Bayesian Models for Zero Truncated Count Data. Asian Journal of Probability and Statistics.

It is important to fit count data with suitable model(s), models such as Poisson Regression, Quassi Poisson, Negative Binomial, to mention but a few have been adopted by researchers to fit zero truncated count data in the past. In recent times, dedicated models for fitting zero truncated count data have been developed, and they are considered sufficient. This study proposed Bayesian multi-level Poisson and Bayesian multi-level Geometric model, Bayesian Monte Carlo Markov Chain Generalized linear Mixed Models (MCMCglmms) of zero truncated Poisson and MCMCglmms Poisson regression model to fit health count data that is truncated at zero. Suitable model selection criteria were used to determine preferred models for fitting zero truncated data. Results obtained showed that Bayesian multi-level Poisson outperformed Bayesian multi-level Poisson Geometric model; also MCMCglmms of zero truncated Poisson outperformed MCMCglmms Poisson

Mitochondrial Genome Sequence and Expression Profiling for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)

We report the assembly of the 14,054 bp near complete sequencing of the mitochondrial genome of the legume pod borer (LPB), Maruca vitrata (Lepidoptera: Crambidae), which we subsequently used to estimate divergence and relationships within the lepidopteran lineage. The arrangement and orientation of the 13 protein-coding, 2 rRNA, and 19 tRNA genes sequenced was typical of insect mitochondrial DNA sequences described to date. The sequence contained a high A+T content of 80.1% and a bias for the use of codons with A or T nucleotides in the 3rd position. Transcript mapping with midgut and salivary gland ESTs for mitochondrial genome annotation showed that translation from protein-coding genes initiates and terminates at standard mitochondrial codons, except for the coxI gene, which may start from an arginine CGA codon. The genomic copy of coxII terminates at a T nucleotide, and a proposed polyadenylation mechanism for completion of the TAA stop codon was confirmed by comparisons to EST data. EST contig data further showed that mature M. vitrata mitochondrial transcripts are monocistronic, except for bicistronic transcripts for overlapping genes nd4/nd4L and nd6/cytb, and a tricistronic transcript for atp8/atp6/coxIII. This processing of polycistronic mitochondrial transcripts adheres to the tRNA punctuated cleavage mechanism, whereby mature transcripts are cleaved only at intervening tRNA gene sequences. In contrast, the tricistronic atp8/atp6/coxIII in Drosophila is present as separate atp8/atp6 and coxIII transcripts despite the lack of an intervening tRNA. Our results indicate that mitochondrial processing mechanisms vary between arthropod species, and that it is crucial to use transcriptional information to obtain full annotation of mitochondrial genomes

Transcriptome Sequencing, and Rapid Development and Application of SNP Markers for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)

The legume pod borer, Maruca vitrata (Lepidoptera: Crambidae), is an insect pest species of crops grown by subsistence farmers in tropical regions of Africa. We present the de novo assembly of 3729 contigs from 454- and Sanger-derived sequencing reads for midgut, salivary, and whole adult tissues of this non-model species. Functional annotation predicted that 1320 M. vitrata protein coding genes are present, of which 631 have orthologs within the Bombyx mori gene model. A homology-based analysis assigned M. vitrata genes into a group of paralogs, but these were subsequently partitioned into putative orthologs following phylogenetic analyses. Following sequence quality filtering, a total of 1542 putative single nucleotide polymorphisms (SNPs) were predicted within M. vitrata contig assemblies. Seventy one of 1078 designed molecular genetic markers were used to screen M. vitrata samples from five collection sites in West Africa. Population substructure may be present with significant implications in the insect resistance management recommendations pertaining to the release of biological control agents or transgenic cowpea that express Bacillus thuringiensis crystal toxins. Mutation data derived from transcriptome sequencing is an expeditious and economical source for genetic markers that allow evaluation of ecological differentiation

