insertions predated the Black Death, leading to an exceptional genome plasticity and increase in rearrangement rate.Comment: Extended abstract of a talk presented at the conference JOBIM 2013, https://colloque.inra.fr/jobim2013_eng/. Full paper submitte

Constraints on Astro-unparticle Physics from SN 1987A

SN 1987A observations have been used to place constraints on the interactions between standard model particles and unparticles. In this study we calculate the energy loss from the supernovae core through scalar, pseudo scalar, vector, pseudo vector unparticle emission from nuclear bremsstrahlung for degenerate nuclear matter interacting through one pion exchange. In order to examine the constraints on $d_{\cal U}=1$ we considered the emission of scalar, pseudo scalar, vector, pseudo vector and tensor through the pair annihilation process $e^+e^-\to {\cal U} \gamma$. In addition we have re-examined other pair annihilation processes. The most stringent bounds on the dimensionless coupling constants for $d_{\cal U} =1$ and $\Lambda_{\cal U}= m_Z$ are obtained from nuclear bremsstrahlung process for the pseudo scalar and pseudo-vector couplings $\bigl|\lambda^{\cal P}_{0,1}\bigr|\leq 4\times 10^{-11}$ and for tensor interaction, the best limit on dimensionless coupling is obtained from $e^+ e^-\to {\cal U} \gamma$ and we get $\bigl|\lambda^{\cal T}\bigr| \leq 6\times 10^{-6}$.Comment: 12 pages, 2 postscript figure

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Brane effective actions, kappa-symmetry and applications

This is a review on brane effective actions, their symmetries and some of their applications. Its first part covers the Green–Schwarz formulation of single M- and D-brane effective actions focusing on kinematical aspects: the identification of their degrees of freedom, the importance of world volume diffeomorphisms and kappa symmetry to achieve manifest spacetime covariance and supersymmetry, and the explicit construction of such actions in arbitrary on-shell supergravity backgrounds. Its second part deals with applications. First, the use of kappa symmetry to determine supersymmetric world volume solitons. This includes their explicit construction in flat and curved backgrounds, their interpretation as Bogomol’nyi–Prasad–Sommerfield (BPS) states carrying (topological) charges in the supersymmetry algebra and the connection between supersymmetry and Hamiltonian BPS bounds. When available, I emphasise the use of these solitons as constituents in microscopic models of black holes. Second, the use of probe approximations to infer about the non-trivial dynamics of strongly-coupled gauge theories using the anti de Sitter/conformal field theory (AdS/CFT) correspondence. This includes expectation values of Wilson loop operators, spectrum information and the general use of D-brane probes to approximate the dynamics of systems with small number of degrees of freedom interacting with larger systems allowing a dual gravitational description. Its final part briefly discusses effective actions for N D-branes and M2-branes. This includes both Super-Yang-Mills theories, their higher-order corrections and partial results in covariantising these couplings to curved backgrounds, and the more recent supersymmetric Chern–Simons matter theories describing M2-branes using field theory, brane constructions and 3-algebra considerations

Inference of ancestral protein-protein interactions using methods from algebraic statistics

Protein-protein interactions are important catalysts for many biological functions. The interaction networks of different organisms may be compared to investigate the process of evolution through which these structures evolve. The parameters used for inference models for such evolutionary processes are usually hard to estimate. This thesis explores approaches developed in algebraic statistics for parametric inference in probabilistic models. Here, we apply the parametric inference approach to Bayesian networks representing the evolution of protein interaction networks. More precisely, we modify the belief propagation algorithm for Bayesian inference to a polytope setting. We apply our program to analyze both simulated and real protein interaction data and compare the results to two well known discrete parsimony inference methods

Variants of the Consecutive Ones Property: Algorithms, Computational Complexity and Applications to Genomics

Genome mapping problems in bioinformatics can be modelled as problems of finding sequences of vertices in hypergraphs, subject to consecutivity constraints. These problems are related to the emph{consecutive ones property}, a well-studied structural property on binary matrices. Many variants of this property have been introduced to include subtleties in the model, such as upper bounds on the number of times a vertex may appear in a sequence, the distance of the input from having the property, and confidence values for the consecutivity constraints. Most problems involving these variants are intractable, and efficient solutions call for restrictions on the structure of the input, exponential time algorithms, or approximations. The following document discusses these problems, from both a theoretical perspective, and from the genomics point of view.We encounter two main classes of problems, divided into models which account for repeated elements in genomes, and those which do not. Orthogonally, we divide the problems into decision and optimization questions. For models with repeats, we discuss when the given input can be used to reconstruct the genome map of interest, and if we can discard a minimal set of encoded consecutivity information from the model to obtain an input which can be used to reconstruct this genome map. We also discuss the problem of ambiguity introduced by repeats, and introduce the concept of emph{repeat spanning intervals} in order to address them. We show that the problem of optimizing over the set of repeat spanning intervals is NP-hard in general, and give an algorithm when the intervals are small. In models without repeated elements, we discuss the problem of optimization byfinding a solution that minimizes the distortion in the consecutivity information, by generalizing the concepts of bandwidth and minimum linear arrangement to hypergraphs. We design approximation algorithms for two versions of the latter problem, with an approximation ratio of $Oleft(sqrt{log n}loglog nright)$.Finally, we provide details of implementations of some of the methods developed for genome mapping and scaffolding on ancestral genomes. We include results on real data for the genome of the Black Death agent, and for ancestral textit{Anopheles} mosquitoes