On estimation of the diagonal elements of a sparse precision matrix

In this paper, we present several estimators of the diagonal elements of the inverse of the covariance matrix, called precision matrix, of a sample of iid random vectors. The focus is on high dimensional vectors having a sparse precision matrix. It is now well understood that when the underlying distribution is Gaussian, the columns of the precision matrix can be estimated independently form one another by solving linear regression problems under sparsity constraints. This approach leads to a computationally efficient strategy for estimating the precision matrix that starts by estimating the regression vectors, then estimates the diagonal entries of the precision matrix and, in a final step, combines these estimators for getting estimators of the off-diagonal entries. While the step of estimating the regression vector has been intensively studied over the past decade, the problem of deriving statistically accurate estimators of the diagonal entries has received much less attention. The goal of the present paper is to fill this gap by presenting four estimators---that seem the most natural ones---of the diagonal entries of the precision matrix and then performing a comprehensive empirical evaluation of these estimators. The estimators under consideration are the residual variance, the relaxed maximum likelihood, the symmetry-enforced maximum likelihood and the penalized maximum likelihood. We show, both theoretically and empirically, that when the aforementioned regression vectors are estimated without error, the symmetry-enforced maximum likelihood estimator has the smallest estimation error. However, in a more realistic setting when the regression vector is estimated by a sparsity-favoring computationally efficient method, the qualities of the estimators become relatively comparable with a slight advantage for the residual variance estimator.Comment: Companion R package at http://cran.r-project.org/web/packages/DESP/index.htm

Wolbachia Symbiont Infections Induce Strong Cytoplasmic Incompatibility in the Tsetse Fly Glossina morsitans

Tsetse flies are vectors of the protozoan parasite African trypanosomes, which cause sleeping sickness disease in humans and nagana in livestock. Although there are no effective vaccines and efficacious drugs against this parasite, vector reduction methods have been successful in curbing the disease, especially for nagana. Potential vector control methods that do not involve use of chemicals is a genetic modification approach where flies engineered to be parasite resistant are allowed to replace their susceptible natural counterparts, and Sterile Insect technique (SIT) where males sterilized by chemical means are released to suppress female fecundity. The success of genetic modification approaches requires identification of strong drive systems to spread the desirable traits and the efficacy of SIT can be enhanced by identification of natural mating incompatibility. One such drive mechanism results from the cytoplasmic incompatibility (CI) phenomenon induced by the symbiont Wolbachia. CI can also be used to induce natural mating incompatibility between release males and natural populations. Although Wolbachia infections have been reported in tsetse, it has been a challenge to understand their functional biology as attempts to cure tsetse of Wolbachia infections by antibiotic treatment damages the obligate mutualistic symbiont (Wigglesworthia), without which the flies are sterile. Here, we developed aposymbiotic (symbiont-free) and fertile tsetse lines by dietary provisioning of tetracycline supplemented blood meals with yeast extract, which rescues Wigglesworthia-induced sterility. Our results reveal that Wolbachia infections confer strong CI during embryogenesis in Wolbachia-free (GmmApo) females when mated with Wolbachia-infected (GmmWt) males. These results are the first demonstration of the biological significance of Wolbachia infections in tsetse. Furthermore, when incorporated into a mathematical model, our results confirm that Wolbachia can be used successfully as a gene driver. This lays the foundation for new disease control methods including a population replacement approach with parasite resistant flies. Alternatively, the availability of males that are reproductively incompatible with natural populations can enhance the efficacy of the ongoing sterile insect technique (SIT) applications by eliminating the need for chemical irradiation

Challenging the Wigglesworthia, Sodalis, Wolbachia symbiosis dogma in tsetse flies : Spiroplasma is present in both laboratory and natural populations

Profiling of wild and laboratory tsetse populations using 16S rRNA gene amplicon sequencing allowed us to examine whether the “Wigglesworthia-Sodalis-Wolbachia dogma” operates across species and populations. The most abundant taxa, in wild and laboratory populations, were Wigglesworthia (the primary endosymbiont), Sodalis and Wolbachia as previously characterized. The species richness of the microbiota was greater in wild than laboratory populations. Spiroplasma was identified as a new symbiont exclusively in Glossina fuscipes fuscipes and G. tachinoides, members of the palpalis sub-group, and the infection prevalence in several laboratory and natural populations was surveyed. Multi locus sequencing typing (MLST) analysis identified two strains of tsetse-associated Spiroplasma, present in G. f. fuscipes and G. tachinoides. Spiroplasma density in G. f. fuscipes larva guts was significantly higher than in guts from teneral and 15-day old male and female adults. In gonads of teneral and 15-day old insects, Spiroplasma density was higher in testes than ovaries, and was significantly higher density in live versus prematurely deceased females indicating a potentially mutualistic association. Higher Spiroplasma density in testes than in ovaries was also detected by fluorescent in situ hybridization in G. f. fuscipe

A model aphid bacterial pathogen: the phytopathogen Dickeya dadantii (Erwinia chrysanthemi) and its insect-specific virulence factors

5-COM (communications sans actes

Dérégulations immunitaires chez les insectes symbiotiques phytophages : vers de nouvelles méthodes de contrôle de ces insectes ravageurs

2-SCL (articles sans comité de lecture

Characterization of the coleoptericin A, an antimicrobial peptide of the weevil Sitophilus zeamais : a putative gene involved in the maintenance of symbiosis

5-COM (communications sans actes

Caractérisation des coléoptéricines A et B du charançon Sitophilus oryzae

5-COM (communications sans actes