A genomic analysis of the insect pest populations of cowpea in West Africa

Cowpea [Vigna unguiculata (L.) Walp (Fabaceae)] is an important and major staple food crop in sub-Saharan Africa, especially in the dry savanna regions of West Africa. The crop provides food, cash, and fodder. As a food crop, cowpea is a primary source of protein for the ever-growing population of both rural and urban dwellers. The fodder and husks from cowpea also form an important source of protein, fiber, and energy for livestock. West Africa accounts for about 80% of the world’s cowpea production. However, insect pests are major constraints to cowpea production in the West African sub-region. The crop is severely attacked at every stage of its growth by different insect pests from the pre-flowering stage right through storage. Damage by insect pests on cowpea can be as high as 80 – 100% if not effectively controlled. Current control measures against the insect pests, which mostly consist of chemical control, are not without limitations. There is a need to develop a more comprehensive IPM strategy against cowpea insect pests by exploiting the knowledge of their biology, location of alternate host plants, and natural enemies, and combining these with the recent advances in genome sequencing technologies. This dissertation consists of five chapters and focuses on the integration of integrated pest management (IPM) and the current trends in genomic sequencing to cowpea IPM in West Africa with the aim of better understanding the insect pest populations of the cowpea crop and defining their population structure and movement patterns. Chapter 1 which serves as the introduction to the whole thesis discusses in detail the advent of the genomics era and how IPM researchers must take advantage of the recent development in genomic practices. It introduces the concept of IPM-omics and how this can be applied to cowpea cropping systems in West Africa. It also discusses the effective deployment of the research output to the end-users. Chapters 2 and 3 answer questions regarding the timing and spatial scale of the migration patterns of one of the major insect pests of cowpea in West Africa, the legume pod borer (Maruca vitrata). I applied a set of microsatellite markers (Chapters 2 and 3) and mitochondrial cox1 haplotype data (Chapter 3) to characterize the M. vitrata populations across locations in West Africa [Burkina Faso, Niger and Nigeria (Chapter 2)] and also on four host plants of M. vitrata [cultivated cowpea (Vigna unguiculata), and three alternative host plants - Pueraria phaseoloides, Loncocarpus sericeus, and Tephrosia candida)] in southern Benin (Chapter 3). The findings from the studies in the two chapters enabled a much clearer understanding of the genetic variability, population structure, and gene flow among M. vitrata populations in those countries and the host plants sampled. Chapter 4 compares the mitochondrial genome of M. vitrata from the New World (Puerto Rico) with the mitochondrial genome of the M. vitrata population from the Old World (Burkina Faso), and also with the mitogenomes of other Crambids. Species from the genus Maruca have a wide distribution from northern Australia and East Asia through sub-Saharan Africa to the Caribbean, Central America, and North America. The species are difficult to distinguish morphologically and have been surmised to be a species complex due to cryptic morphological differences. To be able to study evolutionary patterns among Maruca species, I sequenced and assembled the mitochondrial genome of the Maruca subspecies from Puerto Rico and compared this with the mitochondrial genomes of M. vitrata from West Africa, and also with other available Crambid mitochondrial genomes. The study enabled the estimation of mutation tendencies in M. vitrata and also the construction of phylogenetic relationships, as well as comparative and molecular genome evolution patterns in M. vitrata. Chapter 5 goes beyond my research on M. vitrata and concentrates on other destructive insect pests of cowpea in West Africa. In West Africa, besides M. vitrata, other serious insect pests also attack the cowpea crop. These insect pests include thrips (Megalurothrips sjostedti), aphids (Aphis craccivora) and pod sucking bug complex, (including Clavigralla tomentosicollis and Anoplocnemis curvipes). Collectively, these pests can wipe out a whole cowpea harvest. Part of the constraint in the application of effective control strategies against these pests is the lack of molecular markers that can enable the characterization of the pest populations. For this study, I applied Roche 454 sequencing technology to generate and subsequently assemble contigs from DNA sequencing reads for A. curvipes, A. craccivora, C. tomentosicollis and M. sjostedti. These were then used to detect polymorphisms in the different populations of these insect pests across West Africa. Findings from this study identified putative single nucleotide polymorphisms (SNPs), which can be used for characterizing the populations of the different insect pests, and also identified candidate genes putatively involved in insecticide resistance, regulation of insect growth, and response to disease transmission. Overall, the output from the studies in this dissertation will facilitate the effective evaluation, modification, and optimization of practical cowpea IPM strategies which will in the short- and long-term help in the monitoring of the insect pest populations as well as aid in making decisions as to how, when, and where to apply appropriate control measures

Models for Zero Truncated Count Data in Medicine and Insurance

It is important to fit count data with suitable model(s), models such as Poisson Regression, Quassi Poisson, Negative Binomial, to mention but a few have been adopted by researchers to fit zero truncated count data in the past. In recent times, dedicated models for fitting zero truncated count data have been developed, and they are considered sufficient. This study proposed Bayesian multi-level Poisson and Bayesian multi-level Geometric model, Bayesian Monte Carlo Markov Chain Generalized linear Mixed Models (MCMCglmms) of zero truncated Poisson and MCMCglmms Poisson regression model to fit health count data that is truncated at zero. Data of visits to visit to the doctor of patients under National Health Insurance Scheme in Nigeria was obtained and used to fit the models. Suitable model selection criteria were used to determine preferred models for fitting zero truncated data. Results obtained showed that Bayesian multi-level Poisson outperformed Bayesian multi-level Poisson Geometric model; also MCMCglmms of zero truncated Poisson outperformed MCMCglmms Poisson

Présence, populations et dégâts de l’alucite des céréales Sitotroga cerealella (Olivier) (Lepidoptera,Gelechiidae) sur les stocks de riz au Bénin

Presence, population and damage of the angoumois grain moth, Sitotrogacerealella (Olivier) (Lepidoptera, Gelechiidae), on rice stocks in BeninTheangoumois grain moth, Sitotrogacerealella (Olivier) (Lepidoptera, Gelechiidae) is a major pest on several continents causing major damage to stocks of several cereals(rice, maize, sorghum etc.). This study aimed at analyzing the presence of S. cerealellain key sites of rice production in Benin and evaluating the level of the pest populationand its damage to farmers’ rice stocks. For this purpose, paddy rice samples were collectedfrom 11 sites of peasant stockage. In addition, pheromone traps were placed in farmers’paddy fields to study infestations. The resultsshowed that 70 % of the rice stockswere infested by S. cerealella, with average populations varying from 30 to 300 individualsper kg of paddy. In infested samples, the damage level ranged from 3% to 18 % ofgrains attacked for 2 to 4 months of storage. Pheromone trapping showed that 80 % ofthe rice fields were infested, with an average of 16 individuals captured per trap. Thepresence of this pest is thus confirmed on rice in Benin. This study also shows thatimportant damage can be caused on stored rice as soon as the storage period reaches 3to 4 months

The Effects of A Mosquito Salivary Protein on Sporozoite Traversal of Host Cells

International audienceAbstract Malaria begins when Plasmodium-infected Anopheles mosquitoes take a blood meal on a vertebrate. During the initial probing process, mosquitoes inject saliva and sporozoites into the host skin. Components of mosquito saliva have the potential to influence sporozoite functionality. Sporozoite-associated mosquito saliva protein 1 (SAMSP1; AGAP013726) was among several proteins identified when sporozoites were isolated from saliva, suggesting it may have an effect on Plasmodium. Recombinant SAMSP1 enhanced sporozoite gliding and cell traversal activity in vitro. Moreover, SAMSP1 decreased neutrophil chemotaxis in vivo and in vitro, thereby also exerting an influence on the host environment in which the sporozoites reside. Active or passive immunization of mice with SAMSP1 or SAMSP1 antiserum diminished the initial Plasmodium burden after infection. Passive immunization of mice with SAMSP1 antiserum also added to the protective effect of a circumsporozoite protein monoclonal antibody. SAMSP1 is, therefore, a mosquito saliva protein that can influence sporozoite infectivity in the vertebrate host

Connaissance paysanne des insectes foreurs de tiges du riz et leurs dégâts dans différentes zones écologiques du Benin (Afrique de l’Ouest)

Farmer knowledge of rice stem borers and their damage in various ecologicalzones of Benin (West Africa) In Benin, damage caused by stem borers are a threat to rice production. The presentstudy aimed at evaluating farmer knowledge of these pests in order to find participativesolutions for their monitoring and control in rural areas. An agronomic survey was carriedout with 151 producers in the regions of Zou, collines and Couffo where specimens of rice stem borers and samples of their damage were exhibited to farmers for identification. Field visits were also undertaken in order to observe farmer knowledge. The results recorded show that rice producers in Benin have good knowledge of the main rice stem borers such are SesamiacalamistisHampson (Lepidopera : Noctuidae), ChilozacconiusBleszynski (Lepidoptera : Pyralidae), MaliarphaseparatellaRagonot (Lepidopera : Pyralidae) and Diopsis spp. (Diptera : Diopsidae). Damages caused by stem borers, such as white panicle and dead heart, are also very well recognized by the farmers. The proven knowledge of rice stem borers by farmers would allow agricultural services to take advantage of farmers’ experience and knowledge by associating them in local diagnosis and pest control measures